Evaluation of soybean genotypes for cowpea mild mottle virus resistance through phenotypic reaction and genotypic analysis

Abstract

Cowpea mild mottle virus (CPMMV), a carlavirus nonpersistently transmitted by whiteflies, is an emerging and economically important virus of soybean. The present study aimed to identify soybean genotypes resistant to CPMMV through mechanical inoculation‐based phenotyping and marker trait association using gene‐specific and simple‐sequence repeat (SSR) markers. A set of 500 soybean genotypes was initially screened in the field for CPMMV infection, of which 288 genotypes showing resistance were evaluated further under controlled glasshouse conditions. Among these 288 genotypes, 43 (14.9%) were resistant, 59 (20.5%) were moderately resistant while the remaining 186 (64.6%) were susceptible. A set of five gene‐specific primer pairs, three of which targeted CPMMV R genes, was used for screening the 288 soybean genotypes; 96 genotypes from the 288 (based on disease score) were also genotyped with 24 SSR polymorphic markers for an association study. The mean values of major allele frequency and gene diversity were found to be 0.70 and 0.39, respectively. The polymorphism information content varied from 0.14 to 0.37. Population structure and cluster analysis revealed three subpopulations for the five gene‐specific markers and two distinct subpopulations for the 24 SSR markers, respectively. Neighbour joining‐based clustering analysis categorized the 288 genotypes into two major clusters. Three markers were found to be significantly associated with CPMMV resistance. The BARCSOYSSR0558 marker showed the highest phenotypic variance of 9.6%. The present study will help in identification of CPMMV R genes and breeding new resistant varieties through marker‐assisted selection.