Bulked segregant analysis using next-generation sequencing for identification of genetic loci for charcoal rot resistance in soybean

Charcoal rot, caused by Macrophomina phaseolina in soybean [Glycine max (L).Merr.] is a disease of economic significance in the United States. Chemical and cultural control are not effective and host resistance could be a potential method to control the disease. In this study we report the use of bulked-segregant analysis (BSA) to map the genetic basis of resistance to charcoal rot in soybean PI 567562A, using a QTL-seq approach. Resistant and susceptible bulks from progenies of a biparental population (PI 567562A and PI 567437) were sequenced, and reads were aligned to the PI 567562A genome and used to calculate the SNP-index at each SNP position for the resistant and susceptible bulks. The average distributions of the SNP-index and Δ SNP-index across the genome were estimated for genomic intervals using a sliding window analysis with 2-Mb window size and a 10-kb step. Three genomic regions on chromosomes 5, 8 and 14 were identified with positive values in Δ SNP-index plots that potentially correspond to QTL governing the difference between the R-bulk and S-bulk sub-populations. The current study is the first attempt employing QTL-seq to identify genomic regions that may contain QTL controlling charcoal rot disease resistance in soybean.