1,423 results
Search Results
2. Photosynthetic characteristics and genetic mapping of a yellow-green leaf mutant jym165 in soybean.
- Author
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Zhao Y, Zhu M, Gao H, Zhou Y, Yao W, Zhao Y, Zhang W, Feng C, Li Y, Jin Y, and Xu K
- Subjects
- Chlorophyll metabolism, Phenotype, Starch metabolism, Chloroplasts metabolism, Photosynthesis genetics, Glycine max genetics, Glycine max growth & development, Glycine max physiology, Glycine max metabolism, Plant Leaves genetics, Plant Leaves growth & development, Plant Leaves metabolism, Plant Leaves physiology, Mutation, Chromosome Mapping
- Abstract
Background: Leaves are important sites for photosynthesis and can convert inorganic substances into organic matter. Photosynthetic performance is an important factor affecting crop yield. Leaf colour is closely related to photosynthesis, and leaf colour mutants are considered an ideal material for studying photosynthesis., Results: We obtained a yellow-green leaf mutant jym165, using ethyl methane sulfonate (EMS) mutagenesis. Physiological and biochemical analyses indicated that the contents of chlorophyll a, chlorophyll b, carotenoids, and total chlorophyll in the jym165 mutant decreased significantly compared with those in Jiyu47 (JY47). The abnormal chloroplast development of jym165 led to a decrease in net photosynthetic rate and starch content compared with that of JY47. However, quality traits analysis showed that the sum of oil and protein contents in jym165 was higher than that in JY47. In addition, the regional yield (seed spacing: 5 cm) of jym165 increased by 2.42% compared with that of JY47 under high planting density. Comparative transcriptome analysis showed that the yellow-green leaf phenotype was closely related to photosynthesis and starch and sugar metabolism pathways. Genetic analysis suggests that the yellow-green leaf phenotype is controlled by a single recessive nuclear gene. Using Mutmap sequencing, the candidate regions related of leaf colour was narrowed to 3.44 Mb on Chr 10., Conclusions: Abnormal chloroplast development in yellow-green mutants leads to a decrease in the photosynthetic pigment content and net photosynthetic rate, which affects the soybean photosynthesis pathway and starch and sugar metabolism pathways. Moreover, it has the potentiality to increase soybean yield under dense planting conditions. This study provides a useful reference for studying the molecular mechanisms underlying photosynthesis in soybean., (© 2024. The Author(s).)
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- 2024
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3. 21st International Conference on Animal Blood Groups and Biochemical Polymorphisms. Turin, Italy, 4-8 July 1988. Invited papers.
- Subjects
- Animals, Humans, Blood Group Antigens genetics, Chromosome Mapping, Polymorphism, Genetic
- Published
- 1989
4. Assignment of two mouse genes coinduced with interferon to chromosomes 12 and X.
- Author
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Kelley KA, Pitha PM, Demaeyer-Guignard J, Demaeyer E, and Kozak C
- Subjects
- Animals, Cell Line, Collodion, Cricetinae, Electrophoresis, Polyacrylamide Gel, Genetic Markers, Hybrid Cells metabolism, Interferons biosynthesis, Mice, Newcastle disease virus metabolism, Paper, Chromosome Mapping, Interferons genetics
- Abstract
Two murine cDNAs (pMIF20/11 and pMIF3/10) coinduced with interferon in mouse cells infected with Newcastle disease virus (NDV) were identified previously. By genomic Southern blot analysis of hamster/mouse somatic cell hybrids, the gene hybridizing with pMIF20/11 has been localized on chromosome 12 and the gene hybridizing with pMIF3/10 on chromosome X.
- Published
- 1986
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5. Mapping of the tryptophan genes of Acinetobacter calcoaceticus by transformation.
- Author
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Sawula RV and Crawford IP
- Subjects
- Alcaligenes classification, Alcaligenes enzymology, Cell-Free System, Chromatography, Paper, Culture Media, Cyclohexanecarboxylic Acids, Glutamates metabolism, Glycerophosphates, Hydro-Lyases metabolism, Isomerases metabolism, Mutagens, Mutation, Nitrosoguanidines, Terminology as Topic, Transaminases metabolism, Tryptophan metabolism, Tryptophan Synthase metabolism, ortho-Aminobenzoates, Bacteria, Chromosome Mapping, Chromosomes, Bacterial, Transformation, Genetic, Tryptophan biosynthesis
- Abstract
Auxotrophs of Acinetobacter calcoaceticus blocked in each reaction of the synthetic pathway from chorismic acid to tryptophan were obtained after N-methyl-N'-nitro-N-nitrosoguanidine mutagenesis. One novel class was found to be blocked in both anthranilate and p-aminobenzoate synthesis; these mutants (trpG) require p-aminobenzoate or folate as well as tryptophan (or anthranilate) for growth. The loci of six other auxotrophic classes requiring only tryptophan were defined by growth, accumulation, and enzymatic analysis where appropriate. The trp mutations map in three chromosomal locations. One group contains trpC and trpD (indoleglycerol phosphate synthetase and phosphoribosyl transferase) in addition to trpG mutations; this group is closely linked to a locus conferring a glutamate requirement. Another cluster contains trpA and trpB, coding for the two tryptophan synthetase (EC 4.2.1.20) subunits, along with trpF (phosphoribosylanthranilate isomerase); this group is weakly linked to a his marker. The trpE gene, coding for the large subunit of anthranilate synthetase, is unlinked to any of the above. This chromosomal distribution of the trp genes has not been observed in other organisms.
- Published
- 1972
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6. Genetic analysis of diaminopimelic acid- and lysine-requiring mutants of Escherichia coli.
- Author
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Bukhari AI and Taylor AL
- Subjects
- Carboxy-Lyases biosynthesis, Carboxy-Lyases metabolism, Cell-Free System, Chromatography, Paper, Colorimetry, Conjugation, Genetic, Culture Media, Escherichia coli enzymology, Escherichia coli growth & development, Escherichia coli isolation & purification, Genes, Isomerases metabolism, Lysine biosynthesis, Pimelic Acids biosynthesis, Transduction, Genetic, Chromosome Mapping, Escherichia coli metabolism, Genetics, Microbial, Lysine metabolism, Mutation, Pimelic Acids metabolism
- Abstract
Several diaminopimelic acid (DAP)- and lysine-requiring mutants of Escherichia coli were isolated and studied by genetic, physiological, and biochemical means. The genes concerned with DAP-lysine synthesis map at several different sites on the E. coli chromosome and, therefore, do not constitute a single operon. Three separate loci affecting DAP synthesis are located in the 0 to 2.5 min region of the genetic map. The order of the loci in this region is thr-dapB-pyrA-ara-leu-pan-dapC-tonA-dapD. Two additional DAP genes map in the region between min 47 and 48, with the gene order being gua-dapA-dapE-ctr. The lys locus at min 55 determines the synthesis of the enzyme DAP decarboxylase, which catalyzes the conversion of DAP into lysine. The order of the genes in this region is serA-lysA-thyA.
- Published
- 1971
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7. Cell wall peptidoglycan mutants of Escherichia coli K-12: existence of two clusters of genes, mra and mrb, for cell wall peptidoglycan biosynthesis.
- Author
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Miyakawa T, Matsuzawa H, Matsuhashi M, and Sugino Y
- Subjects
- Alanine metabolism, Carbon Isotopes, Carboxypeptidases metabolism, Cell-Free System, Chromatography, Paper, Escherichia coli enzymology, Escherichia coli isolation & purification, Glucosamine metabolism, Ligases metabolism, Oxidoreductases metabolism, Peptide Synthases metabolism, Phosphoenolpyruvate, Stereoisomerism, Temperature, Transduction, Genetic, Transferases metabolism, Uridine metabolism, Cell Wall metabolism, Chromosome Mapping, Chromosomes, Bacterial, Escherichia coli metabolism, Mutation, Peptidoglycan biosynthesis
- Abstract
Temperature-sensitive mutants of Escherichia coli K-12 which cannot form cell wall peptidoglycan at 42 C were isolated. The thermosensitive steps were characterized biochemically, and the genes coding the enzymes of peptidoglycan synthesis were mapped. These genes were in two clusters: one group, located at about 1.5 min between leu and azi, was designated as mra (murein a); the second group, located at about 77.5 min close to argH and metB, was designated as mrb (murein b, with the order metB-argH-mrb). No simple relations were found between the gene location and the order or localization of enzymes involved in the sequence of reactions of cell wall peptidoglycan biosynthesis.
- Published
- 1972
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8. Germin like protein genes exhibit modular expression during salt and drought stress in elite rice cultivars.
- Author
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Anum J, O'Shea C, Zeeshan Hyder M, Farrukh S, Skriver K, Malik SI, and Yasmin T
- Subjects
- Droughts, Gene Expression Regulation, Plant, Multigene Family, Oryza classification, Oryza genetics, Plant Leaves genetics, Plant Leaves growth & development, Plant Proteins genetics, Plant Roots genetics, Plant Roots growth & development, Real-Time Polymerase Chain Reaction, Salt Stress, Stress, Physiological, Tissue Distribution, Chromosome Mapping methods, Gene Expression Profiling methods, Glycoproteins genetics, Oryza growth & development
- Abstract
Background: Germin-like proteins (GLPs) are ubiquitous plant proteins, which play significant role in plant responses against various abiotic stresses. However, the potential functions of GLPs in rice (Oryza sativa) against salt and drought stress are still unclear., Methods and Results: In this study, transcriptional variation of eight OsGLP genes (OsGLP3-6, OsGLP4-1, OsGLP8-4, OsGLP8-7, OsGLP8-10, OsGLP8-11 and OsGLP8-12) was analyzed in leaves and roots of two economically important Indica rice cultivars, KS282 and Super Basmati, under salt and drought stress at early seedling stage. The relative expression analysis from qRT-PCR indicated the highest increase in expression of OsGLP3-6 in leaves and roots of both rice varieties with a significantly higher expression in KS282. Moreover, relative change in expression of OsGLP8-7, OsGLP8-10 and OsGLP8-11 under salt stress and OsGLP8-7 under drought stress was also commonly higher in leaves and roots of KS282 as compared to Super Basmati. Whereas, OsGLP3-7 and OsGLP8-12 after salt stress and OsGLP8-4 and OsGLP8-12 after drought stress were observed with higher relative expression in roots of Super Basmati than KS282. Importantly, the OsGLP3-6 and OsGLP4-1 from chromosome 3 and 4 respectively showed higher expression in leaves whereas most of the OsGLP genes from chromosome 8 exhibited higher expression in roots., Conclusion: Overall, as a result of this comparative analysis, OsGLP genes showed both general and specific expression profiles depending upon a specific rice variety, stress condition as well as tissue type. These results will increase our understanding of role of OsGLP genes in rice crop and provide useful information for the further in-depth research on their regulatory mechanisms in response to these stress conditions., (© 2021. The Author(s), under exclusive licence to Springer Nature B.V.)
- Published
- 2022
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9. Identification and application of a candidate gene AhAftr1 for aflatoxin production resistance in peanut seed (Arachis hypogaea L.).
- Author
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Yu B, Liu N, Huang L, Luo H, Zhou X, Lei Y, Yan L, Wang X, Chen W, Kang Y, Ding Y, Jin G, Pandey MK, Janila P, Kishan Sudini H, Varshney RK, Jiang H, Liu S, and Liao B
- Subjects
- Plant Proteins genetics, Plant Proteins metabolism, Genetic Linkage, Genes, Plant, Plants, Genetically Modified genetics, Aspergillus genetics, Genotype, Arachis genetics, Arachis microbiology, Arachis immunology, Aflatoxins genetics, Disease Resistance genetics, Quantitative Trait Loci, Plant Diseases microbiology, Plant Diseases genetics, Chromosome Mapping methods, Plant Breeding methods, Seeds genetics
- Abstract
Introduction: Peanut is susceptible to infection of Aspergillus fungi and conducive to aflatoxin contamination, hence developing aflatoxin-resistant variety is highly meaningful. Identifying functional genes or loci conferring aflatoxin resistance and molecular diagnostic marker are crucial for peanut breeding., Objectives: This work aims to (1) identify candidate gene for aflatoxin production resistance, (2) reveal the related resistance mechanism, and (3) develop diagnostic marker for resistance breeding program., Methods: Resistance to aflatoxin production in a recombined inbred line (RIL) population derived from a high-yielding variety Xuhua13 crossed with an aflatoxin-resistant genotype Zhonghua 6 was evaluated under artificial inoculation for three consecutive years. Both genetic linkage analysis and QTL-seq were conducted for QTL mapping. The candidate gene was further fine-mapped using a secondary segregation mapping population and validated by transgenic experiments. RNA-Seq analysis among resistant and susceptible RILs was used to reveal the resistance pathway for the candidate genes., Results: The major effect QTL qAFTRA07.1 for aflatoxin production resistance was mapped to a 1.98 Mbp interval. A gene, AhAftr1 (Arachis hypogaea Aflatoxin resistance 1), was detected structure variation (SV) in leucine rich repeat (LRR) domain of its production, and involved in disease resistance response through the effector-triggered immunity (ETI) pathway. Transgenic plants with overexpression of AhAftr1
(ZH6) exhibited 57.3% aflatoxin reduction compared to that of AhAftr1(XH13) . A molecular diagnostic marker AFTR.Del.A07 was developed based on the SV. Thirty-six lines, with aflatoxin content decrease by over 77.67% compared to the susceptible control Zhonghua12 (ZH12), were identified from a panel of peanut germplasm accessions and breeding lines through using AFTR.Del.A07., Conclusion: Our findings would provide insights of aflatoxin production resistance mechanisms and laid meaningful foundation for further breeding programs., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Production and hosting by Elsevier B.V.)- Published
- 2024
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10. Genetic mapping of regions associated with root system architecture in rice using MutMap QTL-seq.
- Author
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Magar ND, Barbadikar KM, Reddy V, Revadi P, Guha P, Gangatire D, Balakrishnan D, Sharma S, Madhav MS, and Sundaram RM
- Subjects
- Polymorphism, Single Nucleotide genetics, Chromosomes, Plant genetics, Genotype, Oryza genetics, Oryza growth & development, Oryza metabolism, Plant Roots genetics, Plant Roots growth & development, Plant Roots metabolism, Chromosome Mapping, Quantitative Trait Loci genetics
- Abstract
The root system architecture is an important complex trait in rice. With changing climatic conditions and soil nutrient deficiencies, there is an immediate need to breed nutrient-use-efficient rice varieties with robust root system architectural (RSA) traits. To map the genomic regions associated with crucial component traits of RSA viz. root length and root volume, a biparental F
2 mapping population was developed using TI-128, an Ethyl Methane Sulphonate (EMS) mutant of a mega variety BPT-5204 having high root length (RL) and root volume (RV) with wild type BPT-5204. Extreme bulks having high RL and RV and low RL and RV were the whole genome re-sequenced along with parents. Genetic mapping using the MutMap QTL-Seq approach elucidated two genomic intervals on Chr.12 (3.14-3.74 Mb, 18.11-20.85 Mb), and on Chr.2 (23.18-23.68 Mb) as potential regions associated with both RL and RV. The Kompetitive Allele Specific PCR (KASP) assays for SNPs with delta SNP index near 1 were associated with higher RL and RV in the panel of sixty-two genotypes varying in root length and volume. The KASP_SNPs viz. Chr12_S4 (C→T; Chr12:3243938), located in the 3' UTR region of LOC_Os12g06670 encoding a protein kinase domain-containing protein and Chr2_S6 (C→T; Chr2:23181622) present upstream in the regulator of chromosomal condensation protein LOC_Os2g38350. Validation of these genes using qRT-PCR and in-silico studies using various online tools and databases revealed higher expression in TI-128 as compared to BPT- 5204 at the seedling and panicle initiation stages implying the functional role in enhancing RL and RV., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Masson SAS. All rights reserved.)- Published
- 2024
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11. Identification of QTLs associated with yield-related traits and superior genotype prediction using recombinant inbred line population in tobacco.
- Author
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Tong Z, Kamran M, Zhang Q, Lin F, Fang D, Chen X, Zhu T, Xu H, and Xiao B
- Subjects
- Epistasis, Genetic, Plant Breeding methods, Genetic Linkage, Phenotype, Quantitative Trait Loci, Nicotiana genetics, Genotype, Chromosome Mapping methods
- Abstract
Tobacco is an economically significant industrial crop and model plant for genetic research, yet little is known about its genetic architecture. Quantitative trait loci (QTL) analysis was performed for six agronomic traits on an F_7 population of 341 genotypes, parents, and F
1 plants using 1974 SSR markers across two environments. 31 QTLs contributing single-locus additive effects on 13 linkage groups (LGs) and 6 QTL pairs contributing epistatic effects on 6 LGs, were detected by the QTLNetwork 2.0 which was developed for the mixed-linear-model-based composite interval mapping (MCIM). Notably, 5 QTLs and 1 epistatic QTL pair were found to have pleiotropic effects on some genetically related traits. Moreover, the Broad sense heritability of the detected QTLs ranged from 1.05% to 43.33%, while genotype-by-environment interaction heritability spanned from 27.09% to 56.25%. Based on the results of QTL mapping, the potential superior lines for all or specific environments were designed and evaluated. Five major QTLs were finely dissected based on the tobacco reference genome of K326, and 31 candidate genes were predicted. This study offered new insights into the complicated genetic architecture and QTL resources for efficient breeding design for genetic improvement of agronomic traits in tobacco., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)- Published
- 2024
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12. Genetic linkage analysis of stable QTLs in Gossypium hirsutum RIL population revealed function of GhCesA4 in fiber development.
- Author
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Liú R, Xiāo X, Gōng J, Lǐ J, Yán H, Gě Q, Lú Q, Lǐ P, Pān J, Shāng H, Shí Y, Chén Q, Yuán Y, and Gǒng W
- Subjects
- Phenotype, Plant Breeding methods, Plant Proteins genetics, Glucosyltransferases genetics, Gene Expression Regulation, Plant, Gossypium genetics, Quantitative Trait Loci, Cotton Fiber, Genetic Linkage, Chromosome Mapping methods
- Abstract
Introduction: Upland cotton is an important allotetrapolyploid crop providing natural fibers for textile industry. Under the present high-level breeding and production conditions, further simultaneous improvement of fiber quality and yield is facing unprecedented challenges due to their complex negative correlations., Objectives: The study was to adequately identify quantitative trait loci (QTLs) and dissect how they orchestrate the formation of fiber quality and yield., Methods: A high-density genetic map (HDGM) based on an intraspecific recombinant inbred line (RIL) population consisting of 231 individuals was used to identify QTLs and QTL clusters of fiber quality and yield traits. The weighted gene correlation network analysis (WGCNA) package in R software was utilized to identify WGCNA network and hub genes related to fiber development. Gene functions were verified via virus-induced gene silencing (VIGS) and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 strategies., Results: An HDGM consisting of 8045 markers was constructed spanning 4943.01 cM of cotton genome. A total of 295 QTLs were identified based on multi-environmental phenotypes. Among 139 stable QTLs, including 35 newly identified ones, seventy five were of fiber quality and 64 yield traits. A total of 33 QTL clusters harboring 74 QTLs were identified. Eleven candidate hub genes were identified via WGCNA using genes in all stable QTLs and QTL clusters. The relative expression profiles of these hub genes revealed their correlations with fiber development. VIGS and CRISPR/Cas9 edition revealed that the hub gene cellulose synthase 4 (GhCesA4, GH_D07G2262) positively regulate fiber length and fiber strength formation and negatively lint percentage., Conclusion: Multiple analyses demonstrate that the hub genes harbored in the QTLs orchestrate the fiber development. The hub gene GhCesA4 has opposite pleiotropic effects in regulating trait formation of fiber quality and yield. The results facilitate understanding the genetic basis of negative correlation between cotton fiber quality and yield., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Production and hosting by Elsevier B.V.)
- Published
- 2024
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13. piRNAQuest V.2: an updated resource for searching through the piRNAome of multiple species
- Author
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Byapti Ghosh, Arijita Sarkar, Sudip Mondal, Namrata Bhattacharya, Sunirmal Khatua, and Zhumur Ghosh
- Subjects
endocrine system ,ping-pong piRNAs ,Web Browser ,PIWI interacting RNAs ,piRNA cluster ,Species Specificity ,Databases, Genetic ,Animals ,Humans ,RNA, Small Interfering ,Molecular Biology ,Repetitive Sequences, Nucleic Acid ,urogenital system ,piRNA target ,Gene Expression Profiling ,Gene Amplification ,piRNA profile ,Chromosome Mapping ,Computational Biology ,Cell Biology ,Genomics ,Organ Specificity ,Transcriptome ,Software ,Research Article ,Research Paper - Abstract
PIWI interacting RNAs (piRNAs) have emerged as important gene regulators in recent times. Since the release of our first version of piRNAQuest in 2014, lots of novel piRNAs have been annotated in different species other than human, mouse and rat. Such new developments in piRNA research have led us to develop an updated database piRNAQuest V.2. It consists of 92,77,689 piRNA entries for 25 new species of different phylum along with human, mouse and rat. Besides providing primary piRNA features which include their genomic location, with further information on piRNAs overlapping with repeat elements, pseudogenes and syntenic regions, etc., the novel features of this version includes (i) density based cluster prediction, (ii) piRNA expression profile across various healthy and disease systems and (iii) piRNA target prediction. The concept of density-based piRNA cluster identification is robust as it does not consider parametric distribution in its model. The piRNA expression profile for 21 disease systems including cancer have been hosted in addition to 32 tissue specific piRNA expression profile for various species. Further, the piRNA target prediction section includes both predicted and curated piRNA targets within eight disease systems and developmental stages of mouse testis. Further, users can visualize the piRNA-target duplex structure and the ping-pong signature pattern for all the ping-pong piRNA partners in different species. Overall, piRNAQuest V.2 is an updated user-friendly database which will serve as a useful resource to survey, search and retrieve information on piRNAs for multiple species. This freely accessible database is available at http://dibresources.jcbose.ac.in/zhumur/pirnaquest2.
- Published
- 2021
14. Maturation of 23S rRNA includes removal of helix H1 in many bacteria
- Author
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Ralf Bundschuh, Elan A Shatoff, Bryan T Gemler, and Kurt Fredrick
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Models, Molecular ,Biology ,Bacterial Physiological Phenomena ,Ribosome ,Ribosome assembly ,5S ribosomal RNA ,Structure-Activity Relationship ,RRNA modification ,Ribosomal protein ,23S ribosomal RNA ,Escherichia coli ,5S rRNA ,16S rRNA ,RNA Processing, Post-Transcriptional ,RRNA processing ,Molecular Biology ,Genetics ,Base Sequence ,SMART-seq ,Chromosome Mapping ,High-Throughput Nucleotide Sequencing ,23S rRNA ,Cell Biology ,Gene Expression Regulation, Bacterial ,Ribosomal RNA ,50S subunit maturation ,RNA, Bacterial ,RNA, Ribosomal, 23S ,Nucleic Acid Conformation ,RNA-seq ,Research Article ,Research Paper - Abstract
In most bacteria, the three ribosomal RNAs (rRNAs) are encoded together in each of several near-identical operons. As soon as the nascent precursor rRNA emerges from RNA polymerase, ribosome assembly begins. This process entails ribosomal protein binding, rRNA folding, rRNA modification, and rRNA processing. In the model organisms Escherichia coli and Bacillus subtilis, rRNA processing results in similar mature rRNAs, despite substantial differences in the cohort of RNAses involved. A recent study of Flavobacterium johnsoniae, a member of the phylum Bacteroidota (formerly Bacteroidetes), revealed that helix H1 of 23S rRNA is absent from ribosomes, apparently a consequence of rRNA maturation. In this work, we mined RNA-seq data from 19 individual organisms and ocean metatranscriptomic samples to compare rRNA processing across diverse bacterial lineages. We found that mature ribosomes from multiple clades lack H1, and typically these ribosomes also lack an encoded H98. For all groups analysed, H1 is predicted to form in precursor rRNA as part of a longer leader-trailer helix. Hence, we infer that evolutionary loss of H98 sets the stage for H1 removal during 50S subunit maturation.
- Published
- 2021
15. Construction of high-density genetic map based on SLAF-seq and QTL analysis of major traits in sweetpotato [Ipomoea batatas (L.) Lam.].
- Author
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Zhao D, Xiao S, Zhang A, Zhao L, Dai X, Yuan R, Wang J, Wang Y, Li Q, and Zhou Z
- Subjects
- Polymorphism, Single Nucleotide genetics, Genetic Linkage, Phenotype, Ipomoea batatas genetics, Ipomoea batatas metabolism, Quantitative Trait Loci genetics, Chromosome Mapping
- Abstract
Sweetpotato, Ipomoea batatas (L.) Lam., is an important worldwide crop used as feed, food, and fuel. However, its polyploidy, high heterozygosity and self-incompatibility makes it difficult to study its genetics and genomics. Longest vine length (LVL), yield per plant (YPP), dry matter content (DMC), starch content (SC), soluble sugar content (SSC), and carotenoid content (CC) are some of the major agronomic traits being used to evaluate sweetpotato. However limited research has actually examined how these traits are inherited. Therefore, after selecting 212 F
1 from a Xin24 × Yushu10 crossing as the mapping population, this study applied specific-locus amplified fragment sequencing (SLAF-seq), at an average sequencing depth of 26.73 × (parents) and 52.25 × (progeny), to detect single nucleotide polymorphisms (SNPs). This approach generated an integrated genetic map of length 2441.56 cM and a mean distance of 0.51 cM between adjacent markers, encompassing 15 linkage groups (LGs). Based on the linkage map, 26 quantitative trait loci (QTLs), comprising six QTLs for LVL, six QTLs for YPP, ten QTLs for DMC, one QTL for SC, one QTL for SSC, and two QTLs for CC, were identified. Each of these QTLs explained 6.3-10% of the phenotypic variation. It is expected that the findings will be of benefit for marker-assisted breeding and gene cloning of sweetpotato., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Masson SAS. All rights reserved.)- Published
- 2024
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16. Molecular identification of slow rusting resistance Lr46/Yr29 gene locus in selected triticale (× Triticosecale Wittmack) cultivars
- Author
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Agnieszka Tomkowiak, Roksana Skowrońska, Michał Kwiatek, and Jerzy Nawracała
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0106 biological sciences ,0301 basic medicine ,csLV46G22 ,Lr46 ,Biology ,Genes, Plant ,01 natural sciences ,Rust ,03 medical and health sciences ,Plant Genetics • Original Paper ,Genetics ,Cultivar ,Leaf tip necrosis ,Gene ,Disease Resistance ,Plant Diseases ,Slow rusting ,Basidiomycota ,Chromosome ,food and beverages ,Molecular markers ,Chromosome Mapping ,General Medicine ,Phenotypic trait ,Triticale ,Spore ,Fungicide ,Horticulture ,030104 developmental biology ,010606 plant biology & botany ,Xwmc44 - Abstract
Recently, leaf rust and yellow rust caused by the fungi Puccinia triticina Erikss. and P. striiformis Westend f. sp. tritici Eriks and Henn are diseases of increasing threat in triticale (× Triticosecale Wittmack, AABBRR, 2n = 6x = 42) growing areas. The use of genetic resistance is considered the most economical, effective and environmentally friendly method to control the disease and minimize the use of fungicides. Currently, breeding programs mainly relied on race-specific Lr and Yr genes (R), but new races of the rust fungi frequently defeat resistance. There is a small group of genes that causes partial type of resistance (PR) that are characterized by a slow epidemic build up despite a high infection type. In wheat slow rusting resistance genes displayed longer latent periods, low infection frequencies, smaller pustule size and less spore production. Slow rusting Lr46/Yr29 gene, located on chromosome 1B, is being exploited in many wheat breeding programs. So far, there is no information about slow rusting genes in triticale. This paper showed significant differences between the results of identification of wheat molecular markers Xwmc44 and csLV46G22 associated with Lr46/Yr29 in twenty triticale cultivars, which were characterized by high levels of field resistance to leaf and yellow rust. The csLV46G22res marker has been identified in the following cultivars: Kasyno, Mamut and Puzon. Belcanto and Kasyno showed the highest resistance levels in three-year (2016–2018), leaf and yellow rust severity tests under post-registration variety testing program (PDO). Leaf tip necrosis, a phenotypic trait associated with Lr34/Yr18 and Lr46/Yr29 was observed, among others, to Belcanto and Kasyno, which showed the highest resistance for leaf rust and yellow rust. Kasyno could be considered to have Lr46/Yr29 and can be used as a source of slow rust resistance in breeding and importantly as a component of gene pyramiding in triticale.
- Published
- 2020
17. Resolving a QTL complex for height, heading, and grain yield on chromosome 3A in bread wheat
- Author
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Simon Berry, Alba Farre Martinez, Luzie U. Wingen, Sue Freeman, Clare Lister, Simon Griffiths, and Jun Ma
- Subjects
0106 biological sciences ,0301 basic medicine ,Physiology ,QTL ,Population ,Avalon ,Quantitative Trait Loci ,Cadenza ,Locus (genetics) ,Plant Science ,Quantitative trait locus ,Biology ,01 natural sciences ,earliness per se ,Chromosomes ,03 medical and health sciences ,wheat ,Genotype ,Allele ,education ,Gene ,Triticum ,Genetics ,photoperiodism ,education.field_of_study ,flowering ,AcademicSubjects/SCI01210 ,Chromosome ,food and beverages ,Chromosome Mapping ,Vernalization ,Bread ,yield ,Research Papers ,030104 developmental biology ,Phenotype ,Crop Molecular Genetics ,cell wall ,010606 plant biology & botany ,height - Abstract
Crop height (Ht), heading date (Hd), and grain yield (GY) are inter-related in wheat. Independent manipulation of each is important for adaptation and performance. Validated quantitative trait loci (QTLs) for all three co-locate on chromosome 3A in the Avalon×Cadenza population, with increased Ht, Hd, and GY contributed by Cadenza. We asked if these are linked or pleiotropic effects using recombinant lines, and showed that Ht and Hd effects are independent. The Chinese Spring equivalent to the newly defined Ht interval contained a gene cluster involved in cell wall growth and displaying high levels of differential transcript expression. The Hd locus is larger and rearranged compared with the reference genome, but FT2 (Flowering Locus T2) is of particular interest. The Hd effect acted independently of photoperiod and vernalization, but did exhibit seasonal genotype×environment interaction. Recombinants were phenotyped for GY in replicated field experiments. GY was most associated with Cadenza alleles for later Hd, supporting physiological studies using the same lines proposing that ‘late’ alleles at this locus increase spike fertility and grain number (GN). The work has uncoupled height from heading and yield, and shown that one of very few validated GY QTLs in wheat is probably mediated by phenological variation., There are only three validated wheat yield QTLs. Here, one of them was genetically dissected. This showed that the physiological basis of the yield effect is likely to be phenological.
- Published
- 2021
18. Genetic mapping of pollen fertility restoration QTLs in rye (Secale cereale L.) with CMS Pampa
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Agnieszka Niedziela, Waldemar Brukwiński, and Piotr T. Bednarek
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0106 biological sciences ,0301 basic medicine ,Secale ,QTL mapping ,Genetic Markers ,Plant Infertility ,Sterility ,Population ,Quantitative Trait Loci ,Quantitative trait locus ,Biology ,Cytoplasmic male sterility ,01 natural sciences ,Polymorphism, Single Nucleotide ,03 medical and health sciences ,Rye ,Gene mapping ,Plant Genetics • Original Paper ,Genetics ,Plant breeding ,Association mapping ,education ,education.field_of_study ,food and beverages ,Chromosome Mapping ,General Medicine ,biology.organism_classification ,Plant Breeding ,030104 developmental biology ,Phenotype ,Pollen ,010606 plant biology & botany - Abstract
Cytoplasmic male sterility (CMS) is a widely applied plant breeding tool for hybrid seed production. The phenomenon is often caused by chimeric genes with altered open reading frames (ORFs) located in the mitochondrial genomes and expressed as novel genotoxic products that induce pollen abortion. The fertility of CMS plants can be restored by nuclear-encoded genes that inhibit the action of ORFs responsible for pollen sterility. A recombinant inbred line (RIL) mapping population S64/04/01, encompassing 175 individuals, was used for genetic map construction and identification of quantitative trait loci (QTLs) responsible for fertility restoration in rye (Secale cereale L.) with CMS Pampa. The genetic map of all seven rye chromosomes included 15,516 SNP and silicoDArT markers and covered 1070.5 cm. Individual QTLs explaining 60% and 5.5% of the fertility trait’s phenotypic variance were mapped to chromosomes 4R (QRft-4R) and 5R (QRft-5R), respectively. Association mapping identified markers with the highest R2 value of 0.58 (p value = 2.21E-28). Markers showing the highest associations with the trait were also mapped to the 4R chromosome within the QRft-4R region. Based on marker sequence homology, putative genes involved in pollen fertility restoration were suggested. Five silicoDArTs were converted into PCR-based markers for further breeding purposes.
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- 2021
19. TreeMap: a structured approach to fine mapping of eQTL variants
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Pramod Chandrashekar, Biao Zeng, Sudhir Kumar, Li Liu, Maxwell Sanderford, and Greg Gibson
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Statistics and Probability ,Linkage disequilibrium ,AcademicSubjects/SCI01060 ,Colon ,Quantitative Trait Loci ,Gene Expression ,Locus (genetics) ,Genome-wide association study ,Computational biology ,Biology ,Biochemistry ,Hippocampus ,Polymorphism, Single Nucleotide ,Linkage Disequilibrium ,03 medical and health sciences ,0302 clinical medicine ,Genetic linkage ,Humans ,Molecular Biology ,Gene ,030304 developmental biology ,Regulation of gene expression ,0303 health sciences ,Genetics and Population Analysis ,Genetic variants ,Chromosome Mapping ,Original Papers ,Computer Science Applications ,Computational Mathematics ,R package ,Computational Theory and Mathematics ,Expression quantitative trait loci ,030217 neurology & neurosurgery ,Genome-Wide Association Study - Abstract
Motivation Expression quantitative trait loci (eQTL) harbor genetic variants modulating gene transcription. Fine mapping of regulatory variants at these loci is a daunting task due to the juxtaposition of causal and linked variants at a locus as well as the likelihood of interactions among multiple variants. This problem is exacerbated in genes with multiple cis-acting eQTL, where superimposed effects of adjacent loci further distort the association signals. Results We developed a novel algorithm, TreeMap, that identifies putative causal variants in cis-eQTL accounting for multisite effects and genetic linkage at a locus. Guided by the hierarchical structure of linkage disequilibrium, TreeMap performs an organized search for individual and multiple causal variants. Via extensive simulations, we show that TreeMap detects co-regulating variants more accurately than current methods. Furthermore, its high computational efficiency enables genome-wide analysis of long-range eQTL. We applied TreeMap to GTEx data of brain hippocampus samples and transverse colon samples to search for eQTL in gene bodies and in 4 Mbps gene-flanking regions, discovering numerous distal eQTL. Furthermore, we found concordant distal eQTL that were present in both brain and colon samples, implying long-range regulation of gene expression. Availability and implementation TreeMap is available as an R package enabled for parallel processing at https://github.com/liliulab/treemap. Supplementary information Supplementary data are available at Bioinformatics online.
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- 2020
20. Genetic mapping of male sterility and pollen fertility QTLs in triticale with sterilizing Triticum timopheevii cytoplasm
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Marzena Wasiak, Agnieszka Niedziela, Piotr T. Bednarek, Henryk Woś, and Mirosław Pojmaj
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0106 biological sciences ,0301 basic medicine ,Triticum timopheevii ,Cytoplasm ,Plant Infertility ,Sterility ,QTL ,Genetic Linkage ,Population ,Quantitative Trait Loci ,Cytoplasmic male sterility ,medicine.disease_cause ,01 natural sciences ,Polymorphism, Single Nucleotide ,03 medical and health sciences ,Genetic map ,Gene mapping ,Plant Genetics • Original Paper ,Pollen ,Genetics ,medicine ,education ,Triticum ,education.field_of_study ,biology ,Software maintainer ,food and beverages ,Chromosome Mapping ,General Medicine ,Triticale ,biology.organism_classification ,030104 developmental biology ,Fertility ,Phenotype ,010606 plant biology & botany - Abstract
Cytoplasmic male sterility (CMS) phenomenon is widely exploited in commercial hybrid seed production in economically important crop species, including rye, wheat, maize, rice, sorghum, cotton, sugar beets, and many vegetables. Although some commercial successes, little is known about QTLs responsible for the trait in case of triticale with sterilizing Triticum timopheevii (Tt) cytoplasm. Recombinant inbred line (RIL) F6 mapping population encompassing 182 individuals derived from the cross of individual plants representing the HT352 line and cv Borwo was employed for genetic map construction using SNP markers and identification of QTLs conferring pollen sterility in triticale with CMS Tt. The phenotypes of the F1 lines resulting from crossing of the HT352 (Tt) with HT352 (maintainer) × Borwo were determined by assessing the number of the F2 seeds per spike. A genetic map with 21 linkage groups encompasses 29,737 markers and spanned over the distance of 2549 cM. Composite (CIM) and multiple (MIM) interval mappings delivered comparable results. Single QTLs mapped to the 1A, 1B, 2A, 2R, 3B, 3R, 4B, and 5B chromosomes, whereas the 5R and 6B chromosomes shared 3 and 2 QTLs, respectively. The QTLs with the highest LOD score mapped to the 5R, 3R, 1B, and 4B chromosomes; however, the QRft-5R.3 has the highest explained variance of the trait. Supplementary Information The online version contains supplementary material available at 10.1007/s13353-020-00595-z.
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- 2020
21. Analysis of miRNA expression associated with the Lr46 gene responsible for APR resistance in wheat (Triticum aestivum L.)
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Julia Spychała, Roksana Skowrońska, Agata Tyczewska, Jakub Kuczyński, Michał Kwiatek, Tomasz Jędrzejewski, Agnieszka Tomkowiak, and Tomasz Twardowski
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0106 biological sciences ,0301 basic medicine ,Leaf rust ,Lr46 gene ,Resistance ,Quantitative Trait Loci ,miR164 ,Biology ,01 natural sciences ,Rust ,03 medical and health sciences ,Plant Genetics • Original Paper ,Gene Expression Regulation, Plant ,microRNA ,Genetics ,Cultivar ,Common wheat ,Gene ,Triticum ,Disease Resistance ,Plant Diseases ,Plant Proteins ,Inoculation ,Basidiomycota ,fungi ,food and beverages ,Chromosome Mapping ,Puccinia triticina ,General Medicine ,Biotic stress ,Spore ,Horticulture ,MicroRNAs ,030104 developmental biology ,Wheat ,010606 plant biology & botany - Abstract
Lr46/Yr29/Pm39 (Lr46) is a gene for slow rusting resistance in wheat. The aim of the study was to analyze the miRNA expression in selected common wheat cultivars carrying resistance genes, Lr46 among others (HN Rod, Pavon‘S’, Myna‘S’, Frontana‘S’, and Sparrow’S’) in response to leaf rust infection caused by Puccinia triticina Erikss. In the Pavon ‘S’, Myna ‘S’, Frontana‘S’, and Sparow‘S’ varieties a product with a length of 242 bp has been identified, which is specific to the Xwmc44 marker linked to the brown rust resistance gene Lr46. In the next step, the differences in the expression of microRNA (miR5085 and miR164) associated with the Lr46 gene, which is responsible for different resistance of selected wheat cultivars to leaf rust, were examined using emulsion PCR (ddPCR). In the experiment, biotic stress was induced in mature plants by infecting them with fungal spores under controlled conditions in a growth chamber. For analysis the plant material was collected before inoculation and 6, 12, 24, and 48 h after inoculation. The experiments also showed that plant infection with Puccinia triticina resulted in an increase in miR164 expression in cultivars carrying the Lr46 gene. The expression of miR164 remained stable in a control cultivar (HN ROD) lacking this gene. This has proved that miR164 can be involved in leaf rust resistance mechanisms.
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- 2020
22. UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase
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Elena Speretta, Marc Feuermann, Paul Denny, Yvonne Lussi, Antonia Lock, Alexandr Ignatchenko, Philippe Le Mercier, Dushyanth Jyothi, Alexandre Renaux, Ivo Pedruzzi, Emmanuel Boutet, Emanuele Alpi, Claire O'Donovan, Edward Turner, Sandra Orchard, Patrick Masson, Alex Bateman, Peter McGarvey, Emma Hatton-Ellis, Michele Magrane, Alan Bridge, Hema Bye-A-Jee, Ramona Britto, Giuseppe Insana, Shriya Raj, Maria-Jesus Martin, Catherine Rivoire, Penelope Garmiri, Emily Bowler-Barnett, Vishal Joshi, Kate Warner, and Faculty of Sciences and Bioengineering Sciences
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InterPro ,Statistics and Probability ,Protein family ,AcademicSubjects/SCI01060 ,Computer science ,Knowledge Bases ,Databases and Ontologies ,Biochemistry ,DNA sequencing ,03 medical and health sciences ,Annotation ,Resource (project management) ,Databases, Protein ,Gene ,Molecular Biology ,030304 developmental biology ,0303 health sciences ,Information retrieval ,030302 biochemistry & molecular biology ,Chromosome Mapping ,Proteins ,Molecular Sequence Annotation ,Corrigenda ,Original Papers ,Computer Science Applications ,Computational Mathematics ,Functional annotation ,Computational Theory and Mathematics ,UniProt Knowledgebase ,UniProt - Abstract
Motivation The number of protein records in the UniProt Knowledgebase (UniProtKB: https://www.uniprot.org) continues to grow rapidly as a result of genome sequencing and the prediction of protein-coding genes. Providing functional annotation for these proteins presents a significant and continuing challenge. Results In response to this challenge, UniProt has developed a method of annotation, known as UniRule, based on expertly curated rules, which integrates related systems (RuleBase, HAMAP, PIRSR, PIRNR) developed by the members of the UniProt consortium. UniRule uses protein family signatures from InterPro, combined with taxonomic and other constraints, to select sets of reviewed proteins which have common functional properties supported by experimental evidence. This annotation is propagated to unreviewed records in UniProtKB that meet the same selection criteria, most of which do not have (and are never likely to have) experimentally verified functional annotation. Release 2020_01 of UniProtKB contains 6496 UniRule rules which provide annotation for 53 million proteins, accounting for 30% of the 178 million records in UniProtKB. UniRule provides scalable enrichment of annotation in UniProtKB. Availability and implementation UniRule rules are integrated into UniProtKB and can be viewed at https://www.uniprot.org/unirule/. UniRule rules and the code required to run the rules, are publicly available for researchers who wish to annotate their own sequences. The implementation used to run the rules is known as UniFIRE and is available at https://gitlab.ebi.ac.uk/uniprot-public/unifire.
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- 2020
23. Association mapping and genetic dissection of drought-induced canopy temperature differences in rice
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Niteen N. Kadam, Giovanni Melandri, Harro Bouwmeester, Ankush Prashar, Hamlyn G. Jones, Krishna S.V. Jagadish, Gerard van der Linden, Susan R. McCouch, Carolien Ruyter-Spira, and Plant Hormone Biology (SILS, FNWI)
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0106 biological sciences ,0301 basic medicine ,Canopy ,Stomatal conductance ,Crop Physiology ,Physiology ,Population ,Oryza sativa ,Plant Science ,drought ,Quantitative trait locus ,Biology ,Canopy temperature ,01 natural sciences ,03 medical and health sciences ,Genetic variation ,genome-wide association studies (GWAS) ,thermal imaging ,Laboratorium voor Plantenfysiologie ,Association mapping ,education ,Transpiration ,education.field_of_study ,fungi ,Temperature ,Chromosome Mapping ,food and beverages ,Oryza ,PE&RC ,Research Papers ,Droughts ,Plant Breeding ,030104 developmental biology ,Phenotype ,Agronomy ,Plant—Environment Interactions ,haplotype analysis ,EPS ,Laboratory of Plant Physiology ,010606 plant biology & botany ,Genome-Wide Association Study - Abstract
Canopy temperature, detected by thermal imaging, is a good predictor of rice yield performance under drought and shows genetic variation in an association mapping panel., Drought-stressed plants display reduced stomatal conductance, which results in increased leaf temperature by limiting transpiration. In this study, thermal imaging was used to quantify the differences in canopy temperature under drought in a rice diversity panel consisting of 293 indica accessions. The population was grown under paddy field conditions and drought stress was imposed for 2 weeks at flowering. The canopy temperature of the accessions during stress negatively correlated with grain yield (r= –0.48) and positively with plant height (r=0.56). Temperature values were used to perform a genome-wide association (GWA) analysis using a 45K single nucleotide polynmorphism (SNP) map. A quantitative trait locus (QTL) for canopy temperature under drought was detected on chromosome 3 and fine-mapped using a high-density imputed SNP map. The candidate genes underlying the QTL point towards differences in the regulation of guard cell solute intake for stomatal opening as the possible source of temperature variation. Genetic variation for the significant markers of the QTL was present only within the tall, low-yielding landraces adapted to drought-prone environments. The absence of variation in the shorter genotypes, which showed lower leaf temperature and higher grain yield, suggests that breeding for high grain yield in rice under paddy conditions has reduced genetic variation for stomatal response under drought.
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- 2020
24. Optical genome mapping identifies a germline retrotransposon insertion in SMARCB1 in two siblings with atypical teratoid rhabdoid tumors
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Alexander Hoischen, Michael Kwint, Jayne Y. Hehir-Kwa, Madalena Tropa Martins, Roland P. Kuiper, Kornelia Neveling, Freerk van Dijk, Marjolijn C.J. Jongmans, Mariangela Sabatella, Arjen R. Mensenkamp, Jacklyn A. Biegel, Marcel R. Nelen, Tuomo Mantere, Benno Küsters, Esmé Waanders, Maarten H. Lequin, Ronnie Derks, Pieter Wesseling, Luke O’Gorman, Corrie Gidding, Pathology, CCA - Cancer biology and immunology, and CCA - Imaging and biomarkers
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Retroelements ,rhabdoid tumors ,lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4] ,SMARCB1 ,Locus (genetics) ,Biology ,Germline ,Pathology and Forensic Medicine ,Structural variation ,optical imaging ,Germline mutation ,Gene mapping ,medicine ,Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14] ,Humans ,Exome ,Germ-Line Mutation ,Rhabdoid Tumor ,Genetics ,Whole genome sequencing ,Original Paper ,Women's cancers Radboud Institute for Molecular Life Sciences [Radboudumc 17] ,Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7] ,Siblings ,Other Research Radboud Institute for Health Sciences [Radboudumc 0] ,retrotransposon ,Infant, Newborn ,Teratoma ,Chromosome Mapping ,SMARCB1 Protein ,medicine.disease ,Disorders of movement Donders Center for Medical Neuroscience [Radboudumc 3] ,Original Papers ,childhood cancer predisposition ,Atypical teratoid rhabdoid tumor ,Female - Abstract
Contains fulltext : 237894.pdf (Publisher’s version ) (Open Access) In a subset of pediatric cancers, a germline cancer predisposition is highly suspected based on clinical and pathological findings, but genetic evidence is lacking, which hampers genetic counseling and predictive testing in the families involved. We describe a family with two siblings born from healthy parents who were both neonatally diagnosed with atypical teratoid rhabdoid tumor (ATRT). This rare and aggressive pediatric tumor is associated with biallelic inactivation of SMARCB1, and in 30% of the cases, a predisposing germline mutation is involved. Whereas the tumors of both siblings showed loss of expression of SMARCB1 and acquired homozygosity of the locus, whole exome and whole genome sequencing failed to identify germline or somatic SMARCB1 pathogenic mutations. We therefore hypothesized that the insertion of a pathogenic repeat-rich structure might hamper its detection, and we performed optical genome mapping (OGM) as an alternative strategy to identify structural variation in this locus. Using this approach, an insertion of ~2.8 kb within intron 2 of SMARCB1 was detected. Long-range PCR covering this region remained unsuccessful, but PacBio HiFi genome sequencing identified this insertion to be a SINE-VNTR-Alu, subfamily E (SVA-E) retrotransposon element, which was present in a mosaic state in the mother. This SVA-E insertion disrupts correct splicing of the gene, resulting in loss of a functional allele. This case demonstrates the power of OGM and long-read sequencing to identify genomic variations in high-risk cancer-predisposing genes that are refractory to detection with standard techniques, thereby completing the clinical and molecular diagnosis of such complex cases and greatly improving counseling and surveillance of the families involved. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.
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- 2021
25. Refining diffuse large B-cell lymphoma subgroups using integrated analysis of molecular profiles
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Bettina Fabiani, Sylvain Mareschal, Pascaline Etancelin, Tony Petrella, Fabrice Jardin, Bruno Tesson, Sydney Dubois, Jean-Philippe Jais, Christiane Copie-Bergman, Gilles Salles, Elodie Bohers, Corinne Haioun, Pierre-Julien Viailly, Thierry Jo Molina, Philippe Ruminy, Karen Leroy, Hervé Tilly, Pauline Peyrouze, Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques (GPMCND), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Carnot CALYM [Pierre-Benite], Synergie Lyon Cancer-Platform of Bioinformatics-Gilles Thomas, Centre de Recherche en Cancérologie de Lyon (UNICANCER/CRCL), Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Lutte Contre le Cancer Henri Becquerel Normandie Rouen (CLCC Henri Becquerel), Université Lille 2 - Faculté de Médecine, INSERM U955, équipe 9, Département de pathologie [Mondor], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-IFR10-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-IFR10, Service de Pathologie [CHU Saint-Antoine], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Centre de pathologie, Service d'informatique médicale et biostatistiques [CHU Necker], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université Paris-Est Créteil Val-de-Marne - Faculté de médecine (UPEC Médecine), Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Service d'hématologie [Hôpital Edouard Herriot - HCL], Hôpital Edouard Herriot [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Service d'anatomie pathologique [CHU Necker], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Département d'Hématologie, Institut Carnot Lymphome (CALYM), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Faculté de Médecine Henri Warembourg - Université de Lille, Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), and Centre de pathologie [Dijon]
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0301 basic medicine ,Male ,Research paper ,Key genes ,Transcriptomic variability ,DNA Copy Number Variations ,lcsh:Medicine ,[SDV.CAN]Life Sciences [q-bio]/Cancer ,Locus (genetics) ,Computational biology ,Independent component analysis ,Biology ,General Biochemistry, Genetics and Molecular Biology ,Transcriptome ,03 medical and health sciences ,0302 clinical medicine ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,hemic and lymphatic diseases ,medicine ,Biomarkers, Tumor ,Humans ,Genetic Predisposition to Disease ,Copy-number variation ,Gene signatures, prognosis ,Genetic Association Studies ,lcsh:R5-920 ,Gene Expression Profiling ,lcsh:R ,Gene signatures ,Chromosome Mapping ,Computational Biology ,[SDV.MHEP.HEM]Life Sciences [q-bio]/Human health and pathology/Hematology ,Molecular Sequence Annotation ,General Medicine ,Diffuse large B-cell lymphoma ,Gene signature ,medicine.disease ,Immunohistochemistry ,Gene expression profiling ,030104 developmental biology ,030220 oncology & carcinogenesis ,Affymetrix genechip ,Female ,prognosis ,Lymphoma, Large B-Cell, Diffuse ,lcsh:Medicine (General) - Abstract
Background: Gene expression profiling (GEP), next-generation sequencing (NGS) and copy number variation (CNV) analysis have led to an increasingly detailed characterization of the genomic profiles of DLBCL. The aim of this study was to perform a fully integrated analysis of mutational, genomic, and expression profiles to refine DLBCL subtypes. A comparison of our model with two recently published integrative DLBCL classifiers was carried out, in order to best reflect the current state of genomic subtypes. Methods: 223 patients with de novo DLBCL from the prospective, multicenter and randomized LNH-03B LYSA clinical trials were included. GEP data was obtained using Affymetrix GeneChip arrays, mutational profiles were established by Lymphopanel NGS targeting 34 key genes, CNV analysis was obtained by array CGH, and FISH and IHC were performed. Unsupervised independent component analysis (ICA) was applied to GEP data and integrated analysis of multi-level molecular data associated with each component (gene signature) was performed. Findings: ICA identified 38 components reflecting transcriptomic variability across our DLBCL cohort. Many of the components were closely related to well-known DLBCL features such as cell-of-origin, stromal and MYC signatures. A component linked to gain of 19q13 locus, among other genomic alterations, was significantly correlated with poor OS and PFS. Through this integrated analysis, a high degree of heterogeneity was highlighted among previously described DLBCL subtypes. Interpretation: The results of this integrated analysis enable a global and multi-level view of DLBCL, as well as improve our understanding of DLBCL subgroups. Keywords: Diffuse large B-cell lymphoma, Independent component analysis, Transcriptomic variability, Gene signatures, prognosis
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- 2019
26. The transcription factor EGR2 is the molecular linchpin connecting STAT6 activation to the late, stable epigenomic program of alternative macrophage polarization
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Petros Tzerpos, Pal Boto, Attila Bacsi, László Halász, Zsolt Czimmerer, Sascha Sauer, Istvan Szatmari, Anikó Nagy, Gyorgy Hajas, Bence Daniel, Wilhelm K. Berger, Attila Horvath, Gergely Nagy, Szilárd Póliska, Jean Francois-Deleuze, Laszlo Nagy, Zsuzsanna Kolostyak, and Timea Cseh
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Transcriptional Activation ,Macrophage polarization ,Context (language use) ,RNA polymerase II ,Biology ,Epigenesis, Genetic ,03 medical and health sciences ,Mice ,0302 clinical medicine ,Genetics ,Animals ,Humans ,Protein Interaction Domains and Motifs ,Transcription factor ,Conserved Sequence ,Early Growth Response Protein 2 ,030304 developmental biology ,Epigenomics ,STAT6 ,0303 health sciences ,Genome ,Macrophages ,Cell Polarity ,Chromosome Mapping ,Gene signature ,Macrophage Activation ,respiratory system ,Chromatin ,Cell biology ,Mice, Inbred C57BL ,Enhancer Elements, Genetic ,Gene Expression Regulation ,030220 oncology & carcinogenesis ,biology.protein ,Interleukin-4 ,Technology Platforms ,STAT6 Transcription Factor ,Transcriptome ,Outlook ,Developmental Biology ,Research Paper ,Signal Transduction - Abstract
Macrophages polarize into functionally distinct subtypes while responding to microenvironmental cues. The identity of proximal transcription factors (TFs) downstream from the polarization signals are known, but their activity is typically transient, failing to explain the long-term, stable epigenomic programs developed. Here, we mapped the early and late epigenomic changes of interleukin-4 (IL-4)-induced alternative macrophage polarization. We identified the TF, early growth response 2 (EGR2), bridging the early transient and late stable gene expression program of polarization. EGR2 is a direct target of IL-4-activated STAT6, having broad action indispensable for 77% of the induced gene signature of alternative polarization, including its autoregulation and a robust, downstream TF cascade involving PPARG. Mechanistically, EGR2 binding results in chromatin opening and the recruitment of chromatin remodelers and RNA polymerase II. Egr2 induction is evolutionarily conserved during alternative polarization of mouse and human macrophages. In the context of tissue resident macrophages, Egr2 expression is most prominent in the lung of a variety of species. Thus, EGR2 is an example of an essential and evolutionarily conserved broad acting factor, linking transient polarization signals to stable epigenomic and transcriptional changes in macrophages.
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- 2020
27. Genetic architecture of plant stress resistance: multi-trait genome-wide association mapping
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Thoen, Manus P M, Davila Olivas, Nelson H., Kloth, Karen J., Coolen, Silvia, Huang, Ping Ping, Aarts, Mark G M, Bac-Molenaar, Johanna A., Bakker, Jaap, Bouwmeester, Harro J., Broekgaarden, Colette, Bucher, Johan, Busscher-Lange, Jacqueline, Cheng, Xi, Fradin, Emilie F., Jongsma, Maarten A., Julkowska, Magdalena M., Keurentjes, Joost J B, Ligterink, Wilco, Pieterse, Corné M J, Ruyter-Spira, Carolien, Smant, Geert, Testerink, Christa, Usadel, Björn, van Loon, Joop J A, van Pelt, Johan A., van Schaik, Casper C., van Wees, Saskia C M, Visser, Richard G F, Voorrips, Roeland, Vosman, Ben, Vreugdenhil, Dick, Warmerdam, Sonja, Wiegers, Gerrie L., van Heerwaarden, Joost, Kruijer, Willem, van Eeuwijk, Fred A., Dicke, Marcel, Sub Plant-Microbe Interactions, Dynamics of Innovation Systems, Sub Plant-Microbe Interactions, Dynamics of Innovation Systems, Plant Hormone Biology (SILS, FNWI), Plant Cell Biology (SILS, FNWI), and Plant Physiology (SILS, FNWI)
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0106 biological sciences ,0301 basic medicine ,genome‐wide association mapping ,Physiology ,Arabidopsis ,Inheritance Patterns ,Genome-wide association study ,Plant Science ,01 natural sciences ,Wiskundige en Statistische Methoden - Biometris ,Laboratorium voor Plantenveredeling ,Plant Growth Regulators ,Laboratorium voor Plantenfysiologie ,Laboratory of Entomology ,PBR Groei & Ontwikkeling ,Abiotic component ,Genetics ,PBR Kwantitatieve aspecten ,Full Paper ,Entomology & Disease Management ,Chromosome Mapping ,food and beverages ,Full Papers ,PBR Breeding for growth and development ,PE&RC ,Phenotype ,ddc:580 ,Biometris ,Plant Production Systems ,BIOS Applied Metabolic Systems ,Laboratory of Plant Physiology ,DNA, Bacterial ,PBR Non host and insect resistance ,abiotic stress ,genome-wide association mapping ,Quantitative Trait Loci ,Single-nucleotide polymorphism ,Quantitative trait locus ,Biology ,Genes, Plant ,PBR Quantitative aspects of Plant Breeding ,03 medical and health sciences ,biotic stress ,Stress, Physiological ,Groep Koornneef ,BIOS Plant Development Systems ,Mathematical and Statistical Methods - Biometris ,Laboratorium voor Nematologie ,Genetic Association Studies ,Models, Genetic ,Abiotic stress ,Research ,Reproducibility of Results ,Robustness (evolution) ,Biotic stress ,Laboratorium voor Entomologie ,genetic architecture ,Genetic architecture ,Plant Breeding ,030104 developmental biology ,Plantaardige Productiesystemen ,Mutation ,multiple stresses ,EPS ,Laboratory of Nematology ,PBR Non host en Insectenresistentie ,Genome-Wide Association Study ,010606 plant biology & botany - Abstract
The new phytologist 213(3), 1346-1362 (2017). doi:10.1111/nph.14220, Published by Wiley-Blackwell, Oxford [u.a.]
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- 2017
28. Admixture mapping in interspecific Populus hybrids identifies classes of genomic architectures for phytochemical, morphological and growth traits
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C. Alex Buerkle, Stefano Castiglione, Daniel Wegmann, Christian Lexer, Celine Caseys, and Luisa Bresadola
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0106 biological sciences ,0301 basic medicine ,Candidate gene ,Physiology ,Phytochemicals ,fitness- related traits ,Genome-wide association study ,Plant Science ,natural hybrids ,heritability ,01 natural sciences ,Linkage Disequilibrium ,RAD-seq ,admixture mapping ,fitness-related traits ,genomic architecture ,polygenic modeling ,Populus ,2.1 Biological and endogenous factors ,Aetiology ,Genetics ,Genome ,Full Paper ,Chromosome Mapping ,fitness‐related traits ,Biological Sciences ,Full Papers ,Phenotype ,Genome, Plant ,Biotechnology ,Plant Biology & Botany ,Genetic admixture ,Biology ,Quantitative Trait ,03 medical and health sciences ,Quantitative Trait, Heritable ,Hybrid zone ,Genetic ,Species Specificity ,RAD‐seq ,Hybridization ,Heritable ,Gene ,Probability ,Hybrid ,Agricultural and Veterinary Sciences ,Research ,Human Genome ,Plant ,Phenotypic trait ,Heritability ,030104 developmental biology ,Hybridization, Genetic ,Genome-Wide Association Study ,010606 plant biology & botany - Abstract
The genomic architecture of functionally important traits is key to understanding the maintenance of reproductive barriers and trait differences when divergent populations or species hybridize. We conducted a genome-wide association study (GWAS) to study trait architecture in natural hybrids of two ecologically divergent Populus species. We genotyped 472 seedlings from a natural hybrid zone of Populus alba and Populus tremula for genome-wide markers from reduced representation sequencing, phenotyped the plants in common gardens for 46 phytochemical (phenylpropanoid), morphological and growth traits, and used a Bayesian polygenic model for mapping. We detected three classes of genomic architectures: traits with finite, detectable associations of genetic loci with phenotypic variation in addition to highly polygenic heritability; traits with indications for polygenic heritability only; and traits with no detectable heritability. For the first class, we identified genome regions with plausible candidate genes for phenylpropanoid biosynthesis or its regulation, including MYB transcription factors and glycosyl transferases. GWAS in natural, recombinant hybrids represent a promising step towards resolving the genomic architecture of phenotypic traits in long-lived species. This facilitates the fine-mapping and subsequent functional characterization of genes and networks causing differences in hybrid performance and fitness.
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- 2019
29. Dominant inhibition of awn development by a putative zinc‐finger transcriptional repressor expressed at the B1 locus in wheat
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Nikolai M. Adamski, Catherine Chinoy, Paul Nicholson, Curt A. McCartney, Yasmina Bekkaoui, Sateesh Kagale, Qian Zheng, Frank M. You, Tancey Melchkart, J. Allan Feurtado, Martha Clarke, David Konkin, Daiqing Huang, Adrian J. Cutler, Martial Martucci, and A. Steed
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0106 biological sciences ,0301 basic medicine ,Physiology ,Mutant ,Amino Acid Motifs ,Plant Science ,01 natural sciences ,Gene Expression Regulation, Plant ,Chromosome Segregation ,wheat ,Coding region ,B1 Locus ,Triticum ,Genes, Dominant ,Plant Proteins ,Zinc finger ,Genetics ,education.field_of_study ,C2H2 Zinc Finger ,Full Paper ,Chromosome Mapping ,food and beverages ,Genetic Pleiotropy ,Zinc Fingers ,Bread ,Full Papers ,awnletted ,Multigene Family ,Population ,Plant Development ,Locus (genetics) ,Biology ,03 medical and health sciences ,Open Reading Frames ,transcriptional repression ,Deletion mapping ,education ,Gene ,Cell Proliferation ,Polymorphism, Genetic ,Indoleacetic Acids ,zinc finger ,Research ,awn ,transcription repression ,Repressor Proteins ,030104 developmental biology ,Haplotypes ,C2H2 ,Genetic Loci ,Mutation ,EAR motif ,010606 plant biology & botany - Abstract
Summary Awns, bristle‐like structures extending from grass lemmas, provide protection against predators, contribute to photosynthesis and aid in grain dispersal. In wheat, selection of awns with minimal extension, termed awnletted, has occurred during domestication by way of loci that dominantly inhibit awn development, such as Tipped1 (B1), Tipped2 (B2), and Hooded (Hd). Here we identify and characterize the B1 gene. B1 was identified using bulked segregant RNA‐sequencing of an F2 durum wheat population and through deletion mapping of awned bread wheat mutants. Functional characterization was accomplished by gene overexpression while haplotype analyses assessed B1 polymorphisms and genetic variation.Located on chromosome 5A, B1 is a C2H2 zinc finger encoding gene with ethylene‐responsive element binding factor‐associated amphiphilic repression (EAR) motifs. Constitutive overexpression of B1 in awned wheat produced an awnletted phenotype with pleiotropic effects on plant height and fertility. Transcriptome analysis of B1 overexpression plants suggests a role as transcriptional repressor, putatively targeting pathways involved in cell proliferation. Haplotype analysis revealed a conserved B1 coding region with proximal polymorphisms and supported the contention that B1 is mainly responsible for awnletted wheats globally. B1, predominantly responsible for awn inhibition in wheat, encodes a C2H2 zinc finger protein with EAR motifs which putatively functions as a transcriptional repressor.
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- 2019
30. Predicting target genes of non-coding regulatory variants with IRT
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Nilah M. Ioannidis, Zhenqin Wu, and James Zou
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Statistics and Probability ,Candidate gene ,Quantitative Trait Loci ,Inference ,Genome-wide association study ,Computational biology ,Biology ,Biochemistry ,Polymorphism, Single Nucleotide ,DNA sequencing ,03 medical and health sciences ,0302 clinical medicine ,Humans ,Molecular Biology ,Gene ,030304 developmental biology ,Genetic association ,0303 health sciences ,Chromosome Mapping ,Original Papers ,Computer Science Applications ,Histone Code ,Computational Mathematics ,Phenotype ,Computational Theory and Mathematics ,Expression quantitative trait loci ,Trait ,030217 neurology & neurosurgery ,Genome-Wide Association Study - Abstract
Summary Interpreting genetic variants of unknown significance (VUS) is essential in clinical applications of genome sequencing for diagnosis and personalized care. Non-coding variants remain particularly difficult to interpret, despite making up a large majority of trait associations identified in genome-wide association studies (GWAS) analyses. Predicting the regulatory effects of non-coding variants on candidate genes is a key step in evaluating their clinical significance. Here, we develop a machine-learning algorithm, Inference of Connected expression quantitative trait loci (eQTLs) (IRT), to predict the regulatory targets of non-coding variants identified in studies of eQTLs. We assemble datasets using eQTL results from the Genotype-Tissue Expression (GTEx) project and learn to separate positive and negative pairs based on annotations characterizing the variant, gene and the intermediate sequence. IRT achieves an area under the receiver operating characteristic curve (ROC-AUC) of 0.799 using random cross-validation, and 0.700 for a more stringent position-based cross-validation. Further evaluation on rare variants and experimentally validated regulatory variants shows a significant enrichment in IRT identifying the true target genes versus negative controls. In gene-ranking experiments, IRT achieves a top-1 accuracy of 50% and top-3 accuracy of 90%. Salient features, including GC-content, histone modifications and Hi-C interactions are further analyzed and visualized to illustrate their influences on predictions. IRT can be applied to any VUS of interest and each candidate nearby gene to output a score reflecting the likelihood of regulatory effect on the expression level. These scores can be used to prioritize variants and genes to assist in patient diagnosis and GWAS follow-up studies. Availability and implementation Codes and data used in this work are available at https://github.com/miaecle/eQTL_Trees. Supplementary information Supplementary data are available at Bioinformatics online.
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- 2020
31. Diversification of piRNAs expressed in PGCs and somatic cells during embryonic gonadal development
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Jesús del Mazo, Eduardo Larriba, Daniel Fernández-Pérez, Miguel A. Brieño-Enríquez, Odei Barreñada, Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Eunice Kennedy Shriver National Institute of Child Health and Human Development (US), Magee-Womens Research Institute and Foundation, Barreñada, Odei, Fernández-Pérez, D., Larriba, E., Brieño-Enríquez, Miguel A., Del Mazo, Jesús, Barreñada, Odei [0000-0003-2908-8176], Fernández-Pérez, D. [0000-0002-1679-6555], Larriba, E. [0000-0001-8838-4974], Brieño-Enríquez, Miguel A. [0000-0002-8806-0918], and Del Mazo, Jesús [0000-0003-3269-3895]
- Subjects
Male ,Transposable element ,endocrine system ,Somatic cell ,Embryonic Development ,Piwi-interacting RNA ,Biology ,snoRNA ,Mice ,03 medical and health sciences ,0302 clinical medicine ,RNA, Transfer ,piR NA ,Animals ,RNA, Small Interfering ,Small nucleolar RNA ,rRNA ,Gonads ,Molecular Biology ,tRNA ,Repetitive Sequences, Nucleic Acid ,030304 developmental biology ,0303 health sciences ,urogenital system ,PGC ,Chromosome Mapping ,Computational Biology ,Gene Expression Regulation, Developmental ,Genes, rRNA ,Genomics ,Cell Biology ,Ribosomal RNA ,Embryonic stem cell ,Cell biology ,Germ Cells ,030220 oncology & carcinogenesis ,Transfer RNA ,DNA Transposable Elements ,Female ,RNA Interference ,Embryonic gonads ,Transposable elements ,Biogenesis ,Research Paper - Abstract
44 p.-8 fig.-3 tab.-4 fig. supl.-1 tab. supl., piRNAs are small non-coding RNAs known to play a main role in defence against transposable elements in germ cells. However, other potential functions, such as biogenesis and differences in somatic and germline expression of these regulatory elements, are not yet fully unravelled. Here, we analysed a variety of piRNA sequences detected in mouse male and female primordial germ cells (PGCs) and gonadal somatic cells at crucial stages during embryonic differentiation of germ cells (11.5–13.5 days post-coitum). NGS of sncRNA and bioinformatic characterization of piRNAs from PGCs and somatic cells, in addition to piRNAs associated with TEs, indicated functional diversification in both cell types. Differences in the proportion of the diverse types of piRNAs are detected between somatic and germline during development. However, the global diversified patterns of piRNA expression are mainly shared between germ and somatic cells, we identified piRNAs related with molecules involved in ribosome components and translation pathway, including piRNAs derived from rRNA (34%), tRNA (10%) and snoRNA (8%). piRNAs from both tRNA and snoRNA are mainly derived from 3ʹ and 5ʹ end regions. These connections between piRNAs and rRNAs, tRNAs or snoRNAs suggest important functions of specialized piRNAs in translation regulation during this window of gonadal development., This study was supported by the Agencia Estatal de Investigación; Ministerio de Ciencia, Innovación y Universidades (BFU2017-87095-R), Spain. ; ; M.A.B-E was supported by Eunice Kennedy Shriver National Institute of Child Health and Human Development [4R00HD090289-03] and the Magee Auxiliary Research Scholar (MARS).
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- 2020
32. Comparing Methods for Record Linkage for Public Health Action: Matching Algorithm Validation Study
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Brandon L. Guthrie, Mauricio Sadinle, Janet G. Baseman, Tigran Avoundjian, James P. Hughes, Matthew R. Golden, and Julia C. Dombrowski
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Sexually transmitted disease ,public health practice ,Matching (statistics) ,medical record linkage ,Computer science ,Health Informatics ,Context (language use) ,Validation Studies as Topic ,030312 virology ,03 medical and health sciences ,0302 clinical medicine ,Statistics ,Electronic Health Records ,Humans ,Probabilistic analysis of algorithms ,030212 general & internal medicine ,Pandemics ,Original Paper ,0303 health sciences ,Public Health, Environmental and Occupational Health ,Probabilistic logic ,COVID-19 ,Chromosome Mapping ,Reproducibility of Results ,public health surveillance ,Data quality ,Public Health ,data management ,Public aspects of medicine ,RA1-1270 ,Precision and recall ,Algorithms ,Record linkage - Abstract
Background Many public health departments use record linkage between surveillance data and external data sources to inform public health interventions. However, little guidance is available to inform these activities, and many health departments rely on deterministic algorithms that may miss many true matches. In the context of public health action, these missed matches lead to missed opportunities to deliver interventions and may exacerbate existing health inequities. Objective This study aimed to compare the performance of record linkage algorithms commonly used in public health practice. Methods We compared five deterministic (exact, Stenger, Ocampo 1, Ocampo 2, and Bosh) and two probabilistic record linkage algorithms (fastLink and beta record linkage [BRL]) using simulations and a real-world scenario. We simulated pairs of datasets with varying numbers of errors per record and the number of matching records between the two datasets (ie, overlap). We matched the datasets using each algorithm and calculated their recall (ie, sensitivity, the proportion of true matches identified by the algorithm) and precision (ie, positive predictive value, the proportion of matches identified by the algorithm that were true matches). We estimated the average computation time by performing a match with each algorithm 20 times while varying the size of the datasets being matched. In a real-world scenario, HIV and sexually transmitted disease surveillance data from King County, Washington, were matched to identify people living with HIV who had a syphilis diagnosis in 2017. We calculated the recall and precision of each algorithm compared with a composite standard based on the agreement in matching decisions across all the algorithms and manual review. Results In simulations, BRL and fastLink maintained a high recall at nearly all data quality levels, while being comparable with deterministic algorithms in terms of precision. Deterministic algorithms typically failed to identify matches in scenarios with low data quality. All the deterministic algorithms had a shorter average computation time than the probabilistic algorithms. BRL had the slowest overall computation time (14 min when both datasets contained 2000 records). In the real-world scenario, BRL had the lowest trade-off between recall (309/309, 100.0%) and precision (309/312, 99.0%). Conclusions Probabilistic record linkage algorithms maximize the number of true matches identified, reducing gaps in the coverage of interventions and maximizing the reach of public health action.
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- 2020
33. Mapping a double flower phenotype-associated gene DcAP2L in Dianthus chinensis
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Xiaopeng Fu, Xiaoni Zhang, Shengnan Lin, Mohammed Bendahmane, Manzhu Bao, Shaozong Yang, Xiuli Yan, Qijian Wang, Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University [Wuhan] (HZAU), Reproduction et développement des plantes (RDP), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and National Natural Science Foundation of China (NSFC)31872135Fundamental Research Funds for the Central Universities2662018JC036
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0106 biological sciences ,0301 basic medicine ,QTL mapping ,Candidate gene ,Genetic Linkage ,Physiology ,Single-nucleotide polymorphism ,Flowers ,Plant Science ,Biology ,Quantitative trait locus ,Polymorphism, Single Nucleotide ,01 natural sciences ,03 medical and health sciences ,ddRAD ,Dianthus ,Genotype ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,double flower trait ,miR172 ,[SDV.BDD]Life Sciences [q-bio]/Development Biology ,2. Zero hunger ,Genetics ,BSR-seq ,AcademicSubjects/SCI01210 ,fungi ,Chromosome Mapping ,food and beverages ,biology.organism_classification ,Research Papers ,Phenotype ,030104 developmental biology ,[SDE]Environmental Sciences ,Dianthus chinensis ,Petal ,Growth and Development ,Flower formation ,APETALA2 (DcAP2L) ,010606 plant biology & botany - Abstract
An SNP mutation in the miR172 target site of the DcAP2L gene is associated with a double flower phenotype in Dianthus chinensis., The double flower is a highly important breeding trait that affects the ornamental value in many flowering plants. To get a better understanding of the genetic mechanism of double flower formation in Dianthus chinensis, we have constructed a high-density genetic map using 140 F2 progenies derived from a cross between a single flower genotype and a double flower genotype. The linkage map was constructed using double-digest restriction site-associated DNA sequencing (ddRAD-seq) with 2353 single nucleotide polymorphisms (SNPs). Quantitative trait locus (QTL) mapping analysis was conducted for 12 horticultural traits, and major QTLs were identified for nine of the 12 traits. Among them, two major QTLs accounted for 20.7% and 78.1% of the total petal number variation, respectively. Bulked segregant RNA-seq (BSR-seq) was performed to search accurately for candidate genes associated with the double flower trait. Integrative analysis of QTL mapping and BSR-seq analysis using the reference genome of Dianthus caryophyllus suggested that an SNP mutation in the miR172 cleavage site of the A-class flower organ identity gene APETALA2 (DcAP2L) is responsible for double flower formation in Dianthus through regulating the expression of DcAG genes.
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- 2020
34. Seed dormancy release accelerated by elevated partial pressure of oxygen is associated with DOG loci
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Jan Kodde, Leónie Bentsink, Gonda Buijs, and Steven P.C. Groot
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0106 biological sciences ,0301 basic medicine ,EPPO ,Arabidopsis thaliana ,Physiology ,Partial Pressure ,Quantitative Trait Loci ,Arabidopsis ,Germination ,Plant Science ,Common method ,elevated partial pressure of oxygen ,Quantitative trait locus ,Biology ,01 natural sciences ,03 medical and health sciences ,DOG ,BIOS Plant Development Systems ,Laboratorium voor Plantenfysiologie ,Arabidopsis Proteins ,Seed dormancy ,seed dormancy ,food and beverages ,Chromosome Mapping ,Partial pressure ,Delay of Germination ,Plant Dormancy ,Research Papers ,Oxygen ,Horticulture ,030104 developmental biology ,Stratification (seeds) ,Ageing ,Genetic Loci ,quantitative trait loci ,Seeds ,Dormancy ,After-ripening ,Growth and Development ,EPS ,Laboratory of Plant Physiology ,010606 plant biology & botany - Abstract
Storage of seeds under elevated partial pressure of oxygen mimics dry after-ripening at the genetic level, as indicated by identification of DELAY OF GERMINATION quantitative trait loci., Seed dormancy determines the timing of seed germination and may be released by dry storage, also referred to as after-ripening. Studies on dormancy-release mechanisms are often hampered by the long after-ripening requirements of seeds. After-ripening is thought to be mainly caused by oxidative processes during seed dry storage. These processes are also the main cause of seed ageing. Increasing partial oxygen pressure through the elevated partial pressure of oxygen (EPPO) system has been shown to mimic and accelerate dry seed ageing. In this study, we investigated whether the EPPO system may also release primary seed dormancy in Arabidopsis thaliana. EPPO mimics dry after-ripening at the genetic level, as quantitative trait locus (QTL) analysis after EPPO treatment identified the DELAY OF GERMINATION loci DOG1, DOG2, and DOG6 that were first described in a study using dry after-ripening to release seed dormancy. QTL analysis also showed that dormancy release by cold stratification (another common method to break seed dormancy) partly overlaps with release by after-ripening and EPPO treatment. We conclude that EPPO is an appropriate method to mimic and accelerate dormancy release and, as such, may have applications in both research and industry.
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- 2018
35. Genome-wide gene expression analysis of amphioxus (Branchiostoma belcheri) following lipopolysaccharide challenge using strand-specific RNA-seq
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Xiu-Qiang Wang, Jun-Yuan Chen, Qian-Hua Zhu, Bin Xu, Zheng-Qing Xie, and Qi-Lin Zhang
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0301 basic medicine ,Lipopolysaccharides ,strand-specific RNA-seq ,RNA-Seq ,Biology ,immune response ,Transcriptome ,03 medical and health sciences ,0302 clinical medicine ,Immune system ,transcriptome analysis ,Gene expression ,Animals ,Molecular Biology ,Gene ,Lancelets ,Genetics ,Sequence Analysis, RNA ,Gene Expression Profiling ,lipopolysaccharide ,Branchiostoma belcheri ,RNA ,Chromosome Mapping ,Computational Biology ,Reproducibility of Results ,Cell Biology ,Ribosomal RNA ,Molecular biology ,Biological Evolution ,Immunity, Innate ,Gene expression profiling ,evolutionary immunity ,030104 developmental biology ,Gene Ontology ,030217 neurology & neurosurgery ,Research Paper ,Genome-Wide Association Study - Abstract
Amphioxus is the closest living proxy for exploring the evolutionary origin of the immune system in vertebrates. To understand the immune responses of amphioxus to lipopolysaccharide (LPS), 5 ribosomal RNA (rRNA)-depleted libraries of amphioxus were constructed, including one control (0 h) library and 4 treatment libraries at 6, 12, 24, and 48 h post-injection (hpi) with LPS. The transcriptome of Branchiostoma belcheri was analyzed using strand-specific RNA sequencing technology (RNA-seq). A total of 6161, 6665, 7969, and 6447 differentially expressed genes (DEGs) were detected at 6, 12, 24, and 48 hpi, respectively, compared with expression levels at 0 h. We identified amphioxus genes active during the acute-phase response to LPS at different time points after stimulation. Moreover, to better visualize the resolution phase of the immune process during immune response, we identified 6057 and 5235 DEGs at 48 hpi by comparing with 6 and 24 hpi, respectively. Through real-time quantitative PCR (qRT-PCR) analysis of 12 selected DEGs, we demonstrated the accuracy of the RNA-seq data in this study. Functional enrichment analysis of DEGs demonstrated that most terms were related to defense and immune responses, disease and infection, cell apoptosis, and metabolism and catalysis. Subsequently, we identified 1330, 485, 670, 911, and 1624 time-specific genes (TSGs) at 0, 6, 12, 24, and 48 hpi. Time-specific terms at each of 5 time points were primarily involved in development, immune signaling, signal transduction, DNA repair and stability, and metabolism and catalysis, respectively. As this is the first study to report the transcriptome of an organism with primitive immunity following LPS challenge at multiple time points, it provides gene expression information for further research into the evolution of immunity in vertebrates.
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- 2017
36. Rapid mapping and cloning of the virescent-1 gene in cotton by bulked segregant analysis–next generation sequencing and virus-induced gene silencing strategies
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Chenyu Xu, Jiankun Zhu, Kun Chen, Zhanfeng Si, Huaitong Wu, Tianzhen Zhang, Hu Yan, Fengkai Gao, and Jiedan Chen
- Subjects
0106 biological sciences ,0301 basic medicine ,Candidate gene ,map-based clone ,Physiology ,Bulked segregant analysis ,Mutant ,Locus (genetics) ,Plant Science ,Quantitative trait locus ,Biology ,01 natural sciences ,Genome ,cotton ,03 medical and health sciences ,VIGS ,Gene mapping ,Gene Silencing ,Cloning, Molecular ,Gene ,Plant Proteins ,Genetics ,Gossypium ,Chromosome Mapping ,High-Throughput Nucleotide Sequencing ,Research Papers ,virescent ,030104 developmental biology ,Crop Molecular Genetics ,Viruses ,010606 plant biology & botany - Abstract
An improved method of rapid gene mapping and identification was successfully used to map and identify the causal gene at the virescent-1 locus of upland cotton., Map-based gene cloning is a vital strategy for the identification of the quantitative trait loci or genes underlying important agronomic traits. The conventional map-based cloning method is powerful but generally time-consuming and labor-intensive. In this context, we introduce an improved bulked segregant analysis method in combination with a virus-induced gene silencing (VIGS) strategy for rapid and reliable gene mapping, identification and functional verification. This method was applied to a multiple recessive marker line of upland cotton, Texas 582 (T582), and identified unique genomic positions harboring mutant loci, showing the reliability and efficacy of this method. The v1 locus was further fine-mapped. Only one gene, GhCHLI, which encodes one of the subunits of Mg chelatase, was differentially down-regulated in T582 compared with TM-1. A point mutation occurred in the AAA+ conserved region of GhCHLI and led to an amino acid substitution. Suppression of its expression by VIGS in TM-1 resulted in a yellow blade phenotype that was similar to T582. This integrated approach provides a paradigm for the rapid mapping and identification of the candidate genes underlying the genetic traits in plants with large and complex genomes in the future.
- Published
- 2017
37. Fine mapping of a quantitative trait locus for spikelet number per panicle in a new plant type rice and evaluation of a near-isogenic line for grain productivity
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Patrick Lumanglas, Analiza G. Tagle, Ritchel B. Gannaban, Mitsuhiro Obara, Yohei Koide, Yoshimichi Fukuta, Tsutomu Ishimaru, Daisuke Fujita, Nobuya Kobayashi, and Kazuhiro Sasaki
- Subjects
0106 biological sciences ,0301 basic medicine ,Physiology ,Population ,Quantitative Trait Loci ,Introgression ,Plant Science ,Biology ,Quantitative trait locus ,Genes, Plant ,01 natural sciences ,Chromosomes, Plant ,03 medical and health sciences ,quantitative trait locus ,yield component ,Tiller ,Grain yield ,education ,total spikelet number per panicle ,Panicle ,Oryza sativa L ,education.field_of_study ,Oryza sativa ,Crop yield ,near-isogenic line ,Chromosome Mapping ,Oryza ,030104 developmental biology ,Agronomy ,Genetic marker ,Indica Group ,Edible Grain ,010606 plant biology & botany ,Research Paper - Abstract
qTSN12.1 and qTSN12.2 genes for total spikelet number per panicle were detected, qTSN12.2 on rice chromosome 12. Grain yield of a near-isogenic line carrying fine-mapped qTSN12.2 was increased by 18–36%., Total spikelet number per panicle (TSN) is one of the determinants of grain productivity in rice (Oryza sativa L.). In this study, we attempted to detect quantitative trait loci (QTLs) for TSN in the introgression lines with high TSN, derived from the cross of Indica Group variety IR 64 with new plant type lines. Two QTLs were detected on the long arm of chromosome 12: qTSN12.1 in the BC4F2 population of YTH63/IR 64 and qTSN12.2 in the BC4F3 population of YTH83/IR 64. TSN of the main tiller was significantly higher in near-isogenic lines (NILs) for qTSN12.1 (IR 64-NIL1; 188.6) and for qTSN12.2 (IR 64-NIL12; 199.4) than in IR 64 (141.2), owing to a significant increase in both primary and secondary branch numbers. These results suggest the critical function of these QTLs in the promotion of rachis branching at the panicle formation stage. Fine mapping of qTSN12.2 revealed six candidate genes in a 92-kb region of the Nipponbare reference genome sequence between flanking markers RM28746 and RM28753. Detailed phenotyping of agronomic traits of IR 64-NIL12 carrying qTSN12.2 showed drastic changes in plant architecture: this line had lower panicle number, longer culm, and longer and wider leaves compared with IR 64. Percentage of fertility and 1000-grain weight tended to be greater, and grain yield per square meter was also greater in IR 64-NIL12 than in IR 64. The newly identified QTLs will be useful for genetic improvement of the yield potential of Indica Group varieties. The markers tightly linked to qTSN12.2 are available for marker-assisted breeding.
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- 2017
38. Dissecting the genetic components of a quantitative trait locus for blood pressure and renal pathology on rat chromosome 3
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Koh-Tan, H.H. Caline, Dashti, Mohammed, Wang, Ting, Beattie, Wendy, Mcclure, John, Young, Barbara, Dominiczak, Anna F., McBride, Martin W., and Graham, Delyth
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Male ,Quantitative Trait Loci ,Blood Pressure ,Kidney ,Rats, Inbred WKY ,Animals, Congenic ,Rats, Inbred SHR ,congenic ,Animals ,Sodium Chloride, Dietary ,Dynamin I ,Oligonucleotide Array Sequence Analysis ,Gene Expression Profiling ,Wistar–Kyoto rat ,Chromosome Mapping ,High-Throughput Nucleotide Sequencing ,pulse pressure ,Sequence Analysis, DNA ,Chromosomes, Mammalian ,radiotelemetry ,stroke-prone spontaneously hypertensive rat ,Rats ,Stroke ,Hypertension ,gene expression ,next-generation sequencing ,profiling ,ORIGINAL PAPERS: Genetic aspects ,salt-sensitivity ,Molecular Chaperones - Abstract
Background: We have previously confirmed the importance of rat chromosome 3 (RNO3) genetic loci on blood pressure elevation, pulse pressure (PP) variability and renal pathology during salt challenge in the stroke-prone spontaneously hypertensive (SHRSP) rat. The aims of this study were to generate a panel of RNO3 congenic sub-strains to genetically dissect the implicated loci and identify positional candidate genes by microarray expression profiling and analysis of next-generation sequencing data.\ud \ud Method and results: A panel of congenic sub-strains were generated containing Wistar-Kyoto (WKY)-introgressed segments of varying size on the SHRSP genetic background, focused within the first 50 Mbp of RNO3. Haemodynamic profiling during salt challenge demonstrated significantly reduced systolic blood pressure, diastolic blood pressure and PP variability in SP.WKYGla3a, SP.WKYGla3c, SP.WKYGla3d and SP.WKYGla3e sub-strains. Only SBP and DBP were significantly reduced during salt challenge in SP.WKYGla3b and SP.WKYGla3f sub-strains, whereas SP.WKYGla3g rats did not differ in haemodynamic response to SHRSP. Those sub-strains demonstrating significantly reduced PP variability during salt challenge also demonstrated significantly reduced renal pathology and proteinuria. Microarray expression profiling prioritized two candidate genes for blood pressure regulation (Dnm1, Tor1b), localized within the common congenic interval shared by SP.WKYGla3d and SP.WKYGla3f strains, and one candidate gene for salt-induced PP variability and renal pathology (Rabgap1), located within the region unique to the SP.WKYGla3d strain. Comparison of next-generation sequencing data identified variants within additional positional genes that are likely to affect protein function.\ud \ud Conclusion: This study has identified distinct intervals on RNO3-containing genes that may be important for blood pressure regulation and renal pathology during salt challenge.
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- 2017
39. The wheat Seven in Absentia gene is associated with increases in biomass and yield in hot climates
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Chris Brien, Delphine Fleury, Ute Baumann, Pauline Thomelin, Radoslaw Suchecki, Penny J. Tricker, Priyanka Kalambettu, Julien P. Bonneau, and Peter Langridge
- Subjects
0106 biological sciences ,0301 basic medicine ,Hot Temperature ,Positional cloning ,Physiology ,Quantitative Trait Loci ,Triticum aestivum ,drought ,Plant Science ,Quantitative trait locus ,Biology ,Genes, Plant ,01 natural sciences ,Chromosomes, Plant ,heat stress ,03 medical and health sciences ,Genetic variation ,Genotype ,Cereal ,Biomass ,Cultivar ,Water-use efficiency ,Allele ,grain ,Promoter Regions, Genetic ,Gene ,E3 ligase ,Triticum ,Biomass (ecology) ,AcademicSubjects/SCI01210 ,Australia ,positional cloning ,Chromosome Mapping ,food and beverages ,Research Papers ,Plant Breeding ,Phenotype ,030104 developmental biology ,Agronomy ,Plant–Environment Interactions ,010606 plant biology & botany - Abstract
We narrowed down a genetic locus associated with improved physiology and yield components in wheat under heat stress to a gene showing sequence and expression variation., Wheat (Triticum aestivum L.) productivity is severely reduced by high temperatures. Breeding of heat-tolerant cultivars can be achieved by identifying genes controlling physiological and agronomical traits when high temperatures occur and using these to select superior genotypes, but no gene underlying genetic variation for heat tolerance has previously been described. We advanced the positional cloning of qYDH.3BL, a quantitative trait locus (QTL) on bread wheat chromosome 3B associated with increased yield in hot and dry climates. The delimited genomic region contained 12 putative genes and a sequence variant in the promoter region of one gene, Seven in absentia, TaSINA. This was associated with the QTL’s effects on early vigour, root growth, plant biomass, and yield components in two distinct wheat populations grown under various growth conditions. Near isogenic lines carrying the positive allele at qYDH.3BL underexpressed TaSINA and had increased vigour and water use efficiency early in development, as well as increased biomass, grain number, and grain weight following heat stress. A survey of worldwide distribution indicated that the positive allele became widespread from the 1950s through the CIMMYT wheat breeding programme but, to date, has been selected only in breeding programmes in Mexico and Australia.
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- 2019
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40. Identification of novel differentially methylated sites with potential as clinical predictors of impaired respiratory function and COPD
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Riccardo E. Marioni, Yanni Zeng, Ian J. Deary, David J. Porteous, Konrad Rawlik, Andrew M. McIntosh, Mairead L. Bermingham, Stewart M Morris, Paul Redmond, Mark Adams, Rosie M. Walker, Heather C. Whalley, Kathryn L. Evans, Caroline Hayward, and Archie Campbell
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Adult ,Epigenomics ,Male ,Research paper ,Quantitative Trait Loci ,Context (language use) ,Bioinformatics ,Epigenesis, Genetic ,03 medical and health sciences ,Pulmonary Disease, Chronic Obstructive ,0302 clinical medicine ,medicine ,Humans ,Respiratory function ,Genetic Predisposition to Disease ,Genetic Association Studies ,030304 developmental biology ,Genetic association ,Aged ,0303 health sciences ,COPD ,business.industry ,Gene Expression Profiling ,Chromosome Mapping ,Computational Biology ,Molecular Sequence Annotation ,Methylation ,DNA Methylation ,Middle Aged ,medicine.disease ,3. Good health ,Phenotype ,030228 respiratory system ,CpG site ,Case-Control Studies ,DNA methylation ,Cohort ,CpG Islands ,Female ,business ,Genome-Wide Association Study - Abstract
BackgroundThe causes of poor respiratory function and COPD are incompletely understood, but it is clear that genes and the environment play a role. As DNA methylation is under both genetic and environmental control, we hypothesised that investigation of differential methylation associated with these phenotypes would permit mechanistic insights, and improve prediction of COPD. We investigated genome-wide differential DNA methylation patterns using the recently released 850K Illumina EPIC array in the largest single population sample to date.MethodsEpigenome-wide association studies (EWASs) of respiratory function and COPD were performed in peripheral blood samples from the Generation Scotland: Scottish Family Health Study (GS:SFHS) cohort (N=3,791; 274 COPD cases and 2,928 controls). In independent COPD incidence data (N=150), significantly differentially methylated sites (DMSs; p−8) were evaluated for their added predictive power when added to a model including clinical variables, age, sex, height and smoking history using receiver operating characteristic analysis. The Lothian Birth Cohort 1936 (LBC1936) was used to replicate association (N=895) and prediction (N=178) results.FindingsWe identified 29 respiratory function and/or COPD associated DMSs, which mapped to genes involved in alternative splicing, JAK-STAT signalling, and axon guidance. In prediction analyses, we observed significant improvement in discrimination between COPD cases and controls (pInterpretationIdentification of novel DMSs has provided insight into the molecular mechanisms regulating respiratory function and aided prediction of COPD risk.FundingWellcome Trust Strategic Award 10436/Z/14/Z.Research in contextEvidence before this studyWe searched for articles in PubMed published in English up to July 25, 2018, with the search terms “DNA methylation” and “respiratory function”, or “COPD”. We found some evidence for association between differential DNA methylation and both respiratory function and COPD. Of the twelve previous studies identified, eight used peripheral blood samples (sample size [N] range = 100-1,085) and four used lung tissue samples (N range = 24-160). The number of CpG loci analysed range from 27,578 to 485,512. These studies have not identified consistent changes in methylation, most likely due to a combination of factors including small sample sizes, technical issues, phenotypic definitions, and study design. In addition, no previous study has: analysed a sample from a large single cohort; used the recently released Illumina EPIC array (which assesses ~850,000 CpG loci); adjusted methylation data and phenotype for smoking history, or used both prevalent and incident COPD electronic health record data.Added value of this studyTo our knowledge, this is the largest single cohort epigenome-wide association study (EWAS) of respiratory function and COPD to date (N=3,791). After applying stringent genome-wide significance criteria (P −8), we found that DNA methylation levels at 29 CpG sites in peripheral blood were associated with respiratory function or COPD. Of these 29, seven were testable in an independent population sample: all seven showed consistent direction of effect between the two samples and three showed replication (pImplications of all the available evidenceThere is now accumulating evidence that DNA methylation in peripheral blood is associated with respiratory function and COPD.Our study has shown that DNA methylation levels at 29 CpG sites are robustly associated with respiratory function and COPD, provide mechanistic insights, and can improve prediction of COPD risk. Further studies are warranted to improve understanding of the aetiology of COPD and to assess the utility of DNA methylation profiling in the clinical management of this condition.
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- 2019
41. A Gaussian process model and Bayesian variable selection for mapping function-valued quantitative traits with incomplete phenotypic data
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Zitong Li, Jarno Vanhatalo, Mikko J. Sillanpää, Department of Mathematics and Statistics, Organismal and Evolutionary Biology Research Programme, Research Centre for Ecological Change, Environmental and Ecological Statistics Group, and Biostatistics Helsinki
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Statistics and Probability ,EXPRESSION ,Computer science ,Bayesian probability ,Posterior probability ,Quantitative Trait Loci ,Feature selection ,Correlation and dependence ,Quantitative trait locus ,Machine learning ,computer.software_genre ,01 natural sciences ,Biochemistry ,010104 statistics & probability ,03 medical and health sciences ,Bayes' theorem ,symbols.namesake ,Mice ,111 Mathematics ,Animals ,0101 mathematics ,VARYING-COEFFICIENT MODELS ,Molecular Biology ,Gaussian process ,030304 developmental biology ,0303 health sciences ,Models, Genetic ,business.industry ,Model selection ,Genetics and Population Analysis ,Chromosome Mapping ,Bayes Theorem ,ASSOCIATION ,Missing data ,Original Papers ,Computer Science Applications ,Computational Mathematics ,Phenotype ,Computational Theory and Mathematics ,symbols ,MAP ,INFERENCE ,Artificial intelligence ,business ,computer - Abstract
Motivation Recent advances in high dimensional phenotyping bring time as an extra dimension into the phenotypes. This promotes the quantitative trait locus (QTL) studies of function-valued traits such as those related to growth and development. Existing approaches for analyzing functional traits utilize either parametric methods or semi-parametric approaches based on splines and wavelets. However, very limited choices of software tools are currently available for practical implementation of functional QTL mapping and variable selection. Results We propose a Bayesian Gaussian process (GP) approach for functional QTL mapping. We use GPs to model the continuously varying coefficients which describe how the effects of molecular markers on the quantitative trait are changing over time. We use an efficient gradient based algorithm to estimate the tuning parameters of GPs. Notably, the GP approach is directly applicable to the incomplete datasets having even larger than 50% missing data rate (among phenotypes). We further develop a stepwise algorithm to search through the model space in terms of genetic variants, and use a minimal increase of Bayesian posterior probability as a stopping rule to focus on only a small set of putative QTL. We also discuss the connection between GP and penalized B-splines and wavelets. On two simulated and three real datasets, our GP approach demonstrates great flexibility for modeling different types of phenotypic trajectories with low computational cost. The proposed model selection approach finds the most likely QTL reliably in tested datasets. Availability and implementation Software and simulated data are available as a MATLAB package ‘GPQTLmapping’, and they can be downloaded from GitHub (https://github.com/jpvanhat/GPQTLmapping). Real datasets used in case studies are publicly available at QTL Archive. Supplementary information Supplementary data are available at Bioinformatics online.
- Published
- 2019
42. Integration of genetic and physical maps of the Primula vulgaris S locus and localization by chromosome in situ hybridization
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Matthew C. Smith, Jinhong Li, Pat Heslop-Harrison, Philip M. Gilmartin, Farah Badakshi, Margaret A. Webster, Jonathan M. Wright, and Jonathan M. Cocker
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0106 biological sciences ,Genetic Markers ,Chromosomes, Artificial, Bacterial ,Primula vulgaris ,DNA, Plant ,Physiology ,Genetic Linkage ,Plant Development ,Locus (genetics) ,Plant Science ,Flowers ,Biology ,Genes, Plant ,01 natural sciences ,DNA sequencing ,Chromosomes, Plant ,S locus ,Evolution, Molecular ,03 medical and health sciences ,Contig Mapping ,Gene mapping ,chromosome in situ ,Centromere ,genetic map ,Gene ,In Situ Hybridization ,030304 developmental biology ,Genetics ,0303 health sciences ,Contig ,Gene map ,Full Paper ,Base Sequence ,Research ,Chromosome ,food and beverages ,Chromosome Mapping ,Full Papers ,Phenotype ,Primula ,Genetic Loci ,Mutation ,heterostyly ,Genome, Plant ,010606 plant biology & botany - Abstract
Summary Heteromorphic flower development in Primula is controlled by the S locus. The S locus genes, which control anther position, pistil length and pollen size in pin and thrum flowers, have not yet been characterized. We have integrated S‐linked genes, marker sequences and mutant phenotypes to create a map of the P. vulgaris S locus region that will facilitate the identification of key S locus genes. We have generated, sequenced and annotated BAC sequences spanning the S locus, and identified its chromosomal location.We have employed a combination of classical genetics and three‐point crosses with molecular genetic analysis of recombinants to generate the map. We have characterized this region by Illumina sequencing and bioinformatic analysis, together with chromosome in situ hybridization.We present an integrated genetic and physical map across the P. vulgaris S locus flanked by phenotypic and DNA sequence markers. BAC contigs encompass a 1.5‐Mb genomic region with 1 Mb of sequence containing 82 S‐linked genes anchored to overlapping BACs. The S locus is located close to the centromere of the largest metacentric chromosome pair.These data will facilitate the identification of the genes that orchestrate heterostyly in Primula and enable evolutionary analyses of the S locus.
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- 2015
43. The RNA-binding landscape of RBM10 and its role in alternative splicing regulation in models of mouse early development
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Rodor, Julie, FitzPatrick, David R., Eyras, Eduardo, and Cáceres, Javier F.
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Male ,RBM10 ,iCLIP ,Embryonic Development ,RNA-binding proteins ,Stem cells ,Alternative splicing ,mandibular cell line ,stem cells ,TARP syndrome ,Gene Knockout Techniques ,Mice ,RNA, Small Nuclear ,Animals ,RNA, Messenger ,Nucleotide Motifs ,Embryonic Stem Cells ,ICLIP ,Binding Sites ,Chromosome Mapping ,High-Throughput Nucleotide Sequencing ,Molecular Sequence Annotation ,Alternative Splicing ,Phenotype ,Gene Expression Regulation ,Spliceosomes ,Mandibular cell line ,Female ,Research Paper ,Genome-Wide Association Study ,Protein Binding - Abstract
Mutations in the RNA-binding protein, RBM10, result in a human syndromic form of cleft palate, termed TARP syndrome. A role for RBM10 in alternative splicing regulation has been previously demonstrated in human cell lines. To uncover the cellular functions of RBM10 in a cell line that is relevant to the phenotype observed in TARP syndrome, we used iCLIP to identify its endogenous RNA targets in a mouse embryonic mandibular cell line. We observed that RBM10 binds to pre-mRNAs with significant enrichment in intronic regions, in agreement with a role for this protein in pre-mRNA splicing. In addition to protein-coding transcripts, RBM10 also binds to a variety of cellular RNAs, including non-coding RNAs, such as spliceosomal small nuclear RNAs, U2 and U12. RNA-seq was used to investigate changes in gene expression and alternative splicing in RBM10 KO mouse mandibular cells and also in mouse ES cells. We uncovered a role for RBM10 in the regulation of alternative splicing of common transcripts in both cell lines but also identified cell-type specific events. Importantly, those pre-mRNAs that display changes in alternative splicing also contain RBM10 iCLIP tags, suggesting a direct role of RBM10 in these events. Finally, we show that depletion of RBM10 in mouse ES cells leads to proliferation defects and to gross alterations in their differentiation potential. These results demonstrate a role for RBM10 in the regulation of alternative splicing in two cell models of mouse early development and suggests that mutations in RBM10 could lead to splicing changes that affect normal palate development and cause human disease. D.R.F. and J.F.C. were supported by Core funding from the Medical Research Council. J.F.C had also funding from the Wellcome Trust (Grant 095518/Z/11/Z). E.E. was supported by MINECO (Ministerio de Economía y Competitividad) and FEDER (Fondo Europeo de Desarrollo Regional) through grant BIO2014-52566-R, by Sandra Ibarra Foundation for Cancer and by AGAUR (Agència de Gestió d'Ajuts Universitaris i de Recerca) through grant 2014-SGR1121.
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- 2016
44. A single cytosine deletion in the OsPLS1 gene encoding vacuolar-type H+-ATPase subunit A1 leads to premature leaf senescence and seed dormancy in rice
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Yang Xi, Fudeng Huang, Fangmin Cheng, Kunyu Li, Gong Pan, and Gang Pan
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0106 biological sciences ,0301 basic medicine ,Senescence ,Aging ,Vacuolar Proton-Translocating ATPases ,Physiology ,Mutant ,premature leaf senescence ,Plant Science ,Biology ,Genes, Plant ,Real-Time Polymerase Chain Reaction ,01 natural sciences ,03 medical and health sciences ,chemistry.chemical_compound ,Cytosine ,SA ,Gene expression ,Oryza sativa L ,Cloning, Molecular ,Abscisic acid ,health care economics and organizations ,Sequence Deletion ,Genetics ,vacuolar-type H+-ATPase ,Wild type ,Seed dormancy ,OsPLS1 ,seed dormancy ,food and beverages ,Chromosome Mapping ,ROS ,Oryza ,Plant Dormancy ,WRKY protein domain ,Cell biology ,Plant Leaves ,030104 developmental biology ,chemistry ,Dormancy ,Reactive Oxygen Species ,Sequence Analysis ,010606 plant biology & botany ,Research Paper ,Signal Transduction - Abstract
Highlight The OsPLS1 locus that encodes VHA-A1 in rice, was identified by map-based cloning. OsPLS1/VHA-A1 is involved in premature leaf senescence and seed dormancy., Leaf senescence is a programmed developmental process orchestrated by many factors, but its molecular regulation is not yet fully understood. In this study, a novel Oryza sativa premature leaf senescence mutant (ospls1) was examined. Despite normal development in early seedlings, the ospls1 mutant leaves displayed lesion-mimics and early senescence, and a high transpiration rate after tillering. The mutant also showed seed dormancy attributable to physical (defect of micropyle structure) and physiological (abscisic acid sensitivity) factors. Using a map-based cloning approach, we determined that a cytosine deletion in the OsPLS1 gene encoding vacuolar H+-ATPase subunit A1 (VHA-A1) underlies the phenotypic abnormalities in the ospls1 mutant. The OsPSL1/VHA-A1 transcript levels progressively declined with the age-dependent leaf senescence in both the ospls1 mutant and its wild type. The significant decrease in both OsPSL1/VHA-A1 gene expression and VHA enzyme activity in the ospls1 mutant strongly suggests a negative regulatory role for the normal OsPLS1/VHA-A1 gene in the onset of rice leaf senescence. The ospls1 mutant featured higher salicylic acid (SA) levels and reactive oxygen species (ROS) accumulation, and activation of signal transduction by up-regulation of WRKY genes in leaves. Consistent with this, the ospls1 mutant exhibited hypersensitivity to exogenous SA and/or H2O2. Collectively, these results indicated that the OsPSL1/VAH-A1 mutation played a causal role in premature leaf senescence through a combination of ROS and SA signals. To conclude, OsPLS1 is implicated in leaf senescence and seed dormancy in rice.
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- 2016
45. High-density linkage mapping and distribution of segregation distortion regions in the oak genome
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Catherine Bodénès, Antoine Kremer, François Ehrenmann, Christophe Plomion, Emilie Chancerel, Biodiversité, Gènes & Communautés (BioGeCo), and Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)
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0301 basic medicine ,polymorphisme des nucléotides simples ,carte génétique ,high-density linkage map ,Genetic Linkage ,[SDV]Life Sciences [q-bio] ,marqueur génétique ,SNP ,Biology ,Genome ,Polymorphism, Single Nucleotide ,Quercus robur ,analyse de génome ,03 medical and health sciences ,Quercus ,Genetic linkage ,Genetics ,Molecular Biology ,extraction adn ,Chromosome Mapping ,General Medicine ,Reproductive isolation ,Full Papers ,biology.organism_classification ,Genetic load ,reproductive barriers ,segregation distortion ,quercus ,030104 developmental biology ,Quercus petraea ,Genome, Plant ,SNP array - Abstract
International audience; We developed the densest single-nucleotide polymorphism (SNP)-based linkage genetic map to date for the genusQuercus An 8k gene-based SNP array was used to genotype more than 1,000 full-sibs from two intraspecific and two interspecific full-sib families ofQuercus petraeaandQuercus robur A high degree of collinearity was observed between the eight parental maps of the two species. A composite map was then established with 4,261 SNP markers spanning 742 cM over the 12 linkage groups (LGs) of the oak genome. Nine genomic regions from six LGs displayed highly significant distortions of segregation. Two main hypotheses concerning the mechanisms underlying segregation distortion are discussed: genetic load vs. reproductive barriers. Our findings suggest a predominance of pre-zygotic to post-zygotic barriers.
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- 2016
46. Incidentalome from Genomic Sequencing: A Barrier to Personalized Medicine?
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Jiin Ying Lim, Zenia Tiang, Wilson Lek Wen Tan, Angeline Lai, Maggie Brett, Byrappa Venkatesh, Bruno Reversade, Yik Ying Teo, Wendy K.M. Liew, Hai-Yang Law, Jyn Ling Kuan, Ee Shien Tan, Ivy Ng, Roger Foo, Asif Javed, Saumya Shekhar Jamuar, Woei Kang Liew, Ene-Choo Tan, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction & Development (AR&D), and Center for Reproductive Medicine
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0301 basic medicine ,lcsh:Medicine ,Genomics ,030105 genetics & heredity ,Bioinformatics ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Genomic sequencing ,Genetic variation ,Databases, Genetic ,Medicine ,Humans ,Exome ,Precision Medicine ,Gene ,Genetics ,lcsh:R5-920 ,Incidental Findings ,Singapore ,business.industry ,Genome, Human ,lcsh:R ,Chromosome Mapping ,Genetic Variation ,High-Throughput Nucleotide Sequencing ,Molecular Sequence Annotation ,General Medicine ,Precision medicine ,Personalized medicine ,030104 developmental biology ,Cohort ,Mutation ,Human genome ,lcsh:Medicine (General) ,business ,Research Paper - Abstract
Background In Western cohorts, the prevalence of incidental findings (IFs) or incidentalome, referring to variants in genes that are unrelated to the patient's primary condition, is between 0.86% and 8.8%. However, data on prevalence and type of IFs in Asian population is lacking. Methods In 2 cohorts of individuals with genomic sequencing performed in Singapore (total n = 377), we extracted and annotated variants in the 56 ACMG-recommended genes and filtered these variants based on the level of pathogenicity. We then analyzed the precise distribution of IFs, class of genes, related medical conditions, and potential clinical impact. Results We found a total of 41,607 variants in the 56 genes in our cohort of 377 individuals. After filtering for rare and coding variants, we identified 14 potential variants. After reviewing primary literature, only 4 out of the 14 variants were classified to be pathogenic, while an additional two variants were classified as likely pathogenic. Overall, the cumulative prevalence of IFs (pathogenic and likely pathogenic variants) in our cohort was 1.6%. Conclusion The cumulative prevalence of IFs through genomic sequencing is low and the incidentalome may not be a significant barrier to implementation of genomics for personalized medicine., Highlights • We studied the prevalence and type of incidental findings in genomic sequencing data of 377 individuals from South East Asia. • We detected pathogenic variants in 4 individuals and likely pathogenic variants in 2 individuals • Overall, the prevalence of incidental findings in our cohort was 1.6% • The burden of incidental findings may not be a significant barrier to implementation of genomics for personalized medicine Incidental findings (IFs) in genomic sequencing, or incidentalome, refer to variants in genes that may be of medical significance, but unrelated to the patient's primary condition. In analyses of Western cohorts, the prevalence of IFs is reported to be between 0.86% and 8.8%. A study of 196 Korean individuals revealed a frequency of 6–7%. The data on prevalence and type of IFs in Asian populations is lacking. In our cohort of 377 individuals, the cumulative prevalence of IFs is 1.6%, which is similar to what is reported in the Western population. This is the largest study so far that examines IFs specifically in an Asian population. The cumulative prevalence of IFs through genomic sequencing is low and the incidentalome may not be a significant barrier to implementation of genomics for personalized medicine.
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- 2016
47. Next-generation sequencing analysis of lager brewing yeast strains reveals the evolutionary history of interspecies hybridization
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Miki Okuno, Rei Kajitani, Hiroya Morimoto, Takehiko Itoh, Rie Ryusui, and Yukiko Kodama
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0301 basic medicine ,lager beer yeast ,030106 microbiology ,Saccharomyces cerevisiae ,Genome ,DNA sequencing ,Loss of heterozygosity ,Evolution, Molecular ,03 medical and health sciences ,Genetics ,interspecies hybrid ,DNA, Fungal ,Molecular Biology ,Saccharomyces pastorianus ,allopolyploid ,biology ,Strain (biology) ,Saccharomyces eubayanus ,Chromosome Mapping ,General Medicine ,Sequence Analysis, DNA ,Full Papers ,biology.organism_classification ,030104 developmental biology ,Hybridization, Genetic ,loss of heterozygosity ,Ploidy ,Genome, Fungal - Abstract
The lager beer yeast Saccharomyces pastorianus is considered an allopolyploid hybrid species between S. cerevisiae and S. eubayanus. Many S. pastorianus strains have been isolated and classified into two groups according to geographical origin, but this classification remains controversial. Hybridization analyses and partial PCR-based sequence data have indicated a separate origin of these two groups, whereas a recent intertranslocation analysis suggested a single origin. To clarify the evolutionary history of this species, we analysed 10 S. pastorianus strains and the S. eubayanus type strain as a likely parent by Illumina next-generation sequencing. In addition to assembling the genomes of five of the strains, we obtained information on interchromosomal translocation, ploidy, and single-nucleotide variants (SNVs). Collectively, these results indicated that the two groups of strains share S. cerevisiae haploid chromosomes. We therefore conclude that both groups of S. pastorianus strains share at least one interspecific hybridization event and originated from a common parental species and that differences in ploidy and SNVs between the groups can be explained by chromosomal deletion or loss of heterozygosity.
- Published
- 2016
48. Towards understanding the breast cancer epigenome: a comparison of genome-wide DNA methylation and gene expression data
- Author
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Stefan Michiels, Nawaid Usmani, Olga Kovalchuk, Kamal S Saini, Otto Metzger-Filho, Matthew Parliament, and Sandeep Singhal
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0301 basic medicine ,Transcription, Genetic ,Gene Expression ,Breast Neoplasms ,Biology ,Epigenesis, Genetic ,03 medical and health sciences ,breast cancer ,expression ,medicine ,Humans ,Epigenetics ,Promoter Regions, Genetic ,Oligonucleotide Array Sequence Analysis ,Genetics ,DNA methylation ,epigenetics ,Cancer ,Chromosome Mapping ,Promoter ,Epigenome ,Methylation ,DNA ,medicine.disease ,Gene Expression Regulation, Neoplastic ,030104 developmental biology ,Histone ,Oncology ,CpG site ,biology.protein ,CpG Islands ,Female ,microarray ,Research Paper - Abstract
// Sandeep K. Singhal 1, * , Nawaid Usmani 1, * , Stefan Michiels 2, 3 , Otto Metzger-Filho 4 , Kamal S. Saini 5 , Olga Kovalchuk 6, 7, * , Matthew Parliament 1, * 1 Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Canada 2 Service de Biostatistique et d’Epidemiologie, Gustave Roussy, Villejuif, France 3 INSERM U1018, CESP, Universite Paris-Sud, Villejuif, France 4 Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA 5 Quantum Health Analytics SPRL, Liege, Belgium 6 Department of Biological Sciences, University of Lethbridge, Lethbridge, Canada 7 Canada Cancer and Aging Research Laboratories Ltd., Lethbridge, Canada * These authors contributed equally to the work Correspondence to: Matthew Parliament, e-mail: matthew.parliament@albertahealthservices.ca Olga Kovalchuk, e-mail: olga.kovalchuk@uleth.ca and olga.kovalchuk@ccarl.ca Keywords: DNA methylation, breast cancer, epigenetics, expression, microarray Received: August 11, 2015 Accepted: November 16, 2015 Published: December 08, 2015 ABSTRACT Until recently, an elevated disease risk has been ascribed to a genetic predisposition, however, exciting progress over the past years has discovered alternate elements of inheritance that involve epigenetic regulation. Epigenetic changes are heritably stable alterations that include DNA methylation, histone modifications and RNA-mediated silencing. Aberrant DNA methylation is a common molecular basis for a number of important human diseases, including breast cancer. Changes in DNA methylation profoundly affect global gene expression patterns. What is emerging is a more dynamic and complex association between DNA methylation and gene expression than previously believed. Although many tools have already been developed for analyzing genome-wide gene expression data, tools for analyzing genome-wide DNA methylation have not yet reached the same level of refinement. Here we provide an in-depth analysis of DNA methylation in parallel with gene expression data characteristics and describe the particularities of low-level and high-level analyses of DNA methylation data. Low-level analysis refers to pre-processing of methylation data (i.e. normalization, transformation and filtering ), whereas high-level analysis is focused on illustrating the application of the widely used class comparison , class prediction and class discovery methods to DNA methylation data. Furthermore, we investigate the influence of DNA methylation on gene expression by measuring the correlation between the degree of CpG methylation and the level of expression and to explore the pattern of methylation as a function of the promoter region.
- Published
- 2015
49. B chromosomes are associated with redistribution of genetic recombination towards lower-recombination chromosomal regions in perennial ryegrass
- Author
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Julie King, Ann Thomas, Ian Philip King, Ian Armstead, Dylan Phillips, Dagmara Gasior, Caron Evans, John Harper, Wayne Powell, and Glyn Jenkins
- Subjects
0301 basic medicine ,Genetic Markers ,Physiology ,Lolium perenne ,chiasma ,Plant Science ,Biology ,Genetic recombination ,Chromosomes, Plant ,03 medical and health sciences ,Meiosis ,Polyploid ,Lolium ,Plant breeding ,Allele ,Genetics ,Recombination, Genetic ,B chromosome ,B chromosomes, chiasma, genetic mapping, Lolium perenne, meiosis, perennial ryegrass, recombination ,B chromosomes ,perennial ryegrass ,fungi ,Chromosome Mapping ,food and beverages ,Diploidy ,Chiasma ,recombination ,Chromosome Pairing ,030104 developmental biology ,Crop Molecular Genetics ,Pollen ,genetic mapping ,Ploidy ,Research Paper - Abstract
Genetic recombination in perennial ryegrass is redistributed in favour of lower recombination regions of chromosomes in the presence of supernumerary B chromosomes. This has potential applications in plant breeding., Supernumerary ‘B’ chromosomes are non-essential components of the genome present in a range of plant and animal species—including many grasses. Within diploid and polyploid ryegrass and fescue species, including the forage grass perennial ryegrass (Lolium perenne L.), the presence of B chromosomes has been reported as influencing both chromosome pairing and chiasma frequencies. In this study, the effects of the presence/absence of B chromosomes on genetic recombination has been investigated through generating DArT (Diversity Arrays Technology) marker genetic maps for six perennial ryegrass diploid populations, the pollen parents of which contained either two B or zero B chromosomes. Through genetic and cytological analyses of these progeny and their parents, we have identified that, while overall cytological estimates of chiasma frequencies were significantly lower in pollen mother cells with two B chromosomes as compared with zero B chromosomes, the recombination frequencies within some marker intervals were actually increased, particularly for marker intervals in lower recombination regions of chromosomes, namely pericentromeric regions. Thus, in perennial ryegrass, the presence of two B chromosomes redistributed patterns of meiotic recombination in pollen mother cells in ways which could increase the range of allelic variation available to plant breeders.
- Published
- 2018
50. PolymapR-linkage analysis and genetic map construction from F1 populations of outcrossing polyploids
- Author
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Twan Kranenburg, Chris Maliepaard, Richard G. F. Visser, Arwa Shahin, Peter M. Bourke, Roeland E. Voorrips, Paul Arens, Geest, Van, Geert, Johannes Jansen, and Marinus J. M. Smulders
- Subjects
0106 biological sciences ,0301 basic medicine ,Genetic Linkage ,01 natural sciences ,Biochemistry ,PBR Siergewassen ,Laboratorium voor Plantenveredeling ,PBR Siergewassen, Tissue Culture ,Cluster Analysis ,Mathematics ,PBR Kwantitatieve aspecten ,Genetics and Population Analysis ,Chromosome Mapping ,PBR Ornamentals ,PBR Ornamentals, tissue culture and gene transfer ,PE&RC ,Original Papers ,Computer Science Applications ,Computational Mathematics ,Computational Theory and Mathematics ,Section (archaeology) ,Ploidy ,Corrigendum ,Likelihood function ,PBR Biodiversity and genetic variation ,Statistics and Probability ,Context (language use) ,Outcrossing ,Biology ,Chromosomal pairing ,PBR Quantitative aspects of Plant Breeding ,tissue culture and gene transfer ,Polyploidy ,Combinatorics ,03 medical and health sciences ,PBR Biodiversiteit en Genetische Variatie ,Polyploid ,Chromosome (genetic algorithm) ,Gene mapping ,Genetic linkage ,Life Science ,Tissue Culture ,Molecular Biology ,Genotyping ,Linkage (software) ,Tetraploidy ,Plant Breeding ,030104 developmental biology ,Evolutionary biology ,EPS ,Software ,010606 plant biology & botany - Abstract
Motivation Polyploid species carry more than two copies of each chromosome, a condition found in many of the world’s most important crops. Genetic mapping in polyploids is more complex than in diploid species, resulting in a lack of available software tools. These are needed if we are to realize all the opportunities offered by modern genotyping platforms for genetic research and breeding in polyploid crops. Results polymapR is an R package for genetic linkage analysis and integrated genetic map construction from bi-parental populations of outcrossing autopolyploids. It can currently analyse triploid, tetraploid and hexaploid marker datasets and is applicable to various crops including potato, leek, alfalfa, blueberry, chrysanthemum, sweet potato or kiwifruit. It can detect, estimate and correct for preferential chromosome pairing, and has been tested on high-density marker datasets from potato, rose and chrysanthemum, generating high-density integrated linkage maps in all of these crops. Availability and implementation polymapR is freely available under the general public license from the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/package=polymapR. Supplementary information Supplementary data are available at Bioinformatics online.
- Published
- 2018
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