Genome-wide association of single nucleotide polymorphism loci and candidate genes for frogeye leaf spot (Cercospora sojina) resistance in soybean

Abstract

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.

Genetic mapping of the Rcs2 locus in soybean cultivar Kent for resistance to frogeye leaf spot

“…The candidate genes identified in this study would be good candidates for future studies to identify causal polymorphisms for the Rcs2 locus. The gene models annotated as LEUCINE‐RICH REPEAT RECEPTOR‐LIKE KINASE ( LRR‐RLK ) are of particular interest, as LRR‐RLK genes in other areas of the genome have been identified as candidate genes for FLS resistance in past studies (Gu et al., 2021; Pham et al., 2015).…”

Association between Single Nucleotide Polymorphisms of PRKD1 and KCNQ3 Gene and Milk Quality Traits in Gannan Yak (Bos grunniens)

“…The collected tissues were placed in a 1.5 mL frozen tube and stored in liquid nitrogen. After being brought back to the laboratory, the animal tissue genomic DNA was extracted using the magnetic bead method (DP341, Tiangen Biochemical Technology Co., Ltd., Beijing, China) [ 36 ]. For specific extraction steps, please refer to the kit instructions used in this assay.…”

Progress in the Use of Combined Omics for Mungbean Breeding Improvement and Its Potential in Promoting Resistance against Cercospora Leaf Spot

“…Furthermore, in different crops, a range of studies have identified QTL and candidate genes associated with resistance to several leaf spot diseases. Gu et al [102] identified 6 loci and 55 genes associated with resistance to frogeye leaf spot (FLS) in soybean, while Sharma and Lightfoot [103] found QTLs near Satt319 and Satt632 on chromosomes 7 and 8, respectively, in the same species. Chen et al [104] identified 11 QTLs for resistance to grey leaf spot (GLS) in maize.…”