Genetic analysis of resistance to bean leaf crumple virus identifies a candidate LRR-RLK gene.

Bean leaf crumple virus (BLCrV) is a novel begomovirus infecting common bean (Phaseolus vulgaris L.), threatening bean production in Latin America. Genetic resistance is required to ensure yield stability and reduce the use of insecticides, yet the available resistance sources are limited. In this study, three common bean populations containing a total of 559 genotypes were evaluated in different yield and BLCrV resistance trials under natural infection in the field. A genome-wide association study identified the locus BLC7.1 on chromosome Pv07 at 3.31 Mbp, explaining between 8.22% to 16.08% of the phenotypic variation for BLCrV resistance. Comparatively, whole-genome regression models explained 51% to 78% of the variation and identified the same region on Pv07 to confer the resistance. The most significantly associated markers were located within the gene model Phvul.007G040400, which encodes a leucine-rich repeat receptor-like kinase subfamily III member and is likely involved in the innate immune response against the virus. The allelic diversity within this gene revealed five different haplotype groups, one of which was significantly associated with BLCrV resistance. As the same genome region was previously reported with resistance against other geminiviruses affecting common bean, our study highlights the role that historical breeding for virus resistance has played in the accumulation of positive alleles against newly emerging viruses. In addition, we provide novel diagnostic SNP markers for marker-assisted selection to exploit BLC7.1 for breeding against geminivirus diseases in one of the most important food security crops worldwide.