关键词: 舒玛栎, 遗传多样性, 遗传结构, SLAF-seq, SNP

Abstract:

【Objective】Oaks are the most important productive and dominant species in broadleaf forests in the subtropics and temperate zones, and they play irreplaceable roles in forest ecology. As a precious and colorful broadleaf tree species, Quercus shumardii has been extensively utilized for commercial timber production and landscape planting. To provide a theoretical basis for the germplasm protection and variety selection, the genetic diversity and genetic structure of different provenances of Q. shumardii introduced from the USA were evaluated to reveal the characteristics of genetic differentiation and genetic relationships among individuals. 【Method】Thirty-five Quercus individuals were sampled, including 30 individuals from six provenances of Q. shumardii and five individuals of Q. nuttallii as an outgroup. A set of SNP markers was developed based on SLAF sequencing according to a non-reference genome protocol, of which the polymorphic SNP markers with a minor allele frequency (MAF) > 0.05 and miss rate < 0.2 were screened and used for a genotyping. Several software programs such as GenAlex, Arlequin, MEGA, Admixture and Cluster were used for genetic diversity parameter estimation, F statistics and molecular variance analysis, phylogenetic tree construction, genetic structure analysis, and principal component analysis, respectively. 【Result】Average sequencing depth of the 35 Quercus individuals was 11-fold. The values of Q₃₀ and GC content of the seven provenances ranged from 90.24% to 95.12% and from 38.49% to 39.35%, with average values of 93% and 38.9%, respectively. After assembly, 4 256 436 SLAF tags were obtained, and 8 459 025 polymorphic SNP markers were identified, of which the average integrity and the heterozygosity ratio of SNPs was 79.29% and 14.15%, respectively. Among the six different provenances of Q. shumardii, the average effective number of alleles was 1.31, and the percentage of polymorphic loci was 49.21%. The observed and expected heterozygosity (H_o and H_e) ranged from 0.13 to 0.16 (mean 0.15) and 0.17 to 0.21 (mean 0.19), respectively. Average values of polymorphism information content (PIC), Shannon’s information index (I), Nei’s gene diversity (H), and inbreeding coefficient (${F_I}_S$) were 0.15, 0.34, 0.09 and 0.19, respectively. The pairwise genetic differentiation index (F_ST) and genetic distance among provenances of Q. shumardii ranged from 0.08 to 0.18 and from 0.15 to 0.39, respectively. The molecular variance analysis demonstrated that the differentiation among individuals contributed 84.88% of the total variation, and the remaining 15.12% was among populations. Furthermore, the genetic structure results showed that 30 individuals of Q. shumardii originated from three primitive ancestors, of which two groups contained TX and MS provenances, respectively, and the other group contained LA, MO, OH and PA provenances. The cluster analysis demonstrated that all 35 individuals were separated into two clades, i.e., the species Q. shumardii and Q. nuttallii, which belonged to the traditional taxonomy of Quercus. 【Conclusion】A relatively high level of genetic diversity and genetic differentiation was detected in the Q. shumardii population, suggesting that the superior individual tree among populations should be focused on for the variety selection.

Key words: Quercus shumardii, genetic diversity, genetic structure, SLAF-seq, SNP