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Rice (Oryza sativa) is a staple food crop and serves as a model cereal plant. It contains two biosynthetic gene clusters (BGCs) for the production of labdane-related diterpenoids (LRDs), which serve important roles in combating biotic and abiotic stress. While plant BGCs have been subject to genetic analyses, these analyses have been largely confined to the investigation of single genes. CRISPR/Cas9-mediated genome editing was used to precisely remove each of these BGCs, as well as simultaneously knock out both BGCs. Deletion of the BGC from chromosome 2 (c2BGC), which is associated with phytocassane biosynthesis, but not that from chromosome 4 (c4BGC), which is associated with momilactone biosynthesis, led to a lesion mimic phenotype. This phenotype is dependent on two closely related genes encoding cytochrome P450 (CYP) mono-oxygenases, CYP76M7 and CYP76M8, from the c2BGC. However, rather than being redundant, CYP76M7 has been associated with the production of phytocassanes, whereas CYP76M8 is associated with momilactone biosynthesis. Intriguingly, the lesion mimic phenotype is not present in a line with both BGCs deleted. These results reveal directional cross-cluster phytotoxicity, presumably arising from the accumulation of LRD intermediates dependent on the c4BGC in the absence of CYP76M7 and CYP76M8, further highlighting their interdependent evolution and the selective pressures driving BGC assembly.

Necrosis- and ethylene-inducing peptide 1 (Nep1)-like proteins (NLPs) constitute a superfamily of proteins toxic to dicot plants, but the molecular basis of this toxicity remains obscure. Using quantitative trait locus (QTL) analysis we investigated the genetic variation underlying ion leakage in Arabidopsis plants elicited with MoNLP1 derived from Magnaporthe oryzae. The QTL conditioning MoNLP1 toxicity was positionally cloned and further characterized to elucidate its mode of action. MoNLP1-triggered cell death varied significantly across > 250 Arabidopsis accessions and three QTLs were identified conferring the observed variation. The QTL on chromosome 4 was uncovered to encode a leucine-rich repeat (LRR)-only protein designated as NTCD4, which shares high sequence identity with a set of nucleotide-binding LRR proteins. NTCD4 was secreted into the apoplast and physically interacted with multiple NLPs. Apoplastic NTCD4 facilitated the oligomerization of NLP, which was closely associated with toxicity in planta. The natural genetic variation causing D3N change in NTCD4 reduced the secretion efficiency of NTCD4 and the infection of Botrytis cinerea on Arabidopsis plants. These observations demonstrate that the plant-derived NTCD4 is recruited by NLPs to promote toxicity via facilitating their oligomerization, which extends our understanding of a key step in the toxic mode of action of NLPs.

An Oligo-FISH barcode system was developed for two model legumes, allowing the identification of all cowpea and common bean chromosomes in a single FISH experiment, and revealing new chromosome rearrangements. The FISH barcode system emerges as an effective tool to understand the chromosome evolution of economically important legumes and their related species. Current status on plant cytogenetic and cytogenomic research has allowed the selection and design of oligo-specific probes to individually identify each chromosome of the karyotype in a target species. Here, we developed the first chromosome identification system for legumes based on oligo-FISH barcode probes. We selected conserved genomic regions between Vigna unguiculata (Vu, cowpea) and Phaseolus vulgaris (Pv, common bean) (diverged ~ 9.7–15 Mya), using cowpea as a reference, to produce a unique barcode pattern for each species. We combined our oligo-FISH barcode pattern with a set of previously developed FISH probes based on BACs and ribosomal DNA sequences. In addition, we integrated our FISH maps with genome sequence data. Based on this integrated analysis, we confirmed two translocation events (involving chromosomes 1, 5, and 8; and chromosomes 2 and 3) between both species. The application of the oligo-based probes allowed us to demonstrate the participation of chromosome 5 in the translocation complex for the first time. Additionally, we detailed a pericentric inversion on chromosome 4 and identified a new paracentric inversion on chromosome 10. We also detected centromere repositioning associated with chromosomes 2, 3, 5, 7, and 9, confirming previous results for chromosomes 2 and 3. This first barcode system for legumes can be applied for karyotyping other Phaseolinae species, especially non-model, orphan crop species lacking genomic assemblies and cytogenetic maps, expanding our understanding of the chromosome evolution and genome organization of this economically important legume group.

Highlights • Terminal heat stress leads to irreversible damage in wheat. • Marker assisted selection and gene pyramiding for portrayal of heat tolerance. • Allelic frequency and polymorphic information showed significant variability. • Markers xcfa2147 and xwmc671 could be potentail for heat stress tolerance., Terminal heat stress causes irreversible damage to wheat crop productivity. It reduces the vegetative growth and flowering period that consequently declines the efficiency to capture available stem reserves (carbohydrates) in grains. Markers associated with thermotolerant traits ease in marker assisted selection (MAS) for crop improvement. It identifies the genomic regions associated with thermotolerant traits in wheat, but the scarcity of markers is the major hindrance in crop improvement. Therefore, 158 wheat genotypes were subjected to genotyping with 165 simple sequence repeat markers dispersed on three genomes (A, B and D). Allelic frequency and polymorphic information content values were highest on genome A (5.34 (14% greater than the lowest value at genome D) and 0.715 (3% greater than the lowest value at genome D)), chromosome 4 (5.40 (16% greater than the lowest value at chromosome 2) and 0.725 (5% greater than the lowest value at chromosome 6)) and marker xgwm44 (13.0 (84% greater than the lowest value at marker xbarc148) and 0.916 (46% greater than the lowest value at marker xbarc148)). Bayesian based population structure discriminated the wheat genotypes into seven groups based on genetic similarity indicating their ancestral origin and geographical ecotype. Linkage disequilibrium pattern had highest significant (P 0.1 whereas, 58 on genome B at r2 > 0.5. Linkage disequilibrium decay (P 0.1) had larger LD block (5–10 cM) on genome A. Highly significant MTAs (P

Dioecy, the presence of male and female individual, has evolved independently from hermaphroditism in multiple flowering plant lineages. Spinach, an important leafy vegetable crop worldwide, is a dioecious species with an XY sex-determination system. Although some markers that are fully linked to male-determination locus were identified, the male-specific region (MSR) remained unclear. In this research, five male individuals and five female lines were resequenced to identify the male-specific region. We identified a region (∼21 kb) on chromosome 4 (putative sex chromosome) where the five females had a low reads coverage, while the five males had high coverage. A KASP marker, SponR, developed from a single nucleotide polymorphism (SNP) closely linked to the MSR was co-segregating with the sex determination gene in the population of 958 individuals, suggesting that the MSR might be specifically present in male spinach plants.

Cherubism is a rare inherited disorder involving the jaws exclusively and mainly seen in the pediatric population. It has distinctive clinical features and shares radiographic and histopathologic characteristics with other fibro-osseous lesions. Cherubism is caused by a mutation in the SH3BP2 gene located on chromosome 4. Two atypical genetic cases of cherubism from different families that associated with SH3BP2 gene point mutations c.1253C > A and c.1258 G > A in exon 9 were reported. The first case, a 7 years old boy, showed reduced penetrance as the father who is carrying the same mutation did not show any phenotypic features of cherubism. While in the second case, a 6 years old boy, both of his parents proved to be negative for the mutation. Hence the mutation of the child has occurred sporadically. Although the disease seems to be a simple monogenic disease characterized by specific features, a varied genetic presentation can be expected. Understanding such potential influence could highlight possible therapeutic intervention for cherubism.

Objective Bi-allelic mutations in wolframin gene (WFS1) cause Wolfram syndrome 1 (WS1 or DIDMOAD) characterized with non-autoimmune diabetes mellitus (DM), optic atrophy (OA), diabetes insipidus (DI), sensorineural deafness (SND), urinary tract abnormalities, and neuropsychiatric disorders. We evaluated patients presented with an incomplete phenotype of WS1 using homozygosity mapping and subsequent whole-exome sequencing. Patients and methods Four unrelated consanguineous Turkish families (7 affected children), and their unaffected parents and siblings were evaluated. Homozygosity mapping (HZM) was performed, followed by whole-exome sequencing of WFS1. Mutations were classified according to results of "in silico" analyses, protein prediction, and functional consequences. Results Homozygosity mapping confirmed shared homozygous regions on chromosome 4 (chr4p16.1) between the affected individuals, and absent from their unaffected siblings. Exome sequencing identified three novel (c.1215T>A, c.554G>A, c.1525_1540dup) and one known (c. 1522_1523delTA) mutations in WFS1 gene. All mutations were predicted to cause stop codon leading to early termination of protein synthesis and complete loss-of-function. All patients were found to be homozygous for the change, with parents and other unaffected siblings being carriers. Conclusion Our study expands the mutation spectrum of WSF1 mutations with three novel mutations. Homozygosity mapping may provide enrichment for molecular genetic analysis and early diagnosis of WS1 patients with incomplete phenotype, particularly in consanguineous pedigrees.

We report a case of a girl with a chromosomal disorder that has never been described in the literature: inversion of chromosome 4 with an unbalanced translocation between the short arm of chromosome 4 and long arm of chromosome 18. Clinical manifestations of this syndrome included severe growth retardation, very slow weight gain, optic nerve hypoplasia, pronounced delay in mental and motor development, and epilepsy with focal hemiclonic fever-related seizures of varying location. The patient has multiple stigmas of dysembryogenesis, but no abnormalities in the development of internal organs. The somatic status is complicated by chronic liquid aspiration and sleep apnea. Magnetic resonance imaging has demonstrated agenesis of the corpus callosum. In this article, we have summarized the results of clinical observation and electroencephalography findings obtained during several years. The type of epilepsy in this girl does not match Wolf–Hirschhorn syndrome (which is determined by her karyotype), but is similar to epilepsy in patients with aberrations of the long arm of chromosome 18.

Terminal deletions in the long arm of chromosome 4 are an uncommon event, with a worldwide incidence of approximately 0.001%. The majority of these deletions occur de novo. Terminal deletion cases are usually accompanied by clinical findings that include facial and cardiac anomalies, as well as intellectual disability. In this study, we describe the case of a 2-year-old girl, the fourth child born to consanguineous parents. While her karyotype was normal, a homozygous deletion was identified in the chromosome 4q35.2 region by subtelomeric FISH. A heterozygous deletion of the chromosome 4q35.2 region was observed in both parents. According to the literature, this is the first report of a case that has inherited a homozygous deletion of chromosome 4qter from carrier parents. Subsequent array-CGH analyses were performed on both the case and her parents. Whole-exome sequencing was also carried out to determine potential variants. We detected a NM_001111125.3:c.2329G>T (p.Glu777Ter) nonsense variant of the IQSEC2 gene in the girl, a variant that is related to X-linked intellectual disability.

Huntington’s disease (HD) is a neurodegenerative disease that is genetically inherited through an autosomal dominant gene located on chromosome 4. HD is caused by DNA mutation (generally 37 or more repetition of CAG nucleotides) that leads to an excessive stretch of glutamine residues. However, the main pathogenesis pathway resulted by polyglutamine expansion in mutant HD is unknown. The characteristics of this disease mostly appear in adults. Patients who suffer from this disease have shown an inability to control physical movements, emotional problems, speech disturbance, dementia, loss of thinking ability and death occurs between 15-20 years from the time of symptomatic onset. This review article suggested that investigation of mutation in the HD gene can be done by proteomic analysis such as mass spectroscopy, gel electrophoresis, western blotting, chromatographic based technology, and X-ray crystallography. The primary aim of proteomics is to focus on the molecular changes occurring in HD, there by enhancing the effectiveness of treatment.

Human fungal pathogen Candida albicans cannot utilize L-sorbose as a sole carbon source. However, chromosome 5 monosomic strains can grow on sorbose as repressors present on this chromosome get diminished allowing the expression of sorbose utilization gene (SOU1) located on chromosome 4. Functional identification of these repressors has been a difficult task as they are scattered on a large portion of the right arm of chromosome 5. Herein, we have applied the telomere-mediated chromosomal truncation approach to identify a novel repressor for sorbose utilization in this pathogen. Multiple systematic chromosomal truncations were performed on the right arm of Chr5 in the background of csu51∆/CSU51 to minimize the functional region to 6-kb chromosomal stretch. Further, truncation that removes the part of Orf19.3942 strongly suggested its role in sorbose utilization. However, compelling evidence comes from the observation that truncation at 1,044.288-kb position of Chr5 in the strain csu51∆/CSU51 orf19.3942∆/Orf.19.3942 produced Sou+ phenotype; otherwise, the strain remains Sou- . This confirms beyond doubt the role of Orf.19.3942 in the regulation of sorbose utilization and designated as CSU57. Comparison of SOU1 gene expression of Sou+ strains with wild type suggested its role at transcriptional level. Strain carrying double disruption of CSU57 remains Sou- . Co-overexpression of SOU1 and CSU57 together does not make the recipient strain Sou- ; however, multiple tandem copies of CSU57 produced diminished growth compared with control suggesting that it is a weak repressor. Taken together, we report that CSU57 encodes a novel repressor of L-sorbose utilization in this pathogen. TAKE AWAY: CSU57 encodes a repressor for L-sorbose utilization in Candida albicans. Csu57p acts in combination with Csu51p and other regulators. Csu57p exerts its repressing effect at transcriptional level of SOU1 gene. Utilization of sorbose positively correlates to the expression of SOU1 gene. Multiple copies of CSU57 can partially suppress Sou+ phenotype.

ObjectivePrognosis of patients with advanced oesophagogastric adenocarcinoma (mEGAC) is poor and molecular determinants of shorter or longer overall survivors are lacking. Our objective was to identify molecular features and develop a prognostic model by profiling the genomic features of patients with mEGAC with widely varying outcomes.DesignWe profiled 40 untreated mEGACs (20 shorter survivors 36 months) with whole-exome sequencing (WES) and RNA sequencing and performed an integrated analysis of exome, transcriptome, immune profile and pathological phenotypes to identify the molecular determinants, developing an integrated model for prognosis and comparison with The Cancer Genome Atlas (TCGA) cohorts.ResultsKMT2C alterations were exclusively observed in shorter survivors together with high level of intratumour heterogeneity and complex clonal architectures, whereas the APOBEC mutational signatures were significantly enriched in longer survivors. Notably, the loss of heterozygosity in chromosome 4 (Chr4) was associated with shorter survival and ‘cold’ immune phenotype characterised by decreased B, CD8, natural killer cells and interferon-gamma responses. Unsupervised transcriptomic clustering revealed a shorter survivor subtype with distinct expression features (eg, upregulated druggable targets JAK2, MAP3K13 and MECOM). An integrated model was then built based on clinical variables and the identified molecular determinants, which significantly segregated shorter and longer survivors. All the above features and the integrated model have been validated independently in multiple TCGA cohorts.ConclusionThis study discovered novel molecular features prognosticating overall survival in patients with mEGAC and identified potential novel targets in shorter survivors.

Glycophorins are the most abundant sialoglycoproteins on the surface of human erythrocyte membranes. Genetic variation in glycophorin region of human chromosome 4 (containing GYPA, GYPB, and GYPE genes) is of interest because the gene products serve as receptors for pathogens of major public health interest, including Plasmodium sp., Babesia sp., Influenza virus, Vibrio cholerae El Tor Hemolysin, and Escherichia coli. A large structural rearrangement and hybrid glycophorin variant, known as Dantu, which was identified in East African populations, has been linked with a 40% reduction in risk for severe malaria. Apart from Dantu, other large structural variants exist, with the most common being deletion of the whole GYPB gene and its surrounding region, resulting in multiple different deletion forms. In West Africa particularly, these deletions are estimated to account for between 5 and 15% of the variation in different populations, mostly attributed to the forms known as DEL1 and DEL2. Due to the lack of specific variant assays, little is known of the distribution of these variants. Here, we report a modification of a previous GYPB DEL1 assay and the development of a novel GYPB DEL2 assay as high-throughput PCR-RFLP assays, as well as the identification of the crossover/breakpoint for GYPB DEL2. Using 393 samples from three study sites in Ghana as well as samples from HapMap and 1000 G projects for validation, we show that our assays are sensitive and reliable for genotyping GYPB DEL1 and DEL2. To the best of our knowledge, this is the first report of such high-throughput genotyping assays by PCR-RFLP for identifying specific GYPB deletion types in populations. These assays will enable better identification of GYPB deletions for large genetic association studies and functional experiments to understand the role of this gene cluster region in susceptibility to malaria and other diseases.

A Doença de Huntington (DH) é uma doença neurodegenerativa, autossômica dominante e hereditária que ocorre devido a uma mutação genética que gera uma sequência repetitiva de trinucleotídeos CAG, presentes no gene IT-15, gene da huntingtina, localizado no cromossomo 4. O objetivo foi revisar a neuropatologia da doença de Huntington (DH) e a utilização do método CRISPR-Cas9 para silenciar o gene IT-15 e verificar assim, a consequência nos genes HIP14 e HAP1, que possuem interação com a Huntigtina mutada e o resultado desta no organismo do paciente. Foram pesquisados artigos em bases indexadas (Scielo, PubMed e LILACs) com os seguintes descritores: ((Huntington) OR (Proteína Huntingtina)) AND (edição gênica). Também foi utilizada a ferramenta on line GeneMania, acesso livre, para análise de probabilidades e interações gênicas. O silenciamento do gene IT-15 acarreta alterações nas proteínas que interagem com a Huntingtina mutada, levando a perturbações em diversos processos.

In Lotus japonicus, quantitative trait loci (QTLs) for nitrogen fixation activity (acetylene reduction activity, ARA) and seed weight are located in the same region on chromosome 4 as the gene resp...

A 2012–13 survey on Penang Island, Malaysia, revealed the existence of both Drosophila ananassae and Drosophila parapallidosa, the latter of which carries chromosomes Y and 4 from D. ananassae and thus is of hybrid origin. We collected the flies again from the same location in 2018. The hybrid population remained present, which suggests that the D. parapallidosa of hybrid origin does not represent a mere transient population but is stable. Why do these two species coexist irrespective of gene flow? We realized that body size is generally larger in D. ananassae than in D. parapallidosa, which constitutes a new character with which to discriminate these species; previously the number of sex comb teeth was the only diagnostic trait. Character displacement was not detected, however, for those traits. We crossed these two species, which resulted in offspring that had an altered genomic constitution. The body size of D. ananassae was dominant, and the presence of chromosomes Y and 4 did not have a significant effect on body size. By contrast, the presence of chromosome 4 from D. ananassae significantly affected the number of sex comb teeth. Even flies having a genomic constitution similar to that of the Penang D. parapallidosa exhibited a number of sex comb teeth that was intermediate between the two species. We propose that the D. parapallidosa sex comb character underwent selection during evolution of the Penang Island population. Reproductive interference between the species, presumably caused by signal jamming, was detected.

Potato (Solanum tuberosum L.) is one of the most important food crops in the world. The genome of this potato species is autotetraploid and has a high level of heterozygosity, also this potato species is a cross-pollinated plant. These characteristics complicate the genetic analysis and breeding process. The tuber's eye depth is an important trait that affects the suitability of potato varieties for processing. Potato breeding for this trait is based on phenotypic assessment. Identification of the loci that control tuber eye depth would allow diagnostic markers for the marker-assisted selection to be created. The aim of this study is to search for loci associated with the eye depth by analyzing Solanum tuberosum varieties from the GenAgro collection of the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, genotyped using the Illumina 22K SNP potato array DNA chip. The 24 significant markers associated with the "eye depth" trait were identified using 15,214 SNP markers genotyped with the Illumina 22K SNP potato array chip and the general linear model (GLM) taking into account the population structure. Data obtained showed the presence of SNPs in four genomic regions: on chromosome 4 (1 marker in the 3.92 Mb area), 5 (1 marker in the 4.67 Mb area) and 10 (1 marker in the 4.87 Mb area and 21 markers in the region between 48.1-48.9 Mb). The results of localization in the region 48.1-48.9 Mb of chromosome 10 correspond to previously published studies, the remaining three regions were detected for the first time. DNA sections containing SNPs linked to the tuber's eye depth were studied in the SolTub_3.0 potato genome assembly (https://plants.ensembl.org/). KASP markers were developed based on the data obtained. It will be possible to screen the breeding material and to breed the varieties more effectively using current markers associated with a shallow tuber's eye depth.Картофель (Solanum tuberosum L.) – одна из важнейших в мире продовольственных культур. Геном вида автотетраплоидный, отличается высоким уровнем гетерозиготности, этот вид является также перекрестноопыляемым. Все это затрудняет генетический анализ и селекционный процесс. Глубина залегания глазков клубня картофеля продовольственного назначения – важный признак, влияющий на пригодность сортов картофеля для переработки. Селекция по этому признаку ведется на основе фенотипической оценки. Идентификация локусов, контролирующих данный признак, позволила бы проводить маркер-контролируемый отбор гибридов, отбраковывая формы с глубоким залеганием глазков на ранних этапах селекции. Целью настоящего исследования было выявление геномных районов, ассоциированных с глубиной залегания глазков, путем анализа сортообразцов картофеля S. tuberosum L. из коллекции ГенАгро Института цитологии и генетики СО РАН. При использовании 15 214 SNP-маркеров, генотипированных с помощью чипа Illumina 22K SNP potato array, и обобщенной линейной модели (General Linear Model, GLM) с учетом популя- ционной структуры найдены 24 значимых маркера, ассоциированных с признаком «глубина залегания глаз- ков». Полученные данные показали наличие SNP в четырех геномных районах: в хромосомах 4 (1 маркер в районе 3.92 Mб), 5 (1 маркер в районе 4.67 Mб) и 10 (1 маркер, относящийся к району 4.87 Mб, и 21 мар- кер в районе 48.1–48.9 Mб). Сопоставление выявленных геномных районов в нашем исследовании с более ранними работами подтвердило, что локус между 48.1–48.9 Mб был известен ранее, остальные три района обнаружены впервые. Участки ДНК, содержащие SNP, сцепленные с глубиной залегания глазков, были изучены в сборке генома картофеля SolTub_3.0 (https://plants.ensembl.org/), и на основе полученных данных были разработаны КASP-маркеры, при применении которых можно будет более эффективно вести скрининг селекционного материала и селекцию сортов с мелким залеганием глазков.

The impact of environmental factors, such as diet, and the genetic basis of autoimmune pancreatitis (AIP) are largely unknown. Here, we used an experimental murine AIP model to identify the contribution of diet to AIP development, as well as to fine‐map AIP‐associated genes in outbred mice prone to develop the disease. For this purpose, we fed mice of an autoimmune‐prone intercross line (AIL) three different diets (control, calorie‐reduced and western diet) for 6 months, at which point the mice were genotyped and phenotyped for AIP. Overall, 269 out of 734 mice (36.6%) developed AIP with signs of parenchymal destruction, equally affecting mice of both sexes. AIP prevalence and severity were reduced by approximately 50% in mice held under caloric restriction compared to those fed control or western diet. We identified a quantitative trait locus (QTL) on chromosome 4 to be associated with AIP, which is located within a previously reported QTL. This association does not change when considering diet or sex as an additional variable for the mapping. Using whole‐genome sequences of the AIL founder strains, we resolved this QTL to a single candidate gene, namely Map3k7. Expression of Map3k7 was largely restricted to islet cells as well as lymphocytes found in the exocrine pancreas of mice with AIP. Our studies suggest a major impact of diet on AIP. Furthermore, we identify Map3k7 as a novel susceptibility gene for experimental AIP. Both findings warrant clinical translation.

Southern corn rust (SCR) is a prevalent foliar disease that can lead to severe yield losses in maize. Growing SCR-resistant varieties is the most effective way to control the disease. To identify major quantitative trait loci (QTLs) for SCR resistance, a recombinant inbred line population derived from a cross between CIMBL83 (resistant) and Lx9801 (susceptible) was analyzed. The resistance to SCR had high heritability within the population, and a major QTL on chromosome 4 (qSCR4.01), which can explain 48 to 65% of the total phenotypic variation, was consistently detected across multiple environments. Using a progeny-based fine-mapping strategy, we delimited qSCR4.01 to an interval of ∼770 kb. In contrast to other major QTLs for SCR resistance previously reported on the short arm of chromosome 10, qSCR4.01 is a novel QTL and, therefore, a desirable source of SCR resistance in maize breeding programs.

Background ATP-binding cassette (ABC) transporters are involved in the active transportation of various endogenous or exogenous substances. Two ABCG2 gene subfamily members have been identified in birds. A detailed comparative study of the ABCG2 and ABCG2-like genes aid our understanding of their evolutionary history at the molecular level and provide a theoretical reference for studying the specific functions of ABCG2 and ABCG2-like genes in birds. Results We first identified 77 ABCG2/ABCG2-like gene sequences in the genomes of 41 birds. Further analysis showed that both the nucleic acid and amino acid sequences of ABCG2 and ABCG2-like genes were highly conserved and exhibited high homology in birds. However, significant differences in the N-terminal structure were found between the ABCG2 and ABCG2-like amino acid sequences. A selective pressure analysis showed that the ABCG2 and ABCG2-like genes were affected by purifying selection during the process of bird evolution. Conclusions We believe that multiple members of the ABCG2 gene subfamily exist on chromosome 4 in the ancestors of birds. Over the long course of evolution, only the ABCG2 gene was retained on chromosome 4 in birds. The ABCG2-like gene on chromosome 6 might have originated from chromosome replication or fusion. The structural differences between the N terminus of ABCG2 protein and those of ABCG2-like proteins might lead to functional differences between the corresponding genes.

Cowpea (Vigna unguiculate (L.) Walp.) is a worldwide important multifunctional legume crop for food grain, vegetable, fodder, and cover crop. Nevertheless, only limited research has been conducted on agronomic traits. Here, we report quantitative trait locus (QTL) analysis of the days to flowering (DTF) and plant height (PH) using a dense SNP linkage map recently developed from a recombinant inbred line (RIL) population derived from a cross between Golden Eye Cream and IT98K-476-8. The population was phenotyped for DTF and PH through field and greenhouse trials under two environments. The QTLs controlling these traits were mapped using multiple-environment combined and individual trial phenotypic data. The combined data analysis identified one major QTL (qDTF9.1) for DTF, and one major QTL (qPH9.1) and a minor QTL (qPH4.1) for PH. qDTF9.1 and qPH9.1 were adjacent to each other on Chromosome 9 and each explained 29.3% and 29.5% of the phenotypic variation (PVE), respectively. The individual trial data analysis identified a minor QTL (qDTF2.1) on Chromosome 2 for DTF and two minor QTLs (qPH4.1 and qPH4.2) on Chromosome 4 for PH, while the major QTLs, qDTF9.1 and qPH9.1, were consistently identified in all trials conducted. Epistasis analysis revealed that qDTF9.1 interacted with one locus on Chromosome 4, contributed 50% of the PVE, and qPH9.1 interacted with one locus on each of Chromosomes 4 and 6, contributing 30% and 23% of the PVE, respectively, suggesting that epistasis plays an important role in the trait performance. These results, therefore, provide a deeper understanding of the genetic architecture of plant DTF and PH, and molecular tools necessary for cloning the genes and for enhanced cowpea breeding.

Chromosomal rearrangements, such as duplications/deletions, can lead to a variety of genetic disorders. Herein, we reported a prenatal case with right aortic arch and aberrant left subclavian artery, consisting of a complex chromosomal copy number variations. Routine cytogenetic analysis described the chromosomal karyotype as 46,XY, add (2)(q37) for the fetus. However, the chromosomal microarray analysis (CMA) identified a 22.4 Mb duplication in chromosome 4p16.3p15.2, a 3.96 Mb microduplication in 12p11.1q11, and a 1.68 Mb microdeletion in Xp22.31. Fluorescence in situ hybridization (FISH) using a chromosome 4 painting probe was found to hybridize to the terminal of chromosome 2q on the fetus, thus confirming that the extra genetic materials of chromosome 2 was actually trisomy 4p detected through CMA. Meanwhile, the parental karyotypes were normal, which proved that the add (2) was de novo for fetus. The duplication of Wolf-Hirschhorn syndrome critical region (WHSCR) and X-linked recessive ichthyosis associated with Xp22.31 deletion separately were considered potentially pathogenic causes although other abnormalities involving these syndromes were not observed. For prenatal cases, the combined utilization of ultrasonography, traditional cytogenetic, and molecular diagnosis technology will enhance better diagnostic benefits, offer more detailed genetic counselling, and assess the prognosis of the fetuses.

An introgression line RBPH660, derived from wild rice Oryza rufipogon, showed stable resistance to brown planthopper (BPH). Segregation analysis indicated BPH resistance of RBPH660 was controlled by multiple genes/QTLs. By using the bulked segregant analysis (BSA)-seq method, two genomic regions harboring QTLs resistance to BPH were identified from 1.20 to 16.70 Mb on chromosome 4 and from 10.20 to 12.60 Mb on chromosome 9 in RBPH660, respectively. A major resistance locus, designated as Bph35 accounting for 51.27% of the phenotypic variation with a LOD score of 42.51, was mapped to the candidate region of chromosome 4 between InDel (insertion-deletion) markers PSM16 and R4M13. For fine mapping of Bph35, one simple sequence repeat and three newly developed InDel markers were used to screen the recombinants. Finally, the Bph35 locus was delimited in the region from 6.28 to 6.93 Mb and there were 18 predicted protein-encoding genes with a total of 114 non-synonymous single nucleotide polymorphism (SNP) variant sites between the resistant and susceptible parents. Out of these genes, Os04g0193950, encoding a putative NB-ARC (nucleotide- binding adaptor shared by APAF-1, R proteins and CED-4) and LRR (leucine-rich repeat) domain protein with nine non-synonymous SNP substitutions in its coding sequence regions, might be the candidate gene for Bph35. These findings would facilitate the map-based cloning of the Bph35 gene and development of resistant varieties against BPH in rice. Keywords: rice, brown planthopper, Bph35, bulked segregant analysis (BSA)-seq method, gene mapping

Korean army dogs are raised for special purposes and have contributed much to society. However, several diseases occur in dogs. Canine hip dysplasia (CHD) is a musculoskeletal disorder that occurs frequently in Korean army dogs and interferes with their activities. If we could control CHD, this would have a positive effect on their performance. This study performed a genome-wide association study (GWAS) in 69 Korean army dogs to find significant loci for CHD using 170K single nucleotide polymorphisms (SNPs). CHD was classified according to the Norberg angle criterion. The control group comprised 62 dogs classified as relatively normal, and 7 dogs with severe CHD formed the case group. From the GWAS analysis, we concluded that SNPs present on chromosome 4 might have a significant impact on the overall expression of canine hip dysplasia.

Background Although Chromosomal microarray analysis (CMA) is a powerful diagnostic technology for detecting chromosomal copy number variants (CNVs), it detects numerous variants of unknown significance (VUSs), which poses a great challenge for genetic counselling. Terminal deletion of the long arm of chromosome 4 is a rare genetic aberration. Few cases of interstitial deletion sharing the common deleted segment have been reported. Case presentation A male foetus with a 7.22-Mb deletion at chromosome 4q32.2q32.3 was found in the proband. The paternal genotype was normal. His asymptomatic mother with a normal phenotype and intelligence was found to carry the same deletion at the long arm of chromosome 4. The clinical significance of arr[GRCh37] 4q32.2q32.3(162858958_170081268)×1 remains uncertain. To the best of our knowledge, this is the first case report on a VUS of 4q32 deletion and the second report of a heterochromatic CNV involving part of the long arm of chromosome 4 in a phenotypically normal mother and child. The identification of this case contributes to additional understanding of deletion at 4q32.2q32.3. This report may provide a reference for prenatal diagnosis and genetic counselling in patients who have genotypes of similar cytogenetic abnormalities. Conclusions The novel 7.22-Mb deletion at chromosome 4q32.2q32.3 (162858958-170081268) is a VUS. The foetus inherited this VUS from a phenotypically normal mother.

Smoking behaviors, including amount smoked, smoking cessation, and tobacco-related diseases, are altered by the rate of nicotine clearance. Nicotine clearance can be estimated using the nicotine metabolite ratio (NMR) (ratio of 3 ' hydroxycotinine/cotinine), but only in current smokers. Advancing the genomics of this highly heritable biomarker of CYP2A6, the main metabolic enzyme for nicotine, will also enable investigation of never and former smokers. We performed the largest genome-wide association study (GWAS) to date of the NMR in European ancestry current smokers (n = 5185), found 1255 genome-wide significant variants, and replicated the chromosome 19 locus. Fine-mapping of chromosome 19 revealed 13 putatively causal variants, with nine of these being highly putatively causal and mapping to CYP2A6, MAP3K10, ADCK4, and CYP2B6. We also identified a putatively causal variant on chromosome 4 mapping to TMPRSS11E and demonstrated an association between TMPRSS11E variation and a UGT2B17 activity phenotype. Together the 14 putatively causal SNPs explained similar to 38% of NMR variation, a substantial increase from the similar to 20 to 30% previously explained. Our additional GWASs of nicotine intake biomarkers showed that cotinine and smoking intensity (cotinine/cigarettes per day (CPD)) shared chromosome 19 and chromosome 4 loci with the NMR, and that cotinine and a more accurate biomarker, cotinine + 3 ' hydroxycotinine, shared a chromosome 15 locus near CHRNA5 with CPD and Pack-Years (i.e., cumulative exposure). Understanding the genetic factors influencing smoking-related traits facilitates epidemiological studies of smoking and disease, as well as assists in optimizing smoking cessation support, which in turn will reduce the enormous personal and societal costs associated with smoking.

Two major QTL, one for shelf life that corresponds to qSL4 and one, qDEV7, for developmental rate, were identified. Associated markers will be useful in breeding for improved fresh-cut lettuce. Fresh-cut lettuce in packaged salad can have short shelf life, and visible deterioration may start within a week after processing. Yield and developmental rate are an important aspect of lettuce production. Genetic diversity and genome-wide association studies (GWAS) were performed on 493 accessions with the genotypic data of 4615 high-quality single nucleotide polymorphism markers. Population structure (Q), principal component (PC), and phylogenetic analyses displayed genetic relationships associated with lettuce types and geographic distribution. Data for shelf life, yield, developmental rate, and their stability indices were used for statistical analysis, and GWAS was performed by general and mixed linear models. The genetic relationship among the individuals was incorporated into the models using kinship matrix, PC, and Q. Broad-sense heritability (H2) across environments was 0.43 for shelf life, 0.36 for yield, and 0.60 for developmental rate. There was a negative correlation between yield and developmental rate. Significant marker–trait association (SMTA) was detected for shelf life on chromosome 4. The most significant quantitative trait locus (QTL, qSL4, P = 2.23E−17) explained 24% of the total phenotypic variation (R2). The major QTL for developmental rate was detected on chromosome 7 (qDEV7, P = 2.43E−16, R2 = 17%), while additional QTLs with smaller effect were found in all chromosomes. No SMTA was detected for yield. The study identified lettuce accessions with extended and stable shelf life, stable yield, and desirable developmental rate. Molecular markers closely linked to traits can be applied for selection of preferable genotypes and for identification of genes associated with these traits.

Bone size is an important trait for chickens because of its association with osteoporosis in layers and meat production in broilers. Here, we employed high density genotyping platforms to detect candidate genes for bone traits. Estimates of the narrow heritabilities ranged from 0.37 ± 0.04 for shank length to 0.59 ± 0.04 for tibia length. The dominance heritability was 0.12 ± 0.04 for shank length. Using a linear mixed model approach, we identified a promising locus within NCAPG on chromosome 4, which was associated with tibia length and mass, femur length and area, and shank length. In addition, three other loci were associated with bone size or mass at a Bonferroni-corrected genome-wide significance threshold of 1%. One region on chicken chromosome 1 between 168.38 and 171.82 Mb harbored HTR2A, LPAR6, CAB39L, and TRPC4. A second region that accounted for 2.2% of the phenotypic variance was located around WNT9A on chromosome 2, where allele substitution was predicted to be associated with tibia length. Four candidate genes identified on chromosome 27 comprising SPOP, NGFR, GIP, and HOXB3 were associated with tibia length and mass, femur length and area, and shank length. Genome partitioning analysis indicated that the variance explained by each chromosome was proportional to its length.

Korea is considered one of the original centers of Chrysanthemum species, which are important flower crops due to their ornamental and economic values. At present, the genetic resources in wild Chrysanthemum have not been fully exploited. In this study, we evaluated the morphological characteristics and chromosome analysis using forescence in situ hybridization (FISH) technique in four wild Chrysanthemum species to better understand the relationships among species and their evolutionary adaptations to environmental conditions. Although there were some similarities in leaf and flower characteristics, there was high overall variation among the investigated species based on our analysis. Flower diameters ranged from 1.57 ± 0.07 cm (A102) to 3.10 ± 0.10 cm (A7). Also, the RGB values of the white flowers of species A7 were higher than those of the yellow flowers of species A5, A102, and B6. The longest leaf length was observed in species A5 (8.14 ± 0.10 cm), which was dark in color on the upper leaf side, whereas A102 exhibited the shortest leaf length (5.67 ± 0.28 cm) and width (3.20 ± 0.20 cm). FISH karyotype analysis showed that one pair of 5S and three pair of 18S rDNA were observed in all investigated species. The number and distribution pattern of rDNA showed similar arrangement in A5, A102, and B6. One pair of 18S rDNA signals were detected on the terminal region of the short arm chromosomes 3, 7, and 8, respectively. One pair of 5S rDNA signal was located in the interstitial region of chromosome 4. For the A7 species, 5S rDNA were detected in the long arm of chromosome 7 and one pair of 18S rDNA were found in the short arm of chromosomes 2, 5, and 6. According to the results, this study provides basic knowledge on the relationships between the evolution and genomics of Chrysanthemum traits, which are especially important for selecting donor and recipient plants in modern Chrysanthemum breeding programs.

Maize streak virus (MSV) continues to be a major biotic constraint for maize production throughout Africa. Concerning the quantitative nature of inheritance of resistance to MSV disease (MSVD), we sought to identify new loci for MSV resistance in maize using F2:3 population. The mapping population was artificially inoculated with viruliferous leafhoppers under screenhouse and evaluated for MSVD resistance. Using 948 DArT markers, we identified 18 quantitative trait loci (QTLs) associated with different components of MSVD resistance accounting for 3.1–21.4% of the phenotypic variance, suggesting that a total of eleven genomic regions covering chromosomes 1, 2, 3, 4, 5 and 7 are probably required for MSVD resistance. Two new genomic regions on chromosome 4 revealed the occurrence of co-localized QTLs for different parameters associated with MSVD resistance. Moreover, the consistent appearance of QTL on chromosome 7 for MSVD resistance is illustrating the need for fine-mapping of this locus. In conclusion, these QTLs could provide additional source for breeders to develop MSV resistance.

The deletion of the long arm of chromosome 4 is rare, presenting with a variable phenotype depending on the chromosomic area affected. A term newborn with prenatal diagnosis of anhydramnios, dysplastic cystic kidneys, and cardiomegaly was born with generalized subcutaneous edema, several dysmorphic features, and progressive renal failure requiring dialysis. The infant continued to deteriorate and died at 52 days of age. Autopsy confirmed bilateral renal dysplasia with cysts. Array-comparative genomic hybridization (CGH) identified a large deletion on 4q25-q28.3, which is not yet described in association with renal disease. The clinical progression could be expected due to the severity of the perinatal clinical presentation.

In order to study the effects of heat shock treatment on the distribution of rDNA contacts at the region possessing DUX genes inside chromosome 4 we used 4C approach. Our data indicate that the treatment removes the frequent rDNA contacts in this region. The recent data on involvement of superenhancers that are decorated by broad H3K27ac marks in the phase separation mechanisms and the previous data demonstrating that these broad marks are the favorite sites of rDNA contacts taken together with our data on sensitivity of the contacts to the heat shock treatment suggest that the phase separation mechanisms are involved in the reversible rDNA-mediated regulation of gene expression via the contacts.

Muscle fiber characteristics comprise a set of complex traits that influence the meat quality and lean meat production of livestock. However, the genetic and biological mechanisms regulating muscle fiber characteristics are largely unknown in pigs. Based on a genome-wide association study (GWAS) performed on 421 Large White × Min pig F2 individuals presenting well-characterized phenotypes, this work aimed to detect genome variations and candidate genes for five muscle fiber characteristics: percentage of type I fibers (FIB1P), percentage of type IIA fibers (FIB2AP), percentage of type IIB fibers (FIB2BP), diameter of muscle fibers (DIAMF) and number of muscle fibers per unit area (NUMMF). The GWAS used the Illumina Porcine SNP60K genotypic data, which were analyzed by a mixed model. Seven and 10 single nucleotide polymorphisms (SNPs) were significantly associated with DIAMF and NUMMF, respectively (P < 1.10E-06); no SNP was significantly associated with FIB1P, FIB2AP or FIB2B. For DIAMF, the significant SNPs on chromosome 4 were located in the previously reported quantitative trait loci (QTL) interval. Because the significant SNPs on chromosome 6 were not mapped in the previously reported QTL interval, a putative novel QTL was suggested for this locus. None of the previously reported QTL intervals on chromosomes 6 and 14 harbored significant SNPs for NUMMF; thus, new potential QTLs on these two chromosomes are suggested in the present work. The most significant SNPs associated with DIAMF (ALGA0025682) and NUMMF (MARC0046984) explained 12.02% and 11.59% of the phenotypic variation of these traits, respectively. In addition, both SNPs were validated as associated with DIAMF and NUMMF in Beijing Black pigs (P < 0.01). Some candidate genes or non-coding RNAs, such as solute carrier family 44 member 5 and miR-124a-1 for DIAMF, and coiled-coil serine rich protein 2 for NUMMF, were identified based on their close location to the significant SNPs. This study revealed some genome-wide association variants for muscle fiber characteristics, and it provides valuable information to discover the genetic mechanisms controlling these traits in pigs.

HMA (heavy metal associated) is a member of the ATPases protein family involved in metal transport in plants. This study characterizes several HMA3 homologs and infers their molecular functions in different plant species. Arabidopsis AtHMA3 (AT4G30120) was used as a reference to retrieve 11 HMA3 homologs having 97-100% query cover, 535-542 residues, 56983 to 58642 (Da) molecular weight, and 5.74 to 8.16 pI value, 29.10 to 33.89 instability index, and 0.222 to 0.380 grand average of hydropathicity. Topological analyses showed 4 transmembrane domains in these HMA3 homologs positioned similarly in terms of cytoplasmic and non-cytoplasmic regions along with ∼22-28% α-helices, ∼22-28% extended strands, and ∼50% random coils. HMA3 protein of Arabidopsis lyrata subsp. lyrata and Eutrema salsugineum are located at chromosome 2, while others are positioned at chromosome 4. All these HMA3 homologs are localized in the plasma membrane sharing a few common biological and molecular functions. Besides, these HMA3 genes contain 8-9 exons in which promoter positions are varied among the homologs. The cis-acting elements of HMA3 genes were projected to be involved with stress response, anaerobic induction, and light-responsive regulation in plants. Three out of five motifs encode E1-E2_ATPase involved in proton-pumping in the plasma membrane. The Arabidopsis thaliana HMA3 protein clustered with Camelina sativa and Capsella rubella show a close phylogenetic relationship. Also, AtHMA3 exhibits a close association with AtHMA3 with MTPA2, ZAT, NRAMP3, IRT2, and NRAMP2 under the local network of AtHMA3 linked to metal transport. Further, AtHMA3 is most potentially expressed during senescence, germinating seed, seedlings, young rosette, bolting, and young flower. In addition, AtHMA3 showed a significant upregulation (>6.0 fold) under Fe-deficiency. These findings may provide essential background to perform wet-lab experiments to understand the role of HMA3 in metal homeostasis.