生命科学研究2025，Vol.29Issue(2)：123-130,155,9.DOI:10.16605/j.cnki.1007-7847.2024.05.0152
全基因组重测序解析德清朱鹮群体遗传多样性及群体遗传结构
Genetic Diversity and Structure Analysis of Deqing Nipponia nippon Population Based on Whole-genome Resequencing
摘要
Abstract
The genomic single nucleotide polymorphisms(SNPs)in a population of 194 Nipponia nippon in-dividuals were investigated using whole-genome resequencing.The genetic diversity of the population in Deqing was assessed with genetic parameters including minor allele frequency,observed heterozygosity,ex-pected heterozygosity,and polymorphic information content,and the genetic correlation within the population was analyzed by constructing identity by state(IBS)genetic distance matrix and G matrix.A phylogenetic tree based on the IBS genetic distance matrix was also built to analyze and classify the family structure of the Deqing N.nippon population.The results showed that,after quality control,a total of 144 219 SNPs were obtained from the 194 individuals,with the average call rate 0.962,minor allele frequency 0.169±0.050,polymorphic information content 0.276±0.068,and observed heterozygosity and expected heterozygosity 0.338±0.099 and 0.276±0.069,respectively.The inbreeding coefficient was-0.206±0.071,indicating a low level of inbreeding.The IBS genetic distance within this population was 0.218±0.033,and the results of the G matrix analysis were consistent with those of IBS genetic distance matrix,indicating the presence of closely related individuals within the Deqing N.nippon population.Based on phylogenetic tree analysis,the 194 in-dividuals could be classified into 16 lineages.In summary,the genetic diversity of the Deqing N.nippon population is moderate,and there is no significant evidence of extensive inbreeding.However,due to close kinship between certain individuals,there is a risk of inbreeding.Therefore,in future pairing selection,indi-viduals for mating should be chosen based on the classified families to avoid inbreeding.关键词
朱鹮/全基因组重测序/遗传多样性/亲缘关系/家系结构Key words
Nipponia nippon/whole-genome resequencing/genetic diversity/kinship/family structure分类
生物科学引用本文复制引用
邱国强,李瑞,石坚,陈奕洁,袁李莹,杨永春,马翔,宋厚辉,牛冬..全基因组重测序解析德清朱鹮群体遗传多样性及群体遗传结构[J].生命科学研究,2025,29(2):123-130,155,9.基金项目
德清县生态林业综合服务中心项目(ZJXRDQ-2023-DT02) （ZJXRDQ-2023-DT02）
