Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation.

Abstract:

:After domestication, during a process of widespread range extension, barley adapted to a broad spectrum of agricultural environments. To explore how the barley genome responded to the environmental challenges it encountered, we sequenced the exomes of a collection of 267 georeferenced landraces and wild accessions. A combination of genome-wide analyses showed that patterns of variation have been strongly shaped by geography and that variant-by-environment associations for individual genes are prominent in our data set. We observed significant correlations of days to heading (flowering) and height with seasonal temperature and dryness variables in common garden experiments, suggesting that these traits were major drivers of environmental adaptation in the sampled germplasm. A detailed analysis of known flowering-associated genes showed that many contain extensive sequence variation and that patterns of single- and multiple-gene haplotypes exhibit strong geographical structuring. This variation appears to have substantially contributed to range-wide ecogeographical adaptation, but many factors key to regional success remain unidentified.

journal_name

Nat Genet

journal_title

Nature genetics

authors

Russell J,Mascher M,Dawson IK,Kyriakidis S,Calixto C,Freund F,Bayer M,Milne I,Marshall-Griffiths T,Heinen S,Hofstad A,Sharma R,Himmelbach A,Knauft M,van Zonneveld M,Brown JW,Schmid K,Kilian B,Muehlbauer GJ,Stein N,

doi

10.1038/ng.3612

subject

Has Abstract

pub_date

2016-09-01 00:00:00

pages

1024-30

issue

9

eissn

1061-4036

issn

1546-1718

pii

ng.3612

journal_volume

48

pub_type

杂志文章
  • Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution.

    abstract::Enterotoxigenic Escherichia coli (ETEC), a major cause of infectious diarrhea, produce heat-stable and/or heat-labile enterotoxins and at least 25 different colonization factors that target the intestinal mucosa. The genes encoding the enterotoxins and most of the colonization factors are located on plasmids found acr...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.3145

    authors: von Mentzer A,Connor TR,Wieler LH,Semmler T,Iguchi A,Thomson NR,Rasko DA,Joffre E,Corander J,Pickard D,Wiklund G,Svennerholm AM,Sjöling Å,Dougan G

    更新日期:2014-12-01 00:00:00

  • Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene.

    abstract::Allelic heterogeneity in disease-causing genes presents a substantial challenge to the translation of genomic variation into clinical practice. Few of the almost 2,000 variants in the cystic fibrosis transmembrane conductance regulator gene CFTR have empirical evidence that they cause cystic fibrosis. To address this ...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.2745

    authors: Sosnay PR,Siklosi KR,Van Goor F,Kaniecki K,Yu H,Sharma N,Ramalho AS,Amaral MD,Dorfman R,Zielenski J,Masica DL,Karchin R,Millen L,Thomas PJ,Patrinos GP,Corey M,Lewis MH,Rommens JM,Castellani C,Penland CM,Cutting GR

    更新日期:2013-10-01 00:00:00

  • Association of the INS VNTR with size at birth. ALSPAC Study Team. Avon Longitudinal Study of Pregnancy and Childhood.

    abstract::Size at birth is an important determinant of perinatal survival and has also been associated with the risk for cardiovascular disease and type 2 diabetes in adult life. Common genetic variation that regulates fetal growth could therefore influence perinatal survival and predispose to the development of adult disease. ...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng0598-98

    authors: Dunger DB,Ong KK,Huxtable SJ,Sherriff A,Woods KA,Ahmed ML,Golding J,Pembrey ME,Ring S,Bennett ST,Todd JA

    更新日期:1998-05-01 00:00:00

  • Molecular breeding of viruses.

    abstract::Genetic recombination is a major force driving the evolution of many viruses. Recombination between two copackaged retroviral genomes may occur at rates as high as 40% per replication cycle. This enables genetic information to be shuffled rapidly, leading to recombinants with new patterns of mutations and phenotypes. ...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/78132

    authors: Soong NW,Nomura L,Pekrun K,Reed M,Sheppard L,Dawes G,Stemmer WP

    更新日期:2000-08-01 00:00:00

  • The gene mutated in autosomal recessive polycystic kidney disease encodes a large, receptor-like protein.

    abstract::Autosomal recessive polycystic kidney disease (ARPKD) is characterized by dilation of collecting ducts and by biliary dysgenesis and is an important cause of renal- and liver-related morbidity and mortality. Genetic analysis of a rat with recessive polycystic kidney disease revealed an orthologous relationship between...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng833

    authors: Ward CJ,Hogan MC,Rossetti S,Walker D,Sneddon T,Wang X,Kubly V,Cunningham JM,Bacallao R,Ishibashi M,Milliner DS,Torres VE,Harris PC

    更新日期:2002-03-01 00:00:00

  • Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.

    abstract::Microarray analysis has become a widely used tool for the generation of gene expression data on a genomic scale. Although many significant results have been derived from microarray studies, one limitation has been the lack of standards for presenting and exchanging such data. Here we present a proposal, the Minimum In...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng1201-365

    authors: Brazma A,Hingamp P,Quackenbush J,Sherlock G,Spellman P,Stoeckert C,Aach J,Ansorge W,Ball CA,Causton HC,Gaasterland T,Glenisson P,Holstege FC,Kim IF,Markowitz V,Matese JC,Parkinson H,Robinson A,Sarkans U,Schulze-Krem

    更新日期:2001-12-01 00:00:00

  • Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index.

    abstract::Obesity is globally prevalent and highly heritable, but its underlying genetic factors remain largely elusive. To identify genetic loci for obesity susceptibility, we examined associations between body mass index and ∼ 2.8 million SNPs in up to 123,865 individuals with targeted follow up of 42 SNPs in up to 125,931 ad...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.686

    authors: Speliotes EK,Willer CJ,Berndt SI,Monda KL,Thorleifsson G,Jackson AU,Lango Allen H,Lindgren CM,Luan J,Mägi R,Randall JC,Vedantam S,Winkler TW,Qi L,Workalemahu T,Heid IM,Steinthorsdottir V,Stringham HM,Weedon MN,Wheel

    更新日期:2010-11-01 00:00:00

  • Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.

    abstract::To further understanding of the genetic basis of type 2 diabetes (T2D) susceptibility, we aggregated published meta-analyses of genome-wide association studies (GWAS), including 26,488 cases and 83,964 controls of European, east Asian, south Asian and Mexican and Mexican American ancestry. We observed a significant ex...

    journal_title:Nature genetics

    pub_type: 杂志文章,meta分析

    doi:10.1038/ng.2897

    authors: DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium.,Asian Genetic Epidemiology Network Type 2 Diabetes (AGEN-T2D) Consortium.,South Asian Type 2 Diabetes (SAT2D) Consortium.,Mexican American Type 2 Diabetes (MAT2D) Consortium.,

    更新日期:2014-03-01 00:00:00

  • Transposon mutagenesis identifies genetic drivers of Braf(V600E) melanoma.

    abstract::Although nearly half of human melanomas harbor oncogenic BRAF(V600E) mutations, the genetic events that cooperate with these mutations to drive melanogenesis are still largely unknown. Here we show that Sleeping Beauty (SB) transposon-mediated mutagenesis drives melanoma progression in Braf(V600E) mutant mice and iden...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.3275

    authors: Mann MB,Black MA,Jones DJ,Ward JM,Yew CC,Newberg JY,Dupuy AJ,Rust AG,Bosenberg MW,McMahon M,Print CG,Copeland NG,Jenkins NA

    更新日期:2015-05-01 00:00:00

  • PRC1 proteins orchestrate three-dimensional genome architecture.

    abstract::The three-dimensional organization of the genome has an important role in orchestrating gene expression, but its regulation is poorly understood. Now, a new study uncovers a major role for Polycomb components of the PRC1 complex in organizing physical networks of genes that are co-repressed to maintain pluripotency. ...

    journal_title:Nature genetics

    pub_type: 评论,新闻

    doi:10.1038/ng.3411

    authors: Cavalli G

    更新日期:2015-10-01 00:00:00

  • Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial pressure.

    abstract::Numerous genetic loci have been associated with systolic blood pressure (SBP) and diastolic blood pressure (DBP) in Europeans. We now report genome-wide association studies of pulse pressure (PP) and mean arterial pressure (MAP). In discovery (N = 74,064) and follow-up studies (N = 48,607), we identified at genome-wid...

    journal_title:Nature genetics

    pub_type: 杂志文章,meta分析

    doi:10.1038/ng.922

    authors: Wain LV,Verwoert GC,O'Reilly PF,Shi G,Johnson T,Johnson AD,Bochud M,Rice KM,Henneman P,Smith AV,Ehret GB,Amin N,Larson MG,Mooser V,Hadley D,Dörr M,Bis JC,Aspelund T,Esko T,Janssens AC,Zhao JH,Heath S,Laan M,

    更新日期:2011-09-11 00:00:00

  • Variants within the immunoregulatory CBLB gene are associated with multiple sclerosis.

    abstract::A genome-wide association scan of approximately 6.6 million genotyped or imputed variants in 882 Sardinian individuals with multiple sclerosis (cases) and 872 controls suggested association of CBLB gene variants with disease, which was confirmed in 1,775 cases and 2,005 controls (rs9657904, overall P = 1.60 x 10(-10),...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.584

    authors: Sanna S,Pitzalis M,Zoledziewska M,Zara I,Sidore C,Murru R,Whalen MB,Busonero F,Maschio A,Costa G,Melis MC,Deidda F,Poddie F,Morelli L,Farina G,Li Y,Dei M,Lai S,Mulas A,Cuccuru G,Porcu E,Liang L,Zavattari P,M

    更新日期:2010-06-01 00:00:00

  • Mutations in SECISBP2 result in abnormal thyroid hormone metabolism.

    abstract::Incorporation of selenocysteine (Sec), through recoding of the UGA stop codon, creates a unique class of proteins. Mice lacking tRNA(Sec) die in utero, but the in vivo role of other components involved in selenoprotein synthesis is unknown, and Sec incorporation defects have not been described in humans. Deiodinases (...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng1654

    authors: Dumitrescu AM,Liao XH,Abdullah MS,Lado-Abeal J,Majed FA,Moeller LC,Boran G,Schomburg L,Weiss RE,Refetoff S

    更新日期:2005-11-01 00:00:00

  • Estimation of complex effect-size distributions using summary-level statistics from genome-wide association studies across 32 complex traits.

    abstract::We developed a likelihood-based approach for analyzing summary-level statistics and external linkage disequilibrium information to estimate effect-size distributions of common variants, characterized by the proportion of underlying susceptibility SNPs and a flexible normal-mixture model for their effects. Analysis of ...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/s41588-018-0193-x

    authors: Zhang Y,Qi G,Park JH,Chatterjee N

    更新日期:2018-09-01 00:00:00

  • Defective colour vision associated with a missense mutation in the human green visual pigment gene.

    abstract::All red/green colour vision defects described so far have been associated with gross rearrangements within the red/green opsin gene array (Xq28). We now describe a male with severe deuteranomaly without such a rearrangement. A substitution of a highly conserved cysteine by arginine at position 203 in the green opsins ...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng0792-251

    authors: Winderickx J,Sanocki E,Lindsey DT,Teller DY,Motulsky AG,Deeb SS

    更新日期:1992-07-01 00:00:00

  • The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genes.

    abstract::The ratio of X-linked to autosomal diversity was estimated from an analysis of six human genome sequences and found to deviate from the expected value of 0.75. However, the direction of this deviation depends on whether a particular sequence is close to or far from the nearest gene. This pattern may be explained by st...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.651

    authors: Hammer MF,Woerner AE,Mendez FL,Watkins JC,Cox MP,Wall JD

    更新日期:2010-10-01 00:00:00

  • Microdeletions in the human H19 DMR result in loss of IGF2 imprinting and Beckwith-Wiedemann syndrome.

    abstract::The overgrowth- and tumor-associated Beckwith-Wiedemann syndrome results from dysregulation of imprinted genes on chromosome 11p15.5. Here we show that inherited microdeletions in the H19 differentially methylated region (DMR) that abolish two CTCF target sites cause this disease. Maternal transmission of the deletion...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng1410

    authors: Sparago A,Cerrato F,Vernucci M,Ferrero GB,Silengo MC,Riccio A

    更新日期:2004-09-01 00:00:00

  • Indian hedgehog is a major mediator of progesterone signaling in the mouse uterus.

    abstract::The hedgehog family of morphogens are regulators of cell proliferation, differentiation and cell-cell communication. These morphogens have been shown to have important roles in organogenesis, spermatogenesis, stem cell maintenance and oncogenesis. Indian hedgehog (encoded by Ihh) has been shown to be expressed in the ...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng1874

    authors: Lee K,Jeong J,Kwak I,Yu CT,Lanske B,Soegiarto DW,Toftgard R,Tsai MJ,Tsai S,Lydon JP,DeMayo FJ

    更新日期:2006-10-01 00:00:00

  • The extent of linkage disequilibrium in Arabidopsis thaliana.

    abstract::Linkage disequilibrium (LD), the nonrandom occurrence of alleles in haplotypes, has long been of interest to population geneticists. Recently, the rapidly increasing availability of genomic polymorphism data has fueled interest in LD as a tool for fine-scale mapping, in particular for human disease loci. The chromosom...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng813

    authors: Nordborg M,Borevitz JO,Bergelson J,Berry CC,Chory J,Hagenblad J,Kreitman M,Maloof JN,Noyes T,Oefner PJ,Stahl EA,Weigel D

    更新日期:2002-02-01 00:00:00

  • Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis.

    abstract::Sequence variation in human genes is largely confined to single-nucleotide polymorphisms (SNPs) and is valuable in tests of association with common diseases and pharmacogenetic traits. We performed a systematic and comprehensive survey of molecular variation to assess the nature, pattern and frequency of SNPs in 75 ca...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/10297

    authors: Halushka MK,Fan JB,Bentley K,Hsie L,Shen N,Weder A,Cooper R,Lipshutz R,Chakravarti A

    更新日期:1999-07-01 00:00:00

  • Mutations in the gene encoding the serine protease inhibitor, Kazal type 1 are associated with chronic pancreatitis.

    abstract::Chronic pancreatitis (CP) is a continuing or relapsing inflammatory disease of the pancreas. In approximately one-third of all cases, no aetiological factor can be found, and these patients are classified as having idiopathic disease. Pathophysiologically, autodigestion and inflammation may be caused by either increas...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/76088

    authors: Witt H,Luck W,Hennies HC,Classen M,Kage A,Lass U,Landt O,Becker M

    更新日期:2000-06-01 00:00:00

  • The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies.

    abstract::Despite the clinical significance of balanced chromosomal abnormalities (BCAs), their characterization has largely been restricted to cytogenetic resolution. We explored the landscape of BCAs at nucleotide resolution in 273 subjects with a spectrum of congenital anomalies. Whole-genome sequencing revised 93% of karyot...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.3720

    authors: Redin C,Brand H,Collins RL,Kammin T,Mitchell E,Hodge JC,Hanscom C,Pillalamarri V,Seabra CM,Abbott MA,Abdul-Rahman OA,Aberg E,Adley R,Alcaraz-Estrada SL,Alkuraya FS,An Y,Anderson MA,Antolik C,Anyane-Yeboa K,Atkin JF

    更新日期:2017-01-01 00:00:00

  • Identification of DOK genes as lung tumor suppressors.

    abstract::Genome-wide analyses of human lung adenocarcinoma have identified regions of consistent copy-number gain or loss, but in many cases the oncogenes and tumor suppressors presumed to reside in these loci remain to be determined. Here we identify the downstream of tyrosine kinase (Dok) family members Dok1, Dok2 and Dok3 a...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.527

    authors: Berger AH,Niki M,Morotti A,Taylor BS,Socci ND,Viale A,Brennan C,Szoke J,Motoi N,Rothman PB,Teruya-Feldstein J,Gerald WL,Ladanyi M,Pandolfi PP

    更新日期:2010-03-01 00:00:00

  • Molecular basis of Thomsen's disease (autosomal dominant myotonia congenita).

    abstract::Thomsen's disease (autosomal dominant myotonia congenita) has recently been linked to chromosome 7q35 in the region of the human skeletal muscle chloride channel gene (HUMCLC). Single strand conformation polymorphism analysis (SSCP) was used to screen DNA from members of four unrelated pedigrees with this disorder for...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng0493-305

    authors: George AL Jr,Crackower MA,Abdalla JA,Hudson AJ,Ebers GC

    更新日期:1993-04-01 00:00:00

  • Recombination and linkage disequilibrium in Arabidopsis thaliana.

    abstract::Linkage disequilibrium (LD) is a major aspect of the organization of genetic variation in natural populations. Here we describe the genome-wide pattern of LD in a sample of 19 Arabidopsis thaliana accessions using 341,602 non-singleton SNPs. LD decays within 10 kb on average, considerably faster than previously estima...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng2115

    authors: Kim S,Plagnol V,Hu TT,Toomajian C,Clark RM,Ossowski S,Ecker JR,Weigel D,Nordborg M

    更新日期:2007-09-01 00:00:00

  • Pleiotropic fitness effects of the Tre1-Gr5a region in Drosophila melanogaster.

    abstract::The abundance of transposable elements and DNA repeat sequences in mammalian genomes raises the question of whether such insertions represent passive evolutionary baggage or may influence the expression of complex traits. We addressed this question in Drosophila melanogaster, in which the effects of single transposabl...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng1823

    authors: Rollmann SM,Magwire MM,Morgan TJ,Ozsoy ED,Yamamoto A,Mackay TF,Anholt RR

    更新日期:2006-07-01 00:00:00

  • Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation.

    abstract::Methylation of DNA at the dinucleotide CpG is essential for mammalian development and is correlated with stable transcriptional silencing. This transcriptional silencing has recently been linked at a molecular level to histone deacetylation through the demonstration of a physical association between histone deacetylas...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/12664

    authors: Wade PA,Gegonne A,Jones PL,Ballestar E,Aubry F,Wolffe AP

    更新日期:1999-09-01 00:00:00

  • A mouse model of human L1 retrotransposition.

    abstract::The L1 retrotransposon has had an immense impact on the size and structure of the human genome through a variety of mechanisms, including insertional mutagenesis. To study retrotransposition in a living organism, we created a mouse model of human L1 retrotransposition. Here we show that L1 elements can retrotranspose ...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng1022

    authors: Ostertag EM,DeBerardinis RJ,Goodier JL,Zhang Y,Yang N,Gerton GL,Kazazian HH Jr

    更新日期:2002-12-01 00:00:00

  • The chromo and SET domains of the Clr4 protein are essential for silencing in fission yeast.

    abstract::Heritable inactivation of specific regions of the genome is a widespread, possibly universal phenomenon for gene regulation in eukaryotes. Self-perpetuating, clonally inherited chromatin structure has been proposed as the explanation for such phenomena as position-effect variegation (PEV) and control of segment determ...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/566

    authors: Ivanova AV,Bonaduce MJ,Ivanov SV,Klar AJ

    更新日期:1998-06-01 00:00:00

  • Mutations associated with familial melanoma impair p16INK4 function.

    abstract::Cell division is controlled by a series of positive and negative regulators which act at sequential points throughout the cell cycle. Disturbance of these checks could contribute to cancer by allowing excessive cell proliferation. The point in G1 at which cells irrevocably commit to DNA synthesis is controlled by prot...

    journal_title:Nature genetics

    pub_type: 信件

    doi:10.1038/ng0595-114

    authors: Ranade K,Hussussian CJ,Sikorski RS,Varmus HE,Goldstein AM,Tucker MA,Serrano M,Hannon GJ,Beach D,Dracopoli NC

    更新日期:1995-05-01 00:00:00