Genome-Wide Association Study Reveals a QTL Region for Ashy Stem Blight Resistance in PRA154 Andean Common Bean

Ashy stem blight (ASB) caused by Macrophomina phaseolina (Tassi) Goidanich affects the common bean (Phaseolus vulgaris L.) at all growing stages. Higher levels of resistance were observed in Andean common beans, but specific resistant quantitative trait loci (QTLs) conferring resistance to this pathogen have not been reported in this gene pool. The objectives of this research were to: (i) conduct a genome-wide association study (GWAS) and QTL mapping for resistance in the Andean breeding line PRA154; and (ii) identify single nucleotide polymorphism (SNP) markers and candidate genes for ASB resistance. Phenotyping was conducted under greenhouse conditions by inoculating the 107 F_6:7 recombinant inbred lines (RILs) derived from the cross between the susceptible cultivar 'Verano' and the partial-resistant breeding line PRA154 twice with the M. phaseolina isolate PRI21. Genotyping was performed with 109,040 SNPs distributed across all 11 P. vulgaris chromosomes. A novel major QTL was located between 28,761,668 and 31,263,845 bp, extending 2.5 Mbp on chromosome Pv07, and the highest significant SNP markers were Chr07_28761668_A_G, Chr07_29131720_G_A, and Chr07_31263845_C_T with the highest LOD (more than 10 in most of the cases) and R-squared values, explaining 40% of the phenotypic variance of the PRI21 isolate. The gene Phvul.007G173900 (methylcrotonyl-CoA carboxylase alpha chain and mitochondrial 3-methylcrotonyl-CoA carboxylase 1 [MCCA]) with a size of 10,891 bp, located between 29,131,591 and 29,142,481 bp on Pv07, was identified as one candidate for ASB resistance in PRA154, and it contained Chr07_29131720_G_A. The QTL and genetic marker information could be used to assist common bean breeders to develop germplasm and cultivars with ASB resistance through molecular breeding.