Development of SNP molecular markers of Pinus bungeana based on SLAF-seq technology

  Objective  This paper aims to develop a large number of specific SNP molecular markers in the whole genome of Pinus bungeana, and provide enough resources of molecular markers for key gene mapping, marker assisted selection and germplasm resource evaluation of P. bungeana.

  Method  In this study, 52 P. bungeana resources from five populations were used as materials, and the genome of P. taeda was selected as reference genome. A large number of specific SNP sites were developed on polymorphic SLAF tags using specific length amplification fragment sequencing (SLAF-seq), and a batch of high-quality SNP sites were filtered out for genetic diversity analysis of different populations of P. bungeana.

  Result  Through sequence comparative analysis, 23 597 049 SLAF tags were obtained, including 370 659 polymorphic SLAF tags and 1 291 290 SNPs of P. bungeana population were developed. Under the condition of missing rate was less than 20% and minor gene frequency (MAF) was greater than 5%, a total of 346 840 SNPs with high consistency were obtained, accounting for 26.9% of the total SNPs, including 9 SNP loci with mutation only in Jiufeng, Beijing (JF) population, 148 SNP loci with mutation only in Lantian, Shaanxi (LT) population, 425 SNP loci with mutation only in Maiji Mountain, Gansu (MJS) population, 1 466 SNP loci with mutation only in Wuzi Mountain, Shaanxi (WZS) population, 4 SNP loci with mutation only in Baiwa Mountain, Shanxi (BWS) population. Genetic diversities of 5 P. bungeana populations were analyzed based on 346 840 SNPs, and the results showed that there were significant differences in genetic diversity among different populations of P. bungeana, among which the level of genetic diversity was relatively high in MJS and WZS population, and relatively low in JF population.

  Conclusion  The results showed that SLAF-seq technology can be used to develop a large number of SNP markers in the whole genome, and the developed SNP markers showed abundant genetic polymorphisms in different populations of P. bungeana. The results of this study lay a foundation for the identification of germplasm resources, QTL mapping, construction of genetic linkage map and association analysis of important traits of P. bungeana, and are of great significance for the protection of germplasm resources and molecular marker assisted breeding of P. bungeana in the future.