Population structure and linkage disequilibrium in US barley germplasm: implications for association mapping

Authors: HAMBLIN, MARTHA - Cornell University; CLOSE, TIMOTHY - University Of California; BHAT, PRASANNA - University Of California; Chao, Shiaoman; ABRAHAM, K. JOSEPH - Case Western Reserve University (CWRU); BLAKE, TOM - Montana State University; BROOKS, WYNSE - Virginia Polytechnic Institution & State University; COOPER, BLAKE - Busch Agriculture Resources, Inc; GRIFFEY, CARL - Virginia Polytechnic Institution & State University; HAYES, PATRICK - Oregon State University; HOLE, DAVID - University Of Utah; HORSLEY, RICHARD - North Dakota State University; Obert, Donald; SMITH, KEVIN - University Of Minnesota; ULLRICH, STEVEN - Washington State University; MUEHLBAUER, GARY - University Of Minnesota; Jannink, Jean-Luc

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/6/2009
Publication Date: 4/1/2010
Citation: Hamblin, M.T., Close, T.J., Bhat, P.R., Chao, S., Abraham, K., Blake, T., Brooks, W.S., Cooper, B., Griffey, C.A., Hayes, P.M., Hole, D.J., Horsley, R.D., Obert, D.E., Smith, K.P., Ullrich, S.E., Muehlbauer, G.J., Jannink, J. 2010. Population structure and linkage disequilibrium in US barley germplasm: implications for association mapping. Crop Science. 50:556-566.

Interpretive Summary: The Barley Coordinated Agricultural Project (Barley CAP) is developing a large association mapping resource of elite barley lines that have been genotyped and phenotyped. The study reported in this manuscript begins to answer the questions concerning how best to implement association mapping using this resource and what mapping precision it may provide. A first question is that of identifying population structure within the resource, that is, identifying sets of lines more strongly related to each other than to the rest of the lines. These sets define appropriate materials and inference space for an analysis. The study showed that some structure was related to spike type and growth habit but also strongly influenced by breeding program. To answer the question of whether sets of lines in different subpopulations might be pooled, the study assessed the phase of allelic association in the different sets. That is, within different sets, are the same alleles at different markers usually co-inherited or not? We found that, relative to the range of genetic distance between subpopulations in barley, the correlation in allelic phase decays quickly: only the most similar barley subpopulations should be pooled for any given analysis.

Technical Abstract: Previous studies have shown that there is considerable population structure in cultivated barley, with the strongest structure corresponding to differences in row number and growth habit. US barley breeding programs include 6-row and 2-row types and winter and spring types in all combinations. To facilitate mapping of complex traits in breeding germplasm, 1816 barley lines from ten US breeding programs were scored with 1536 SNP genotyping assays. The number of SNPs segregating within breeding programs varied from 854 to 1398. Model-based analysis of population structure showed the expected clustering by row type and growth habit, however there was additional structure, some of which corresponded to the breeding programs. The model that fit the data best had seven populations: three 2-row spring, two 6-row spring, and two 6-row winter. Average linkage disequilibrium (LD) within populations decayed over a distance of 20-30 cM, but some populations showed long-range LD suggestive of admixture. Genetic distance (allele-sharing) between populations varied from 0.11 (6-row spring vs. 6-row spring) to 0.45 (2-row spring vs. 6-row spring). Analyses of pairwise LD revealed that the phase of allelic associations was not well correlated between populations, particularly when their allele-sharing distance was > 0.2. These results suggest that pooling divergent barley populations for purposes of association mapping may be inadvisable.