Genetic Diversity Assessment and Core Germplasm Screening of Blackcurrant (Ribes nigrum) in China via Expressed Sequence Tag–Simple Sequence Repeat Markers

Blackcurrant (<i>Ribes nigrum</i> L.) has high nutritional value for human health due to its abundant vitamin C, flavonoids, and organic acids. However, its breeding and genetic research have been severely hindered by the lack of scientific tools such as molecular markers. Here, we identified 14,258 EST-SSR loci from 9531 CDS sequences with lengths greater than 1 kb, which comprised 6211 mononucleotide repeats, 4277 dinucleotide repeats, and 2469 trinucleotide repeats. We then randomly selected 228 EST-SSR loci for PCR amplification and gel electrophoresis imaging in the <i>Ribes</i> collection of Northeast Agricultural University (95 blackcurrant cultivars and 12 other <i>Ribes</i> accessions). As a result, 31 pairs of markers produced clear and reproducible bands of the expected size. Based on the 107 <i>Ribes</i> accessions, the allele number (<i>Na</i>), information index (<i>I</i>), observed heterozygosity (<i>Ho</i>), expected heterozygosity (<i>He</i>), and polymorphic information content (<i>PIC</i>) of the 31 markers were 2-5, 0.23-1.32, 0.07-0.71, 0.11-0.68, and 0.14-0.67, respectively. For the blackcurrant gene pool, neighbor-joining and population structure analysis revealed three clusters, which did not align well with their geographical origins. Based on the results, two sets with 21 and 19 blackcurrant cultivars were identified by Power Core (PC) and Core Hunter (CH) programs. The integrated core germplasm (IC) set with 27 cultivars derived from the PC and CH sets harbored abundant genetic diversity, where the allele retention rate accounted for 98.9% of the blackcurrant gene pool. The SSR markers, data, and core germplasms presented in this study lay a solid foundation for the phylogenetic study, molecular breeding, and conservation genetics of <i>Ribes</i>, especially <i>Ribes nigrum</i>.