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Genome-wide association mapping: a case study in bread wheat (Triticum aestivum L.)

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Abstract

Association-based trait mapping is an innovative methodology based on linkage disequilibrium. Studies in plants, especially in cereals, are rare. A genome-wide association study of wheat is reported, in which a large number of diversity array technology markers was used to genotype a winter wheat core collection of 96 accessions. The germplasm was structured into two sub-populations. Twenty agronomic traits were measured in field trials conducted over up to eight growing seasons. Association analysis was performed with two different approaches, the general linear model incorporating the Q-matrix only and the mixed linear model including also the kinship-matrix. In total, 385 marker–trait associations significant in both models were detected. The intrachromosomal location of many of these coincided with those of known major genes or quantitative trait loci, but others were detected in regions where no known genes have been located to date. These latter presumptive loci provide opportunities for further wheat improvement, based on a marker approach.

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References

  • Agrama HA, Eizenga GC, Yan W (2007) Association mapping of yield and its components in rice cultivars. Mol Breed 19:341–356

    Article  Google Scholar 

  • Aranzana MJ, Kim S, Zhao K, Bakker E, Horton M et al (2005) Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet 1(5):e60

    Article  PubMed  Google Scholar 

  • Blanco A, De Giovanni C, Laddomada B, Sciancalepore A, Simeone R, Devos KM, Gale MD (1996) Quantitative trait loci influencing grain protein content in tetraploid wheats. Plant Breed 115:310–316

    Article  Google Scholar 

  • Blanco A, Bellomo MP, Lotti C, Manglio T, Pasqualone A, Simeone R, Troccoli A, Di Fonzo N (1998) Genetic mapping of sedimentation volume across environments using recombinant inbred lines of durum wheat. Plant Breed 117:413–417

    Article  Google Scholar 

  • Börner A, Schumann E, Fürste A, Cöster H, Leithold B, Röder MS, Weber WE (2002) Mapping of quantitative trait loci determining agronomic important characters in hexaploid wheat (Triticum aestivum L.). Theor Appl Genet 105:921–936

    Article  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 

  • Breseghello F, Sorrells ME (2006a) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172:1165–1177

    Article  PubMed  Google Scholar 

  • Breseghello F, Sorrells ME (2006b) Association analysis as a strategy for improvement of quantitative traits in plants. Crop Sci 46:1323–1330

    Article  Google Scholar 

  • Cadalen T, Sourdille P, Charmet G, Tixier MH, Gay G, Boeuf C, Bernard S, Leroy P, Bernard M (1998) Molecular markers linked to genes affecting plant height in wheat using a doubled-haploid population. Theor Appl Genet 96:933–940

    Article  CAS  Google Scholar 

  • Comadran J, Thomas WTB, 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 

  • Crossa J, Burgueno J, Dreisigacker S, Vargas M, Herrera-Foessel SA, Lillemo M, Singh RP, Trethowan R, Warburton M, Franco J, Reynolds M, Crouch JH, Ortiz R (2007) Association analysis of historical bread wheat germplasm using additive genetic covariance of relatives and population structure. Genetics 177:1889–1913

    Article  CAS  PubMed  Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    Article  CAS  PubMed  Google Scholar 

  • Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587

    CAS  PubMed  Google Scholar 

  • Flint-Garcia SA, Thornsberry JM, Buckler ES IV (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54:357–374

    Article  CAS  PubMed  Google Scholar 

  • Gervais L, Dedryver F, Morlais J-Y, Bodusseau V, Negre S, Bilous M, Groos C, Trottet M (2003) Mapping of quantitative trait loci for field resistance to Fusarium head blight in an European winter wheat. Theor Appl Genet 106:961–970

    CAS  PubMed  Google Scholar 

  • Huang XQ, Cloutier S, Lycar L, Radovanovic N, Humphreys DG, Noll JS, Somers DJ, Brown PD (2006) Molecular detection of QTLs for agronomic and quality traits in a doubled haploid population derived from two Canadian wheats (Triticum aestivum L.). Theor Appl Genet 113:753–766

    Article  CAS  PubMed  Google Scholar 

  • ICC (2008) http://www.icc.or.at/methods3.php

  • Ivandic V, Hackett CA, Nevo E, Keith R, Thomas WTB, Forster BP (2002) Analysis of simple sequence repeats (SSRs) in wild barley from the fertile crescent: associations with ecology, geography and flowering time. Plant Mol Biol 48:511–527

    Article  CAS  PubMed  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  Google Scholar 

  • Kang HM, Zaitlen NA, Wade CM, Kirby A, Heckermann D, Daly MJ, Eskin E (2008) Efficient control of population structure in model organism association mapping. Genetics 178:1709–1723

    Article  PubMed  Google Scholar 

  • Kobiljski B, Quarrie S, Denčić S, Kirby J, Ivegěs M (2002) Genetic diversity of the Novi Sad Wheat collection revealed by microsatellites. Cell Mol Biol Lett 7:685–694

    CAS  PubMed  Google Scholar 

  • Kraakman ATW, Niks RE, Van den Berg PM, 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  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 

  • Kuchel H, Hollambi G, Langridge P, Williams K, Jefferies SP (2006) Identification of genetic loci associated with ear emergence in bread wheat. Theor Appl Genet 113:1103–1112

    Article  CAS  PubMed  Google Scholar 

  • Kumar N, Kulwal PL, Balyan HS, Gupta PK (2007) QTL mapping for yield and yield contributing traits in two mapping populations of bread wheat. Mol Breed 19(2):63–177

    Article  Google Scholar 

  • Laurie DA, Pratchett N, Bezant J, Snape JW (1995) RFLP mapping of five major genes and eight quantitative trait loci controlling flowering time in a winter × spring barley (Hordeum vulgare L.) cross. Genome 38:575–585

    CAS  PubMed  Google Scholar 

  • Leonova I, Pestsova E, Salina E, Efremova T, Röder M, Börner A (2003) Mapping of the Vrn-B1 gene in Triticum aestivum using microsatellite markers. Plant Breed 122:209–212

    Article  CAS  Google Scholar 

  • Maccaferri M, Sanguineti MC, Noli E, Tuberosa R (2005) Population structure and long-range linkage disequilibrium in a durum wheat elite collection. Mol Breed 15:271–289

    Article  CAS  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. doi:10.1186/1471-2156-7-6

    Article  PubMed  Google Scholar 

  • Matthies IE, Weise S, Röder MS (2008) Association of haplotype diversity in the a-amylase gene amy1 with malting quality parameters in barley. Mol Breed 23(1):139–152

    Article  Google Scholar 

  • McCartney CA, Somers DJ, Humphreys DG, Lukow O, Ames N, Noll J, Cloutier S, McCallum BD (2005) Mapping quantitative trait loci controlling agronomic traits in the spring wheat cross RL4452 × ‘AC Domain’. Genome 48:870–883

    CAS  PubMed  Google Scholar 

  • McIntosh RA, Yamazaki Y, Dubcovsky J, Rogers J, Morris C, Somers DJ, Apples R, Devos KM (2008) Catalogue of gene symbols for wheat. http://www.shigen.nig.ac.jp/wheat/komugi/genes/symbolClassList.jsp

  • Miura H, Nakagawa M, Worland AJ (1999) Control of ear emergence time by chromosome 3A of wheat. Plant Breed 118:85–87

    Article  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Quarrie SA, Dodig D, Pekiç S, Kirby J, Kobiljski B (2003) Prospects for marker-assisted selection of improved drought responses in wheat. Bulg J Plant Physiol (special issue):83–95

  • Quarrie SA, Steed A, Calestani C, Semikhodskii A, Lebreton C, Chinoy C, Steele N, Pljevljakusic D, Waterman E, Weyen J, Schondelmaier J, Habash DZ, Farmer P, Saker L, Clarkson DT, Abugalieva A, Yessimbekova M, Turuspekov Y, Abugalieva S, Tuberosa R, Sanguineti MC, Hollington PA, Aragues R, Royo A, Dodig D (2005) A high-density genetic map of hexaploid wheat (Triticum aestivum L.) from the cross Chinese Spring × SQ1 and its use to compare QTLs for grain yield across a range of environments. Theor Appl Genet 110:865–880

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Rostoks N, Mudie S, Cardle L, Russell J, 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 Genom 274:515–527

    Article  CAS  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 inbred crop varieties. Proc Natl Acad Sci USA 103:18656–18661

    Article  CAS  PubMed  Google Scholar 

  • Roy JK, Bandopadhyay R, Rustgi S, Balyan HS, Gupta PK (2006) Association analysis of agronomically important traits using SSR, SAMPL and AFLP markers in bread wheat. Curr Sci 90:683–689

    CAS  Google Scholar 

  • Skøt L, Humphreys MO, Armstead I, Heywood S, Skøt KP, Sanderson R, Thomas ID, Chorlton KH, Hamilton NRS (2004) An association mapping approach to identify flowering time genes in natural populations of Lolium perenne (L.). Mol Breed 15:233–245

    Article  Google Scholar 

  • Snape JW, Law CN, Worland AJ (1977) Whole chromosome analysis of height in wheat. Heredity 38:25–26

    Article  Google Scholar 

  • Somers D, Banks T, DePauw R, Fox S, Clarke J, Pozniak C, McCartney C (2007) Genome-wide linkage disequilibrium analysis in bread wheat and durum wheat. Genome 50(6):557–567. doi:10.1139/G07-031

    Article  CAS  PubMed  Google Scholar 

  • Stich B, Melchinger AE, Frisch M, Maurer HP, Heckenberger M, Reif J (2005) Linkage disequilibrium in European elite maize germplasm investigated with SSRs. Theor Appl Genet 111:723–730

    Article  PubMed  Google Scholar 

  • Stich B, Möhring J, Piepho H-P, Heckenberger M, Buckler ES, Melchinger AE (2008) Comparison of mixed-model approaches for association mapping. Genetics 178:1745–1754

    Article  PubMed  Google Scholar 

  • Tommasini L, Schnurbusch T, Fossati D, Mascher F, Keller B (2007) Association mapping of Stagonospora nodorum blotch resistance in modern European winter wheat varieties. Theor Appl Genet 115:697–708

    Article  CAS  PubMed  Google Scholar 

  • Tóth B, Galiba G, Fehér E, Sutka J, Snape JW (2003) Mapping genes affecting flowering time and frost resistance on chromosome 5B of wheat. Theor Appl Genet 107:509–514

    Article  PubMed  Google Scholar 

  • UN Country Code (2009) http://unstats.un.org/unsd/methods/m49/m49alpha.htm

  • Weir BS (1996) Genetic data analysis II: methods for discrete population genetic data. Sinauer Associates Inc., Sunderland

    Google Scholar 

  • Wenzl P, Carling J, Kudrna D, Jaccoud D, Huttner E, Kleinhofs A, Kilian A (2004) Diversity arrays technology (DArT) for whole-genome profiling of barley. Proc Natl Acad Sci USA 101(26):9915–9920

    Article  CAS  PubMed  Google Scholar 

  • Wenzl P, Li H, Carling J, Zhou M, Raman H, Paul E, Hearnden P, Maier C, Xia L, Caig V, Ovesná J, Cakir M, Poulsen D, Wang J, Raman R, Smith KP, Muehlbauer GJ, Chalmers KJ, Kleinhofs A, Huttner E, Kilian A (2006) A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits. BMC Genomics 7:206. doi:10.1186/1471-2164-7-206

    Article  PubMed  Google Scholar 

  • Yu J, Buckler ES (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotechnol 17:155–160

    CAS  PubMed  Google Scholar 

  • Yu J, Pressoir G, Briggs WH, Vroh Bi I, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB et al (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 

  • Yu J, Zhang Z, Zhu C, Tabanao DA, Pressoir G, Tuinstra MR, Kresovich S, Todhunter RJ, Buckler ES (2009) Simulation appraisal of the adequacy of number of background markers for relationship estimation in association mapping. Plant Genome 2:63–77. doi:10.3835/plantgenome2008.09.0009

    Article  CAS  Google Scholar 

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Acknowledgments

The authors thank Susanne Dreisigacker, CIMMT, Mexico for providing the mapping data as well as Inge Matthies, IPK Gatersleben, Germany for her constructive discussions during the course of study.

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Authors and Affiliations

  1. Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Corrensstraße 3, 06466, Gatersleben, Germany

    K. Neumann & A. Börner

  2. Institute of Field and Vegetable Crops, M. Gorkog 30, 21000, Novi Sad, Serbia

    B. Kobiljski & S. Denčić

  3. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502 324, India

    R. K. Varshney

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  1. K. Neumann
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  2. B. Kobiljski
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  3. S. Denčić
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  4. R. K. Varshney
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  5. A. Börner
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Correspondence to A. Börner.

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Neumann, K., Kobiljski, B., Denčić, S. et al. Genome-wide association mapping: a case study in bread wheat (Triticum aestivum L.). Mol Breeding 27, 37–58 (2011). https://doi.org/10.1007/s11032-010-9411-7

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  • DOI: https://doi.org/10.1007/s11032-010-9411-7

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