Genome-wide microsatellite characterization and marker development in Diospyros oleifera

Diospyros oleifera, a diploid Diospyros, have a wide range of applications in biomedical science and the food, wood, and chemical industries. In addition, it is an excellent model plant to study Diospyros. While, to date, the genome-wide mining of SSRs (or Microsatellite) in D. oleifera is still absent. In this study, we constituted the first deep characterization of genome-wide microsatellites for D. oleifera and developed polymorphic SSR markers across Diospyros lotus and Diospyros kaki. A total of 330,507 SSRs were identified from D. oleifera genome with an average density of 385.95 SSRs per Mb, representing a higher SSR density. D. oleifera SSR motifs are not randomly distributed across genomic regions and motif types. Although, the distribution of SSRs differed slightly among D. oleifera chromosomes, only chromosomes 1 and 5 had considerably high densities. There are significantly lower frequencies of SSRs in the coding regions than that in the whole genomic region, which was only about 3.49% of the density of the D. oleifera genome (13.48/Mb vs. 385.95/Mb). Of the different SSR motif types, mononucleotide repeats (47.63%) were the most abundant in genome, while trinucleotide repeats (68.57%; 1924) were the most abundant in coding regions. Therefore, unlike in the D. oleifera genome, the AT-rich motif lost its numerical dominance in the coding regions. In addition, 231,809 primer pairs were identified, and 87.65% were high-resolution markers in the D. oleifera genome, which generated no more than three in silico products. 25,387 potential for interspecific polymorphic SSR markers between two Diospyros species were also identified. An amplification rate of 92% from testing Diospyros species were clarified through with a subset of candidate polymorphic markers (100 markers) test. Then, 29 novel polymorphism SSR markers were employed to distinguish among 12 Diospyros accessions with high mean PIC values of 0.6009. Thus, these SSR locus we identified in this study had the potential to reveal genotypic diversity in Diospyros.

Automated summary

This study characterized the genome-wide microsatellites in D. oleifera and developed polymorphic SSR markers for Diospyros lotus and Diospyros kaki. A total of 330,507 SSRs were identified from the D. oleifera genome, with an average density of 385.95 SSRs per Mb. Mononucleotide repeats were the most abundant in the genome, while trinucleotide repeats were the most abundant in the coding regions.