Single Nucleotide Polymorphism Detection of the Rcs3 Gene for Resistance to Frogeye Leaf Spot in Soybean

Abstract

Frogeye leaf spot (FLS), caused by Cercospora sojina Hara, has become a more frequent disease in soybean, Glycine max (L.) Merr., across the USA. The Rcs3 gene provides resistance to all known races of C. sojina To provide resources for efficient marker‐assisted selection (MAS) of Rcs3, we developed and evaluated several single nucleotide polymorphisms (SNP) and insertions or deletions (InDels) markers linked to Rcs3 We surveyed 13 bacterial artificial chromosome (BAC) end sequences that were anchored with simple sequence repeat (SSR) markers Satt244 and Satt547 along with the two SSRs containing clones in six soybean cultivars (Davis, Cook, and Young that have the Rcs3 allele and Blackhawk, Bragg, and Lee that have the rcs3 allele) for SNPs. A total of 19 SNPs/InDels were identified and validated, but only 11 mapped near Rcs3 in a F2 population of Davis × Blackhawk. The Rcs3 gene was positioned near Satt244 and 0.50 cM from SNPs AZ573TA150 and AZ573CA393. None of the SNPs or InDels identified appeared to contribute directly to the Rcs3 phenotype, but 11 mapped within a 3‐cM interval surrounding Rcs3 These 11 markers were further validated for association with Rcs3 and for their potential in MAS in 64 lines and cultivars. Our results suggest that the two markers AZ573TA150 and AZ573CA393 could be used in MAS for Rcs3. Allele specific oligonucleotide probes specific for MAS were developed for a direct hybridization assay on a Luminex 100 flow cytometry platform.