Multilocus genome-wide association study reveals genomic regions associated with resistance to red leaf blotch in soybean

Soybean [Glycine max (L.) Merr.] is a widely grown crop used for food, feed, and industrial purposes. However, a fungal disease known as Red Leaf Blotch (RLB), poses a significant threat to soybean production, and developing resistant varieties is a key management strategy. In this study, a total of 323 genetically diverse soybean genotypes of the USDA Germplasm Collection were phenotyped at RLB hotspot locations in Ethiopia (Pawe, Metu, and Asosa) in the 2024 cropping season. These genotypes were genotyped using the SoySNP50K Illumina Infinium BeadChip. A final filtered set of 38,281 SNP markers was used for multilocus genome-wide association studies to identify genomic regions associated with RLB resistance. A LOD score > 3 was used as the significance threshold. The results of the population structure analysis showed that the tested soybean genotypes were grouped into four different clusters. Linkage disequilibrium decay occurred at approximately 229 kb. ML-GWAS revealed that six quantitative trait nucleotides (QTNs) were significantly associated with RLB resistance. These QTNs are linked to 153 functional candidate genes, which are primarily involved in pathogen defense responses. Notably, key genes encode transcription factors (WRKY, HBP-1b, MYB5 repressors, bZIPs), kinases, Ser/Thr phosphatase 2 A regulatory subunits, zinc finger proteins, nodulins, amino acid transporters, and CMP-sialic acid domain-containing proteins. The identified quantitative trait nucleotides provide a valuable opportunity for consideration in advanced molecular breeding initiatives aimed at improving RLB resistance in soybean. It would be beneficial for future research efforts to emphasize validating these candidate genes and elucidating their gene interactions.