Population structure revealed by different marker types (SSR or DArT) has an impact on the results of genome-wide association mapping in European barley cultivars

Ayoub M, Symons SJ, Edney MJ, Mather DE (2002) QTLs affecting kernel size and shape in a two-rowed by six-rowed barley cross. Theor Appl Genet 105:237–247

Barr AR, Jeffries SP, Broughton S, Chalmers KJ, Kretschmer JM, Boyd WJR, Collins HM, Roumeliotis S, Logue SJ, Coventry SJ, Moody DB, Read BJ, Poulsen D, Lance RCM, Platz GJ, Park RF, Panozzo JF, Karakousis A, Lim P, Verbyla AP, Eckermann PJ (2003a) Mapping and QTL analysis of the barley population Alexis × Sloop. Aust J Agric Res 54:1117–1123

Barr AR, Karakousis A, Lance RCM, Logue SJ, Manning S, Chalmers KJ, Kretschmer JM, Boyd WJR, Collins HM, Roumeliotis S, Coventry SJ, Moody DB, Read BJ, Poulsen D, Li CD, Platz GJ, Inkerman PA, Panozzo JF, Cullis BR, Smith AB, Lim P, Langridge P (2003b) Mapping and QTL analysis of the barley population Chebec × Harrington. Aust J Agric Res 54:1125–1130

Beattie AD, Edney MJ, Scoles GJ, Rossnagel BG (2010) Association mapping of malting quality data from Western Canadian two-row barley cooperative trials. Crop Sci 50:1649–1663

Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57:289–300

Bezant J, Laurie D, Pratchett N, Chojecki J, Kearsey M (1997) Mapping QTL controlling yield and yield components in a spring barley (Hordeum vulgare L.) cross using marker regression. Mol Breed 3:29–38

Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331

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

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

Camus-Kulandaivelu L, Veyrieras J, Gouesnard B, Charcosset A, Manicacci D (2007) Evaluating the reliability of structure outputs case of relatedness between individuals. Crop Sci 47:887–890

Cleveland WS (1979) Robust locally weighted regression and smoothing scatterplots. J Am Stat Assoc 74:829–836

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

Comadran J, Ramsay L, MacKenzie K, Hayes P, Close TJ, Muehlbauer G, Stein N, Waugh R (2011) Patterns of polymorphism and linkage disequilibrium in cultivated barley. Theor Appl Genet. doi: 10.1007/s00122-010-1466-7

Falush D, Stephens M, Pritchard JK (2003) Inference of population structure: extensions to linked loci and correlated allele frequencies. Genetics 164:1567–1587

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

Hamblin MT, Warburton ML, Buckler ES (2007) Empirical comparison of simple sequence repeats and single nucleotide polymorphisms in assessment of maize diversity and relatedness. PLoS One 2(12):e1367

Han F, Romagosa I, Ullrich SE, Jones BL, Hayes PM, Wesenberg DM (1997a) Molecular marker-assisted selection for malting quality traits in barley. Mol Breed 3:427–437

Han F, Ullrich SE, Kleinhofs A, Jones BL, Hayes PM, Wesenberg DM (1997b) Fine structure mapping of the barley chromosome-1 centromere region containing malting-quality QTLs. Theor Appl Genet 95:903–910

Hardy OJ, Vekemans X (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes 2:618–620

Haseneyer G, Stracke S, Paul C, Einfeldt C, Broda A, Piepho HP, Graner A, Geiger HH (2009) Population structure and phenotypic variation of a spring barley world collection set up for association studies. Plant Breed 129(3):271–279

Hayes PM, Liu BH, Knapp SJ, Chen F, Jones B, Blake T, Franckowiak J, Rasmusson D, Sorrells M, Ulrich SE, Wesenberg D, Kleinhofs A (1993) Quantitative trait locus effects and environmental interaction in a sample of North American barley germplasm. Theor Appl Genet 87:392–401

Herz MP (2000) Kartierung quantitativer vererbter Eigenschaften einschließlich Brauqualität und Resistenz gegen Krankheiten mit molekularen Markern in Gerste. PhD-Thesis. Technische Universität München (TUM), Lehrstuhl für Pflanzenzüchtung

Hill WG, Robertson A (1968) Linkage disequilibrium in finite populations. Theor Appl Genet 38:226–231

Holm S (1979) A simple sequentially rejective multiple test procedure. Scand J Stat 6(2):65–70

Jaccard P (1908) Nouvelles recherches sur la distribution florale. Bull Soc Vaud Sci Nat 44:223–270

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

Kennedy BW, Quinton M, Vanarendonk JAM (1992) Estimation of effects of single genes on quantitative traits. J Anim Sci 70:2000–2012

Kjaer B, Jensen J (1996) Quantitative trait loci for grain yield and yield components in a cross between a six-rowed and a two-rowed barley. Euphytica 90:39–48

Krumnacker K (2009) Untersuchung der funktionellen Assoziation von Kandidatengenen in Zusammenhang mit der Malzqualität der Gerste durch Transkriptomkartierung. PhD-Thesis. Technische Universität München (TUM), Lehrstuhl für Pflanzenzüchtung

Larson SR, Habernicht DK, Blake TK, Adamson M (1997) Backcross gains for six-rowed grain and malt qualities with introgression of a feed barley yield QTL. J Am Soc Brew Chem 55:52–57

Li JZ, Huang XQ, Heinrichs F, Ganal MW, Röder MS (2005) Analysis of QTLs for yield, yield components, and malting quality in a BC3-DH population of spring barley. Theor Appl Genet 110:356–363

Liu K, Muse SV (2005) PowerMarker: integrated analysis environment for genetic marker data. Bioinformatics 21(9):2128–2129

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

Marquez-Cedillo LA, Hayes PM, Jones BL, Kleinhofs A, Legge WG, Rossnagel BG, Sato K, Ullric E, Wesenberg DM (2000) QTL analysis of malting quality in barley based on doubled-haploid progeny of two elite North American varieties representing different germplasm pools. Theor Appl Genet 101:173–184

Marquez-Cedillo LA, Hayes PM, Kleinhofs A, Legge WG, Rossnagel BG, Sato K, Ullrich SE, Wesenberg DM (2001) QTL analysis of agronomic traits in barley based on the doubled haploid progeny of two elite North American varieties representing different germplasm groups. Theor Appl Genet 103:625–637

Mather DE, Tinker NA, LaBerge DE, Edney M, Jones BL, Rossnagel BG, Legge WG, Briggs KG, Irvine RB, Falk DE, Kasha KJ (1997) Regions of the genome that affect grain and malt quality in a North American two-row barley cross. Crop Sci 37:544–554

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

Matthies IE, Weise S, Förster J, Röder MS (2009b) Association mapping and marker development of the candidate genes (1→3),(1→4)-β-d-Glucan-4-glucanohydrolase and (1→4)-β-Xylan-endohydrolase 1 for malting quality in barley. Euphytica 170:109–122

Mezmouk S, Dubreuil P, Bosio M, Décousset L, Charcosset A, Praud S, Mangin B (2011) Effect of population structure corrections on the results of association mapping tests in complex maize diversity panels. Theor Appl Genet 122:1149–1160

Nei M, Li WH (1979) Mathematical models for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76:5269–5273

Oziel A, Hayes PM, Chen FQ, Jones B (1996) Application of quantitative trait locus mapping to the development of winter-habit malting barley. Plant Breed 115:43–51

Plaschke J, Ganal MW, Röder MS (1995) Detection of genetic diversity in closely related bread wheat using microsatellite markers. Theor Appl Genet 91:1001–1007

Pourkheirandish M, Komatsuda T (2007) The importance of barley genetics and domestication in a global perspective. Ann Bot 100:999–1008

Pritchard JK, Rosenberg NA (1999) Use of unlinked genetic markers to detect population stratification in association studies. Am J Hum Genet 65:220–228

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

Pswarayi A, van Eeuwijk FA, Ceccarelli S, Grando S, Comadran J, Russell JR, Pecchioni N, Tondelli A, Akar T, Al-Yassin A, Benbelkacem A, Ouabbou H, Thomas WTB, Romagosa I (2008) Changes in allele frequencies in landraces, old and modern barley cultivars of marker loci close to QTL for grain yield under high and low input conditions. Euphytica 163:435–447

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

Ritland K (1996) Estimators for pairwise relatedness and individual inbreeding coefficients. Genet Res 67:175–186

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

Russell JR, Ellis RP, Thomas WTB, Waugh R, Provan J, Booth A, Fuller J, Lawrence P, Young G, Powell W (2000) A retrospective analysis of spring barley germplasm development from ‘foundation genotypes’ to currently successful cultivars. Mol Breed 6:553–568

Russell J, Booth A, Fuller J, 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

Schmalenbach I, Léon J, Pillen K (2009) Identifcation and verification of QTLs for agronomic traits using wild barley introgression lines. Theor Appl Genet 118:483–497

Searle SR (1987) Linear models for unbalanced data. Wiley, New York

Smith JSC, Kresovich S, Hopkins MS, Mitchell SE, Dean RE, Woodman WL, Lee M, Porter K (2000) Genetic diversity among elite Sorghum inbred lines assessed with simple sequence repeats. Crop Sci 40:226–232

Sneath PHA (1957) Some thoughts on bacterial classification. J Gen Microbiol 17:184–200

Stracke S, Haseneyer G, Veyrieras JB, Geiger HH, Sauer S, Graner A, Piepho HP (2009) Association mapping reveals gene action and interactions in the determination of flowering time in barley. Theor Appl Genet 118(2):259–273

Szücs P, Blake VC, Bhat PR, Chao S, Close TJ, Cuesta-Marcos A, Muehlbauer GJ, Ramsay L, Waugh R, Hayes PM (2009) An integrated resource for barley linkage map and malting quality QTL alignment. Plant Genome 2:134–140

Tinker NA, Mather DE, Rossnagel BG, Kasha KJ, Kleinhofs A, Hayes PM, Falk DE, Ferguson T, Shugar LP, Legge WG, Irvine RB, Choo TM, Briggs KG, Ullrich SE, Franckowiak JD, Blake TK, Graf RJ, Dofing SM, Saghai Maroof MA, Scoles GJ, Hoffman D, Dahleen LS, Kilian A, Chen F, Biyashev RM, Kudrna DA, Steffenson BJ (1996) Regions of the genome that affect agronomic performance in two-row barley. Crop Sci 36:1053–1062

Ullrich SE, Han F (1997) Genetic complexity of the malt extract trait in barley suggested by QTL analysis. J Am Soc Brew Chem 55(1):1–4

van Hintum TJL (2007) Data resolution: a jackknife procedure for determining the consistency of molecular marker datasets. Theor Appl Genet 115:343–349

van Inghelandt D, Melchinger AE, Lebreton C, Stich B (2010) Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers. Theor Appl Genet 120:1289–1299

Varshney RK, Marcel TC, Ramsay L, Russell J, Röder MS, Stein N, Waugh R, Langridge P, Niks RE, Graner A (2007) A high density barley microsatellite consensus map with 775 SSR loci. Theor Appl Genet 114:1091–1103

Waugh R, Jannink JL, Muehlbauer GL, Ramsay L (2009) The emergence of whole genome association scans in barley. Curr Opin Plant Biol 12:1–5

Weir BS (1996) Genetic data analysis II. Sinauer, Massachusetts

Weise S, Scholz U, Röder MS, Matthies IE (2009) A comprehensive database of malting quality traits in brewing barley. Barley Genet Newsl 39:1–4

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

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

Wenzl P, Raman H, Wang J, Zhou M, Huttner E, Kilian A (2007) A DArT platform for quantitative bulked segregant analysis. BMC Genomics 8:196

Worch S, Kalladan R, Harshavardhan VT, Pietsch C, Korzun V, Kuntze L, Börner A, Wobus U, Röder MS, Sreenivasulu N (2011) Haplotyping, linkage mapping and expression analysis of barley genes regulated by terminal drought stress influencing seed quality. BMC Plant Biol 11:1

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

Yu J, Pressoir G, Briggs WH, Vroh Bi I, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, 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

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(1):63–77

Zhang LY, Marchand S, Tinker NA, Belzile F (2009) Population structure and linkage disequilibrium in barley assessed by DArT markers. Theor Appl Genet 119(1):43–52