Skip to main content
SpringerLink
Log in

Genome-Wide Association Scans (GWAS)

  • Chapter
  • First Online:
Biotechnological Approaches to Barley Improvement

Part of the book series: Biotechnology in Agriculture and Forestry ((AGRICULTURE,volume 69))

Abstract

Genome-wide association scans (GWAS) provide a mechanism to assess variation that segregates in a gene pool, rather than in a biparental population. Fashioned originally in human genetics, it has become popular in plant genetic research over the last decade [Waugh et al. (Curr Opin Plant Biol 12:218–222, 2009)]. GWAS is attractive because it potentially provides an opportunity to exploit existing and extensive phenotypic data collected during the plant registration process, thus making it directly relevant to current breeding material. It also holds the promise of increasing genetic resolution because GWAS populations typically contain more genetic breakpoints and more alleles than are found in conventional mapping populations. However, GWAS approaches also raise issues in genetic analysis. These are largely caused by the origins and history of the population, which introduce a tendency to reveal significant false-positive associations due to factors other than genetic linkage. Here, we summarise some of the progress and the problems that have been encountered in establishing effective GWAS in barley and the approaches that have been developed or applied to take account of them.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Atwell S, Huang YS, Vilhjálmsson BJ, Willems G, Horton M, Li Y, Meng D, Platt A, Tarone AM, Hu TT, Jiang R, Muliyati NW, Zhang X, Amer MA, Baxter I, Brachi B, Chory J, Dean C, Debieu M, de Meaux J, Ecker JR, Faure N, Kniskern JM, Jones JD, Michael T, Nemri A, Roux F, Salt DE, Tang C, Todesco M, Traw MB, Weigel D, Marjoram P, Borevitz JO, Bergelson J, Nordborg M (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465:627–631

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Aulchenko YS, de Koning D-J, Haley C (2007) Genomewide rapid association using mixed model and regression: a fast and simple method for genomewide pedigree-based quantitative trait loci association analysis. Genetics 177:577–585

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635

    Article  CAS  PubMed  Google Scholar 

  • Büschges R, Hollricher K, Panstruga R, Simons G, Wolter M, Frijters A, van Daelen R, van der Lee T, Diergaarde P, Groenendijk J, Töpsch S, Vos P, Salamini F, Schulze-Lefert P (1997) The barley Mlo gene: a novel control element of plant pathogen resistance. Cell 88:695–705

    Article  PubMed  Google Scholar 

  • Caldwell KS, Russell J, Langridge P, Powell W (2006) Extreme population-dependent linkage disequilibrium detected in an inbreeding plant species, Hordeum vulgare. Genetics 172:557–567

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Casas AM, Djemel A, Ciudad FJ, Yahiaoui S, Ponce LJ, Contreras-Moreira B, Gracia MP, Lasa JM, Igartua E (2011) HvFT1 (VrnH3) drives latitudinal adaptation in Spanish barleys. Theor Appl Genet 122:1293–1304

    Article  CAS  PubMed  Google Scholar 

  • Cavanagh C, Morell M, Mackay I, Powell W (2008) From mutations to MAGIC: resources for gene discovery, validation and delivery in crop plants. Curr Opin Plant Biol 11:215–221

    Article  PubMed  Google Scholar 

  • Ceccarelli S, Grando S, Leur JAG (1987) Genetic diversity in barley landraces from Syria and Jordan. Euphytica 36:389–405

    Article  Google Scholar 

  • Chutimanitsakun Y, Nipper RW, Cuesta-Marcos A, Cistué L, Corey A, Filichkina T, Johnson EA, Hayes PM (2011) Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley. BMC Genomics 2011:4

    Article  Google Scholar 

  • Close TJ, Bhat PR, Lonardi S, Wu Y, Rostoks N, Ramsay L, Druka A, Stein N, Svensson JT, Wanamaker S, Bozdag S, Roose ML, Moscou MJ, Chao S, Varshney RK, Szucs P, Sato K, Hayes PM, Matthews DE, Kleinhofs A, Muehlbauer GJ, DeYoung J, Marshall DF, Madishetty K, Fenton RD, Condamine P, Graner A, Waugh R (2009) Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics 10:582

    Article  PubMed Central  PubMed  Google Scholar 

  • Cockram J, White J, Zuluaga D, Smith D, Comadran J, Macaulay M, Luo ZW, Kearsey MJ, Werner P, Harrap D, Tapsell C, Liu H, Hedley PE, Stein N, Schulte D, Steuernagel B, Marshall DF, Thomas WTB, Ramsay L, Mackay I, Balding DJ, Waugh R, O’Sullivan D (2010) Genome-wide association mapping of morphological traits to candidate gene resolution in the un-sequenced barley genome. Proc Natl Acad Sci U S A 107:21611–21616

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Comadran J, Thomas WT, van Eeuwijk FA, Ceccarelli S, Grando S, Stanca AM, Pecchioni N, Akar T, Al-Yassin A, Benbelkacem A, Ouabbou H, Bort J, Romagosa I, Hackett CA, Russell JR (2009) Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin. Theor Appl Genet 119:175–187

    Article  CAS  PubMed  Google Scholar 

  • Comadran J, Ramsay L, MacKenzie K, Hayes P, Close TJ, Muehlbauer G, Stein N, Waugh R (2011a) Patterns of polymorphism and linkage disequilibrium in cultivated barley. Theor Appl Genet 122:523–531

    Article  PubMed Central  PubMed  Google Scholar 

  • Comadran J, Russell JR, Booth A, Pswarayi A, Ceccarelli S, Grando S, Stanca AM, Pecchioni N, Akar T, Al-Yassin A, Benbelkacem A, Ouabbou H, Bort J, van Eeuwijk FA, Thomas WT, Romagosa I (2011b) Mixed model association scans of multi-environmental trial data reveal major loci controlling yield and yield related traits in Hordeum vulgare in Mediterranean environments. Theor Appl Genet 122:1363–1373

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Comadran J, Kilian B, Russell J, Ramsay L, Stein N, Ganal M, Shaw P, Bayer M, Thomas WTB, Marshall D, Hedley P, Tondelli A, Pecchioni N, Francia E, Korzun V, Walther A, Waugh R (2012) A homologue of Antirrhinum CENTRORADIALIS is a component of the quantitative photoperiod and vernalization independent EARLINESS PER SE 2 locus in cultivated barley. Nat Genet 44:1388–1392

    Article  CAS  PubMed  Google Scholar 

  • Cuesta-Marcos A, Szucs P, Close TJ, Filichkin T, Muehlbauer GJ, Smith KP, Hayes PM (2010) Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure. BMC Genomics 11:707

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12:499–510

    Article  CAS  PubMed  Google Scholar 

  • Druka A, Franckowiak J, Lundqvist U, Bonar N, Alexander J, Houston K, Radovic S, Shahinnia F, Vendramin V, Morgante M, Stein N, Waugh R (2011) Genetic dissection of barley morphology and development. Plant Physiol 155:617–627

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell Sharon E (2011) A robust, simple genotyping-by-sequencing (gbs) approach for high diversity species. PLoS One 6:e19379

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Fan JB, Oliphant A, Shen R, Kermani BG, Garcia F, Gunderson KL, Hansen M, Steemers F, Butler SL, Deloukas P, Galver L, Hunt S, Mcbride C, Bibikova M, Rubano T, Chen J, Wickham E, Doucet D, Chang W, Campbell D, Zhang B, Kruglyak S, Bentley D, Haas J, Rigault P, Zhou L, Stuelpnagel J, Chee MS (2003) Highly parallel SNP genotyping. Cold Spring Harb Symp Quant Biol LXVIII:69–78

    Article  Google Scholar 

  • Graner A, Jahoor A, Schondelmaier J, Siedler H, Pillen K, Fischbeck G, Wenzel G, Herrmann RG (1990) Construction of an RFLP map of barley. Theor Appl Genet 83:250–256

    Google Scholar 

  • Graner A, Streng S, Kellermann A, Schiemann A, Bauer E, Waugh R, Pellio B, Ordon F (1998) Molecular mapping and genetic fine-structure of the rym5 locus encoding resistance to different strains of the barley yellow mosaic virus complex. Theor Appl Genet 98:285–290

    Article  Google Scholar 

  • Hamblin MT, Close TJ, Bhat PR, Chao S, Kling JG, Joseph Abraham K, Blake T, Brooks WS, Cooper B, Griffey CA, Hayes PM, Hole DJ, Horsley RD, Obert DE, Smith KP, Ullrich SE, Muehlbauer GJ, Jannink JL (2010) Population structure and linkage disequilibrium in U.S. barley germplasm: implications for association mapping. Crop Sci 50:556

    Article  CAS  Google Scholar 

  • Haseneyer G, Stracke S, Paul C, Einfeldt C, Broda A, Piepho HP, Graner A, Geiger HH (2010) Population structure and phenotypic variation of a spring barley world collection set up for association studies. Plant Breed 129:271–279

    Article  CAS  Google Scholar 

  • Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z, Li M, Fan D, Guo Y, Wang A, Wang L, Deng L, Li W, Lu Y, Weng Q, Liu K, Huang T, Zhou T, Jing Y, Li W, Lin Z, Buckler ES, Qian Q, Zhang QF, Li J, Han B (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42:961–967

    Article  CAS  PubMed  Google Scholar 

  • Igartua E, Gracia MP, Lasa JM, Medina B, Molina-Cano JL, Montoya JL, Romagosa I (1998) The Spanish barley core collection. Genet Resour Crop Evol 45:475–481

    Article  Google Scholar 

  • Jaccoud D, Peng K, Feinstein D, Kilian A (2001) Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Res 29:E25

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Jones H, Civáň P, Cockram J, Leigh FJ, Smith LM, Jones MK, Charles MP, Molina-Cano JL, Powell W, Jones G, Brown TA (2011) Evolutionary history of barley cultivation in Europe revealed by genetic analysis of extant landraces. BMC Evol Biol 11:320

    Article  PubMed Central  PubMed  Google Scholar 

  • Kang HM, Sul JH, Service SK, Zaitlen NA, Kong SY, Freimer NB, Sabatti C, Eskin E (2010) Variance component model to account for sample structure in genome-wide association studies. Nat Genet 42:348–354

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kim S, Plagnol V, Hu TT, Toomajian C, Clark RM, Ossowski S, Ecker JR, Weigel D, Nordborg M (2007) Recombination and linkage disequilibrium in Arabidopsis thaliana. Nat Genet 39:1151–1155

    Article  CAS  PubMed  Google Scholar 

  • Kleinhofs A, Kilian A, Saghai Marrof MA, Biyashev RM, Hayes P, Chen FQ, Lapitan N, Fenwick A, Blake TK, Kanazin V, Ananiev E, Dahleen L, Kudrna D, Bollinger J, Knapp SJ, Liu B, Sorells M, Heun M, Franckowiak JD, Hoffman D, Skadsen R, Steffenson BJ (1993) A molecular, isozyme and morphological map of the barley (Hordeum vulgare) genome. Theor Appl Genet 86:705–712

    Article  CAS  PubMed  Google Scholar 

  • Komatsuda T, Pourkheirandish M, He C, Azhaguvel P, Kanamori H, Perovic D, Stein N, Graner A, Wicker T, Tagiri A, Lundqvist U, Fujimura T, Matsuoka M, Matsumoto T, Yano M (2007) Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I–class homeobox gene. Proc Natl Acad Sci U S A 104:1424–1429

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kraakman ATW (2005) Mapping of yield, yield stability, yield adaptability and other traits in barley using linkage disequilibrium mapping and linkage analysis. PhD Dissertation 3772, Wageningen University

    Google Scholar 

  • Kraakman ATW, Niks RE, Van den Berg PMMM, Stam P, Van Eeuwijk FA (2004) Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics 168:435–446

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kraakman ATW, Martinez F, Mussiraliev B, van Eeuwijk FA, Niks RE (2006) Linkage disequilibrium mapping of morphological, resistance, and other agronomically relevant traits in modern spring barley cultivars. Mol Breed 17:41–58

    Article  CAS  Google Scholar 

  • Lee JM, Davenport GF, Marshall D, Ellis TH, Ambrose MJ, Dicks J, van Hintum TJ, Flavell AJ (2005) GERMINATE: a generic database for integrating genotypic and phenotypic information for plant genetic resource collections. Plant Physiol 139:619–631

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Lippert C, Listgarten J, Liu Y, Kadie CM, Davidson RI, Heckerman D (2011) FaST linear mixed models for genome-wide association studies. Nat Methods 8:833–835

    Article  CAS  PubMed  Google Scholar 

  • Mackay I, Powell W (2007) Methods for linkage disequilibrium mapping in crops. Trends Plant Sci 12:57–63

    Article  CAS  PubMed  Google Scholar 

  • Malysheva-Otto LV, Ganal MW, Röder MS (2006) Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L). BMC Genet 7:6

    Article  PubMed Central  PubMed  Google Scholar 

  • Massman J, Cooper B, Horsley R, Neate S, Dill-Macky R, Chao S, Dong Y, Schwarz P, Muehlbauer GJ, Smith KP (2011) Genome-wide association mapping of Fusarium head blight resistance in contemporary barley breeding germplasm. Mol Breed 27:439–454

    Article  Google Scholar 

  • Matthies IE, Weise S, Roder MS (2009) Association of haplotype diversity in the alpha-amylase gene amy1 with malting quality parameters in barley. Mol Breed 23:139–152

    Article  CAS  Google Scholar 

  • Matthies IE, Sharma S, Weise S, Roder MS (2012) Sequence variation in the barley genes encoding sucrose synthase I and sucrose phosphate synthase II, and its association with variation in grain traits and malting quality. Euphytica 184:73–83

    Article  CAS  Google Scholar 

  • McMullen MD, Kresovich S, Villeda HS, Bradbury P, Li H, Sun Q, Flint-Garcia S, Thornsberry J, Acharya C, Bottoms C, Brown P, Browne C, Eller M, Guill K, Harjes K, Kroon D, Lepak N, Mitchell SE, Peterson B, Pressoir G, Romero S, Rosas OM, Salvo S, Yates H, Hanson M, Jones E, Smith S, Glaubitz JC, Goodman M, Ware D, Holland JB, Buckler ES (2009) Genetic properties of the maize nested association mapping population. Science 325:737–740

    Article  CAS  PubMed  Google Scholar 

  • Milne I, Shaw P, Stephen G, Bayer M, Cardle L, Thomas WTB, Flavell AJ, Marshall DF (2010) Flapjack – graphical genotype visualization. Bioinformatics 26:3133–3134. doi:10.1093/bioinformatics/btq580#_blank

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Moragues M, Comadran J, Waugh R, Milne I, Flavell AJ, Russell JR (2010) Effects of ascertainment bias and marker number on estimations of barley diversity from high throughput SNP genotype data. Theor Appl Genet 120:1525–1534

    Article  CAS  PubMed  Google Scholar 

  • Morrell PL, Toleno DM, Lundy KE, Clegg MT (2005) Low levels of linkage disequilibrium in wild barley (Hordeum vulgare ssp. spontaneum) despite high rates of self-fertilization. Proc Natl Acad Sci U S A 102:2442–2447

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Nielsen R (2000) Estimation of population parameters and recombination rates from single nucleotide polymorphisms. Genetics 154:931–942

    CAS  PubMed Central  PubMed  Google Scholar 

  • Nilsson NO, Säll T, Bengtsson BO (1993) Chiasma and recombination data in plants: are compatible? Trends Genet 9:344–348

    Article  CAS  PubMed  Google Scholar 

  • Nordborg M, Borevitz JO, Bergelson J, Berry CC, Chory J, Hagenblad J, Kreitman M, Maloof JN, Noyes T, Oefner PJ, Stahl EA, Weigel D (2002) The extent of linkage disequilibrium in Arabidopsis thaliana. Nat Genet 30:190–193

    Article  CAS  PubMed  Google Scholar 

  • Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C, Zheng H, Bakker E, Calabrese P, Gladstone J, Goyal R, Jakobsson M, Kim S, Morozov Y, Padhukasahasram B, Plagnol V, Rosenberg NA, Shah C, Wall JD, Wang J, Zhao K, Kalbfleisch T, Schulz V, Kreitman M, Bergelson J (2005) The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol 3:e196

    Article  PubMed Central  PubMed  Google Scholar 

  • Pasam RK, Sharma R, Malosetti M, van Eeuwijk FA, Haseneyer G, Kilian B, Graner A (2012) Genome-wide association studies for agronomical traits in a world-wide spring barley collection. BMC Plant Biol 12:16

    Article  PubMed Central  PubMed  Google Scholar 

  • Patterson N, Price AL, Reich D (2006) Population structure and eigenanalysis. PLoS Genet 2:e190

    Article  PubMed Central  PubMed  Google Scholar 

  • Podlich DW, Cooper M (1998) QU-GENE: a platform for quantitative analysis of genetic models. Bioinformatics 14:632–653

    Article  CAS  PubMed  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed Central  PubMed  Google Scholar 

  • Ramsay L, Comadran J, Druka A, Marshall DF, Thomas WTB, Macaulay M, MacKenzie K, Simpson CG, Fuller J, Bonar N, Hayes PM, Lundqvist U, Franckowiak JD, Close TJ, Muehlbauer G, Waugh R (2011) INTERMEDIUM-C, a modifier of lateral spikelet fertility in barley is an ortholog of the maize domestication gene TEOSINTE BRANCHED 1. Nat Genet 43:169–172

    Article  CAS  PubMed  Google Scholar 

  • Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, Doebley J, Kresovich S, Goodman MM, Buckler ES IV (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci U S A 98:11479–11484

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Rode J, Ahlemeyer J, Friedt W, Ordon F (2012) Identification of marker-trait associations in the German winter barley breeding gene pool (Hordeum vulgare L.). Mol Breed 30:831–843. doi:10.1007/s11032-011-9667-6

    Article  Google Scholar 

  • Rosenblum EB, Novembre J (2007) Ascertainment bias in spatially structured populations: a case study in the eastern fence lizard. J Hered 98:331–336

    Article  PubMed  Google Scholar 

  • Rostoks N, Mudie S, Cardle L, Russell JR, Ramsay L, Booth A, Svensson JT, Wanamaker SI, Walia H, Rodriguez EM, Hedley PE, Liu H, Morris J, Close TJ, Marshall DF, Waugh R (2005) Genome wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress. Mol Genet Genomics 274:515–527

    Article  CAS  PubMed  Google Scholar 

  • Rostoks N, Ramsay L, MacKenzie K, Cardle L, Bhat PR, Roose ML, Svensson JT, Stein N, Varshney RK, Marshall DF, Graner A, Close TJ, Waugh R (2006) Recent history of artificial outcrossing facilitates whole genome association mapping in elite crop varieties. Proc Natl Acad Sci U S A 103:18656–18661

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Roy JK, Smith KP, Muehlbauer GJ, Chao S, Close TJ, Steffenson BJ (2010) Association mapping of spot blotch resistance in wild barley. Mol Breed 26:243–256

    Article  PubMed Central  PubMed  Google Scholar 

  • Russell J, Booth A, Fuller JD, Baum M, Ceccarelli S, Grando S, Powell W (2003) Patterns of polymorphism detected in the chloroplast and nuclear genomes of barley landraces sampled from Syria and Jordan. Theor Appl Genet 107:413–421

    Article  CAS  PubMed  Google Scholar 

  • Russell J, Booth A, Fuller F, Harrower B, Hedley P, Machray G, Powell W (2004) A comparison of sequence-based polymorphism and haplotype content in transcribed and anonymous regions of the barley genome. Genome 47:389–398

    Article  CAS  PubMed  Google Scholar 

  • Russell JR, Dawson IK, Flavell AJ, Steffenson B, Weltzien E, Booth A, Ceccarelli S, Grando S, Waugh R (2011) Analysis of more than 1,000 SNPs in geographically-matched samples of landrace and wild barley indicates secondary contact and chromosome-level differences in diversity around domestication genes. New Phytol 191:564–578

    Article  PubMed  Google Scholar 

  • Schlotterer C, Harr B (2002) Single nucleotide polymorphisms derived from ancestral populations show no evidence for biased diversity estimates in Drosophila melanogaster. Mol Ecol 11:947–950

    Article  PubMed  Google Scholar 

  • Steffenson BJ, Olivera P, Roy JK, Jin Y, Smith KP, Muehlbauer GJ (2007) A walk on the wild side: mining wild wheat and barley collections for rust resistance genes. Aust J Agric Res 2007:532–544

    Article  Google Scholar 

  • Stein N, Perovic D, Kumlehn J, Pellio B, Stracke S, Streng S, Ordon F, Graner A (2005) The eukaryotic translation initiation factor 4E confers multiallelic recessive Bymovirus resistance in Hordeum vulgare (L.). Plant J 42:912–922

    Article  CAS  PubMed  Google Scholar 

  • Storz JF, Kelly JK (2008) Effects of spatially varying selection on nucleotide diversity and linkage disequilibrium: insights from deer mouse globin genes. Genetics 180:367–379

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Thomas WTB (2003) Prospects for molecular breeding of barley. Ann Appl Biol 142:1–12

    Article  CAS  Google Scholar 

  • Tian F, Bradbury PJ, Brown PJ, Hung H, Sun Q, Flint-Garcia S, Rocheford TR, McMullen MD, Holland JB, Buckler ES (2011) Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet 43:159–162

    Article  CAS  PubMed  Google Scholar 

  • Todesco M, Balasubramanian S, Hu TT, Traw MB, Horton M, Epple P, Kuhns C, Sureshkumar S, Schwartz C, Lanz C, Laitinen RAE, Huang Y, Chory J, Lipka V, Borevitz JO, Dangl JL, Bergelson J, Nordborg M, Weigel D (2010) Natural allelic variation underlying a major fitness trade-off in Arabidopsis thaliana. Nature 465:632–636

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Turner A, Beales J, Faure S, Dunford RP, Laurie DA (2005) The pseudo-response regulator Ppd-H1 provides adaptation to photoperiod in barley. Science 310:1031–1034

    Article  CAS  PubMed  Google Scholar 

  • von Zitzewitz J, Cuesta-Marcos A, Condon F, Castro AJ, Chao S, Corey A, Filichkin T, Fisk SP, Gutierrez L, Haggard K, Karsai I, Muehlbauer GJ, Smith KP, Veisz O, Hayes PM (2011) The genetics of winterhardiness in barley: perspectives from genome-wide association mapping. Plant Genome 4:76–91

    Article  Google Scholar 

  • VSN International (2011) GenStat for Windows (14th edn). VSN International, Hemel Hempstead (Web page: GenStat.co.uk)

    Google Scholar 

  • Wang M, Jiang N, Jia TY, Leach L, Cockram J, Comadran J, Shaw P, Waugh R, Luo ZW (2012) Genome-wide association mapping of agronomic and morphologic traits in highly structured populations of barley cultivars. Theor Appl Genet 124:233–246

    Article  PubMed  Google Scholar 

  • Waugh R, Jannink JL, Muehlbauer GJ, Ramsay L (2009) The emergence of whole genome association scans in barley. Curr Opin Plant Biol 12:218–222

    Article  CAS  PubMed  Google Scholar 

  • Waugh R, Marshall DF, Thomas WTB, Comadran J, Russell JR, Close T, Stein N, Hayes P, Muehlbauer G, Cockram J, O’Sullivan D, Mackay I, Flavell AJ, AGOUEB, BarleyCAP, Ramsay L (2010) Whole-genome association mapping in elite inbred crop varieties. Genome 53:967–972

    Google Scholar 

  • Wei F, Gobelman-Werner K, Morroll SM, Kurth J, Mao L, Wing R, Leister D, Schulze-Lefert P, Wise RP (1999) The Mla (powdery mildew) resistance cluster is associated with three NBS-LRR gene families and suppressed recombination within a 240-kb DNA interval on chromosome 5S (1HS) of barley. Genetics 153:1929–1948

    CAS  PubMed Central  PubMed  Google Scholar 

  • Yan L, Fu D, Li C, Blechl A, Tranquilli G, Bonafede M, Sanchez A, Valarik M, Yasuda S, Dubcovsky J (2006) The wheat and barley vernalization gene VRN3FT. Proc Natl Acad Sci U S A 103:19581–19586

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Yan J, Shah T, Warburton ML, Buckler ES, McMullen MD, Crouch J (2009) Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers. PLoS One 4:e8451

    Article  PubMed Central  PubMed  Google Scholar 

  • Yu J, Pressoir G, Briggs WH, Bi IV, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Holland JB, Kresovich S, Buckler ES (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203–208

    Article  CAS  PubMed  Google Scholar 

  • Zhang LY, Marchand S, Tinker NA, Belzile F (2009) Population structure and linkage disequilibrium in barley assessed by DArT markers. Theor Appl Genet 119:43–52

    Article  CAS  PubMed  Google Scholar 

  • Zhang Z, Eroz E, Lai C-Q, Todhunter HK, Gore MA, Bradbury PJ, Yu J, Arnett DK, Ordovas JM, Buckler ES (2010) Mixed linear model approach adapted for genome-wide association studies. Nat Genet 42:355–360

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Zhou H, Muehlbauer G, Steffenson B (2012) Population structure and linkage disequilibrium in elite barley breeding germplasm from the United States. J Zhejiang Univ Sci B 13:438–451

    Article  PubMed Central  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland

    Robbie Waugh, Bill Thomas, Luke Ramsay & Joanne Russell

  2. Division of Plant Sciences, The University of Dundee, JHI Campus, Invergowrie, Dundee, DD2 DA, Scotland

    Robbie Waugh & Andrew Flavell

  3. LIMAGRAIN Europe, BP1, 63720, Chappes, France

    Jordi Comadran

Authors
  1. Robbie Waugh
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Bill Thomas
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Andrew Flavell
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Luke Ramsay
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jordi Comadran
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Joanne Russell
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Robbie Waugh .

Editor information

Editors and Affiliations

  1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany

    Jochen Kumlehn

  2. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany

    Nils Stein

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Waugh, R., Thomas, B., Flavell, A., Ramsay, L., Comadran, J., Russell, J. (2014). Genome-Wide Association Scans (GWAS). In: Kumlehn, J., Stein, N. (eds) Biotechnological Approaches to Barley Improvement. Biotechnology in Agriculture and Forestry, vol 69. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-44406-1_18

Download citation

Publish with us

Policies and ethics

Search

Navigation