Background: Frogeye leaf spot (FLS) is a destructive fungal disease that affects soybean production. The most economical and effective strategy to control FLS is the use of resistant cultivars. However, the use of a limited number of resistant loci in FLS management will be countered by the emergence of new high-virulence Cercospora sojina races. Therefore, we identified quantitative trait loci (QTL) that control resistance to FLS and identified novel resistant genes using a genome-wide association study (GWAS) on 234 Chinese soybean cultivars. Results: A total of 30,890 single nucleotide polymorphism (SNP) markers were used to estimate linkage disequilibrium (LD) and population structure. The GWAS results showed four loci (p < 0.0001) distributed over chromosomes (Chr.) 5 and 20, that are significantly associated with FLS resistance. No previous studies have reported resistance loci in these regions. Subsequently, 45 genes in the two resistance-related haplotype blocks were annotated. Among them, Glyma20g31630 encoding pyruvate dehydrogenase (PDH), Glyma05g28980, which encodes mitogen-activated protein kinase 7 (MPK7), and Glyma20g31510, Glyma20g31520 encoding calcium-dependent protein kinase 4 (CDPK4) in the haplotype blocks deserves special attention. Conclusions: This study showed that GWAS can be employed as an effective strategy for identifying disease resistance traits in soybean and narrowing SNPs and candidate genes. The prediction of candidate genes in the haplotype blocks identified by disease resistance loci can provide a useful reference to study systemic disease resistance.

Plant height is a key agronomic trait in soybeans, directly influencing yield potential and agronomic performance. In this study, the tall-stem cultivar Heinong 63 and the dwarf-stem cultivar Longken 3077, along with their F₂ populations, were used as experimental materials. A preliminary mapping using the bulk segregant analysis sequencing (BSA-Seq) approach enabled us to locate the target locus within a 1.8 Mb interval, which was subsequently narrowed to a 48.3 kb region using simple sequence repeat (SSR) and insertion and deletion (InDel) markers. The interval was designated as PH19-31 and contained nine annotated genes. One InDel marker, PL7, was developed within this fine-mapped region. Based on an expression analysis of the nine candidate genes, Glyma.19G230000 and Glyma.19G230200 were identified as potential regulators of plant height in soybeans. This study provides valuable materials and technical support for the cloning of plant height-related genes and the molecular breeding of soybeans.