中国海洋大学学报（自然科学版）2025，Vol.55Issue(12)：64-78,15.DOI:10.16441/j.cnki.hdxb.20240294
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
Genome-Wide Association Study Reveals Genetic Loci for Important Growth Traits of Gemetophyte in Neopyropia yezoensis
摘要
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 pheno-typic 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 dif-ferent subgroups.The subgroups division were not in accordance with geographical location.The rela-tively 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 devel-opment.This study furnishes a set of candidate genetic markers and crucial evidence for molecular breeding of N.yezoensis.关键词
条斑紫菜/生长性状/全基因组重测序/全基因组关联分析/遗传位点Key words
Neopyropia yezoensis/growth traits/genome-wide re-sequencing/genome-wide associa-tion study/genetic loci分类
生物学引用本文复制引用
王士宽,唐磊,王俊皓,于欣孜,孔凡娜,茅云翔..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):64-78,15.基金项目
国家重点研究发展计划项目(2023YFD2400101)资助 Supported by the National Key Research and Development Program of China(2023YFD2400101) （2023YFD2400101）
