What's Under a QTL? Gene Expression Changes Following Infection by Phytophthora sojae

Partial resistance in soybean is mediated by quantitative trait loci (QTL). Two QTL on Chr. 19 in resistant cultivar 'Conrad' were identified that confer broad-spectrum resistance to multiple Phytophthora sojae isolates. In this study, these two QTL were dissected by sequence and expression analysis of genes from the resistant and susceptible genotypes. A total of 1025 single nucleotide polymorphisms (SNPs) were identified between the resistant cultivar Conrad and susceptible cultivar ‘Sloan’ through sequencing of 153 genes. In comparison to both Sloan and Williams82, Conrad had 304 SNPs in 54 genes, and there were 11 genes in which SNPs were unique to Conrad. Expression patterns of 19 genes in these regions in response to inoculation with P. sojae were examined in Conrad, Sloan, and four selected recombinant inbred lines (RILs) from the Conrad × Sloan F_6:8 population. A list of candidate genes with significantly different infection response between the resistant and susceptible lines were identified, including those involved in signal transduction, hormone-mediated pathways, plant cell structural modification, ubiquitination, and basal resistance. These findings suggest a complex defense network with multiple mechanisms underlying individual soybean QTL conferring resistance to P. sojae. This study also provides putative candidate genes and SNP markers for fine mapping and marker-assisted resistance breeding for this trait.