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On-line Access: 2012-06-06

Received: 2011-12-31

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Journal of Zhejiang University SCIENCE B 2012 Vol.13 No.6 P.438-451


Population structure and linkage disequilibrium in elite barley breeding germplasm from the United States

Author(s):  Hao Zhou, Gary Muehlbauer, Brian Steffenson

Affiliation(s):  Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA; more

Corresponding email(s):   zhoux222@umn.edu

Key Words:  Association mapping (AM), Structure, Linkage disequilibrium (LD)

Hao Zhou, Gary Muehlbauer, Brian Steffenson. Population structure and linkage disequilibrium in elite barley breeding germplasm from the United States[J]. Journal of Zhejiang University Science B, 2012, 13(6): 438-451.

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author="Hao Zhou, Gary Muehlbauer, Brian Steffenson",
journal="Journal of Zhejiang University Science B",
publisher="Zhejiang University Press & Springer",

%0 Journal Article
%T Population structure and linkage disequilibrium in elite barley breeding germplasm from the United States
%A Hao Zhou
%A Gary Muehlbauer
%A Brian Steffenson
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%P 438-451
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%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.B1200003

T1 - Population structure and linkage disequilibrium in elite barley breeding germplasm from the United States
A1 - Hao Zhou
A1 - Gary Muehlbauer
A1 - Brian Steffenson
J0 - Journal of Zhejiang University Science B
VL - 13
IS - 6
SP - 438
EP - 451
%@ 1673-1581
Y1 - 2012
PB - Zhejiang University Press & Springer
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DOI - 10.1631/jzus.B1200003

Cultivated barley is known to have a complex population structure and extensive linkage disequilibrium (LD). To conduct robust association mapping (AM) studies of economically important traits in US barley breeding germplasm, population structure and LD decay were examined in a complete panel of US barley breeding germplasm (3840 lines) genotyped with 3072 single nucleotide polymorphisms (SNPs). Nine subpopulations (sp1‒sp9) were identified by the program structure and subsequently confirmed by principle component analysis (PCA). Out of the nine subpopulations, seven were very similar to the respective subpopulations identified by Hamblin et al. (2010) which were based on half of the germplasm and half of the SNP markers, but two subpopulations were found to be new. One subpopulation was dominated by six-rowed spring lines from Utah State University (UT) and the other was composed of six-rowed spring lines from multiple breeding programs (USDA-ARS Aberdeen (AB), Busch Agricultural Resources Inc. (BA), UT, and Washington State University (WA)). LD was found to decay across a range from 4.0 to 19.8 cM. This result indicates that the germplasm genotyped with 3072 SNPs would be robust for mapping and possibly identifying the causal polymorphisms contributing to disease resistance and perhaps other traits.

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article


[1]Atwell, S., Huang, Y.S., Vilhjálmsson, B.J., Willems, G., Horton, M., Li, Y., Meng, D., Platt, A., Tarone, A.M., Hu, T.T., 2010. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature, 465(7298):627-631.

[2]Barrett, J.C., Fry, B., Maller, J., Daly, M.J., 2005. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics, 21(2):263-265.

[3]Bhangale, T.R., Rieder, M.J., Nickerson, D.A., 2008. Estimating coverage and power for genetic association studies using near-complete variation data. Nat. Genet., 40(7):841-843.

[4]Boyko, A.R., Boyko, R.H., Boyko, C.M., Parker, H.G., Castelhano, M., Corey, L., Degenhardt, J.D., Auton, A., Hedimbi, M., Kityo, R., 2009. Complex population structure in African village dogs and its implications for inferring dog domestication history. PNAS, 106(33):13903-13908.

[5]Bradbury, P.J., Zhang, Z., Kroon, D.E., Casstevens, T.M., Ramdoss, Y., Buckler, E.S., 2007. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics, 23(19):2633-2635.

[6]Breseghello, F., Sorrells, M.E., 2006. Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics, 172(2):1165-1177.

[7]Chao, S., Zhang, W., Dubcovsky, J., Sorrells, M., 2007. Evaluation of genetic diversity and genome-wide linkage disequilibrium among US wheat (Triticum aestivum L.) germplasm representing different market classes. Crop Sci., 47(3):1018-1030.

[8]Cleveland, W.S., 1979. Robust locally weighted regression and smoothing scatterplots. J. Am. Stat. Assoc., 74(368):829-836.

[9]Close, T.J., Bhat, P.R., Lonardi, S., Wu, Y., Rostoks, N., Ramsay, L., Druka, A., Stein, N., Svensson, J.T., Wanamaker, S., et al., 2009. Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics, 10(1):582.

[10]Comadran, J., Thomas, W.T.B., van Eeuwijk, F.A., Ceccarelli, S., Grando, S., Stanca, A.M., Pecchioni, N., Akar, T., Al-Yassin, A., Benbelkacem, A., 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(1):175-187.

[11]Condón, F., Gustus, C., Rasmusson, D.C., Smith, K.P., 2008. Effect of advanced cycle breeding on genetic diversity in barley breeding germplasm. Crop Sci., 48(3):1027-1036.

[12]Cornuet, J.M., Luikart, G., 1996. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics, 144(4):2001-2014.

[13]D′Hoop, B.B., Paulo, M.J., Mank, R.A., van Eck, H.J., van Eeuwijk, F.A., 2008. Association mapping of quality traits in potato (Solanum tuberosum L.). Euphytica, 161(1-2):47-60.

[14]Dragalin, V., Fedorov, V., Patterson, S., Jones, B., 2003. Kullback-Leibler divergence for evaluating bioequivalence. Stat. Med., 22(6):913-930.

[15]Ewens, W.J., Spielman, R.S., 1995. The transmission/ disequilibrium test: history, subdivision, and admixture. Am. J. Hum. Genet., 57(2):455-464.

[16]Falush, D., Stephens, M., Pritchard, J.K., 2003. Inference of population structure using multilocus genotype data linked loci and correlated allele frequencies. Genetics, 164(4):1567-1587.

[17]Fan, J.B., Oliphant, A., Shen, R., Kermani, B.G., Garcia, F., Gunderson, K.L., Hansen, M., Steemers, F., Butler, S.L., Deloukas, P., et al., 2003. Highly parallel SNP genotyping. Cold Spring Harb. Symp. Quant. Biol., 68:69-78.

[18]Flint-Garcia, S.A., Thornsberry, J.M., 2003. Structure of linkage disequilibrium in plants. Annu. Rev. Plant Biol., 54(1):357-374.

[19]Frazer, K.A., Ballinger, D.G., Cox, D.R., Hinds, D.A., Stuve, L.L., Gibbs, R.A., Belmont, J.W., Boudreau, A., Hardenbol, P., Leal, S.M., 2007. A second generation human haplotype map of over 3.1 million SNPs. Nature, 449(7164):851-861.

[20]González-Martínez, S.C., Wheeler, N.C., Ersoz, E., Nelson, C.D., Neale, D.B., 2007. Association genetics in Pinus taeda L. I. Wood property traits. Genetics, 175(1):399-409.

[21]Gunderson, K.L., Kruglyak, S., Graige, M.S., Garcia, F., Kermani, B.G., Zhao, C., Che, D., Dickinson, T., Wickham, E., Bierle, J., 2004. Decoding randomly ordered DNA arrays. Genome Res., 14(5):870-877.

[22]Haldane, J.B.S., 1919. The combination of linkage values and the calculation of distances between the loci of linked factors. J. Genet., 8(29):309-320.

[23]Hamblin, M.T., Close, T.J., Bhat, P.R., Chao, S., Kling, J.G., Abraham, K.J., Blake, T., Brooks, W.S., Cooper, B., Griffey, C.A., et al., 2010. Population structure and linkage disequilibrium in US barley germplasm: implications for association mapping. Crop Sci., 50(2):556-566.

[24]Horsley, R.D., Schwarz, P.B., Hammond, J.J., 1995. Genetic diversity in malt quality of North American six-rowed spring barley. Crop Sci., 35(1):113-118.

[25]Hyten, D.L., Choi, I.Y., Song, Q., Shoemaker, R.C., Nelson, R.L., Costa, J.M., Specht, J.E., Cregan, P.B., 2007. Highly variable patterns of linkage disequilibrium in multiple soybean populations. Genetics, 175(4):1937-1944.

[26]Jannink, J.L., Walsh, B., 2002. Association Mapping in Plant Populations. In: Kang, M.S. (Ed.), Quantitative Genetics Genomics and Plant Breeding. CAB International, Wallingford, UK, p.59-68.

[27]Jolliffe, I., 2002. Principal Component Analysis. Springer-Verlag, New York, NY.

[28]Kang, H.M., Sul, J.H., 2010. Variance component model to account for sample structure in genome-wide association studies. Nat. Genet., 42(4):348-354.

[29]Kang, H.M., Zaitlen, N.A., Wade, C.M., Kirby, A., Heckerman, D., Daly, M.J., Eskin, E., 2008. Efficient control of population structure in model organism association mapping. Genetics, 178(3):1709-1723.

[30]Ku, C.S., Loy, E.Y., Pawitan, Y., Chia, K.S., 2010. The pursuit of genome-wide association studies: where are we now? J. Hum. Genet., 55(4):195-206.

[31]Malysheva-Otto, L.V., Ganal, M.W., Roder, M.S., 2006. Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.). BMC Genet., 7(1):6-18.

[32]Mangin, B., Siberchicot, A., Nicolas, S., Doligez, A., This, P., Cierco-Ayrolles, C., 2012. Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness. Heredity, 108(3):285-291.

[33]Martin, J.M., 1991. Diversity among North American spring barley cultivars based on coefficients of parentage. Crop Sci., 31(5):1131-1137.

[34]Massman, J., Cooper, B., Horsley, R., Neate, S., Dill-Macky, R., Chao, S., Dong, Y., Schwarz, P., Muehlbauer, G.J., Smith, K.P., 2011. Genome-wide association mapping of Fusarium head blight resistance in contemporary barley breeding germplasm. Mol. Breed., 27(4):439-454.

[35]McVean, G., 2009. A genealogical interpretation of principal components analysis. PLoS Genet., 5(10):e1000686.

[36]Metzker, M.L., 2009. Sequencing technologies—the next generation. Nat. Rev. Genet., 11(1):31-46.

[37]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(6):1149-1160.

[38]Mikel, M.A., Kolb, F.L., 2008. Genetic diversity of contemporary North American barley. Crop Sci., 48(4):1399-1407.

[39]Nordborg, M., Borevitz, J.O., Bergelson, J., Berry, C.C., Chory, J., Hagenblad, J., Kreitman, M., Maloof, J.N., Noyes, T., Oefner, P.J., 2002. The extent of linkage disequilibrium in Arabidopsis thaliana. Nat. Genet., 30(2):190-193.

[40]Palaisa, K., Morgante, M., Tingey, S., Rafalski, A., 2004. Long-range patterns of diversity and linkage disequilibrium surrounding the maize Y1 gene are indicative of an asymmetric selective sweep. PNAS, 101(26):9885-9890.

[41]Pallotta, M.A., Asayama, S., Reinheimer, J.M., Davies, P.A., Barr, A.R., Jefferies, S.P., Chalmers, K.J., Lewis, J., Collins, H.M., Roumeliotis, S., et al., 2003. Mapping and QTL analysis of the barley population Amagi Nijo× WI2585. Aust. J. Agric. Res., 54(12):1141-1144.

[42]Patterson, N., Price, A.L., Reich, D., 2006. Population structure and eigenanalysis. PLoS Genet., 2(12):e190.

[43]Pritchard, J.K., Rosenberg, N.A., 1999. Use of unlinked genetic markers to detect population stratification in association studies. Am. J. Hum. Genet., 65(1):220-228.

[44]Pritchard, J.K., Stephens, M., Donnelly, P., 2000. Inference of population structure using multilocus genotype data. Genetics, 155(2):945.

[45]Rafalski, A., 2002. Applications of single nucleotide polymorphisms in crop genetics. Curr. Opin. Plant Biol., 5(2):94-100.

[46]Remington, D.L., Thornsberry, J.M., Matsuoka, Y., Wilson, L.M., Whitt, S.R., Doebley, J., Kresovich, S., Goodman, M.M., Buckler IV, E.S., 2001. Structure of linkage disequilibrium and phenotypic associations in the maize genome. PNAS, 98(20):11479-11484.

[47]Risch, N., Merikangas, K., 1996. The future of genetic studies of complex human diseases. Science, 273(5281):1516-1517.

[48]Rostoks, N., Ramsay, L., MacKenzie, K., Cardle, L., Bhat, P.R., Roose, M.L., Svensson, J.T., Stein, N., Varshney, R.K., Marshall, D.F., 2006. Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties. PNAS, 103(49):18656-18661.

[49]Saisho, D., Purugganan, M.D., 2007. Molecular phylogeography of domesticated barley traces expansion of agriculture in the old world. Genetics, 177(3):1765-1776.

[50]Skøt, L., Humphreys, J., Humphreys, M.O., Thorogood, D., Gallagher, J., Sanderson, R., Armstead, I.P., Thomas, I.D., 2007. Association of candidate genes with flowering time and water-soluble carbohydrate content in Lolium perenne (L.). Genetics, 177(1):535-547.

[51]Song, B.H., Windsor, A.J., Schmid, K.J., Ramos-Onsins, S., Schranz, M.E., Heidel, A.J., Mitchell-Olds, T., 2009. Multilocus patterns of nucleotide diversity, population structure and linkage disequilibrium in Boechera stricta, a wild relative of Arabidopsis. Genetics, 181(3):1021-1033.

[52]Thornsberry, J.M., Goodman, M.M., Doebley, J., Kresovich, S., Nielsen, D., Buckler, E.S., 2001. Dwarf8 polymorphisms associate with variation in flowering time. Nat. Genet., 28(3):286-289.

[53]Watterson, G.A., Guess, H.A., 1977. Is the most frequent allele the oldest? Theor. Popul. Biol., 11(2):141-160.

[54]Wei, X., Jackson, P.A., McIntyre, C.L., Aitken, K.S., Croft, B., 2006. Associations between DNA markers and resistance to diseases in sugarcane and effects of population substructure. Theor. Appl. Genet., 114(1):155-164.

[55]Wilson, L.M., Whitt, S.R., Ibáñez, A.M., Rocheford, T.R., Goodman, M.M., Buckler, E.S., 2004. Dissection of maize kernel composition and starch production by candidate gene association. Plant Cell, 16(10):2719-2733.

[56]Würschum, T., Maurer, H.P., Kraft, T., Janssen, G., Nilsson, C., Reif, J.C., 2011. Genome-wide association mapping of agronomic traits in sugar beet. Theor. Appl. Genet., 2(2):1-11.

[57]Wych, R.D., Rasmusson, D.C., 1983. Genetic improvement in malting barley cultivars since 1920. Crop Sci., 23(6):1037-1040.

[58]Yu, J., Pressoir, G., Briggs, W.H., Bi, I.V., Yamasaki, M., Doebley, J.F., McMullen, M.D., Gaut, B.S., Nielsen, D.M., Holland, J.B., 2005. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat. Genet., 38(2):203-208.

[59]Zhang, Z., Ersoz, E., Lai, C.Q., Todhunter, R.J., Tiwari, H.K., Gore, M.A., Bradbury, P.J., Yu, J., Arnett, D.K., Ordovas, J.M., 2010. Mixed linear model approach adapted for genome-wide association studies. Nat. Genet., 42(4):355-360.

[60]Zhou, H., 2011. Association Mapping of Multiple Disease Resistance in US Barley Breeding Germplasm. PhD Thesis, University of Minnesota, St. Paul, USA.

[61]Zhu, C.G., Buckler, M., Yu, E.S., 2008. Status and prospects of association mapping in plants. Plant Genome, 1(1):5-20.

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