云南农业大学学报（自然科学）2017，Vol.32Issue(5)：811-817,7.DOI:10.16211/j.issn.1004-390X(n).2017.05.009
基于SNP的基因组近交系数衡量群体遗传多样性的准确性
Accuracy of Measuring Population Genetic Diversity by Using Genomic Inbreeding Coefficient Based on SNP
摘要
Abstract
[Purpose] To investigate the accuracy of measuring population genetic diversity by using genomic inbreeding coefficient based on SNP markers (FSNP).[Method] Continuous 50-generation breeding in a closed population was simulated and assumed that there were 1 000 evenly spaced SNPs on a couple of autosomes which genetic length was 100 cM.The effects of population size,sire ratio,number of SNPs used to compute the FSNP (NSNP) and initial allelic frequency of each SNP (p) on the accuracy of measuring population genetic diversity by using FSNP were determined,which considered the inbreeding coefficient based on pedigree (Fped) as a control,and the correlation coefficients between FSNP,Fped and genomic observed homozygosity (HOMobs),rSNrP and rped were set as the indexes of measuring the accuracy.[Result] The accuracy of measuring the population genetic diversity by using FSNP was higher in general,which with less influence of population size and sex ratio,and would not decrease with the increase of generations,when compared to using Fped.The accuracy of measuring the population genetic diversity by using FSNP was higher,when NSNP was larger and P was closer to 0.5.[Conclusion] In practice,it could be ensured that rSNP was higher than rped,and FSNP could be used to implement a timely and dynamic monitoring of the genetic diversity effectively,when the NSNP was equal or more than 20 percent of the number of whole genomic SNP (NSNP ≥200 in present experiment) and covered all the chromosomes;it would help to increase the accuracy of monitoring the genetic diversity and preserve the genetic variation within population that controlling the p value at medium level.关键词
近交系数/基因组/SNP标记/系谱信息/遗传多样性Key words
inbreeding coefficient/genome/SNP marker/pedigree information/genetic diversity分类
生物科学引用本文复制引用
王孝义,李明丽,胡伟,严达伟,鲁绍雄..基于SNP的基因组近交系数衡量群体遗传多样性的准确性[J].云南农业大学学报（自然科学）,2017,32(5):811-817,7.基金项目
NSFC-云南联合基金项目(U1402266) （U1402266）
云南省高校科技创新团队支持计划(云教科[2014] 22号) （云教科[2014] 22号）
云南省现代农业生猪产业技术体系建设项目(2017KJTX0013). （2017KJTX0013）
