Genome-wide association study for charcoal rot resistance in soybean harvested in Kazakhstan

Charcoal rot (CR) caused by the fungal pathogen Macrophomina phaseolina is a devastating disease affecting soybean (Glycine max (L.) Merrill.) worldwide. Identifying the genetic factors associated with resistance to charcoal rot is crucial for developing disease-resistant soybean cultivars. In this research, we conducted a genome-wide association study (GWAS) using different models and genotypic data to unravel the genetic determinants underlying soybean resistance to сharcoal rot. The study relied on a panel of 252 soybean accessions, comprising commercial cultivars and breeding lines, to capture genetic variations associated with resistance. The phenotypic evaluation was performed under natural conditions during the 2021–2022 period. Disease severity and survival rates were recorded to quantify the resistance levels in the accessions. Genotypic data consisted of two sets: the results of genotyping using the Illumina iSelect 6K SNP (single-nucleotide polymorphism) array and the results of whole-genome resequencing. The GWAS was conducted using four different models (MLM, MLMM, FarmCPU, and BLINK) based on the GAPIT platform. As a result, SNP markers of 11 quantitative trait loci associated with CR resistance were identified. Candidate genes within the identified genomic regions were explored for their functional annotations and potential roles in plant defense responses. The findings from this study may further contribute to the development of molecular breeding strategies for enhancing CR resistance in soybean cultivars. Marker-assisted selection can be efficiently employed to accelerate the breeding process, enabling the development of cultivars with improved resistance to сharcoal rot. Ultimately, deploying resistant cultivars may significantly reduce yield losses and enhance the sustainability of soybean production, benefiting farmers and ensuring a stable supply of this valuable crop.