2,259 results
Search Results
2. Identification of the PP2C gene family in paper mulberry (Broussonetia papyrifera) and its roles in the regulation mechanism of the response to cold stress
- Author
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Naizhi Chen, Xianjun Peng, Bohan Zhang, and Shihua Shen
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0106 biological sciences ,0301 basic medicine ,Gene Expression ,Bioengineering ,Genes, Plant ,01 natural sciences ,Applied Microbiology and Biotechnology ,Synteny ,03 medical and health sciences ,Protein Domains ,Gene Expression Regulation, Plant ,010608 biotechnology ,Arabidopsis ,Gene Duplication ,Phosphoprotein Phosphatases ,Gene family ,Protein Interaction Maps ,Phosphorylation ,Promoter Regions, Genetic ,Gene ,Phylogeny ,Plant Proteins ,Genetics ,biology ,Kinase ,Cold-Shock Response ,Paper mulberry ,Chromosome Mapping ,Promoter ,General Medicine ,Broussonetia ,biology.organism_classification ,030104 developmental biology ,Multigene Family ,Genome, Plant ,Biotechnology ,Signal Transduction - Abstract
To study the possible roles of type-2C protein phosphatases (PP2Cs) which have been confirmed to play roles in the response to diverse abiotic stresses in paper mulberry, we launched a series of genomic and functional studies of BpPP2Cs. Sixty-three PP2C proteins in paper mulberry (Broussonetia papyrifera) were classified into 13 clades. Four BpPP2Cs with kinase domains were verified to be highly conserved in organisms ranging from algae to dicots. Seven pairs of BpPP2C genes were found to be expanding, and 18 BpPP2C genes had orthologues in Arabidopsis. BpPP2Cs showed broad expression in different tissues; the expression levels of 18 BpPP2Cs were changed and the phosphorylation levels of seven BpPP2C proteins increased at low temperature. Cold-response elements were found in the promoter region of 31 BpPP2Cs. Finally, Bp01g0320 was found to act as a hub protein and Bp01g0512 and Bp09g1278 played key roles in the ABA-signaling pathway and MAPK cascades, respectively. These results suggest that the PP2C gene family of paper mulberry is evolutionarily conserved and participates the regulation of the response to cold stress, which will play a vital role in further research on phosphatases in paper mulberry.
- Published
- 2020
3. Colloquium paper: genome-wide patterns of population structure and admixture among Hispanic/Latino populations
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Katarzyna, Bryc, Christopher, Velez, Tatiana, Karafet, Andres, Moreno-Estrada, Andy, Reynolds, Adam, Auton, Michael, Hammer, Carlos D, Bustamante, and Harry, Ostrer
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Male ,Principal Component Analysis ,Genome, Human ,Colloquium Papers ,Chromosome Mapping ,Computational Biology ,Bayes Theorem ,Hispanic or Latino ,DNA, Mitochondrial ,United States ,Genetics, Population ,Sex Factors ,Cluster Analysis ,Humans ,Female ,Genome-Wide Association Study - Abstract
Hispanic/Latino populations possess a complex genetic structure that reflects recent admixture among and potentially ancient substructure within Native American, European, and West African source populations. Here, we quantify genome-wide patterns of SNP and haplotype variation among 100 individuals with ancestry from Ecuador, Colombia, Puerto Rico, and the Dominican Republic genotyped on the Illumina 610-Quad arrays and 112 Mexicans genotyped on Affymetrix 500K platform. Intersecting these data with previously collected high-density SNP data from 4,305 individuals, we use principal component analysis and clustering methods FRAPPE and STRUCTURE to investigate genome-wide patterns of African, European, and Native American population structure within and among Hispanic/Latino populations. Comparing autosomal, X and Y chromosome, and mtDNA variation, we find evidence of a significant sex bias in admixture proportions consistent with disproportionate contribution of European male and Native American female ancestry to present-day populations. We also find that patterns of linkage-disequilibria in admixed Hispanic/Latino populations are largely affected by the admixture dynamics of the populations, with faster decay of LD in populations of higher African ancestry. Finally, using the locus-specific ancestry inference method LAMP, we reconstruct fine-scale chromosomal patterns of admixture. We document moderate power to differentiate among potential subcontinental source populations within the Native American, European, and African segments of the admixed Hispanic/Latino genomes. Our results suggest future genome-wide association scans in Hispanic/Latino populations may require correction for local genomic ancestry at a subcontinental scale when associating differences in the genome with disease risk, progression, and drug efficacy, as well as for admixture mapping.
- Published
- 2010
4. Schizophrenia: from the brain to peripheral markers. A consensus paper of the WFSBP task force on biological markers
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Micha Gawlik, Dorit Ben-Shachar, Gerald Stöber, Norbert Müller, Johannes Kornhuber, Peter Riederer, Michal Cardon, Toshikazu Saito, Andrea Schmitt, Assen Jablensky, Alfred N. Fonteh, Edna Grünblatt, Johannes Thome, Bob Oranje, Thomas F. McNeil, Marat Uzbekov, Michal Schwartz, Birte Glenthøj, Peter Falkai, Nuria Durany, Yong Ku Kim, Mohamed Saoud, University of Zurich, and Stober, G
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Predictive validity ,Genetic Markers ,Schizophrenia (object-oriented programming) ,610 Medicine & health ,Disease ,Biology ,2738 Psychiatry and Mental Health ,03 medical and health sciences ,0302 clinical medicine ,Humans ,Genetic Predisposition to Disease ,Biomarker discovery ,Biological Psychiatry ,Brain ,Chromosome Mapping ,10058 Department of Child and Adolescent Psychiatry ,Phenotype ,030227 psychiatry ,3. Good health ,Psychiatry and Mental health ,Genetic marker ,Trait ,Schizophrenia ,Identification (biology) ,Schizophrenic Psychology ,2803 Biological Psychiatry ,Neuroscience ,030217 neurology & neurosurgery ,Biomarkers - Abstract
Objective. The phenotypic complexity, together with the multifarious nature of the so-called "schizophrenic psychoses", limits our ability to form a simple and logical biologically based hypothesis for the disease group. Biological markers are defined as biochemical, physiological or anatomical traits that are specific to particular conditions. An important aim of biomarker discovery is the detection of disease correlates that can be used as diagnostic tools. Method. A selective review of the WFSBP Task Force on Biological Markers in schizophrenia is provided from the central nervous system to phenotypes, functional brain systems, chromosomal loci with potential genetic markers to the peripheral systems. Results. A number of biological measures have been proposed to be correlated with schizophrenia. At present, not a single biological trait in schizophrenia is available which achieves sufficient specificity, selectivity and is based on causal pathology and predictive validity to be recommended as diagnostic marker. Conclusions. With the emergence of new technologies and rigorous phenotypic subclassification the identification of genetic bases and assessment of dynamic disease related alterations will hopefully come to a new stage in the complex field of psychiatric research.
- Published
- 2009
5. Identification and application of a candidate gene AhAftr1 for aflatoxin production resistance in peanut seed (Arachis hypogaea L.).
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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
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- 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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6. piRNAQuest V.2: an updated resource for searching through the piRNAome of multiple species
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Byapti Ghosh, Arijita Sarkar, Sudip Mondal, Namrata Bhattacharya, Sunirmal Khatua, and Zhumur Ghosh
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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
7. REPORT on the Fifth International Workshop on Chromosome 9 held at Eynsham, Oxfordshire, UK, September 4–6, 1996
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POVEY, S, ATTWOOD, J, CHADWICK, B, FREZAL, J, HAINES, JL, KNOWLES, M, KWIATKOWSKI, DJ, OLOPADE, OI, SLAUGENHAUPT, S, SPURR, NK, SMITH, M, STEEL, K, WHITE, JA, and PERICAK‐VANCE, MA
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Genetics ,Animals ,Chromosome Aberrations ,Chromosome Disorders ,Chromosome Mapping ,Chromosomes ,Human ,Pair 9 ,Computational Biology ,Humans ,Mice ,Rats ,Species Specificity ,algorithm ,animal cell ,basal cell carcinoma ,bladder cancer ,cancer genetics ,cardiomyopathy ,chromosome 9 ,chromosome analysis ,chromosome map ,conference paper ,consensus sequence ,data analysis ,ehlers danlos syndrome ,friedreich ataxia ,gene location ,gene locus ,gene mapping ,hearing loss ,human ,human cell ,hypoplasia ,lymphatic leukemia ,marker gene ,meiosis ,mouse ,muscular dystrophy ,neuropathy ,nomenclature ,nonhuman ,priority journal ,sex determination ,tuberous sclerosis ,tumor suppressor gene ,workshop ,Clinical Sciences ,Genetics & Heredity - Abstract
The Fifth International workshop on chromosome 9 comprised a gathering of 36 scientists from seven countries and included a fairly even distribution of interests along chromosome 9 as well as a strong input from more global activities and from comparative mapping. At least eight groups had participated in the goal set at the previous workshop which was to improve the fine genetic mapping in different regions of chromosome 9 by meiotic breakpoint mapping in allocated regions and this has resulted in some greatly improved order information. Excellent computing facilities were available and all contributed maps were entered not only into SIGMA (and thence submitted to GDB) but also into a dedicated version of ACEDB which can be accessed on the Web in the form of one of 28 slices into which the chromosome has been arbitrarily divided. It was generally agreed that the amount of data is now overwhelming and that the integration and validation of all data is not only unrealistic in a short meeting but probably impossible until the whole chromosome has been sequenced and fully annotated. Sequence-ready contigs presented at the meeting totalled about 3 MB which is about one fiftieth of the estimated length. The single biggest barrier to integration of maps is the problem of non-standard nomenclature of loci. In the past 2 workshops efforts have been made to compare traditional 'consensus' maps made by human insight (still probably best for small specific regions) with those generated with some computer assistance (such as SIGMA) and those generated objectively by defined computer algorithms such as ldb. Since no single form of map or representation is entirely satisfactory for all purposes the maps reproduced in the published version of the report are confined to one of the genetic maps, in which Genethon and older markers have been incorporated, a Sigma map of the genes as symbols together with a listing of known 'disease' genes on chromosome 9, and a revised assessment of the mouse map together with a list of mouse loci predicted to be on human chromosome 9. One of the 25 ACEDB slices is also shown to illustrate strengths and weaknesses of this approach. Workshop files include not only all maps available at the time but also details of loci and details of the meiotic breakpoints in the CEPH families.
- Published
- 1997
8. A new Cannabis genome assembly associates elevated cannabidiol (CBD) with hemp introgressed into marijuana
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Todd P. Michael, Shane G. Poplawski, S. Timothy Motley, Clemon Dabney, George D. Weiblen, Christopher J. Schwartz, Jonathan P. Wenger, and Christopher J. Grassa
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0106 biological sciences ,0301 basic medicine ,Physiology ,medicine.medical_treatment ,Population ,Plant Science ,01 natural sciences ,Genome ,domestication ,03 medical and health sciences ,Cannabidiolic acid synthase ,medicine ,Cannabidiol ,Dronabinol ,Tetrahydrocannabinol ,education ,Cannabis ,Genetics ,education.field_of_study ,Full Paper ,biology ,Cannabinoids ,Research ,Chromosome Mapping ,food and beverages ,Full Papers ,hemp ,biology.organism_classification ,cannabidiol (CBD) ,030104 developmental biology ,Tetrahydrocannabinolic acid ,tetrahydrocannabinol (THC) ,Cannabinoid ,marijuana ,010606 plant biology & botany ,medicine.drug - Abstract
Summary Demand for cannabidiol (CBD), the predominant cannabinoid in hemp (Cannabis sativa), has favored cultivars producing unprecedented quantities of CBD. We investigated the ancestry of a new cultivar and cannabinoid synthase genes in relation to cannabinoid inheritance.A nanopore‐based assembly anchored to a high‐resolution linkage map provided a chromosome‐resolved genome for CBDRx, a potent CBD‐type cultivar. We measured cannabinoid synthase expression by cDNA sequencing and conducted a population genetic analysis of diverse Cannabis accessions. Quantitative trait locus mapping of cannabinoids in a hemp × marijuana segregating population was also performed.Cannabinoid synthase paralogs are arranged in tandem arrays embedded in long terminal repeat retrotransposons on chromosome 7. Although CBDRx is predominantly of marijuana ancestry, the genome has cannabidiolic acid synthase (CBDAS) introgressed from hemp and lacks a complete sequence for tetrahydrocannabinolic acid synthase (THCAS). Three additional genomes, including one with complete THCAS, confirmed this genomic structure. Only cannabidiolic acid synthase (CBDAS) was expressed in CBD‐type Cannabis, while both CBDAS and THCAS were expressed in a cultivar with an intermediate tetrahydrocannabinol (THC) : CBD ratio.Although variation among cannabinoid synthase loci might affect the THC : CBD ratio, variability among cultivars in overall cannabinoid content (potency) was also associated with other chromosomes.
- Published
- 2021
9. Maturation of 23S rRNA includes removal of helix H1 in many bacteria
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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
10. Report and abstracts of the First International Workshop on Chromosome 9. Held at Girton College Cambridge, UK, 22-24 March, 1992.
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Povey, S, Smith, M, Haines, J, Kwiatkowski, D, Fountain, J, Bale, A, Abbott, C, Jackson, I, Lawrie, M, and Hultén, M
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DNA ,Single Stranded ,single stranded DNA ,animal ,chromosome 9 ,chromosome map ,comparative study ,conference paper ,genetic linkage ,genetics ,human ,molecular genetics ,mouse ,nucleotide sequence ,tuberous sclerosis ,Animal ,Base Sequence ,Chromosome Mapping ,Chromosomes ,Human ,Pair 9 ,Comparative Study ,DNA ,Single-Stranded ,Human ,Linkage ,Mice ,Molecular Sequence Data ,Support ,Non-U.S. Gov't ,Support ,U.S. Gov't ,Non-P.H.S. ,Support ,U.S. Gov't ,P.H.S. ,Tuberous Sclerosis ,Clinical Sciences ,Genetics & Heredity ,Genetics - Published
- 1992
11. REPORT on the First International Workshop on Chromosome 9 held at Girton College Cambridge, UK, 22–24 March, 1992
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POVEY, S, SMITH, M, HAINES, J, KWIATKOWSKI, D, FOUNTAIN, J, BALE, A, ABBOTT, C, JACKSON, I, LAWRIE, M, and HULTÉN, M
- Subjects
Biological Sciences ,Genetics ,Animals ,Base Sequence ,Chromosome Mapping ,Chromosomes ,Human ,Pair 9 ,DNA ,Single-Stranded ,Genetic Linkage ,Humans ,Mice ,Molecular Sequence Data ,Tuberous Sclerosis ,chromosomal localization ,chromosome 9 ,chromosome 9p ,chromosome 9q ,chromosome analysis ,chromosome map ,conference paper ,friedreich ataxia ,gene ,gene mapping ,genetic linkage ,genetic polymorphism ,human ,major clinical study ,normal human ,priority journal ,pulsed field gel electrophoresis ,telomere ,torsion dystonia ,tuberous sclerosis ,Clinical Sciences ,Genetics & Heredity - Published
- 1992
12. Genetic Heterogeneity in Tuberous Sclerosis
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SMITH, MOYRA, YOSHIYAMA, K, WAGNER, C, FLODMAN, P, and SMITH, B
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Ataxia Telangiectasia ,Cell Movement ,Chromosome Mapping ,Chromosomes ,Human ,Pair 9 ,Forecasting ,Genetic Linkage ,Humans ,Likelihood Functions ,Neurons ,Polymorphism ,Restriction Fragment Length ,Tuberous Sclerosis ,chromosome 11q ,conference paper ,family study ,female ,gene mapping ,genetic heterogeneity ,genetic linkage ,human ,major clinical study ,male ,marker gene ,priority journal ,tuberous sclerosis ,Human ,Linkage ,Support ,Non-U.S. Gov't ,Support ,U.S. Gov't ,P.H.S. ,General Science & Technology - Published
- 1991
13. An Attempt to Map Two Genes for Tuberous Sclerosis Using Novel Two‐Point Methodsa
- Author
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POVEY, S, ATTWOOD, J, JANSSEN, LAJ, BURLEY, M, SMITH, M, FLODMAN, P, MORTON, NE, EDWARDS, JH, SAMPSON, JR, YATES, JRW, HAINES, JL, AMOS, J, SHORT, MP, SANDKUYL, LA, HALLEY, DJJ, FRYER, AE, BECH‐HANSEN, T, MUELLER, R, AL‐GHAZALI, L, SUPER, M, and OSBORNE, J
- Subjects
Adult ,Chromosome Mapping ,Chromosomes ,Human ,Pair 11 ,Chromosomes ,Human ,Pair 9 ,Genetic Linkage ,Humans ,Likelihood Functions ,Polymorphism ,Restriction Fragment Length ,Tuberous Sclerosis ,conference paper ,family study ,female ,gene mapping ,human ,major clinical study ,male ,marker gene ,priority journal ,tuberous sclerosis ,Human ,Linkage ,Support ,Non-U.S. Gov't ,General Science & Technology - Published
- 1991
14. A Comparative Study on Genetic Heterogeneity in Tuberous Sclerosis: Evidence for One Gene on 9q34 and a Second Gene on 11q22–23a
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JANSSEN, LAJ, POVEY, S, ATTWOOD, J, SANDKUYL, LA, LINDHOUT, D, FLODMAN, P, SMITH, M, SAMPSON, JR, HAINES, JL, MERKENS, EC, FLEURY, P, SHORT, P, AMOS, J, and HALLEY, DJJ
- Subjects
Biological Sciences ,Genetics ,Chromosome Mapping ,Chromosomes ,Human ,Pair 11 ,Chromosomes ,Human ,Pair 9 ,Genes ,Genetic Linkage ,Humans ,Likelihood Functions ,Tuberous Sclerosis ,chromosome 11q ,chromosome 9q ,conference paper ,female ,genetic heterogeneity ,genetic linkage ,human ,male ,priority journal ,tuberous sclerosis ,Genes ,Structural ,Human ,Linkage ,Support ,Non-U.S. Gov't ,General Science & Technology - Published
- 1991
15. Molecular identification of slow rusting resistance Lr46/Yr29 gene locus in selected triticale (× Triticosecale Wittmack) cultivars
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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
16. Sequence‐based mapping identifies a candidate transcription repressor underlying awn suppression at the B1 locus in wheat
- Author
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Martin Sarinelli, Daolin Fu, Eduard Akhunov, Priyanka Tyagi, Gina Brown-Guedira, Qunqun Hao, Alina Akhunova, J. Paul Murphy, Noah DeWitt, Mohammed Guedira, Edwin Lauer, Katherine W. Jordan, and David Marshall
- Subjects
0106 biological sciences ,0301 basic medicine ,Candidate gene ,Transcription, Genetic ,Physiology ,wheat (Triticum aestivum) ,Plant Science ,01 natural sciences ,Suppression, Genetic ,Gene Expression Regulation, Plant ,Chromosome Segregation ,Coding region ,Inbreeding ,Association mapping ,Triticum ,Plant Proteins ,Recombination, Genetic ,Zinc finger ,Genetics ,Full Paper ,B1 locus ,positional cloning ,Chromosome Mapping ,food and beverages ,Organ Size ,Full Papers ,Up-Regulation ,Genetic Markers ,zinc finger protein ,Positional cloning ,Quantitative Trait Loci ,Locus (genetics) ,Quantitative trait locus ,Biology ,Genes, Plant ,03 medical and health sciences ,Amino Acid Sequence ,Gene ,Genetic Association Studies ,Base Sequence ,Research ,Repressor Proteins ,030104 developmental biology ,Haplotypes ,Genetic Loci ,fine mapping ,awns ,Gene Deletion ,Genome-Wide Association Study ,010606 plant biology & botany - Abstract
Summary Awns are stiff, hair‐like structures which grow from the lemmas of wheat (Triticum aestivum) and other grasses that contribute to photosynthesis and play a role in seed dispersal. Variation in awn length in domesticated wheat is controlled primarily by three major genes, most commonly the dominant awn suppressor Tipped1 (B1). This study identifies a transcription repressor responsible for awn inhibition at the B1 locus.Association mapping was combined with analysis in biparental populations to delimit B1 to a distal region of 5AL colocalized with QTL for number of spikelets per spike, kernel weight, kernel length, and test weight.Fine‐mapping located B1 to a region containing only two predicted genes, including C2H2 zinc finger transcriptional repressor TraesCS5A02G542800 upregulated in developing spikes of awnless individuals. Deletions encompassing this candidate gene were present in awned mutants of an awnless wheat. Sequence polymorphisms in the B1 coding region were not observed in diverse wheat germplasm whereas a nearby polymorphism was highly predictive of awn suppression.Transcriptional repression by B1 is the major determinant of awn suppression in global wheat germplasm. It is associated with increased number of spikelets per spike and decreased kernel size.
- Published
- 2019
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
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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
- Author
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Agnieszka Niedziela, Waldemar Brukwiński, and Piotr T. Bednarek
- Subjects
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.
- Published
- 2021
19. De Novo Genome Assembly of the Japanese Wheat Cultivar Norin 61 Highlights Functional Variation in Flowering Time and Fusarium-Resistant Genes in East Asian Genotypes
- Author
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Sean Walkowiak, Sudharsan Padmarasu, Martin Mascher, Emily Delorean, Georg Haberer, Masaomi Hatakeyama, Curtis J. Pozniak, Tomohiro Ban, Kanako Kawaura, Kentaro Shimizu, Jesse Poland, Shuhei Nasuda, Toshiaki Tameshige, Tetsuya Nakazaki, Dario Copetti, Juan J. Gutierrez-Gonzalez, Kazuki Murata, Klaus F. X. Mayer, Nils Stein, Thomas Wicker, Fuminori Kobayashi, Hiroyuki Tsuji, Rie Shimizu-Inatsugi, Jun Sese, Axel Himmelbach, Catharine Aquino, Kazusa Nishimura, Moeko Okada, Gary J. Muehlbauer, Tony Kuo, Manuel Spannagl, Cécile Monat, and Hirokazu Handa
- Subjects
0106 biological sciences ,0301 basic medicine ,Physiology ,Sequence assembly ,Plant Science ,AcademicSubjects/SCI01180 ,Bread wheat ,01 natural sciences ,Genome ,chemistry.chemical_compound ,Fusarium ,Genotype ,Cultivar ,Phylogeny ,Triticum ,Disease Resistance ,2. Zero hunger ,Genetics ,Asia, Eastern ,Chromosome Mapping ,food and beverages ,General Medicine ,Norin 61 ,ddc ,Florigen ,Genome, Plant ,Rapid Paper ,Locus (genetics) ,Flowers ,Asian germplasm ,Biology ,Genes, Plant ,Chromosomes, Plant ,Polyploidy ,Cytogenetics ,03 medical and health sciences ,Adaptation ,Asian Germplasm ,Bread Wheat ,Genome Assembly ,Allele ,Gene ,Genetic Association Studies ,Genome assembly ,AcademicSubjects/SCI01210 ,Genetic Variation ,Sequence Analysis, DNA ,Cell Biology ,030104 developmental biology ,chemistry ,Sequence Alignment ,010606 plant biology & botany - Abstract
Bread wheat is a major crop that has long been the focus of basic and breeding research. Assembly of its genome has been difficult because of its large size and allohexaploid nature (AABBDD genome). Following the first reported assembly of the genome of the experimental strain Chinese Spring (CS), the 10+ Wheat Genomes Project was launched to produce multiple assemblies of worldwide modern cultivars. The only Asian cultivar in the project is Norin 61, a representative Japanese cultivar adapted to grow across a broad latitudinal range, mostly characterized by a wet climate and a short growing season. Here, we characterize the key aspects of its chromosome-scale genome assembly spanning 15 Gb with a raw scaffold N50 of 22 Mb. Analysis of the repetitive elements identified chromosomal regions unique to Norin 61 that encompass a tandem array of the pathogenesis-related 13 family. We report novel copy-number variations in the B homeolog of the florigen gene FT1/VRN3, pseudogenization of its D homeolog and the association of its A homeologous alleles with the spring/winter growth habit. Furthermore, the Norin 61 genome carries typical East Asian functional variants different from CS, ranging from a single nucleotide to multi-Mb scale. Examples of such variation are the Fhb1 locus, which confers Fusarium head-blight resistance, Ppd-D1a, which confers early flowering, Glu-D1f for Asian noodle quality and Rht-D1b, which introduced semi-dwarfism during the green revolution. The adoption of Norin 61 as a reference assembly for functional and evolutionary studies will enable comprehensive characterization of the underexploited Asian bread wheat diversity.
- Published
- 2020
20. The B chromosome ofSorghum purpureosericeumreveals the first pieces of its sequence
- Author
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Kateřina Holušová, Jana Čížková, Miroslava Karafiátová, Martina Bednářová, Jan Bartoš, Nicolas Blavet, and Mahmoud Said
- Subjects
Genetic Markers ,0106 biological sciences ,0301 basic medicine ,In situ ,medicine.medical_specialty ,Physiology ,Sorghum purpureosericeum ,Plant Science ,01 natural sciences ,cytogenetics ,Chromosomes, Plant ,pollen nuclei ,03 medical and health sciences ,chemistry.chemical_compound ,medicine ,In Situ Hybridization, Fluorescence ,Sorghum ,Sequence (medicine) ,Genetics ,B chromosome ,B chromosomes ,biology ,medicine.diagnostic_test ,AcademicSubjects/SCI01210 ,repeat analysis ,flow cytometry ,Cytogenetics ,Chromosome Mapping ,food and beverages ,biology.organism_classification ,Research Papers ,030104 developmental biology ,Crop Molecular Genetics ,chemistry ,Ploidy ,DNA ,010606 plant biology & botany ,Fluorescence in situ hybridization - Abstract
More than a century has passed since the B chromosomes were first discovered. Today we know much of their variability, morphology, and transmission to plant progeny. With the advent of modern technologies, B chromosome research has accelerated, and some of their persistent mysteries have since been uncovered. Building on this momentum, here we extend current knowledge of B chromosomes in Sorghum purpureosericeum to the sequence level. To do this, we estimated the B chromosome size at 421 Mb, sequenced DNA from flow-sorted haploid pollen nuclei of both B-positive (B+) and B-negative (B0) plants, and performed a repeat analysis on the Illumina raw sequence data. This analysis revealed nine putative B-specific clusters, which were then used to develop B chromosome-specific markers. Additionally, cluster SpuCL4 was identified and verified to be a centromeric repeat. We also uncovered two repetitive clusters (SpuCL168 and SpuCL115), which hybridized exclusively on the B chromosome under fluorescence in situ hybridization and can be considered as robust cytogenetic markers. Given that B chromosomes in Sorghum are rather unstable across all tissues, our findings could facilitate expedient identification of B+ plants and enable a wide range of studies to track this chromosome type in situ., We sequenced plants of the tropical grass Sorghum purpureosericeum carrying B chromosomes. Based on repeat clustering, we assigned nine clusters to B chromosome and developed B-specific PCR and cytogenetic markers.
- Published
- 2020
21. 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.
- Published
- 2020
22. 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.
- Published
- 2020
23. Genome-wide analyses reveal footprints of divergent selection and popping-related traits in CIMMYT’s maize inbred lines
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Delin Li, Amalio Santacruz Varela, Huihui Li, Natalia Palacios Rojas, Jiankang Wang, Denise E. Costich, Natália Carolina de Almeida Silva, Jing Li, Cristian Zavala Espinosa, Patrick S. Schnable, Viridiana Trejo Pastor, and Awais Rasheed
- Subjects
0106 biological sciences ,0301 basic medicine ,genetic structures ,Physiology ,Quantitative Trait Loci ,Single-nucleotide polymorphism ,Genome-wide association study ,Plant Science ,Biology ,quality traits ,Polymorphism, Single Nucleotide ,Zea mays ,01 natural sciences ,Genome ,03 medical and health sciences ,Inbred strain ,popping traits ,GWAS ,SNP ,Allele ,Selection (genetic algorithm) ,Genetics ,AcademicSubjects/SCI01210 ,tropical maize landrace ,Chromosome Mapping ,Research Papers ,Phenotype ,EigenGWAS ,Plant Breeding ,030104 developmental biology ,Plant—Environment Interactions ,maize adaptation ,Research Article ,Genome-Wide Association Study ,010606 plant biology & botany - Abstract
Sequencing-based technology reveals popping characteristics in maize, establishing a benchmark for popcorn genetics, and supporting a gradual selection process for popping traits., Popcorn (Zea mays L. var. Everta) is the most ancient type of cultivated maize. However, there is little known about the genetics of popping-related traits based on genotyping-by-sequencing (GBS) technology. Here, we characterized the phenotypic variation for seven popping-related traits in maize kernels among 526 CIMMYT inbred lines (CMLs). In total, 155 083 high-quality single nucleotide polymorphism (SNP) markers were identified by a GBS approach. Several trait-associated loci were detected by genome-wide association study for color, popping expansion volume, shape, pericarp, flotation index, floury/vitreous, and protein content, explaining a majority of the observed phenotypic variance, and these were validated by a diverse panel comprising 764 tropical landrace accessions. Sixty two of the identified loci were recognized to have undergone selection. On average, there was a 55.27% frequency for alleles that promote popping in CMLs. Our work not only pinpoints previously unknown loci for popping-related traits, but also reveals that many of these loci have undergone selection. Beyond establishing a new benchmark for the genetics of popcorn, our study provides a foundation for gene discovery and breeding. It also presents evidence to investigate the role of a gradual loss of popping ability as a by-product of diversification of culinary uses throughout the evolution of teosinte–to–modern maize.
- Published
- 2020
24. Temperature response of wheat affects final height and the timing of stem elongation under field conditions
- Author
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Steven Yates, Andreas Hund, Lukas Kronenberg, Norbert Kirchgessner, Martin P. Boer, and Achim Walter
- Subjects
0106 biological sciences ,0301 basic medicine ,Canopy ,Candidate gene ,Physiology ,Plant Science ,Development ,Quantitative trait locus ,01 natural sciences ,plant height ,LIDAR ,03 medical and health sciences ,field phenotyping ,GWAS ,physiology ,temperature response ,wheat ,Genetic variation ,Arabidopsis thaliana ,Allele ,Association mapping ,Triticum ,030304 developmental biology ,2. Zero hunger ,0303 health sciences ,biology ,AcademicSubjects/SCI01210 ,Phenology ,Temperature ,Chromosome Mapping ,food and beverages ,15. Life on land ,PE&RC ,biology.organism_classification ,Horticulture ,Phenotype ,Biometris ,030104 developmental biology ,Plant—Environment Interactions ,Adaptation ,Research Paper ,Genome-Wide Association Study ,010606 plant biology & botany - Abstract
Temperature response of stem elongation in wheat grown under field conditions indicated that temperature response is highly heritable and linked to the flowering pathway., In wheat, temperature affects the timing and intensity of stem elongation. Genetic variation for this process is therefore important for adaptation. This study investigates the genetic response to temperature fluctuations during stem elongation and its relationship to phenology and height. Canopy height of 315 wheat genotypes (GABI wheat panel) was scanned twice weekly in the field phenotyping platform (FIP) of ETH Zurich using a LIDAR. Temperature response was modelled using linear regressions between stem elongation and mean temperature in each measurement interval. This led to a temperature-responsive (slope) and a temperature-irresponsive (intercept) component. The temperature response was highly heritable (H2=0.81) and positively related to a later start and end of stem elongation as well as final height. Genome-wide association mapping revealed three temperature-responsive and four temperature-irresponsive quantitative trait loci (QTLs). Furthermore, putative candidate genes for temperature-responsive QTLs were frequently related to the flowering pathway in Arabidopsis thaliana, whereas temperature-irresponsive QTLs corresponded to growth and reduced height genes. In combination with Rht and Ppd alleles, these loci, together with the loci for the timing of stem elongation, accounted for 71% of the variability in height. This demonstrates how high-throughput field phenotyping combined with environmental covariates can contribute to a smarter selection of climate-resilient crops.
- Published
- 2020
25. A chromosome‐scale genome assembly reveals a highly dynamic effector repertoire of wheat powdery mildew
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Lukas Kunz, Andreas Wehrli, Seraina Schudel, Manuel Poretti, Marion C. Müller, Beat Keller, Simone Oberhänsli, Thomas Wicker, Alexandros G. Sotiropoulos, Fabrizio Menardo, Salim Bourras, Coraline R. Praz, University of Zurich, and Keller, Beat
- Subjects
0106 biological sciences ,0301 basic medicine ,DNA Copy Number Variations ,Transcription, Genetic ,Physiology ,Genes, Fungal ,Blumeria graminis ,Plant Science ,580 Plants (Botany) ,01 natural sciences ,Genome ,UFSP13-7 Evolution in Action: From Genomes to Ecosystems ,03 medical and health sciences ,10126 Department of Plant and Microbial Biology ,Ascomycota ,Gene mapping ,Gene Expression Regulation, Fungal ,1110 Plant Science ,Copy-number variation ,avirulence genes ,Gene ,Triticum ,Genomic organization ,Recombination, Genetic ,Genetics ,Bacterial artificial chromosome ,Polymorphism, Genetic ,Full Paper ,biology ,Effector ,Research ,copy number variation ,Chromosome Mapping ,food and beverages ,1314 Physiology ,Full Papers ,biology.organism_classification ,recombination ,030104 developmental biology ,Multigene Family ,DNA Transposable Elements ,powdery mildew ,Chromosomes, Fungal ,Genome, Fungal ,010606 plant biology & botany - Abstract
Blumeria graminis f. sp. tritici (B.g. tritici) is the causal agent of the wheat powdery mildew disease. The highly fragmented B.g. tritici genome available so far has prevented a systematic analysis of effector genes that are known to be involved in host adaptation. To study the diversity and evolution of effector genes we produced a chromosome‐scale assembly of the B.g. tritici genome. The genome assembly and annotation was achieved by combining long‐read sequencing with high‐density genetic mapping, bacterial artificial chromosome fingerprinting and transcriptomics. We found that the 166.6 Mb B.g. tritici genome encodes 844 candidate effector genes, over 40% more than previously reported. Candidate effector genes have characteristic local genomic organization such as gene clustering and enrichment for recombination‐active regions and certain transposable element families. A large group of 412 candidate effector genes shows high plasticity in terms of copy number variation in a global set of 36 isolates and of transcription levels. Our data suggest that copy number variation and transcriptional flexibility are the main drivers for adaptation in B.g. tritici. The high repeat content may play a role in providing a genomic environment that allows rapid evolution of effector genes with selection as the driving force.
- Published
- 2018
26. Analysis of miRNA expression associated with the Lr46 gene responsible for APR resistance in wheat (Triticum aestivum L.)
- Author
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Julia Spychała, Roksana Skowrońska, Agata Tyczewska, Jakub Kuczyński, Michał Kwiatek, Tomasz Jędrzejewski, Agnieszka Tomkowiak, and Tomasz Twardowski
- Subjects
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.
- Published
- 2020
27. Blood DNA methylation sites predict death risk in a longitudinal study of 12, 300 individuals
- Author
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Juan E. Castillo-Fernandez, Riccardo E. Marioni, Andrea A. Baccarelli, Luigi Ferrucci, Steve Horvath, Joel Schwartz, Daniel Levy, Luke C. Pilling, Rahul Gondalia, James S. Pankow, Naomi R. Wray, Allan C. Just, Ian J. Deary, Toshiko Tanaka, Melanie Waldenberger, Wen Zhang, Gao Xu, Allan F. McRae, Phil S. Tsaho, Holger Prokisch, James D. Stewart, Tim Assimes, Rory P. Wilson, Cavin K. Ward-Caviness, John M. Starr, Weihua Guan, Yun Li, Devin Absher, Pantel S. Vokonas, Peter M. Visscher, Mike Mendelson, Ann Zenobia Moore, Agha Golareh, Chunyu Liu, Jan Bressler, Eric A. Whitsel, Ake T. Lu, Pei-Chien Tsai, Joanne M. Murabito, Lifang Hou, Tim D. Spector, Annette Peters, Guosheng Zhang, Tianxiao Huan, Elena Colicino, Jordana T. Bell, Stefania Bandinelli, Brian H. Chen, and Douglas P. Kiel
- Subjects
Adult ,Male ,Oncology ,Aging ,medicine.medical_specialty ,Longitudinal study ,Quantitative Trait Loci ,epigenome-wide association studies ,Risk Assessment ,Epigenesis, Genetic ,450K ,Cohort Studies ,Intergenic region ,Meta-Analysis as Topic ,Predictive Value of Tests ,Cause of Death ,Internal medicine ,Mendelian randomization ,medicine ,Humans ,Longitudinal Studies ,Gene ,Aged ,450k ,Dna Methylation ,All-cause Mortality ,Epigenome-wide Association Studies ,DNA methylation ,business.industry ,aging ,Chromosome Mapping ,Cell Biology ,Methylation ,Middle Aged ,Genetic epidemiology ,Chronic Disease ,all-cause mortality ,Female ,Risk assessment ,business ,Follow-Up Studies ,Genome-Wide Association Study ,Research Paper - Abstract
DNA methylation has fundamental roles in gene programming and aging that may help predict mortality. However, no large-scale study has investigated whether site-specific DNA methylation predicts all-cause mortality. We used the Illumina-HumanMethylation450-BeadChip to identify blood DNA methylation sites associated with all-cause mortality for 12, 300 participants in 12 Cohorts of the Heart and Aging Research in Genetic Epidemiology (CHARGE) Consortium. Over an average 10-year follow-up, there were 2,561 deaths across the cohorts. Nine sites mapping to three intergenic and six gene-specific regions were associated with mortality (P < 9.3x10-7) independently of age and other mortality predictors. Six sites (cg14866069, cg23666362, cg20045320, cg07839457, cg07677157, cg09615688)—mapping respectively to BMPR1B, MIR1973, IFITM3, NLRC5, and two intergenic regions—were associated with reduced mortality risk. The remaining three sites (cg17086398, cg12619262, cg18424841)—mapping respectively to SERINC2, CHST12, and an intergenic region—were associated with increased mortality risk. DNA methylation at each site predicted 5%¬¬–15% of all deaths. We also assessed the causal association of those sites to age-related chronic diseases by using Mendelian randomization, identifying weak causal relationship between cg18424841 and cg09615688 with coronary heart disease. Of the nine sites, three (cg20045320, cg07839457, cg07677157) were associated with lower incidence of heart disease risk and two (cg20045320, cg07839457) with smoking and inflammation in prior CHARGE analyses. Methylation of cg20045320, cg07839457, and cg17086398 was associated with decreased expression of nearby genes (IFITM3, IRF, NLRC5, MT1, MT2, MARCKSL1) linked to immune responses and cardiometabolic diseases. These sites may serve as useful clinical tools for mortality risk assessment and preventative care.
- Published
- 2020
28. Genetic basis of phenotypic plasticity and genotype × environment interactions in a multi-parental tomato population
- Author
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Laurent Derivot, Isidore Diouf, Laurence Moreau, Frédérique Bitton, Shai Koussevitzky, Yolande Carretero, Mathilde Causse, Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Gautier semences, Hazera – Seeds of Growth, Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-16-CE20-0014,TomEpiSet,La parthénocarpie comme une stratégie pour surmonter la baisse de nouaison et du rendement en fruits chez la tomate dans des conditions de stress thermique(2016), and ANR-13-ADAP-0013,AdapTom,Diversité et bases génétiques, génomiques et (éco)physiologiques de l'adaptation de la tomate à une limitation en eau et à d'autres stress environnementaux(2013)
- Subjects
genotype × environment interaction (G×E) ,0106 biological sciences ,0301 basic medicine ,Candidate gene ,Genotype ,QTL ,Physiology ,Population ,Context (language use) ,Abiotic stresses ,MAGIC population ,Plant Science ,tomato ,Quantitative trait locus ,Biology ,eXtra Botany ,Insights ,phenotypic plasticity ,01 natural sciences ,03 medical and health sciences ,Solanum lycopersicum ,Plant breeding ,Adaptation ,multiple stress ,genotype×environment ,education ,2. Zero hunger ,Genetics ,education.field_of_study ,Phenotypic plasticity ,AcademicSubjects/SCI01210 ,fungi ,Chromosome Mapping ,food and beverages ,genotype x environment interaction (GxE) ,15. Life on land ,Adaptation, Physiological ,Research Papers ,Genetic architecture ,Plant Breeding ,[SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding ,Phenotype ,climate change ,030104 developmental biology ,Crop Molecular Genetics ,breeding ,Gene-Environment Interaction ,010606 plant biology & botany - Abstract
Measurements of agronomic and fruit quality traits in a multi-environment trial using a multi-parental advanced generation intercross population identify QTLs for plasticity and QTL × environment interactions in response to abiotic stresses in tomato., Deciphering the genetic basis of phenotypic plasticity and genotype × environment interactions (G×E) is of primary importance for plant breeding in the context of global climate change. Tomato (Solanum lycopersicum) is a widely cultivated crop that can grow in different geographical habitats and that displays a great capacity for expressing phenotypic plasticity. We used a multi-parental advanced generation intercross (MAGIC) tomato population to explore G×E and plasticity for multiple traits measured in a multi-environment trial (MET) comprising optimal cultural conditions together with water deficit, salinity, and heat stress over 12 environments. Substantial G×E was observed for all the traits measured. Different plasticity parameters were estimated by employing Finlay–Wilkinson and factorial regression models and these were used together with genotypic means for quantitative trait loci (QTL) mapping analyses. In addition, mixed linear models were also used to investigate the presence of QTL × environment interactions. The results highlighted a complex genetic architecture of tomato plasticity and G×E. Candidate genes that might be involved in the occurrence of G×E are proposed, paving the way for functional characterization of stress response genes in tomato and for breeding climate-adapted cultivars.
- Published
- 2020
29. UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase
- Author
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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
- Subjects
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.
- Published
- 2020
30. A complex network of QTL for thousand-kernel weight in the rye genome
- Author
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Piotr Masojć, Paweł Milczarski, Anna Bienias, and Piotr Kruszona
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QTL mapping ,0106 biological sciences ,0301 basic medicine ,Genotype ,Secale cereale L ,Quantitative Trait Loci ,Population ,Quantitative trait locus ,Biology ,01 natural sciences ,Genome ,Two-loci interactions ,Chromosomes, Plant ,03 medical and health sciences ,Plant Genetics • Original Paper ,Inbred strain ,Gene interaction ,Genetics ,Allele ,education ,Selection (genetic algorithm) ,education.field_of_study ,Secale ,High-density map ,food and beverages ,Chromosome Mapping ,DArT markers ,Epistasis, Genetic ,General Medicine ,Phenotype ,030104 developmental biology ,Thousand-kernel weight ,Seeds ,Epistasis ,010606 plant biology & botany - Abstract
Here, QTL mapping for thousand-kernel weight carried out within a 541 × Ot1-3 population of recombinant inbred lines using high-density DArT-based map and three methods (single-marker analysis with F parametric test, marker analysis with the Kruskal–Wallis K* nonparametric test, and the recently developed analysis named genes interaction assorting by divergent selection with χ2 test) revealed 28 QTL distributed over all seven rye chromosomes. The first two methods showed a high level of consistency in QTL detection. Each of 13 QTL revealed in the course of gene interaction assorting by divergent selection analysis coincided with those detected by the two other methods, confirming the reliability of the new approach to QTL mapping. Its unique feature of discriminating QTL classes might help in selecting positively acting QTL and alleles for marker-assisted selection. Also, interaction among seven QTL for thousand-kernel weight was analyzed using gene interaction assorting by the divergent selection method. Pairs of QTL showed a predominantly additive relationship, but epistatic and complementary types of two-loci interactions were also revealed. Electronic supplementary material The online version of this article (10.1007/s13353-020-00559-3) contains supplementary material, which is available to authorized users.
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- 2020
31. Identification of a minimal region of loss on chromosome 6q27 associated with poor survival of high-risk neuroblastoma patients
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Annalisa Pezzolo, Martina Morini, Alberto Garaventa, Marina Podestà, and Marzia Ognibene
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Adult ,0301 basic medicine ,Cancer Research ,Adolescent ,Loss of Heterozygosity ,Disease ,Cohort Studies ,Loss of heterozygosity ,Neuroblastoma ,Young Adult ,03 medical and health sciences ,0302 clinical medicine ,Databases, Genetic ,Humans ,Medicine ,Genes, Tumor Suppressor ,Young adult ,Child ,Survival rate ,Aged ,Pharmacology ,Comparative Genomic Hybridization ,business.industry ,Chromosome Mapping ,Chromosome ,Middle Aged ,medicine.disease ,Gene Expression Regulation, Neoplastic ,Survival Rate ,030104 developmental biology ,Oncology ,030220 oncology & carcinogenesis ,Cancer research ,Molecular Medicine ,Chromosomes, Human, Pair 6 ,business ,Haploinsufficiency ,human activities ,Research Paper ,Cohort study - Abstract
Patients with high-risk neuroblastoma (HR-NB) often initially respond to therapy, but afterward they become resistant and disease recurred. Unfortunately, it does not exist one or more specific chromosome defects associated with relapse or refractory NB. Recently, genomic evidence from primary tumors indicated that the distal region of chromosome 6q is loss in HR-NB patients with fatal outcome. We identified a minimal common region of loss of chromosome 6q27 spanning an area of 2.09 Mb by high-resolution DNA copy number data of a small cohort of HR-NB samples carrying 6q loss. This region of loss harbored five genes T, SFT2D1, RPS6KA2, FGFR1OP, and UNC93A. We found that low SFT2D1, RPS6KA2, and FGFR1OP gene expression predicted poor outcome in HR-NB patients using public R2 Platform. Further functional studies will be essential to confirm the presumed tumor suppressor gene(s) located within 6q27 region. These results suggest that SFT2D1, RPS6KA2, and FGFR1OP genes may be responsible for poor prognosis of HR-NB tumors with 6q27 loss, and their haploinsufficiency may be crucial in accelerating tumor progression.
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- 2020
32. Genome-wide DNA copy number profiling and bioinformatics analysis of ovarian cancer reveals key genes and pathways associated with distinct invasive/migratory capabilities
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MeiMei Huang, Guanyu Ruan, Guifen Liu, Lili Chen, and Pengming Sun
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copy number variations (CNVs) ,Aging ,DNA Copy Number Variations ,Genome-Wide DNA Copy Number ,Loss of Heterozygosity ,Computational biology ,Biology ,Genome ,Loss of heterozygosity ,Cell Movement ,Transcription (biology) ,Cell Line, Tumor ,Protein Interaction Mapping ,Gene expression ,metastasis ,Humans ,Gene Regulatory Networks ,Protein Interaction Maps ,Copy-number variation ,Neoplasm Metastasis ,Gene ,Transcription factor ,Cell Proliferation ,Neoplasm Staging ,Proportional Hazards Models ,Ovarian Neoplasms ,Chromosome Mapping ,Computational Biology ,Cell Biology ,invasion ,Prognosis ,ovarian cancer ,protein/DNA array ,Female ,Research Paper ,Genome-Wide Association Study ,Signal Transduction - Abstract
Ovarian cancer (OC) metastasis presents major hurdles that must be overcome to improve patient outcomes. Recent studies have demonstrated copy number variations (CNVs) frequently contribute to alterations in oncogenic drivers. The present study used a CytoScan HD Array to analyse CNVs and loss of heterozygosity (LOH) in the entire genomes of 6 OC patients and human OC cell lines to determine the genetic target events leading to the distinct invasive/migratory capacities of OC. The results showed that LOH at Xq11.1 and Xp21.1 and gains at 8q21.13 were novel, specific CNVs. Ovarian cancer-related CNVs were then screened by bioinformatics analysis. In addition, transcription factors-target gene interactions were predicted with information from PASTAA analysis. As a result, six genes (i.e., GAB2, AKT1, EGFR, COL6A3, UGT1A1 and UGT1A8) were identified as strong candidates by integrating the above data with gene expression and clinical outcome data. In the transcriptional regulatory network, 4 known cancer-related transcription factors (TFs) interacted with 6 CNV-driven genes. The protein/DNA arrays revealed 3 of these 4 TFs as potential candidate gene-related transcription factors in OC. We then demonstrated that these six genes can serve as potential biomarkers for OC. Further studies are required to elucidate the pathogenesis of OC.
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- 2020
33. 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
34. 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
35. Organ-specific small non-coding RNA responses in domestic (Sudani) ducks experimentally infected with highly pathogenic avian influenza virus (H5N1)
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Ahmed A.H. Ali, Fatma Abdallah, Ramon O. Vidal, Robert Geffers, Mohamed Samir, Stefan Bonn, Vincenzo Capece, Ashraf Hussein, Frank Pessler, Frauke Seehusen, University of Zurich, and Pessler, Frank
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virology [Influenza in Birds] ,animal diseases ,viruses ,virology [Ducks] ,pathogenicity [Influenza A Virus, H5N1 Subtype] ,10184 Institute of Veterinary Pathology ,Piwi-interacting RNA ,Biology ,medicine.disease_cause ,genetics [Ducks] ,Virus ,1307 Cell Biology ,03 medical and health sciences ,0302 clinical medicine ,Transcription (biology) ,ddc:570 ,1312 Molecular Biology ,medicine ,Animals ,genetics [MicroRNAs] ,Small nucleolar RNA ,Molecular Biology ,030304 developmental biology ,0303 health sciences ,Influenza A Virus, H5N1 Subtype ,Gene Expression Profiling ,Chromosome Mapping ,metabolism [Influenza in Birds] ,virus diseases ,RNA ,genetics [Organ Specificity] ,Cell Biology ,physiology [Influenza A Virus, H5N1 Subtype] ,Non-coding RNA ,Virology ,Influenza A virus subtype H5N1 ,MicroRNAs ,Ducks ,genetics [Influenza in Birds] ,Viral replication ,Organ Specificity ,Influenza in Birds ,030220 oncology & carcinogenesis ,Host-Pathogen Interactions ,RNA, Small Untranslated ,570 Life sciences ,biology ,genetics [Host-Pathogen Interactions] ,genetics [RNA, Small Untranslated] ,Research Paper - Abstract
The duck represents an important reservoir of influenza viruses for transmission to other avian and mammalian hosts, including humans. The increased pathogenicity of the recently emerging clades of highly pathogenic avian influenza (HPAI) viruses of the H5N1 subtype in ducks features systemic viral spread and organ-to-organ variation in viral transcription and tissue damage. We previously reported that experimental infection of Sudani ducks (Cairina moschata) with an Egyptian HPAI (H5N1) virus (clade 2.2.1.2) features high viral replication and severe tissue damage in lung, but lower viral replication and only mild histological changes in brain. Little is known about the involvement of miRNA in organ-specific responses to H5N1 viruses in ducks, and involvement of the other classes of small noncoding RNA (sncRNA) has not been investigated so far. Following RNA sequencing, we have annotated the duck sncRNome and compared global expression changes of the four major sncRNA classes (miRNAs, piRNAs, snoRNAs, snRNAs) between duck lung and brain during a 120 h time course of infection with this HPAI strain. We find major organ-specific differences in miRNA, piRNA and snoRNA populations even before infection and substantial reprogramming of all sncRNA classes throughout infection, which was less pronounced in brain. Pathway prediction analysis of miRNA targets revealed enrichment of inflammation-, infection- and apoptosis-related pathways in lung, but enrichment of metabolism-related pathways (including tryptophan metabolism) in brain. Thus, organ-specific differences in sncRNA responses may contribute to differences in viral replication and organ damage in ducks infected with isolates from this emerging HPAI clade, and likely other strains.
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- 2019
36. 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
37. Genetic architecture underlying variation in floral meristem termination in Aquilegia
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Molly B. Edwards, Ya Min, Scott A. Hodges, Elena M. Kramer, and Evangeline S. Ballerini
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Candidate gene ,biology ,Physiology ,Aquilegia ,Meristem ,Stamen ,Chromosome Mapping ,Flowers ,Plant Science ,Quantitative trait locus ,biology.organism_classification ,Research Papers ,Genetic architecture ,Gene Expression Regulation, Plant ,Evolutionary biology ,Gene ,Whorl (botany) - Abstract
Floral organs are produced by floral meristems (FMs), which harbor stem cells in their centers. Since each flower only has a finite number of organs, the stem cell activity of a FM will always terminate at a specific time point, a process termed floral meristem termination (FMT). Variation in the timing of FMT can give rise to floral morphological diversity, but how this process is fine-tuned at a developmental and evolutionary level is poorly understood. Flowers from the genus Aquilegia share identical floral organ arrangement except for stamen whorl numbers (SWN), making Aquilegia a well-suited system for investigation of this process: differences in SWN between species represent differences in the timing of FMT. By crossing A. canadensis and A. brevistyla, quantitative trait locus (QTL) mapping has revealed a complex genetic architecture with seven QTL. We identified potential candidate genes under each QTL and characterized novel expression patterns of select candidate genes using in situ hybridization. To our knowledge, this is the first attempt to dissect the genetic basis of how natural variation in the timing of FMT is regulated and our results provide insight into how floral morphological diversity can be generated at the meristematic level.
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- 2021
38. Genetic map‐guided genome assembly reveals a virulence‐governing minichromosome in the lentil anthracnose pathogen Colletotrichum lentis
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Curtis J. Pozniak, Vijai Bhadauria, Sabine Banniza, Aurelie Cohen-Skalie, Li Li, Jerlene Halliday, and Ron MacLachlan
- Subjects
0106 biological sciences ,0301 basic medicine ,disease resistance ,Genetic Linkage ,Physiology ,conditionally dispensable chromosomes ,legumes ,Quantitative Trait Loci ,Population ,Virulence ,Single-nucleotide polymorphism ,Genomics ,Plant Science ,Quantitative trait locus ,Biology ,Polymorphism, Single Nucleotide ,01 natural sciences ,Genome ,03 medical and health sciences ,Minichromosome ,genomics ,Colletotrichum ,education ,Gene ,Plant Diseases ,2. Zero hunger ,Genetics ,education.field_of_study ,Full Paper ,Research ,genotyping‐by‐whole‐genome shotgun sequencing ,Chromosome Mapping ,pathogens ,Full Papers ,030104 developmental biology ,Lens Plant ,Chromosomes, Fungal ,Genome, Fungal ,effectors ,010606 plant biology & botany - Abstract
Colletotrichum lentis causes anthracnose, which is a serious disease on lentil and can account for up to 70% crop loss. Two pathogenic races, 0 and 1, have been described in the C. lentis population from lentil. To unravel the genetic control of virulence, an isolate of the virulent race 0 was sequenced at 1481‐fold genomic coverage. The 56.10‐Mb genome assembly consists of 50 scaffolds with N 50 scaffold length of 4.89 Mb. A total of 11 436 protein‐coding gene models was predicted in the genome with 237 coding candidate effectors, 43 secondary metabolite biosynthetic enzymes and 229 carbohydrate‐active enzymes (CAZymes), suggesting a contraction of the virulence gene repertoire in C. lentis. Scaffolds were assigned to 10 core and two minichromosomes using a population (race 0 × race 1, n = 94 progeny isolates) sequencing‐based, high‐density (14 312 single nucleotide polymorphisms) genetic map. Composite interval mapping revealed a single quantitative trait locus (QTL), qClVIR‐11, located on minichromosome 11, explaining 85% of the variability in virulence of the C. lentis population. The QTL covers a physical distance of 0.84 Mb with 98 genes, including seven candidate effector and two secondary metabolite genes. Taken together, the study provides genetic and physical evidence for the existence of a minichromosome controlling the C. lentis virulence on lentil.
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- 2018
39. 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
40. Genome-wide association mapping of the architecture of susceptibility to the root-knot nematode Meloidogyne incognita in Arabidopsis thaliana
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Marcel Dicke, Casper van Schaik, Geert Smant, Jan E. Kammenga, S. Warmerdam, Octavina C.A. Sukarta, Johannes Helder, Jaap Bakker, Aska Goverse, Marian Oortwijn, Jose L. Lozano-Torres, and Mark G. Sterken
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0106 biological sciences ,0301 basic medicine ,Arabidopsis thaliana ,Physiology ,Arabidopsis ,Plant Science ,Plant Roots ,01 natural sciences ,susceptibility ,brassinosteroid signalling ,Gene Expression Regulation, Plant ,Meloidogyne incognita ,Laboratory of Entomology ,genome‐wide association ,Association mapping ,PBR Groei & Ontwikkeling ,Genetics ,Full Paper ,biology ,Reproduction ,Chromosome Mapping ,food and beverages ,Full Papers ,PBR Breeding for growth and development ,allelic variation ,PE&RC ,F‐box protein ,Terra incognita ,F-box protein ,Quantitative Trait Loci ,Quantitative trait locus ,Polymorphism, Single Nucleotide ,Chromosomes, Plant ,03 medical and health sciences ,Genetic variation ,Animals ,Root-knot nematode ,Genetic Predisposition to Disease ,Tylenchoidea ,Laboratorium voor Nematologie ,Plant Diseases ,Research ,Laboratorium voor Entomologie ,biology.organism_classification ,Genetic architecture ,030104 developmental biology ,Mutation ,genome-wide association ,EPS ,Laboratory of Nematology ,Genome-Wide Association Study ,010606 plant biology & botany - Abstract
Summary Susceptibility to the root‐knot nematode Meloidogyne incognita in plants is thought to be a complex trait based on multiple genes involved in cell differentiation, growth and defence. Previous genetic analyses of susceptibility to M. incognita have mainly focused on segregating dominant resistance genes in crops. It is not known if plants harbour significant genetic variation in susceptibility to M. incognita independent of dominant resistance.To study the genetic architecture of susceptibility to M. incognita, we analysed nematode reproduction on a highly diverse set of 340 natural inbred lines of Arabidopsis thaliana with genome‐wide association mapping. We observed a surprisingly large variation in nematode reproduction among these lines.Genome‐wide association mapping revealed four quantitative trait loci (QTLs) located on chromosomes 1 and 5 of A. thaliana significantly associated with reproductive success of M. incognita, none of which harbours typical resistance gene homologues. Mutant analysis of three genes located in two QTLs showed that the transcription factor BRASSINAZOLE RESISTANT1 and an F‐box family protein may function as (co‐)regulators of susceptibility to M. incognita in Arabidopsis.Our data suggest that breeding for loss‐of‐susceptibility, based on allelic variants critically involved in nematode feeding, could be used to make crops more resilient to root‐knot nematodes.
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- 2018
41. Gene-set association and epistatic analyses reveal complex gene interaction networks affecting flowering time in a worldwide barley collection
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Camilla Beate Hill, Xiao-Qi Zhang, David Moody, Tefera Tolera Angessa, Tianhua He, Paul Telfer, Kefei Chen, Chengdao Li, and Sharon Westcott
- Subjects
epistasis ,0106 biological sciences ,0301 basic medicine ,Genotype ,Physiology ,Quantitative Trait Loci ,Epistasis and functional genomics ,Genome-wide association study ,Single-nucleotide polymorphism ,Flowers ,Plant Science ,heritability ,Biology ,phenology ,Polymorphism, Single Nucleotide ,01 natural sciences ,Linkage Disequilibrium ,03 medical and health sciences ,Gene interaction ,gene-set association analysis ,Barley ,Genetic variation ,GWAS ,Gene Regulatory Networks ,Genetic association ,2. Zero hunger ,Genetics ,fungi ,target capture ,Chromosome Mapping ,food and beverages ,Epistasis, Genetic ,Hordeum ,flowering time ,Heritability ,Research Papers ,030104 developmental biology ,Crop Molecular Genetics ,Epistasis ,next-generation sequencing ,target enrichment ,Genome-Wide Association Study ,010606 plant biology & botany - Abstract
Using gene-set association test and epistasis analysis, this research achieved higher statistical power with potentially high accuracy, and detected significant genes and gene networks that influence flowering time in barley., Single-marker genome-wide association studies (GWAS) have successfully detected associations between single nucleotide polymorphisms (SNPs) and agronomic traits such as flowering time and grain yield in barley. However, the analysis of individual SNPs can only account for a small proportion of genetic variation, and can only provide limited knowledge on gene network interactions. Gene-based GWAS approaches provide enormous opportunity both to combine genetic information and to examine interactions among genetic variants. Here, we revisited a previously published phenotypic and genotypic data set of 895 barley varieties grown in two years at four different field locations in Australia. We employed statistical models to examine gene–phenotype associations, as well as two-way epistasis analyses to increase the capability to find novel genes that have significant roles in controlling flowering time in barley. Genetic associations were tested between flowering time and corresponding genotypes of 174 putative flowering time-related genes. Gene–phenotype association analysis detected 113 genes associated with flowering time in barley, demonstrating the unprecedented power of gene-based analysis. Subsequent two-way epistasis analysis revealed 19 pairs of gene×gene interactions involved in controlling flowering time. Our study demonstrates that gene-based association approaches can provide higher capacity for future crop improvement to increase crop performance and adaptation to different environments.
- Published
- 2019
42. Development of molecular markers associated with resistance to Meloidogyne incognita by performing quantitative trait locus analysis and genome-wide association study in sweetpotato
- Author
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Rumi Sasai, Hiroaki Tabuchi, Yoshihiro Okada, Kazuki Kishimoto, Akira Kobayashi, Yuki Monden, Shusei Sato, Sachiko Isobe, Akihide Kuramoto, Kenta Shirasawa, and Makoto Tahara
- Subjects
QTL mapping ,0106 biological sciences ,Genetic Linkage ,Quantitative Trait Loci ,Genome-wide association study ,Single-nucleotide polymorphism ,Quantitative trait locus ,Polymorphism, Single Nucleotide ,01 natural sciences ,03 medical and health sciences ,Genetic linkage ,Genotype ,Genetics ,Meloidogyne incognita ,Animals ,GWAS ,Tylenchoidea ,Ipomoea batatas ,Nematode Infections ,Molecular Biology ,sweetpotato ,Disease Resistance ,Plant Diseases ,marker-assisted breeding ,030304 developmental biology ,0303 health sciences ,Polymorphism, Genetic ,biology ,polyploids ,fungi ,Chromosome Mapping ,food and beverages ,General Medicine ,Full Papers ,biology.organism_classification ,Genetic marker ,Terra incognita ,Genome-Wide Association Study ,Microsatellite Repeats ,010606 plant biology & botany - Abstract
The southern root-knot nematode, Meloidogyne incognita, is a pest that decreases yield and the quality of sweetpotato [Ipomoea batatas (L.) Lam.]. There is a demand to produce resistant cultivars and develop DNA markers to select this trait. However, sweetpotato is hexaploid, highly heterozygous, and has an enormous genome (∼3 Gb), which makes genetic linkage analysis difficult. In this study, a high-density linkage map was constructed based on retrotransposon insertion polymorphism, simple sequence repeat, and single nucleotide polymorphism markers. The markers were developed using F1 progeny between J-Red, which exhibits resistance to multiple races of M. incognita, and Choshu, which is susceptible to multiple races of such pest. Quantitative trait locus (QTL) analysis and a genome-wide association study detected highly effective QTLs for resistance against three races, namely, SP1, SP4, and SP6-1, in the Ib01-6 J-Red linkage group. A polymerase chain reaction marker that can identify genotypes based on single nucleotide polymorphisms located in this QTL region can discriminate resistance from susceptibility in the F1 progeny at a rate of 70%. Thus, this marker could be helpful in selecting sweetpotato cultivars that are resistant to multiple races of M. incognita.
- Published
- 2019
43. Genetic architecture of leaf photosynthesis in rice revealed by different types of reciprocal mapping populations
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Takayuki Ochiai, Naoto Ichihara, Shunsuke Adachi, Toshio Yamamoto, Takashi Ikka, Masaki Uchida, Chikako Otsuka, Kazuya Soda, Katsuhiko Kondo, Taiichiro Ookawa, Ryoji Karimata, Toshiyuki Takai, Tadamasa Ueda, Masahiro Yamashita, Tadashi Hirasawa, Toru Nakae, Risako Ao, and Ruri Nakano
- Subjects
0106 biological sciences ,0301 basic medicine ,Stomatal conductance ,Physiology ,Quantitative Trait Loci ,Plant Science ,Quantitative trait locus ,phenology ,01 natural sciences ,Japonica ,chromosome segment substitution line ,03 medical and health sciences ,quantitative trait locus ,Backcross inbred line ,Inbred strain ,Cultivar ,Allele ,Alleles ,photosynthesis ,biology ,rice ,fungi ,Chromosome Mapping ,food and beverages ,Oryza ,yield ,biology.organism_classification ,Research Papers ,Genetic architecture ,Plant Leaves ,Horticulture ,030104 developmental biology ,Crop Molecular Genetics ,stomatal conductance ,Backcrossing ,reciprocal mapping population ,nitrogen content ,010606 plant biology & botany - Abstract
Several reliable QTLs for leaf photosynthesis were detected using reciprocal mapping populations derived from japonica and indica rice varieties with different photosynthetic capacities., The improvement of leaf net photosynthetic rate (An) is a major challenge in enhancing crop productivity. However, the genetic control of An among natural genetic accessions is still poorly understood. The high-yielding indica cultivar Takanari has the highest An of all rice cultivars, 20–30% higher than that of the high-quality japonica cultivar Koshihikari. By using reciprocal backcross inbred lines and chromosome segment substitution lines derived from a cross between Takanari and Koshihikari, we identified three quantitative trait loci (QTLs) where the Takanari alleles enhanced An in plants with a Koshihikari genetic background and five QTLs where the Koshihikari alleles enhanced An in plants with a Takanari genetic background. Two QTLs were expressed in plants with both backgrounds (type I QTL). The expression of other QTLs depended strongly on genetic background (type II QTL). These beneficial alleles increased stomatal conductance, the initial slope of An versus intercellular CO2 concentration, or An at CO2 saturation. Pyramiding of these alleles consistently increased An. Some alleles positively affected biomass production and grain yield. These alleles associated with photosynthesis and yield can be a valuable tool in rice breeding programs via DNA marker-assisted selection.
- Published
- 2019
44. Unraveling the genetic architecture of grain size in einkorn wheat through linkage and homology mapping and transcriptomic profiling
- Author
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Chun-Ming Liu, Kang Yu, Jiazhu Sun, Aimin Zhang, Wenlong Yang, Wei Yang, Dongcheng Liu, Shancen Zhao, Lixin Yin, Chi Zhang, Dongzhi Wang, and Yong Chen
- Subjects
Candidate gene ,Genetic Linkage ,Physiology ,Sequence assembly ,Single-nucleotide polymorphism ,Plant Science ,Quantitative trait locus ,Biology ,Genome ,RAD-seq, RNA-seq ,Gene mapping ,high-density genetic map ,Gene ,Triticum ,Plant Proteins ,grain size ,Genetics ,Comparative genomics ,Einkorn wheat (Triticum monococcum) ,Gene Expression Profiling ,Chromosome Mapping ,food and beverages ,Heritability ,Research Papers ,Genetic architecture ,Crop Molecular Genetics ,quantitative trait loci ,Edible Grain ,Transcriptome - Abstract
Genome-wide linkage and homology mapping revealed 17 genomic regions harboring 42 QTLs affecting grain size in einkorn wheat. Transcriptomic analysis identified 20 genes involved in grain development and starch biosynthesis with differential expression between two parental lines., Understanding the genetic architecture of grain size is a prerequisite to manipulating grain development and improving the potential crop yield. In this study, we conducted a whole genome-wide quantitative trait locus (QTL) mapping of grain-size-related traits by constructing a high-density genetic map using 109 recombinant inbred lines of einkorn wheat. We explored the candidate genes underlying QTLs through homologous analysis and RNA sequencing. The high-density genetic map spanned 1873 cM and contained 9937 single nucleotide polymorphism markers assigned to 1551 bins on seven chromosomes. Strong collinearity and high genome coverage of this map were revealed by comparison with physical maps of wheat and barley. Six grain size-related traits were surveyed in five environments. In total, 42 QTLs were identified; these were assigned to 17 genomic regions on six chromosomes and accounted for 52.3–66.7% of the phenotypic variation. Thirty homologous genes involved in grain development were located in 12 regions. RNA sequencing identified 4959 genes differentially expressed between the two parental lines. Twenty differentially expressed genes involved in grain size development and starch biosynthesis were mapped to nine regions that contained 26 QTLs, indicating that the starch biosynthesis pathway plays a vital role in grain development in einkorn wheat. This study provides new insights into the genetic architecture of grain size in einkorn wheat; identification of the underlying genes enables understanding of grain development and wheat genetic improvement. Furthermore, the map facilitates quantitative trait mapping, map-based cloning, genome assembly, and comparative genomics in wheat taxa.
- Published
- 2019
45. The multi-allelic APRR2 gene is associated with fruit pigment accumulation in melon and watermelon
- Author
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Arthur A. Schaffer, Adi Faigenboim, Yaakov Tadmor, Joseph Burger, Lea Vexler, Edward S. Buckler, Ayala Meir, Vitaly Portnoy, Asaf Dafna, Amnon Levi, Nurit Katzir, Elad Oren, Galil Tzuri, Merav Kenigswald, and Amit Gur
- Subjects
Chlorophyll ,QTL ,Physiology ,Melon ,Quantitative Trait Loci ,Single-nucleotide polymorphism ,Genome-wide association study ,Plant Science ,Quantitative trait locus ,Biology ,Genes, Plant ,Deep sequencing ,Citrullus ,Pigment accumulation ,melon ,GWAS ,RNA-Seq ,Allele ,APRR2 ,Gene ,Alleles ,BSA-Seq ,Genetics ,Pigmentation ,fruit quality ,carotenoids ,watermelon ,Chromosome Mapping ,food and beverages ,Research Papers ,Cucurbitaceae ,Phenotype ,Crop Molecular Genetics ,Fruit ,Genome, Plant ,Genome-Wide Association Study - Abstract
Color and pigment contents are important aspects of fruit quality and consumer acceptance of cucurbit crops. Here, we describe the independent mapping and cloning of a common causative APRR2 gene regulating pigment accumulation in melon and watermelon. We initially show that the APRR2 transcription factor is causative for the qualitative difference between dark and light green rind in both crops. Further analyses establish the link between sequence or expression level variations in the CmAPRR2 gene and pigment content in the rind and flesh of mature melon fruits. A genome-wide association study (GWAS) of young fruit rind color in a panel composed of 177 diverse melon accessions did not result in any significant association, leading to an earlier assumption that multiple genes are involved in shaping the overall phenotypic variation in this trait. Through resequencing of 25 representative accessions and allelism tests between light rind accessions, we show that multiple independent single nucleotide polymorphisms in the CmAPRR2 gene are causative of the light rind phenotype. The multi-haplotypic nature of this gene explains the lack of detection power obtained through genotyping by sequencing-based GWAS and confirms the pivotal role of this gene in shaping fruit color variation in melon. This study demonstrates the power of combining bi- and multi-allelic designs with deep sequencing, to resolve lack of power due to high haplotypic diversity and low allele frequencies. Due to its central role and broad effect on pigment accumulation in fruits, the APRR2 gene is an attractive target for carotenoid bio-fortification of cucurbit crops., A multi-allelic APRR2 gene was shown to be a common broad effect regulator of fruit pigmentation in melon and watermelon.
- Published
- 2019
46. De novo whole-genome assembly in Chrysanthemum seticuspe, a model species of Chrysanthemums, and its application to genetic and gene discovery analysis
- Author
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Kenji Taniguchi, Makoto Kusaba, Yohei Higuchi, Kenta Shirasawa, Katsuhiko Sumitomo, Hiroyasu Yamaguchi, Yoshihiro Nakano, Masafumi Yagi, Tamotsu Hisamatsu, Hideki Hirakawa, Michiharu Nakano, Masaji Koshioka, Sachiko Isobe, and Soichiro Nagano
- Subjects
0106 biological sciences ,Chrysanthemum ,Genetic Linkage ,Sequence assembly ,Computational biology ,Biology ,01 natural sciences ,Genome ,Genetic analysis ,DNA sequencing ,03 medical and health sciences ,Genetics ,Molecular Biology ,Gene ,Genome size ,Phylogeny ,Illumina dye sequencing ,030304 developmental biology ,0303 health sciences ,Polymorphism, Genetic ,Whole Genome Sequencing ,Chrysanthemum morifolium ,Chromosome Mapping ,Molecular Sequence Annotation ,General Medicine ,Full Papers ,biology.organism_classification ,linkage map ,Chrysanthemum seticuspe ,genome sequence assembly ,humanities ,flowering genes ,Genome, Plant ,010606 plant biology & botany - Abstract
Cultivated chrysanthemum (Chrysanthemum morifolium Ramat.) is one of the most economically important ornamental crops grown worldwide. It has a complex hexaploid genome (2n = 6x = 54) and large genome size. The diploid Chrysanthemum seticuspe is often used as a model of cultivated chrysanthemum, since the two species are closely related. To expand our knowledge of the cultivated chrysanthemum, we here performed de novo whole-genome assembly in C. seticuspe using the Illumina sequencing platform. XMRS10, a C. seticuspe accession developed by five generations of self-crossing from a self-compatible strain, AEV2, was used for genome sequencing. The 2.72 Gb of assembled sequences (CSE_r1.0), consisting of 354,212 scaffolds, covered 89.0% of the 3.06 Gb C. seticuspe genome estimated by k-mer analysis. The N50 length of scaffolds was 44,741 bp. For protein-encoding genes, 71,057 annotated genes were deduced (CSE_r1.1_cds). Next, based on the assembled genome sequences, we performed linkage map construction, gene discovery and comparative analyses for C. seticuspe and cultivated chrysanthemum. The generated C. seticuspe linkage map revealed skewed regions in segregation on the AEV2 genome. In gene discovery analysis, candidate flowering-related genes were newly found in CSE_r1.1_cds. Moreover, single nucleotide polymorphism identification and annotation on the C. × morifolium genome showed that the C. seticuspe genome was applicable to genetic analysis in cultivated chrysanthemums. The genome sequences assembled herein are expected to contribute to future chrysanthemum studies. In addition, our approach demonstrated the usefulness of short-read genome assembly and the importance of choosing an appropriate next genome sequencing technology based on the purpose of the post-genome analysis.
- Published
- 2019
47. The transcription factor EGR2 is the molecular linchpin connecting STAT6 activation to the late, stable epigenomic program of alternative macrophage polarization
- Author
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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
- Subjects
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.
- Published
- 2020
48. Introducing differential RNA-seq mapping to track the early infection phase for
- Author
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Laura, Wicke, Falk, Ponath, Lucas, Coppens, Milan, Gerovac, Rob, Lavigne, and Jörg, Vogel
- Subjects
Gene Expression Regulation, Viral ,phage-host interaction ,Sequence Analysis, RNA ,Chromosome Mapping ,Molecular Sequence Annotation ,Gene Expression Regulation, Bacterial ,Genome, Viral ,differential expression ,DNA-Binding Proteins ,Gene Ontology ,Bacterial Proteins ,Biofilms ,dRNA-seq ,Antibiosis ,Pseudomonas aeruginosa ,RNA, Viral ,Transcription Initiation Site ,Adhesins, Bacterial ,Pseudomonas Phages ,Transcriptome ,transcription start site ,Bacterial Outer Membrane Proteins ,Research Article ,Research Paper ,Bacteriophage ɸKZ - Abstract
As part of the ongoing renaissance of phage biology, more phage genomes are becoming available through DNA sequencing. However, our understanding of the transcriptome architecture that allows these genomes to be expressed during host infection is generally poor. Transcription start sites (TSSs) and operons have been mapped for very few phages, and an annotated global RNA map of a phage – alone or together with its infected host – is not available at all. Here, we applied differential RNA-seq (dRNA-seq) to study the early, host takeover phase of infection by assessing the transcriptome structure of Pseudomonas aeruginosa jumbo phage ɸKZ, a model phage for viral genetics and structural research. This map substantially expands the number of early expressed viral genes, defining TSSs that are active ten minutes after ɸKZ infection. Simultaneously, we record gene expression changes in the host transcriptome during this critical metabolism conversion. In addition to previously reported upregulation of genes associated with amino acid metabolism, we observe strong activation of genes with functions in biofilm formation (cdrAB) and iron storage (bfrB), as well as an activation of the antitoxin ParD. Conversely, ɸKZ infection rapidly down-regulates complexes IV and V of oxidative phosphorylation (atpCDGHF and cyoABCDE). Taken together, our data provide new insights into the transcriptional organization and infection process of the giant bacteriophage ɸKZ and adds a framework for the genome-wide transcriptomic analysis of phage–host interactions.
- Published
- 2020
49. Present‐day sympatry belies the evolutionary origin of a high‐order polyploid
- Author
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Jacob A. Tennessen, Na Wei, Tia-Lynn Ashman, and Aaron Liston
- Subjects
0301 basic medicine ,Sympatry ,Fragaria cascadensis ,Physiology ,polyploid origin ,Plant Science ,Biology ,subgenome ,Chromosomes, Plant ,Evolution, Molecular ,Polyploidy ,03 medical and health sciences ,Polyploid ,Phylogenetics ,Genetic algorithm ,targeted sequence capture ,Phylogeny ,Genetics ,Base Sequence ,Full Paper ,Research ,fungi ,sex expression ,Chromosome Mapping ,food and beverages ,Full Papers ,15. Life on land ,biology.organism_classification ,linkage map ,phylogenetics ,030104 developmental biology ,Evolutionary biology ,Sympatric speciation ,decaploid Fragaria ,Hybrid speciation ,Ploidy - Abstract
Summary Disentangling the evolutionary histories of polyploids, especially those with high ploidies, can reveal fundamental processes in speciation. Despite occurring frequently during evolution, the origins of many extant polyploid plant species remain largely unknown. By integrating linkage mapping, polyploid phylogeny and sex-determining region (SDR) in a unified framework, we statistically evaluated evolutionary hypotheses concerning the origin of a recently recognized decaploid strawberry (Fragaria cascadensis). The maximum-likelihood phylogenies and topology tests across homeologous groups consistently rejected the seemingly parsimonious hypothesis of ‘contemporary sympatric speciation’ via hybridization between octoploid and diploid congeners. Instead, most chromosomes supported ‘ancient hybrid speciation’ between a maternal octoploid progenitor ancestral to extant octoploid strawberries and a paternal, extinct Fragaria iinumae-like diploid progenitor, probably in Beringia during the Pleistocene. The absence of a shared SDR between the decaploid and other Fragaria is also consistent with an older origin rather than a recent hybrid origin in situ. Our study reveals a long evolutionary history of the decaploid despite its recent discovery, and highlights the pitfalls of inferring polyploid origins from niche/range alone or combined with morphology. It can serve as an exemplary starting step towards building much-needed model systems of established polyploids that have been, and remain to be, recognized.
- Published
- 2017
50. Genetic architecture of plant stress resistance: multi-trait genome-wide association mapping
- Author
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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)
- Subjects
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.]
- Published
- 2017
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