Evaluation of the Population Structure of the Ziwuling Black Goat Based on Super-GBS
This study aimed to assess the genetic diversity and population structure of the Ziwuling black goat,laying the groundwork for the preservation and utilization of this breed.The whole-genome SNP analysis of a total of 99 adult Ziwuling black goats(10 males and 89 females)was performed by super-genotyping by sequencing(super-GBS).Genetic diversity parameters in-cluding observed heterozygosity(Ho),expected heterozygosity(He),polymorphic information content(PIC),nucleotide diversity(Pi),effective allele number(Ne),and minor allele fre-quency(MAF)were calculated using Plink software.Principal component analysis and construc-tion of genetic relationship G matrix were conducted using GCTA software.IBS genetic distance matrix was built using Plink software,and a heatmap was plotted using R language.A phyloge-netic tree was constructed using PHYLP,while runs of homozygosity(ROH)were detected using the detect RUNS tool.A total of 996 042 SNPs were detected in the 99 individuals of Ziwuling black goats.The PIC,Pi,Ne,and MAF values of Ziwuling black goats were 0.161,0.193,1.295,0.130,respectively,indicating a relatively low genetic diversity with Ho(0.167)lower than He(0.192).Both the G matrix and IBS genetic distance results showed that most in-dividuals in the Ziwuling black goat population had distant genetic relationships.The principal component analysis revealed no obvious differentiation within the Ziwuling black goat population,while the phylogenetic tree indicated that the rams could be roughly divided into 6 lineages,with few rams in each lineage.The inbreeding coefficient FROH of the Ziwuling black goat population was 0.049 6,suggesting a relatively low level of inbreeding within the population.In conclusion,the genetic diversity of the Ziwuling black goat population is relatively low,with most individuals having distant kinship relations and a low level of inbreeding within the group.It is recommended to pay attention to the breeding of offspring in order to avoid loss of genetic diversity in the fu-ture.
Ziwuling black goatSuper-GBSpopulation structuregenetic diversityfamily structurekinship
万方数据
维普
