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United States Department of Agriculture

Agricultural Research Service

Research Project: IMPROVEMENT OF PEST RESISTANCE AND QUALITY TRAITS OF SOYBEAN Title: Joint QTL analyses for partial resistance to Phytophthora sojae using six nested inbred populations with heterogeneous conditions

Authors
item Lee, Sungwoo -
item Mian, Rouf
item Sneller, Clay -
item Wang, Hehe -
item Dorrance, Anne -
item Mchale, Leah -

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 31, 2013
Publication Date: November 19, 2013
Citation: Lee, S., Mian, R.M., Sneller, C.H., Wang, H., Dorrance, A., Mchale, L.K. 2013. Joint QTL analyses for partial resistance to Phytophthora sojae using six nested inbred populations with heterogeneous conditions. Theoretical and Applied Genetics. 127:429-444.

Interpretive Summary: Partial resistance to Phytophthora root and stem rot in soybean is controlled by multiple quantitative trait loci (QTL) or genes with small effects. With traditional QTL mapping approaches, power to detect such 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. However, 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 inbreeding 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.

Technical Abstract: 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.

Last Modified: 12/28/2014
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