Xin Qirui, Qing Jun, He Yanhong
College of Forestry, Inner Mongolia Agricultural University, Hohhot 010019, China.
Curr Issues Mol Biol. 2024 Dec 13;46(12):14106-14118. doi: 10.3390/cimb46120844.
Based on the single nucleotide polymorphism (SNP) markers developed by whole genome resequencing (WGRS), the relationship and population genetic structure of 53 common apricot () varieties were analyzed to provide a theoretical basis for revealing the phylogenetic relationship and classification of the common apricot. WGRS was performed on 53 common apricot varieties, and high-quality SNP sites were obtained after alignment with the "" apricot genome as a reference. Phylogenetic analysis, G matrix analysis, principal component analysis, and population structure analysis were performed using Genome-wide Complex Trait Analysis (GCTA), FastTree, Admixture, and other software. The average comparison ratio between the sequencing results and the reference genome was 97.66%. After strict screening, 88,332,238 high-quality SNP sites were finally obtained. Based on the statistical SNP variation type, it was found that had the largest number of variations (3,951,322) and the lowest base transition/base transversion ratio (ts/tv = 1.77), indicating that its gene exchange events occurred less frequently. Based on the SNP point estimation of the relationship and genetic distance between samples, the relationship between species was 1.41-0.01, among which and had the closest relationship of 1.41, and and had the farthest relationship of 0.01. The genetic distance between species was 0.00367-0.264344, the genetic distance between and was the closest, and the genetic distance between and was the farthest, which was the largest. Phylogenetic tree, PCA, and genetic structure analysis results all divided 53 common apricot varieties into four groups, and the classification results were consistent. The SNP markers mined using WGRS technology are useful not only to analyze the variation of common apricots, but also to effectively identify their kinship and genetic structure, which plays a critical role in the classification and utilization of common apricot germplasm resources.
基于全基因组重测序（WGRS）开发的单核苷酸多态性（SNP）标记，对53个普通杏品种的亲缘关系和群体遗传结构进行分析，为揭示普通杏的系统发育关系和分类提供理论依据。对53个普通杏品种进行全基因组重测序，以“”杏基因组为参考进行比对后获得高质量SNP位点。使用全基因组复杂性状分析（GCTA）、FastTree、Admixture等软件进行系统发育分析、G矩阵分析、主成分分析和群体结构分析。测序结果与参考基因组的平均比对率为97.66%。经过严格筛选，最终获得88332238个高质量SNP位点。基于统计的SNP变异类型，发现变异数量最多（3951322个）且碱基转换/碱基颠换比最低（ts/tv = 1.77），表明其基因交换事件发生频率较低。基于SNP对样本间亲缘关系和遗传距离的估计，品种间亲缘关系为1.41 - 0.01，其中与亲缘关系最密切，为1.41，与亲缘关系最远，为0.01。品种间遗传距离为0.00367 - 0.264344，与遗传距离最近，与遗传距离最远，最大。系统发育树、主成分分析和遗传结构分析结果均将53个普通杏品种分为4组，分类结果一致。利用WGRS技术挖掘的SNP标记不仅有助于分析普通杏的变异，还能有效鉴定其亲缘关系和遗传结构，对普通杏种质资源的分类和利用具有关键作用。
