在. 中进行针和枝特征变异分析及相关 SNP 位点挖掘。

Needle and Branch Trait Variation Analysis and Associated SNP Loci Mining in .

机构信息

College of Forestry and Grassland, Jilin Agricultural University, Changchun 130118, China.

State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, the Chinese Academy of Forestry, 1958 Box, Beijing 100091, China.

出版信息

Int J Mol Sci. 2024 Sep 23;25(18):10212. doi: 10.3390/ijms251810212.

DOI:10.3390/ijms251810212

PMID:39337698

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11432355/

Abstract

Needles play key roles in photosynthesis and branch growth in . However, genetic variation and SNP marker mining associated with needle and branch-related traits have not been reported yet. In this study, we examined 131 samples of unrelated genotypes from provenance trails. We investigated phenotypic data for seven needle and one branch-related traits before whole genome resequencing (WGRS) was employed to perform a genome-wide association study (GWAS). Subsequently, the results were used to screen single nucleotide polymorphism (SNP) loci that were significantly correlated with the studied traits. We identified a total of 243,090,868 SNP loci, and among them, we discovered a total of 161 SNP loci that were significantly associated with these traits using a general linear model (GLM). Based on the GWAS results, Kompetitive Allele-Specific PCR (KASP), designed based on the DNA of population samples, were used to validate the loci associated with phenotypes. In total, 20 KASP markers were selected from the 161 SNPs loci, and BSBM01000635.1_4693780, BSBM01000114.1_5114757, and BSBM01000114.1_5128586 were successfully amplified, were polymorphic, and were associated with the phenotypic variation. These developed KASP markers could be used for the genetic improvement of needle and branch-related traits in .

摘要

在中，针对于光合作用和侧枝生长，针扮演着关键的角色。然而，与针和侧枝相关的性状的遗传变异和 SNP 标记挖掘尚未被报道。在这项研究中，我们检测了 131 个来自不同起源的样本。在全基因组重测序（WGRS）之前，我们对七个与针和一个侧枝相关的性状进行了表型数据的调查，以便进行全基因组关联研究（GWAS）。随后，利用这些结果筛选与研究性状显著相关的单核苷酸多态性（SNP）位点。我们总共鉴定出 243,090,868 个 SNP 位点，其中，我们使用一般线性模型（GLM）总共发现了 161 个与这些性状显著相关的 SNP 位点。基于 GWAS 的结果，使用基于群体样本 DNA 的 Kompetitive Allele-Specific PCR（KASP），对与表型相关的基因座进行了验证。总共从 161 个 SNP 位点中选择了 20 个 KASP 标记，BSBM01000635.1_4693780、BSBM01000114.1_5114757 和 BSBM01000114.1_5128586 成功扩增、多态性并与表型变异相关。这些开发的 KASP 标记可以用于改进的针和侧枝相关性状的遗传改良。