Genome-wide identification of simple sequence repeat (SSR) markers in Capsicum chinense Jacq. with high potential for use in pepper introgression breeding

Capsicum chinense, is closely related to Capsicum annuum L., and the two species share a common gene pool. There are a limited number of cultivated C. chinense varieties; yet, it is acknowledged that C. chinense germplasm harbors useful alleles for important traits such as fruit yield, disease resistance, accumulation of secondary metabolites and technological fruit characters. Besides, it is feasible to obtain fertile progeny from interspecific crosses of C. chinense and C. annuum. Consequently, C. chinense has high breeding potential for improvement of several different traits in pepper breeding. In the present work, C. chinense genome assembly was mined for trinucleotide simple sequence repeats (SSRs) and repeat loci were converted to 53,749 PCR markers. Marker transferability to C. annuum genome was analyzed with high-stringency cross-species mapping parameters, identifying 17,992 transferable markers. Selecting for interspecific polymorphisms and eliminating redundant loci resulted in 4994 SSR markers distributed over the 12 pepper chromosomes with high potential for interspecific polymorphisms between the two pepper species. Laboratory experiments with a subset of candidate polymorphic markers (36 markers) resulted in an amplification rate of 100% from both pepper species and 31 markers produced polymorphic alleles. Thus, in silico marker development and cross-species mapping analyses proved highly efficient in accuracy of primer design and detection of interspecific sequence divergence. The large set of genome-anchored SSR markers introduced in the present work has high potential for polymorphisms. Therefore, the marker set constitutes a useful genomic resource for broadening the genetic base of cultivated pepper with favorable C. chinense alleles.