Genome-wide association study reveals novel loci and candidate gene for resistance to frogeye leaf spot (Cercospora sojina) in soybean

Authors: MCDONALD, SAMUEL - University Of Georgia; BUCK, JAMES - University Of Georgia; Song, Qijian; LI, ZENGLU - University Of Georgia

Submitted to: Molecular Genetics and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/19/2022
Publication Date: 1/5/2023
Citation: McDonald, S., Buck, J., Song, Q., Li, Z. 2023. Genome-wide association study reveals novel loci and candidate gene for resistance to frogeye leaf spot (Cercospora sojina) in soybean. Molecular Genetics and Genomics. https://doi.org/10.1007/s00438-022-01986-z.
DOI: https://doi.org/10.1007/s00438-022-01986-z

Interpretive Summary: Frogeye leaf spot is a foliar disease of soybean caused by a fungus. In severe infections, foliar lesions can coalesce and cover more than 30% of the leaf area, at which time the leaves often wither and abscise. In 2020, the yield loss estimates due to FLS in the United States exceeded 160 thousand metric tons. The disease can also diminish quality for soybean processing. The disease was one of the five most yield-reducing diseases in the southern United States and recently has become a growing problem in the midwestern and northern growing regions of the United States due to warmer winters and the growing of susceptible cultivars. Limited sources of resistance have been identified and used in modern soybean breeding and carries the risk that available resistance may be overcome by fungus variants. Researchers at the University of Georgia and USDA-ARS, Beltsville, MD identified a new source of resistance in soybean. Through analysis of 329 different soybeans, they identified genomic regions that control disease resistance. They identified a gene designated as Glyma.11g230400 in one region that contributed to the most pronounced disease resistance and developed a molecular marker to track the gene. Identification of these genomic regions and development of molecular markers to track these regions will facilitate combining new sources of resistance with known available sources to enhance soybean resistance to frogeye leaf spot and accelerate disease resistance breeding.

Technical Abstract: Frogeye leaf spot, caused by the fungus Cercospora sojina, is a threat to soybeans in the southeastern and, more recently, midwestern United States. Limited genetic resistance to the disease has been reported, and only three sources of resistance have been used in modern soybean breeding. To discover novel sources and identify the genomic locations of resistance, a GWAS was conducted using a panel of 329 soybean accessions selected to maximize genetic diversity. Accessions were phenotyped using a 1-5 visual rating and by counting lesion number and measuring the percent of leaf area diseased using image analysis. Eight novel loci on eight chromosomes were identified for three traits utilizing the FarmCPU or BLINK models, of which a locus on chromosome 11 was highly significant across all model-trait combinations. Using the SoySNP50K Beadchip and variant information from 65 of the accessions that have been sequenced, KASP markers were designed to target SNPs in the gene model Glyma.11g230400, a leucine-rich repeat receptor-like protein kinase. GSM990, a KASP marker designed to detect a missense mutation in Glyma.11g230400, was the most significant for all three traits in a genome-wide association and may be useful to select for resistance to frogeye leaf spot in soybean breeding.