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为解决条斑紫菜(Neopyropia yezoensis)遗传育种研究中缺乏生长性状遗传位点的问题，本研究针对条斑紫菜配子体的4个重要生长性状展开了全基因组关联分析(Genome-wide association study, GWAS)。首先，在相同环境下纯化培养了130个单一基因型条斑紫菜个体，并测量了叶长、叶宽、鲜质量和干质量这4个与生长相关的表型数据，进而分析并发现条斑紫菜不同生长性状的变异系数(Coefficient of variation)为32.63%～50.95%,各性状之间存在显著的相关性。利用全基因组重测序技术获得每个个体的基因型。对重测序数据质检后，共得到405 999个高质量的单核苷酸多态性(Single nucleotide polymorphism, SNP)位点，其中53 077个位点位于外显子区域，SNPs位点转换与颠换的数量之比为1.23。群体结构分析发现，研究群体可以分为4个亚群，不同亚群之间存在明显的遗传差异，而分群情况并非严格按照地理位置划分。测序个体之间的亲缘关系较远，连锁不平衡(Linkage disequilibrium, LD)衰减距离较小，这表明样本的遗传变异比较丰富。本研究利用混合线性模型(Q+K)进行了性状关联位点的筛选，共筛选出90个显著关联位点，其中67个位点与叶长显著相关，17个位点与叶宽显著相关，4个位点与鲜质量显著相关，2个位点与干质量显著相关，这些位点能够解释16.12%～24.85%的表型变异。在显著性位点上、下游20 kb范围内筛选，得到39个可能与生长性状相关的候选基因，基因功能涉及细胞增殖、控制细胞代谢途径以及调控植物的生长发育等。本文为条斑紫菜分子育种研究的开展提供了候选遗传位点和重要依据。
Abstract：In order to address the paucity of genetic loci associated with growth traits in the genetic breeding studies of Neopyropia yezoensis, the genome-wide association study(GWAS) was conducted for 4 important growth traits in gametophytes of N. yezoensis. One hundred and thirty thalli of N. yezoensis with single genotype were cultured under the same environment. Four growth-related phenotypic values of thallus length, thallus width, fresh mass and dry mass were measured. Study revealed that the coefficient of variation of different growth traits of thalli ranged from 32.63% to 50.95%, and there were significant correlations among the four traits. The genotype of each individual were obtained by whole genome re-sequencing. After quality inspection of the re-sequencing data, a total of 405 999 high-quality SNPs were obtained, of which 53 077 sites were in the exon region, and the ratio of SNPs transitions to translocations was 1.23. Population structure analysis found that the population in this work could be divided into 4 subgroups, and there were obvious genetic differences between any two different subgroups. The subgroups division were not in accordance with geographical location. The relatively distant phylogenetic relationship among the individuals and the short range of LD decay distance indicated that the genetic variation was relatively rich in the population. The mixed linear model(Q+K) was used to screen the associated loci of traits. A total of 90 significant SNP markers were detected, of which 67 loci were correlated with thallus length, 17 loci were correlated with thallus width, 4 loci were correlated with fresh mass, and 2 loci were correlated with dry mass, which could explain 16.12% to 24.85% of the observed phenotypic variation. A total of 39 candidate genes were identified within a 20 kb range upstream and downstream of the SNP site with significant association. The gene functions involved cell proliferation, control of cell metabolic pathways, and regulation of plant growth and development. This study furnishes a set of candidate genetic markers and crucial evidence for molecular breeding of N. yezoensis.
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基本信息:
DOI：10.16441/j.cnki.hdxb.20240294
中图分类号:S917.3
引用信息:
[1]王士宽,唐磊,王俊皓,等.基于全基因组关联分析挖掘条斑紫菜配子体生长性状遗传位点[J].中国海洋大学学报(自然科学版),2025,55(12):64-78.DOI:10.16441/j.cnki.hdxb.20240294.
基金信息:
国家重点研究发展计划项目(2023YFD2400101)资助~~