Identification of anthracnose resistance loci introgressed from P. coccineus into P. vulgaris combining BSA and WGS

Bean anthracnose is a race-specific disease, in which numerous pathogenic variants have been described. Phaseolus coccineus L. (Pc) exhibits a high level of resistance to this disease and other common diseases that affect Phaseolus vulgaris L. (Pv). Lines (HYB) derived from the interspecific cross Pv × (Pv × Pc) were developed at SERIDA. The goal of this study was to investigate the inheritance of resistance to race 38 identified in the HYB028 line, as well as to identify the genomic regions responsible for this resistance. A segregating population was developed from the cross HYB28 (resistant to race 38) × Midas (susceptible). The obtained F2 plants were multiplied in greenhouse. The response to race 38 was evaluated under controlled conditions with at least 16 F3 seedlings per F2 plant. The observed F2 segregation was 21 resistant, 40 heterozygous, and 24 susceptible, which fitted the expected ratio for one gene (χ²1:2:1= 0.21, p =0.78). F2:3 families with the heterozygous genotype showed segregation that conformed to a 3 resistant:1 susceptible ratio, indicating the dominant nature of this resistance. Two bulks (Resistant & Susceptible) with 10 F2 plants each were established and genotyped using whole-genome sequencing (WGS). Sequencing reads from different genotypes were aligned using the bean genome G19833 v2 (ncbi accession GCA_000499845.2). A total of 5,766,560 SNPs were detected and reduced to 5,432,040 SNPs after filtering (SNP with missing values or physically close positions were removed). Bulked segregant analysis was implemented using the package QTLseqR, which revealed two statistically significant regions on chromosomes Pv07 and Pv11, likely associated with anthracnose resistance. The variants identified by WGS can be used to develop molecular markers to be tested in the F2 population for their involvement in resistance by linkage analysis. The innovative aspect of this work is the use of P. coccineus as a donor to broaden resistance to anthracnose and the combination of BSA and WGS as a rapid and cost-effective approach for identifying genomic regions associated with complex traits.