Leveraging ddRADseq for Uncovering New Genome-Wide and Polymorphic SSR Markers in Japanese Plum (Prunus salicina Lindl.)

Abstract

Reduced representation libraries, like ddRADseq, enable simultaneous detection and genotyping of polymorphic simple sequence repeats (SSRs) in a wide range of species. Plum is a species with different breeding qualities and adaptations to diverse environments, making it interesting to evaluate genetic diversity. We employed ddRADseq data from two contrasting landrace representatives from the Paraná River Delta ecosystem to develop polymorphic SSR loci for the Japanese plum (Prunus salicina). In 38,330 genomic regions sequenced, 588 microsatellite motifs were found, and PCR primer pairs were designed. PCR efficiency and specificity were analyzed in silico allowing positive amplification of 418 (71%) SSRs. Sixty-two out of 588 SSRs (10.5%) exhibited polymorphism. Among these, 20 were validated and amplified by wet lab experiments. Seven of them were selected to characterize 26 individuals of P. salicina. Forty-two alleles were detected (3–9 alleles/locus). The observed and expected heterozygosity values ranged from 0.34–0.89 and from 0.60–0.81, respectively. Polymorphism information content values varied from 0.52 to 0.77. Allele sharing distance values between individuals indicated that the 26 plum landraces are genetically unique. When P. salicina ddRADseq sequences were compared with a P. persica reference genome, a lower percentage of reads were mapped, but all validated SSRs could be located. ddRADseq is proving to be an efficient, cost-effective, and reliable technology for discovering and developing novel SSR markers, with considerable potential for application in non-model species. It allows the pre-selection of polymorphic SSRs valuable for studying genetic diversity in P. salicina and has potential for transferability to other related species, including P. persica.