Genetic diversity and assessment of markers linked to resistance and pungency genes in Capsicum germplasm

Abstract

The use of germplasm as source of resistances to biotic stresses represents an important strategy in pepper in order to improve susceptible cultivars and release new resistant varieties. The study of the relationships among genotypes within germplasm collections is useful for genetic improvement as well as for the management of genetic resources. In the present study, 59 accessions belonging to nine different species have been genotyped with a set of ten simple sequence repeats (SSR) and eleven allele specific molecular markers linked to major genes and QTLs for pathogen resistance and pungency. Results allowed to select promising genotypes in terms of content of resistance alleles and to identify highly polymorphic SSR pairs which can be used for species discrimination and hybrid identification. The diversity pattern of the SSR loci revealed a number of distinct alleles per locus, ranging from 3 to 11 with an average of 6.3. Hierarchical analysis allowed to distinguish several clusters each including the different species under study with genetic similarities in the range of 7–100 %. The most distant genotypes from the C. annuum accessions belong to C. baccatum and C. pubescens. The differentiation of the accessions on the basis of the presence of resistance and pungency associated markers, allowed to identify 17 clusters in which the resistance genes were differently distributed. Tsw, L 4 and Pvr4 resulted to be most represented within the genotypes of the collection. Accessions belonging to C. chinense and C. frutescens resulted to be the most interesting ones for pyramiding multiple resistance genes, confirming the need of interspecific crosses in breeding programs in order to transfer useful alleles from domesticated Capsicum spp. to varieties and landraces of cultivated pepper.