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Joint QTL analyses for partial resistance to Phytophthora sojae using six nested inbred populations with heterogeneous conditions

Sungwoo Lee, M. A. Rouf Mian, Clay H. Sneller, Hehe Wang, Anne E. Dorrance, Leah K. McHale
Theoretical and applied genetics 2014 v.127 no.2 pp. 429-444
Phytophthora sojae, alleles, case studies, chromosomes, inbred lines, phenotypic variation, population growth, population size, quantitative trait loci, soybeans
Partial resistance to Phytophthora sojae in soybean is controlled by multiple quantitative trait loci (QTL). With traditional QTL mapping approaches, power to detect these QTL, frequently of small effect, can be limited by population size. Joint linkage QTL analysis of nested recombinant inbred line (RIL) populations provides improved power to detect QTL through increased population size, recombination, and allelic diversity, yet, uniform development and phenotyping of multiple RIL populations can prove difficult. In this study, the effectiveness of joint linkage QTL analysis was evaluated on combinations of two to six nested RIL populations differing in generation, phenotypic assay method, and/or marker set used in genotyping. In comparison to linkage analysis in a single population, identification of QTL by joint linkage analysis was only minimally affected by differing phenotypic methods used among populations when phenotypic data was standardized. In contrast, genotyping of populations with only partially overlapping sets of markers had a marked negative effect on QTL detection by joint linkage analysis. In total, 16 genetic regions with QTL for partial resistance against P. sojae were identified, including four novel QTL on chromosomes 4, 9, 12, and 16, as well as significant genotype-by-isolate interactions. Resistance alleles from PI 427106 or PI 427105B contributed to a major QTL on chromosome 18, explaining 10 to 45% of the phenotypic variance. This case study provides guidance on the application of joint linkage QTL analysis of data from populations with heterogenous assay conditions and a genetic framework for partial resistance to P. sojae.