Genome-wide Identification of Powdery Mildew Resistance in Common Bean

Abstract

Background Genome-wide association studies (GWAS) was utilized to detect genetic variations related to the powdery mildew (PM) resistance and several agronomic traits in common bean. However, its application in common bean and the PM interactions to identify genes and their location in the common bean genome has not been fully addressed. Results Genome-wide association studies (GWAS) through marker-trait association are useful molecular tools for identification of disease resistance and other agronomic traits. SNP genotyping with a BeadChip containing 5398 SNPs was used to detect genetic variations related to resistance to PM disease in a panel of 206 genotypes grown under field conditions for two consecutive years. Significant SNPs identified on chromosome 4 and 10 were repeatable, confirming the reliability of the phenotypic data scored from the genotypes grown in two locations within two years. A cluster of resistance genes was revealed on the chromosome 4 of common bean genome among which CNL and TNL like resistance genes were identified. Furthermore, two resistance genes Phavu_010G1320001g and Phavu_010G136800g were also identified on pv10; further sequence analysis showed that these genes were homologs to the Arabidopsis disease resistance protein (RLM1A-like) and the putative disease resistance protein (At4g11170.1), respectively. Two LRR receptor-like kinases (RLK) were also identified on pv11 in samples collected in 2018 only. Many genes encoding auxin-responsive protein, TIFY10A protein, growth-regulating factor 5-like, ubiquitin-like protein, cell wall protein RBR3-like protein related to PM resistance were identified nearby significant SNPs. These results suggested that the resistance to PM pathogen involves a network of many genes constitutively co-expressed and may generate several layers of defense barriers or inducible reactions. Conclusion Our results provide new insights into common bean and PM interactions, and revealed putative resistance genes as well as their location on common bean genome that could be used for marker-assisted selection, functional genomic study approaches to confirm the role of these putative genes; hence, developing common bean resistance lines to the PM disease.