Analysis of germplasm genetic diversity and construction of a core collection in Camellia oleifera C.Abel by integrating novel simple sequence repeat markers

Camellia oleifera C.Abel is an important oilseed crop. While germplasm resources have been widely collected and conserved, their genetic diversity remained to be explored effectively. Therefore, genomic libraries were constructed and sequenced, and all clean reads were assembled into 673,863 unigenes. In total, 27,953 SSRs were detected from all the unigenes, and 17,517 SSR primer pairs were successfully designed. Furthermore, we re-evaluated the genetic diversity of the germplasm bank of C. oleifera using 22 SSR markers. The number of alleles (Na), the effective number of alleles (Ne), the Shannon index (I), the polymorphic information index (PIC) ranged from 4 to 25 (mean of 11.41), 2.014 to 9.284 (mean of 4.800), 0.716 to 2.471 (mean of 1.682), 0.380 to 0.883 (mean of 0.717), respectively. Finally, a core collection consisting of 45 samples (15% of the 300 trees in the entire germplasm bank) was developed, the genetic diversity parameters of which showed nonsignificant differences from the entire germplasm bank. Genomic SSR development, the re-evaluation of genetic diversity and the development of a core collection from the germplasm bank in this study provided useful tools, abundant genetic resources and an effective collection for the utilization and deep exploration of C. oleifera.