Construction of a SNP fingerprinting of exotic pine germplasm resources in China based on 51K liquid- phased probes

Abstract

【Background】Slash pine (Pinus elliottii), loblolly pine (P. taeda), caribbean pine (P. caribaea) and their hybrid pine are the major timber species in China, which have been introduced from North America for 100 years. Distinguishing them is challenging due to the nutritional organs similarity and the combined characteristics inherited from their parent species in hybrid pines. 【Results】In this study, we aimed at constructing a set of DNA fingerprint of 38 pine varieties including four kinds of pines species for accurately identifying them. The genotypes of 38 pines were captured by 51K liquid-phased probes developed by our team and 5,60,567 SNPs were genotyped by the following next-generation sequencing. A total of 344 core SNPs were obtained through the screening of the minor allele frequency, miss rate, heterozygosity rate and other parameter conditions. Additionally, employing the Random Forest model in conjunction with PCA led to the retention of 28 SNPs demonstrating identification capabilities for the pine varieties. 【Conclusions】The DNA fingerprint of the 38 pine varieties was successfully established using the set of 28 SNPs, which serve as a valuable reference for identifying the exotic pine varieties, managing germplasm , and conducting genetic diversity analysis.