Genome-wide association study for resistance to Macrophomina phaseolina in maize (Zea mays L.)

Maize (Zea mays L.) is a frequently used food source in human and animal nutrition. Macrophomina phaseolina is a fungal pathogen causing charcoal rot disease in many plants, especially maize. This pathogen causes high yield losses in maize. The development of resistant maize genotypes is of great importance in controlling this disease. In this study, the population structure of 120 different maize genotypes with varying levels of disease resistance was determined and genome-wide association studies were performed. Each genotype was subjected to the pathogen under controlled conditions and their phenotypic responses to the disease were analyzed. Afterwards, single nucleotide polymorphisms were determined by DArT-seq sequencing. After filtering the SNP data, 37,470 clean SNPs were obtained. The population structure was analyzed with STRUCTURE software, and it was determined that the population was divided into two subgroups. The relationship between phenotypic and genotypic data was analyzed using the MLM (Q + K) model in TASSEL software. As a result, seven SNPs markers located on four different chromosomes were associated with disease resistance. The related markers can be used in the future for the development of maize varieties resistant to M. phaseolina by marker-assisted selection.