Evaluation of Joint Linkage QTL Analyses for Partial Resistance to Phytophthora Sojae Using Six Soybean Nested Inbred Populations.

Joint linkage QTL analysis (JLA) as applied to nested recombinant inbred line (RIL) populations can facilitate QTL detection of complex traits conferred by multiple loci of small effects through increased population size, recombination, and allelic diversity. Partial resistance to Phytophthora sojae in soybean is an economically important quantitative trait, controlled by many loci with small effects and is thus amenable to study by JLA. In this research, we assessed six nested inbred line populations for partial resistance to P. sojae. The six populations were assayed using heterogeneous phenotypic and genotypic assays. We examined the effectiveness of JLA on combinations of two to six nested inbred line populations differing in inbreeding generation, phenotypic assay method, and/or marker set used in genotyping. Compared to QTL analysis in the six single RIL populations, differing phenotypic assay method negligibly affected detection of QTL in JLA once phenotypic data was standardized. In contrast, genotyping populations with different sets of markers negatively affected QTL detection by JLA. A total of 16 loci associated with partial resistance to P. sojae were identified, four of which were novel (chromosomes 4, 9, 12, and 16). A major QTL on chromosome 18 explained 10 to 45% of the phenotypic variance with the resistance alleles of the QTL were provided by the parental lines PI 427106 and PI 427105B. This case study provides a genetic frame work for partial resistance to P. sojae and illustrates the application of JLA to mapping populations assayed by heterogeneous methods.