Fine Mapping of Candidate Gene(s) That Controls the Resistance of Frogeye Leaf Spot Disease in Soybean

Frogeye leaf spot (FLS) caused by the fungus Cercospora sojina Hara, may cause a significant yield loss in regions with a warm and humid climate. Two soybean lines, PI 594891 and PI 594774, were identified to carry a high level of resistance similar to that conditioned by the Rcs3 gene in 'Davis'. Previously, we reported that the resistance to FLS in these two PIs was controlled by a novel QTL on chromosome 13 that is different from the Rcs3. To fine map the QTL from these two PIs, F_2:3 seeds from the crosses between PI 594891 and PI 594774, and FLS susceptible genotype 'Blackhawk' were genotyped with KASP markers designed based on the SoySNP 50k Infinium Chip data to identify recombinants and locate candidate genes. Analysis of lines carrying key recombinationss helped narrow the FLS-resistance QTL region in PI 594891 from 3.3 Mb to a 75kb region with five annotated genes. The resistance gene in PI 594774 was fine-mapped into a 540 kb region that encompasses the 72 kb region found in PI 594891. Sequencing five candidate genes in PI 594891 identified three genes that have several mutations in the promoter, intron, 5', and 3' UTR regions. qPCR analysis showed a difference in expression levels of these genes in the PIs compared to Blackhawk in the presence of C. sojina. The mutant SNPs were used to develop KASP assays to select the resistance alleles on chromosome 13 from the two PIs for marker-assisted selection.