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Population Genetics
Contrasting evolutionary genome dynamics between domesticated and wild yeasts
Apr 18, 2017   Nature Genetics Add nature.com free-link Cancel
Yue JX, Li J, Aigrain L, Hallin J, Persson K, Oliver K, Bergström A, Coupland P, Warringer J, Lagomarsino MC, Fischer G, Durbin R, Liti G
Contrasting evolutionary genome dynamics between domesticated and wild yeasts
Apr 18, 2017
Nature Genetics
Structural rearrangements have long been recognized as an important source of genetic variation, with implications in phenotypic diversity and disease, yet their detailed evolutionary dynamics remain elusive. Here we use long-read sequencing to generate end-to-end genome assemblies for 12 strains representing major subpopulations of the partially domesticated yeast Saccharomyces cerevisiae and its wild relative Saccharomyces paradoxus. These population-level high-quality genomes with comprehensive annotation enable precise definition of chromosomal boundaries between cores and subtelomeres and a high-resolution view of evolutionary genome dynamics. In chromosomal cores, S. paradoxus shows faster accumulation of balanced rearrangements (inversions, reciprocal translocations and transpositions), whereas S. cerevisiae accumulates unbalanced rearrangements (novel insertions, deletions and duplications) more rapidly. In subtelomeres, both species show extensive interchromosomal reshuffling, with a higher tempo in S. cerevisiae. Such striking contrasts between wild and domesticated yeasts are likely to reflect the influence of human activities on structural genome evolution.
Association between BRCA1 P871L polymorphism and cancer risk: evidence from a meta-analysis
Apr 21, 2017   Oncotarget
Miao L, Yu Y, Ji Y, Zhang B, Yuan Z, Du Y, Zhu L, Wang R, Chen N, Yuan H
Association between BRCA1 P871L polymorphism and cancer risk: evidence from a meta-analysis
Apr 21, 2017
Oncotarget
Breast cancer 1 (BRCA1) gene makes great contributions to the repair of DNA. The association between BRCA1 P871L polymorphism and cancer risk has been investigated in a growing number of studies, but the conclusions are not conclusive. To obtain a comprehensive conclusion, we performed a meta-analysis of 24 studies with 13762 cases and 22388 controls. The pooled results indicated that BRCA1 gene P871L variant decreased risk of overall cancer (homozygous model: odds ratio (OR) = 0.89, 95%confidence interval (CI) = 0.79-1.00; recessive model: OR = 0.89, 95% CI = 0.80-0.99). The stratified analysis observed decreased risk associated with BRCA1 P871L in subgroups among Asians and high score studies, but not Caucasians or low score studies. In conclusion, despite several limitations, this meta-analysis suggested that BRCA1 P871L genetic variation may be associated with decreased susceptibility to cancer.
Genetic variants associated with the root system architecture of oilseed rape (Brassica napus L.) under contrasting phosphate supply
Apr 21, 2017   DNA Research : An International Journal For Rapid Publication Of Reports On Genes And Genomes
Wang X, Chen Y, Thomas CL, Ding G, Xu P, Shi D, Grandke F, Jin K, Cai H, Xu F, Yi B, Broadley MR, Shi L
Genetic variants associated with the root system architecture of oilseed rape (Brassica napus L.) under contrasting phosphate supply
Apr 21, 2017
DNA Research : An International Journal For Rapid Publication Of Reports On Genes And Genomes
Breeding crops with ideal root system architecture for efficient absorption of phosphorus is an important strategy to reduce the use of phosphate fertilizers. To investigate genetic variants leading to changes in root system architecture, 405 oilseed rape cultivars were genotyped with a 60K Brassica Infinium SNP array in low and high P environments. A total of 285 single-nucleotide polymorphisms were associated with root system architecture traits at varying phosphorus levels. Nine single-nucleotide polymorphisms corroborate a previous linkage analysis of root system architecture quantitative trait loci in the BnaTNDH population. One peak single-nucleotide polymorphism region on A3 was associated with all root system architecture traits and co-localized with a quantitative trait locus for primary root length at low phosphorus. Two more single-nucleotide polymorphism peaks on A5 for root dry weight at low phosphorus were detected in both growth systems and co-localized with a quantitative trait locus for the same trait. The candidate genes identified on A3 form a haplotype 'BnA3Hap', that will be important for understanding the phosphorus/root system interaction and for the incorporation into Brassica napus breeding programs. © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.
A comprehensive analysis of rare genetic variation in amyotrophic lateral sclerosis in the UK
Apr 21, 2017   Brain : A Journal Of Neurology
Morgan S, Shatunov A, Sproviero W, Jones AR, Shoai M,   . . . . . .   , Orrell RW, Fratta P, Hardy J, Pittman A, Al-Chalabi A
A comprehensive analysis of rare genetic variation in amyotrophic lateral sclerosis in the UK
Apr 21, 2017
Brain : A Journal Of Neurology
Amyotrophic lateral sclerosis is a progressive neurodegenerative disease of motor neurons. About 25 genes have been verified as relevant to the disease process, with rare and common variation implicated. We used next generation sequencing and repeat sizing to comprehensively assay genetic variation in a panel of known amyotrophic lateral sclerosis genes in 1126 patient samples and 613 controls. About 10% of patients were predicted to carry a pathological expansion of the C9orf72 gene. We found an increased burden of rare variants in patients within the untranslated regions of known disease-causing genes, driven by SOD1, TARDBP, FUS, VCP, OPTN and UBQLN2. We found 11 patients (1%) carried more than one pathogenic variant (P = 0.001) consistent with an oligogenic basis of amyotrophic lateral sclerosis. These findings show that the genetic architecture of amyotrophic lateral sclerosis is complex and that variation in the regulatory regions of associated genes may be important in disease pathogenesis. © The Author (2017). Published by Oxford University Press on behalf of the Guarantors of Brain.
Stuck in fragments: Population genetics of the Endangered collared brown lemur Eulemur collaris in the Malagasy littoral forest
Apr 21, 2017   American Journal Of Physical Anthropology
Bertoncini S, D'Ercole J, Brisighelli F, Ramanamanjato JB, Capelli C, Tofanelli S, Donati G
Stuck in fragments: Population genetics of the Endangered collared brown lemur Eulemur collaris in the Malagasy littoral forest
Apr 21, 2017
American Journal Of Physical Anthropology
The Endangered collared brown lemur (Eulemur collaris) is the largest primate living in the littoral forest of southeastern Madagascar, a top priority habitat for biodiversity conservation on the island. Because this lemur is a key seed-disperser, an evaluation of the structure and connectivity of the populations surviving in the forest fragments is urgently needed to guide conservation plans. Genetic variability at autosomal microsatellites and mitochondrial DNA was investigated in a total of 49 collared brown lemurs sampled by non-invasive methods in three littoral forest fragments and in the nearby lowland humid forest. The overall genetic diversity of E. collaris in the southeastern coastal region of Madagascar was lower than in other populations, as well as in other lemur species. The population appears highly structured, with less variable and more inbred groups inhabiting the littoral forest fragments compared to the inland area. Major barriers to gene flow were identified isolating littoral forest fragments from each other and from the inland lowland humid forest. Medium to long-term drift and scarce gene flow is the scenario that best explains the current genetic distribution. Habitat discontinuities such as rivers and grassland between forest fragments played a major role in structuring the population. A common history of size contraction is pointed out by several genetic estimators, indicating a possible ecological crisis triggered around 1,300 years ago. The adoption of strategies aimed at facilitating gene flow and population growth appears crucial to delay further loss of genetic diversity. © 2017 Wiley Periodicals, Inc.
Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome
Apr 21, 2017   Scientific Reports
Johnston HR, Hu YJ, Gao J, O'Connor TD, Abecasis GR,   . . . . . .   , Beaty TH, Mathias RA, Barnes KC, Qin ZS, CAAPA Consortium
Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome
Apr 21, 2017
Scientific Reports
A primary goal of The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) is to develop an 'African Diaspora Power Chip' (ADPC), a genotyping array consisting of tagging SNPs, useful in comprehensively identifying African specific genetic variation. This array is designed based on the novel variation identified in 642 CAAPA samples of African ancestry with high coverage whole genome sequence data (~30× depth). This novel variation extends the pattern of variation catalogued in the 1000 Genomes and Exome Sequencing Projects to a spectrum of populations representing the wide range of West African genomic diversity. These individuals from CAAPA also comprise a large swath of the African Diaspora population and incorporate historical genetic diversity covering nearly the entire Atlantic coast of the Americas. Here we show the results of designing and producing such a microchip array. This novel array covers African specific variation far better than other commercially available arrays, and will enable better GWAS analyses for researchers with individuals of African descent in their study populations. A recent study cataloging variation in continental African populations suggests this type of African-specific genotyping array is both necessary and valuable for facilitating large-scale GWAS in populations of African ancestry.
Comprehensive assessment showed no associations of variants at the SLC10A1 locus with susceptibility to persistent HBV infection among Southern Chinese
Apr 21, 2017   Scientific Reports
Zhang Y, Li Y, Wu M, Cao P, Liu X,   . . . . . .   , Shen H, Zeng YX, He F, Zhang H, Zhou G
Comprehensive assessment showed no associations of variants at the SLC10A1 locus with susceptibility to persistent HBV infection among Southern Chinese
Apr 21, 2017
Scientific Reports
The sodium taurocholate cotransporting polypeptide (NTCP) encoded by SLC10A1 was recently demonstrated to be a functional receptor for hepatitis B virus (HBV). The role of SLC10A1 polymorphisms, particularly the Ser267Phe variant (rs2296651) in exon 4, has been frequently investigated in regard to risk of persistent HBV infection. However, these investigations have generated conflicting results. To examine whether common genetic variation at the SLC10A1 locus is associated with risk of persistent HBV infection, haplotype-tagging and imputed single nucleotide polymorphisms (SNPs) were assessed in two case-control sample sets, totally including 2,550 cases (persistently HBV infected subjects, PIs) and 2,124 controls (spontaneously recovered subjects, SRs) of Southern Chinese ancestry. To test whether rare or subpolymorphic SLC10A1 variants are associated with disease risk, the gene's exons in 244 cases were sequenced. Overall, we found neither SNPs nor haplotypes of SLC10A1 showed significant association in the two sample sets. Furthermore, no significant associations of rare variants or copy number variation covering SLC10A1 were observed. Finally, expression quantitative trait locus analyses revealed that SNPs potentially affecting SLC10A1 expression also showed no significant associations. We conclude that genetic variation at the SLC10A1 locus is not likely a major risk factor of persistent HBV infection among Southern Chinese.
SLCO1B1 polymorphisms and plasma estrone conjugates in postmenopausal women with ER+ breast cancer: genome-wide association studies of the estrone pathway
Apr 21, 2017   Breast Cancer Research And Treatment
Dudenkov TM, Ingle JN, Buzdar AU, Robson ME, Kubo M,   . . . . . .   , Williard CV, Kalari KR, Nakamura Y, Wang L, Weinshilboum RM
SLCO1B1 polymorphisms and plasma estrone conjugates in postmenopausal women with ER+ breast cancer: genome-wide association studies of the estrone pathway
Apr 21, 2017
Breast Cancer Research And Treatment
Estrone (E1), the major circulating estrogen in postmenopausal women, promotes estrogen-receptor positive (ER+) breast tumor growth and proliferation. Two major reactions contribute to E1 plasma concentrations, aromatase (CYP19A1) catalyzed E1 synthesis from androstenedione and steroid sulfatase (STS) catalyzed hydrolysis of estrone conjugates (E1Cs). E1Cs have been associated with breast cancer risk and may contribute to tumor progression since STS is expressed in breast cancer where its activity exceeds that of aromatase. We performed genome-wide association studies (GWAS) to identify SNPs associated with variation in plasma concentrations of E1Cs, E1, and androstenedione in 774 postmenopausal women with resected early-stage ER+ breast cancer. Hormone concentrations were measured prior to aromatase inhibitor therapy. Multiple SNPs in SLCO1B1, a gene encoding a hepatic influx transporter, displayed genome-wide significant associations with E1C plasma concentrations and with the E1C/E1 ratio. The top SNP for E1C concentrations, rs4149056 (p = 3.74E-11), was a missense variant that results in reduced transporter activity. Patients homozygous for the variant allele had significantly higher average E1C plasma concentrations than did other patients. Furthermore, three other SLCO1B1 SNPs, not in LD with rs4149056, were associated with both E1C concentrations and the E1C/E1 ratio and were cis-eQTLs for SLCO1B3. GWAS signals of suggestive significance were also observed for E1, androstenedione, and the E1/androstenedione ratio. These results suggest a mechanism for genetic variation in E1C plasma concentrations as well as possible SNP biomarkers to identify ER+ breast cancer patients for whom STS inhibitors might be of clinical value.
Rs4878104 contributes to Alzheimer's disease risk and regulates DAPK1 gene expression
Apr 21, 2017   Neurological Sciences : Official Journal Of The Italian Neurological Society And Of The Italian Society Of Clinical Neurophysiology
Hu Y, Cheng L, Zhang Y, Bai W, Zhou W, Wang T, Han Z, Zong J, Jin S, Zhang J, Jiang Q, Liu G
Rs4878104 contributes to Alzheimer's disease risk and regulates DAPK1 gene expression
Apr 21, 2017
Neurological Sciences : Official Journal Of The Italian Neurological Society And Of The Italian Society Of Clinical Neurophysiology
In 2006, a candidate gene study reported death-associated protein kinase 1 (DAPK1) rs4878104 variant to be significantly associated with Alzheimer's disease (AD) risk. However, the following studies showed inconsistent association results. Here, we conducted an updated analysis to investigate the potential association between rs4878104 and AD using a total of 60,751 samples (20,161 AD cases and 40,590 controls). In the pooled population, the results based on the allele and genotype genetic models show that rs4878104 variant is not significantly associated with AD risk. Interestingly, we identified rs4878104 variant to be significantly associated with AD risk in American population and Chinese population in subgroup analysis. Using multiple large-scale expression quantitative trait loci datasets, we further found that rs4878104 T allele could significantly regulate increased DAPK1 expression in European population. These findings suggest that rs4878104 may contribute AD susceptibility by modifying DAPK1 expression in European population.
Genome-Wide Association Study for Pre-harvest Sprouting Resistance in a Large Germplasm Collection of Chinese Wheat Landraces
Apr 21, 2017   Frontiers In Plant Science
Zhou Y, Tang H, Cheng MP, Dankwa KO, Chen ZX,   . . . . . .   , Pu ZE, Wei YM, Zheng YL, Hickey LT, Wang JR
Genome-Wide Association Study for Pre-harvest Sprouting Resistance in a Large Germplasm Collection of Chinese Wheat Landraces
Apr 21, 2017
Frontiers In Plant Science
Pre-harvest sprouting (PHS) is mainly caused by the breaking of seed dormancy in high rainfall regions, which leads to huge economic losses in wheat. In this study, we evaluated 717 Chinese wheat landraces for PHS resistance and carried out genome-wide association studies (GWAS) using to 9,740 DArT-seq and 178,803 SNP markers. Landraces were grown across six environments in China and germination testing of harvest-ripe grain was used to calculate the germination rate (GR) for each accession at each site. GR was highly correlated across all environments. A large number of landraces (194) displayed high levels of PHS resistance (i.e., mean GR < 0.20), which included nine white-grained accessions. Overall, white-grained accessions displayed a significantly higher mean GR (42.7-79.6%) compared to red-grained accessions (19.1-56.0%) across the six environments. Landraces from mesic growing zones in southern China showed higher levels of PHS resistance than those sourced from xeric areas in northern and north-western China. Three main quantitative trait loci (QTL) were detected by GWAS: one on 5D that appeared to be novel and two co-located with the grain color transcription factor Tamyb10 on 3A and 3D. An additional 32 grain color related QTL (GCR-QTL) were detected when the set of red-grained landraces were analyzed separately. GCR-QTL occurred at high frequencies in the red-grained accessions and a strong correlation was observed between the number of GCR-QTL and GR (R2 = 0.62). These additional factors could be critical for maintaining high levels of PHS resistance and represent targets for introgression into white-grained wheat cultivars. Further, investigation of the origin of haplotypes associated with the three main QTL revealed that favorable haplotypes for PHS resistance were more common in accessions from higher rainfall zones in China. Thus, a combination of natural and artificial selection likely resulted in landraces incorporating PHS resistance in China.
Network-assisted analysis of GWAS data identifies a functionally-relevant gene module for childhood-onset asthma
Apr 21, 2017   Scientific Reports
Liu Y, Brossard M, Sarnowski C, Vaysse A, Moffatt M, Margaritte-Jeannin P, Llinares-López F, Dizier MH, Lathrop M, Cookson W, Bouzigon E, Demenais F
Network-assisted analysis of GWAS data identifies a functionally-relevant gene module for childhood-onset asthma
Apr 21, 2017
Scientific Reports
The number of genetic factors associated with asthma remains limited. To identify new genes with an undetected individual effect but collectively influencing asthma risk, we conducted a network-assisted analysis that integrates outcomes of genome-wide association studies (GWAS) and protein-protein interaction networks. We used two GWAS datasets, each consisting of the results of a meta-analysis of nine childhood-onset asthma GWASs (5,924 and 6,043 subjects, respectively). We developed a novel method to compute gene-level P-values (fastCGP), and proposed a parallel dense-module search and cross-selection strategy to identify an asthma-associated gene module. We identified a module of 91 genes with a significant joint effect on childhood-onset asthma (P 
CXCR6 gene characterization in two ethnically distinct South African populations and association with viraemic disease control in HIV-1-infected black South African individuals
Apr 21, 2017   Clinical Immunology (Orlando, Fla.)
Picton ACP, Paximadis M, Chaisson RE, Martinson NA, Tiemessen CT
CXCR6 gene characterization in two ethnically distinct South African populations and association with viraemic disease control in HIV-1-infected black South African individuals
Apr 21, 2017
Clinical Immunology (Orlando, Fla.)
CXCR6 genetic variation was described for HIV-1-uninfected black (n=41) and Caucasian (n=40) South Africans. We also investigated the CXCR6 rs2234358 and rs2234355 single nucleotide polymorphisms in HIV-1 disease control in 124 HIV-1-infected drug-naïve black individuals [elite controllers (n=11), viraemic controllers (VCs, n=30), high viral load long-term nonprogressors (HVL LTNPs, n=11) and progressors (n=72)] compared to healthy controls (HCs; n=232). The rs2234358-T allele was underrepresented in VCs (40.0%) compared to HCs (59%, P=0.006), HVL LTNPs (72.7%, P=0.012) and progressors (59%, P=0.014). The rs2234358-TT genotype was underrepresented in VCs (7%) compared to progressors (32%; OR=6.57, P=0.006) and HCs (35%; OR=7.18, P=0.001, Pbonferroni=0.034). The rs2234355-GA genotype was overrepresented in VCs (80%) compared to HCs (50.4%; OR=0.25, P=0.003) and progressors (29.17%; OR=0.10, P=3.8×10-5, Pbonferroni=0.001). The combination of rs2234355-GA in the absence of rs2234358-TT was overrepresented in VCs (80%) compared to HCs (32.6%, OR=0.12, P=1×10-6, Pbonferroni=3.4×10-5) and to progressors (16.7%; OR=0.05, P
Characterization of bimodal chronotype and its association with sleep: A population-based study
Apr 20, 2017   Chronobiology International
Tempaku PF, Ramirez Arruda J, Mazzotti DR, Gonçalves BSB, Pedrazzoli M, Bittencourt L, Tufik S
Characterization of bimodal chronotype and its association with sleep: A population-based study
Apr 20, 2017
Chronobiology International
The circadian system coordinates internal events in a daily schedule to make sure that the body systems are synchronized to environmental time and internal cues. One important behavioral aspect of the circadian system is the chronotype. It is usually assessed through subjective questionnaires, being the Horne-Ostberg Morningness-Eveningness Questionnaire (MEQ) one of the most used. It classifies individuals into three major categories: morning, evening, and intermediate types. Recently, it has been hypothesized the existence of a fourth chronotype, the bimodal type, through an algorithm derived from the MEQ responses. Bimodals answer as morning-types in some questions, and as evening-types in others, resulting in an intermediate total score. To better characterize this phenotype, the present study aimed to detect and characterize the frequency of the bimodal chronotype in the EPISONO, a large population-based cohort, as well as to verify the association between bimodality and sleep parameters and genetic variation in the PER3 gene. Of the 1,042 individuals who participated of the EPISONO, 857 had MEQ filled correctly. We found that 16% of our sample were bimodal types. We observed that bimodal individuals were significantly younger and had lower body mass index. The association between PER3 VNTR genotype and gender with bimodal chronotype was not significant. However, we found an association between bimodality and Epworth Sleepiness Scale (EES) and apnea-hypopnea index (AHI). We did not find a statistically significant difference between bimodals and intermediate non-bimodals for the studied variables. Lastly, it was observed that the most significant predictors for bimodal chronotype were female gender, AHI, and EES. In conclusion, the present work provides more evidence that the bimodal type might have to be considered when classifying chronotype and its association with young age and sleepiness may be due to the influence of social and environmental factors.
Squamate Conserved Loci (SqCL): a unified set of conserved loci for phylogenomics and population genetics of squamate reptiles
Apr 18, 2017   Molecular Ecology Resources
Singhal S, Grundler M, Colli G, Rabosky DL
Squamate Conserved Loci (SqCL): a unified set of conserved loci for phylogenomics and population genetics of squamate reptiles
Apr 18, 2017
Molecular Ecology Resources
The identification of conserved loci across genomes, along with advances in target capture methods and high-throughput sequencing, has helped spur a phylogenomics revolution by enabling researchers to gather large numbers of homologous loci across clades of interest with minimal upfront investment in locus design. Target capture for vertebrate animals is currently dominated by two approaches - anchored hybrid enrichment (AHE) and ultraconserved elements (UCE) - and both approaches have proven useful for addressing questions in phylogenomics, phylogeography, and population genomics. However, these two sets of loci have minimal overlap with each other; moreover, they do not include many traditional loci that that have been used for phylogenetics. Here, we combine across UCE, AHE, and traditional phylogenetic gene locus sets to generate the Squamate Conserved Loci (SqCL) set, a single integrated probe set that can generate high-quality and highly complete data across all three loci types. We use these probes to generate data for 44 phylogenetically-disparate taxa that collectively span approximately 33% of terrestrial vertebrate diversity. Our results generated an average of 4.29 Mb across 4709 loci per individual, of which an average of 2.99 Mb was sequenced to high enough coverage (≥10×) to use for population genetic analyses. We validate the utility of these loci for both phylogenomic and population genomic questions, provide a comparison among these locus sets of their relative usefulness, and suggest areas for future improvement. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
Quantitative Trait Locus Mapping for Verticillium wilt Resistance in an Upland Cotton Recombinant Inbred Line Using SNP-Based High Density Genetic Map
Apr 20, 2017   Frontiers In Plant Science
Palanga KK, Jamshed M, Rashid MHO, Gong J, Li J,   . . . . . .   , Dilnur T, Li W, Li P, Gong W, Yuan Y
Quantitative Trait Locus Mapping for Verticillium wilt Resistance in an Upland Cotton Recombinant Inbred Line Using SNP-Based High Density Genetic Map
Apr 20, 2017
Frontiers In Plant Science
Verticillium wilt (VW) caused by Verticillium dahlia Kleb is one of the most destructive diseases of cotton. Numerous efforts have been made to improve the resistance of upland cotton against VW, with little progress achieved due to the paucity of upland cotton breeding germplasms with high level of resistance to VW. Gossypium barbadense was regarded as more resistant compared to upland cotton; however, it is difficult to apply the resistance from G. barbadense to upland cotton improvement because of the hybrid breakdown and the difficulty to fix resistant phenotype in their interspecific filial. Here we reported QTLs related to VW resistance identified in upland cotton based on 1 year experiment in greenhouse with six replications and 4 years investigations in field with two replications each year. In total, 119 QTLs of disease index (DI) and of disease incidence (DInc) were identified on 25 chromosome of cotton genome except chromosome 13 (c13). For DI, 62 QTLs explaining 3.7-12.2% of the observed phenotypic variations were detected on 24 chromosomes except c11 and c13. For DInc, 59 QTLs explaining 2.3-21.30% of the observed PV were identified on 19 chromosomes except c5, c8, c12-c13, c18-c19, and c26. Seven DI QTLs were detected to be stable in at least environments, among which six have sGK9708 alleles, while 28 DInc QTLs were detected to be stable in at least environments. Eighteen QTL clusters containing 40 QTLs were identified on 13 chromosomes (c1-c4, c6-c7, c10, c14, c17 c20-c22, and c24-c25). Most of the stable QTLs aggregated into these clusters. These QTLs and clusters identification can be an important step toward Verticillium wilt resistant gene cloning in upland cotton and provide useful information to understand the complex genetic bases of Verticillium wilt resistance.
Effects of drought stress on global gene expression profile in leaf and root samples of Dongxiang wild rice (Oryza rufipogon)
Apr 20, 2017   Bioscience Reports
Zhang F, Zhou Y, Zhang M, Luo X, Xie J
Effects of drought stress on global gene expression profile in leaf and root samples of Dongxiang wild rice (Oryza rufipogon)
Apr 20, 2017
Bioscience Reports
Drought is a serious constraint to rice production throughout the world, and although Dongxiang wild rice ( Oryza rufipogon , DXWR) possesses a high degree of drought resistance, the underlying mechanisms of this trait remains unclear. In the present study, cDNA libraries were constructed from the leaf and root tissues of drought-stressed and untreated DXWR seedlings, and transcriptome sequencing was performed with the goal of elucidating the molecular mechanisms involved in drought stress response. The results indicated that 11,231 transcripts were differentially expressed in the leaves (4,040 up-regulated and 7,191 down-regulated) and 7,025 transcripts were differentially expressed in the roots (3,097 up-regulated and 3,928 down-regulated). Among these differentially expressed genes, the detection of many transcription factors and functional genes demonstrated that multiple regulatory pathways were involved in drought resistance. Meanwhile, the differentially expressed genes were also annotated with Gene Ontology terms and key pathways via functional classification and Kyoto Encyclopedia of Gene and Genomes pathway mapping, respectively. A set of the most interesting candidate genes was then identified by combining the differentially expressed genes with previously identified drought-resistant quantitative trait loci. The present work provides abundant genomic information for functional dissection of the drought resistance of DXWR, and findings will further the current understanding of the biological regulatory mechanisms of drought resistance in plants and facilitate the breeding of new drought-resistant rice cultivars. ©2017 The Author(s).
Improving genetic diagnosis in Mendelian disease with transcriptome sequencing
Apr 20, 2017   Science Translational Medicine
Cummings BB, Marshall JL, Tukiainen T, Lek M, Donkervoort S,   . . . . . .   , Muntoni F, Clarke NF, Cooper ST, Bönnemann CG, MacArthur DG
Improving genetic diagnosis in Mendelian disease with transcriptome sequencing
Apr 20, 2017
Science Translational Medicine
Exome and whole-genome sequencing are becoming increasingly routine approaches in Mendelian disease diagnosis. Despite their success, the current diagnostic rate for genomic analyses across a variety of rare diseases is approximately 25 to 50%. We explore the utility of transcriptome sequencing [RNA sequencing (RNA-seq)] as a complementary diagnostic tool in a cohort of 50 patients with genetically undiagnosed rare muscle disorders. We describe an integrated approach to analyze patient muscle RNA-seq, leveraging an analysis framework focused on the detection of transcript-level changes that are unique to the patient compared to more than 180 control skeletal muscle samples. We demonstrate the power of RNA-seq to validate candidate splice-disrupting mutations and to identify splice-altering variants in both exonic and deep intronic regions, yielding an overall diagnosis rate of 35%. We also report the discovery of a highly recurrent de novo intronic mutation in COL6A1 that results in a dominantly acting splice-gain event, disrupting the critical glycine repeat motif of the triple helical domain. We identify this pathogenic variant in a total of 27 genetically unsolved patients in an external collagen VI-like dystrophy cohort, thus explaining approximately 25% of patients clinically suggestive of having collagen VI dystrophy in whom prior genetic analysis is negative. Overall, this study represents a large systematic application of transcriptome sequencing to rare disease diagnosis and highlights its utility for the detection and interpretation of variants missed by current standard diagnostic approaches. Copyright © 2017, American Association for the Advancement of Science.
Identifying selectively important amino acid positions associated with alternative habitat environments in fish mitochondrial genomes
Apr 20, 2017   Mitochondrial DNA. Part A, DNA Mapping, Sequencing, And Analysis
Xia JH, Li HL, Zhang Y, Meng ZN, Lin HR
Identifying selectively important amino acid positions associated with alternative habitat environments in fish mitochondrial genomes
Apr 20, 2017
Mitochondrial DNA. Part A, DNA Mapping, Sequencing, And Analysis
Fish species inhabitating seawater (SW) or freshwater (FW) habitats have to develop genetic adaptations to alternative environment factors, especially salinity. Functional consequences of the protein variations associated with habitat environments in fish mitochondrial genomes have not yet received much attention. We analyzed 829 complete fish mitochondrial genomes and compared the amino acid differences of 13 mitochondrial protein families between FW and SW fish groups. We identified 47 specificity determining sites (SDS) that associated with FW or SW environments from 12 mitochondrial protein families. Thirty-two (68%) of the SDS sites are hydrophobic, 13 (28%) are neutral, and the remaining sites are acidic or basic. Seven of those SDS from ND1, ND2 and ND5 were scored as probably damaging to the protein structures. Furthermore, phylogenetic tree based Bayes Empirical Bayes analysis also detected 63 positive sites associated with alternative habitat environments across ten mtDNA proteins. These signatures could be important for studying mitochondrial genetic variation relevant to fish physiology and ecology.
QTL analysis and dissection of panicle components in rice using advanced backcross populations derived from Oryza Sativa cultivars HR1128 and 'Nipponbare'
Apr 19, 2017   PloS One
Sun Z, Yin X, Ding J, Yu D, Hu M,   . . . . . .   , Jiang B, Yuan G, Duan M, Yuan D, Fang J
QTL analysis and dissection of panicle components in rice using advanced backcross populations derived from Oryza Sativa cultivars HR1128 and 'Nipponbare'
Apr 19, 2017
PloS One
Panicle traits are among the most important agronomic characters which directly relate to yield in rice. Grain number (GN), panicle length (PL), primary branch number (PBN), and secondary branch number (SBN) are the major components of rice panicle structure, and are all controlled by quantitative trait loci (QTLs). In our research, four advanced backcross overlapping populations (BIL152, BIL196a, BIL196b, and BIL196b-156) carrying introgressed segments from chromosome 6 were derived from an indica/japonica cross that used the super-hybrid rice restorer line HR1128 and the international sequenced japonica cultivar 'Nipponbare' as the donor and recurrent parents, respectively. The four panicle traits, GN, PL, PBN, and SBN, were evaluated for QTL effects using the inclusive composite interval mapping (ICIM) method in populations over two years at two sites. Results showed that a total of twelve QTLs for GN, PL, PBN, and SBN were detected on chromosome 6. Based on marker loci physical positions, the QTLs were found to be tightly linked to three important chromosomal intervals described as RM7213 to RM19962, RM20000 to RM20210, and RM412 to RM20595. Three QTLs identified in this study, PL6-5, PBN6-1, and PBN6-2, were found to be novel compared with previous studies. A major QTL (PL6-5) for panicle length was detected in all four populations at two locations, and its position was narrowed down to a 1.3Mb region on chromosome 6. Near isogenic lines (NILs) carrying PL6-5 will be developed for fine mapping of the QTL, and our results will provide referable information for gene excavation of panicle components in rice.
Construction of a high-density linkage map and fine mapping of QTLs for growth and gonad related traits in blunt snout bream
Apr 19, 2017   Scientific Reports
Wan SM, Liu H, Zhao BW, Nie CH, Wang WM, Gao ZX
Construction of a high-density linkage map and fine mapping of QTLs for growth and gonad related traits in blunt snout bream
Apr 19, 2017
Scientific Reports
High-density genetic maps based on SNPs are essential for fine mapping loci controlling specific traits for fish species. Using restriction-site associated DNA tag sequencing (RAD-Seq) technology, we identified 42,784 SNPs evenly distributed across the Megalobrama amblycephala genome. Based on 2 parents and 187 intra-specific hybridization progenies, a total of 14,648 high-confidence SNPs were assigned to 24 consensus linkage groups (LGs) of maternal and paternal map. The total length of the integrated map was 3,258.38 cM with an average distance of 0.57 cM among 5676 effective loci, thereby representing the first high-density genetic map reported for M. amblycephala. A total of eight positive quantitative trait loci (QTLs) were detected in QTL analysis. Of that, five QTL explained ≥35% of phenotypic variation for growth traits and three QTL explained ≥16% phenotypic variation for gonad related traits. A total of 176 mapped markers had significant hits in the zebrafish genome and almost all of the 24 putative-chromosomes of M. amblycephala were in relatively conserved synteny with chromosomes of zebrafish. Almost all M. amblycephala and zebrafish chromosomes had a 1:1 correspondence except for putative-chromosome 4, which mapped to two chromosomes of zebrafish caused by the difference in chromosome numbers between two species.
Gene-set analysis shows association between FMRP targets and autism spectrum disorder
Apr 19, 2017   European Journal Of Human Genetics : EJHG
Jansen A, Dieleman GC, Smit AB, Verhage M, Verhulst FC, Polderman TJC, Posthuma D
Gene-set analysis shows association between FMRP targets and autism spectrum disorder
Apr 19, 2017
European Journal Of Human Genetics : EJHG
Autism spectrum disorder (ASD) is a heterogeneous group of disorders characterized by problems with social interaction, communication, and repetitive and restricted behavior. Despite its high heritability and the substantial progress made in elucidating genetic associations, the corresponding biological mechanisms are largely unknown. Our objective is to investigate the contribution of common genetic variation to biological pathways functionally involved in ASD. We conducted gene-set analyses to identify ASD-associated functional biological pathways using the statistical tools MAGMA and INRICH. Gene-set selection was based on previously reported associations with psychiatric disorders and resulted in testing of specific synaptic and glial sets, a glutamate pathway gene-set, mitochondrial gene-sets and gene-sets consisting of fragile X mental retardation protein (FMRP) targets. In total 32 gene-sets were tested. We used Psychiatric Genomics Consortium genome-wide association studies summary statistics of ASD. The study is based on the largest ASD sample to date (N=5305). We found one significantly associated gene-set consisting of FMRP-targeting transcripts (MAGMA: p corr.=0.014, INRICH: p corr.=0.031; all competitive P-values). The results indicate the involvement of FMRP-targeted transcripts in ASD in common genetic variation. This novel finding is in line with the literature as FMRP has been linked to fragile X syndrome, ASD and cognitive development in whole-exome sequencing and copy number variant studies. This gene-set has also been linked to Schizophrenia suggesting that FMRP-targeted transcripts might be involved in a general mechanism with shared genetic etiology between psychiatric disorders.European Journal of Human Genetics advance online publication, 19 April 2017; doi:10.1038/ejhg.2017.55.
Genetic interplay between human longevity and metabolic pathways - a large-scale eQTL study
Apr 19, 2017   Aging Cell
Häsler R, Venkatesh G, Tan Q, Flachsbart F, Sinha A, Rosenstiel P, Lieb W, Schreiber S, Christensen K, Christiansen L, Nebel A
Genetic interplay between human longevity and metabolic pathways - a large-scale eQTL study
Apr 19, 2017
Aging Cell
Human longevity is a complex phenotype influenced by genetic and environmental components. Unraveling the contribution of genetic vs. nongenetic factors to longevity is a challenging task. Here, we conducted a large-scale RNA-sequencing-based expression quantitative trait loci study (eQTL) with subsequent heritability analysis. The investigation was performed on blood samples from 244 individuals from Germany and Denmark, representing various age groups including long-lived subjects up to the age of 104 years. Our eQTL-based approach revealed for the first time that human longevity is associated with a depletion of metabolic pathways in a genotype-dependent and independent manner. Further analyses indicated that 20% of the differentially expressed genes are influenced by genetic variants in cis. The subsequent study of twins showed that the transcriptional activity of a third of the differentially regulated genes is heritable. These findings suggest that longevity-associated biological processes such as altered metabolism are, to a certain extent, also the driving force of longevity rather than just a consequence of old age. © 2017 The Authors. Aging Cell published by the Anatomical Society and John Wiley & Sons Ltd.
MicroRNAs as biomarkers for psychiatric disorders with a focus on autism spectrum disorder: Current progress in genetic association studies, expression profiling, and translational research
Apr 18, 2017   Autism Research : Official Journal Of The International Society For Autism Research
Hu Y, Ehli EA, Boomsma DI
MicroRNAs as biomarkers for psychiatric disorders with a focus on autism spectrum disorder: Current progress in genetic association studies, expression profiling, and translational research
Apr 18, 2017
Autism Research : Official Journal Of The International Society For Autism Research
MicroRNAs (miRNAs) are a group of small noncoding RNA molecules, 18-25 nucleotides in length, which can negatively regulate gene expression at the post-transcriptional level by binding to messenger RNAs. About half of all identified miRNAs in humans are expressed in the brain and display regulatory functions important for many biological processes related to the development of the central nervous system (CNS). Disruptions in miRNA biogenesis and miRNA-target interaction have been related to CNS diseases, including psychiatric disorders. In this review, we focus on the role of miRNAs in autism spectrum disorder (ASD) and summarize recent findings about ASD-associated genetic variants in miRNA genes, in miRNA biogenesis genes, and miRNA targets. We discuss deregulation of miRNA expression in ASD and functional validation of ASD-related miRNAs in animal models. Including miRNAs in studies of ASD will contribute to our understanding of its etiology and pathogenesis and facilitate the discrimination between different disease subgroups. Autism Res 2017. © 2017 International Society for Autism Research, Wiley Periodicals, Inc. © 2017 International Society for Autism Research, Wiley Periodicals, Inc.
A Bayesian Group Sparse Multi-Task Regression Model for Imaging Genetics
Apr 18, 2017   Bioinformatics (Oxford, England)
Greenlaw K, Szefer E, Graham J, Lesperance M, Nathoo FS, Alzheimer’s Disease Neuroimaging Initiative
A Bayesian Group Sparse Multi-Task Regression Model for Imaging Genetics
Apr 18, 2017
Bioinformatics (Oxford, England)
Recent advances in technology for brain imaging and high-throughput genotyping have motivated studies examining the influence of genetic variation on brain structure. Wang et al. (Bioinformatics, 2012) have developed an approach for the analysis of imaging genomic studies using penalized multi-task regression with regularization based on a novel group l2,1-norm penalty which encourages structured sparsity at both the gene level and SNP level. While incorporating a number of useful features, the proposed method only furnishes a point estimate of the regression coefficients; techniques for conducting statistical inference are not provided. A new Bayesian method is proposed here to overcome this limitation. We develop a Bayesian hierarchical modeling formulation where the posterior mode corresponds to the estimator proposed by Wang et al. (Bioinformatics, 2012), and an approach that allows for full posterior inference including the construction of interval estimates for the regression parameters. We show that the proposed hierarchical model can be expressed as a three-level Gaussian scale mixture and this representation facilitates the use of a Gibbs sampling algorithm for posterior simulation. Simulation studies demonstrate that the interval estimates obtained using our approach achieve adequate coverage probabilities that outperform those obtained from the nonparametric bootstrap. Our proposed methodology is applied to the analysis of neuroimaging and genetic data collected as part of the Alzheimer's Disease Neuroimaging Initiative (ADNI), and this analysis of the ADNI cohort demonstrates clearly the value added of incorporating interval estimation beyond only point estimation when relating SNPs to brain imaging endophenotypes. Software and sample data is available as an R package 'bgsmtr' that can be downloaded from The Comprehensive R Archive Network (CRAN).
Genomic data for 78 chickens from 14 populations
Apr 21, 2017   GigaScience
Li D, Che T, Chen B, Tian S, Zhou X,   . . . . . .   , Yang M, Zhou R, Li R, Zhu Q, Li M
Genomic data for 78 chickens from 14 populations
Apr 21, 2017
GigaScience
Since the domestication of the red jungle fowls ( Gallus gallus ) (dating back to ∼10,000 B.P.) in Asia, domestic chickens ( Gallus gallus domesticus ) have been subjected to the combined effects of natural selection and human-driven artificial selection; this has resulted in marked phenotypic diversity in a number of traits, including behavior, body composition, egg production and skin color. Population genomic variations through diversifying selection have not been fully investigated. The whole genomes of 78 domestic chickens were sequenced to an average of 18-fold coverage for each bird. By combining this data with publicly available genomes of 5 wild red jungle fowls and 8 Xishuangbanna game fowls, we conducted a comprehensive comparative genomics analysis of 91 chickens from 17 populations. After aligning ∼21.30 gigabases (Gb) of high quality data from each individual to the reference chicken genome, we identified ∼6.44 million (M) SNPs for each population. These SNPs included 1.10 M novel SNPs in 17 populations that were absent in the current chicken dbSNP (Build 145) entries. The current data is important for population genetics and further studies in chicken, and will serve as a valuable resource for investigating diversifying selection and candidate genes for selective breeding in chicken.

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