Genome-wide Identification And Population Genetic Analysis Of Copy Number Variations In Seven Goat Populations

As a major class of genetic variations in higher organisms（e.g.,mammals）,structural variations include copy number variations（CNVs）,inversions and translocations.CNVs are now defined as duplications and insertions/deletions of DNA sequences≥50 bp in length between individuals within a species.Previous studies have demonstrated that copy number variations（CNVs）are involved in animal domestication and genetic adaptation to local environments at the population level.However,it remains largely unknown for the characteristics of CNVs in the goat genome.Here we sought to investigate genetic diversity,population structure,and population differentiation in domestic goats on the aspect of CNV by exploiting the whole-genome sequence data of 38 goats from three Chinese breeds（Chengdu Brown,Jintang Black,and Tibetan Cashmere）and the public genome sequence data of 26 goats from three other breeds（two Moroccan and one Chinese breed）and 21 Bezoar ibexes.In brief,the main results were as follows:A total of 208,649 CNVs,including 190,773 deletions and 17,876 duplications were identified in 85 goats sampled from seven populations.We found that the number of CNVs on each chromosome increased significantly with the chromosome length(t test,P=2×10^-16)using an univariate linear regression analysis.In total,2394 CNVRs were obtained by merging overlapping CNVs.The total length of all the CNVRs was 266.71 Mb and covered10.80%of the goat autosomal genome.The numbers of CNVs and CNVRs with different lengths showed L-shaped distributions.The principal component analysis based on genome-wide deletion and duplication genotypes showed that the seven goat populations could be divided into three groups:Chinese goats（CB,JT,TC,SC）,Moroccan goats（MD,MN）and Bezoar Ibexes（BI）.Moreover,the results of genetic admixture analysis showed that the ancestral origins of the seven goat populations could be divided into two categories:Chinese goat and Bezoar Ibex,when the optimal number of ancestral population K=2.When the optimal number of ancestral population K=3,the two Moroccan goat populations can be classified into another original group.The population differentiation index(F_ST)values were calculated.Based on a threshold of top 5%,a total of 310,296,297,230,285 loci were identified with a pairwise comparison between CB(F_ST>0.45),JT(F_ST>0.43),TC(F_ST>0.37),SC(F_ST>0.60),MD+MN(F_ST>0.34),and BI.Based on the functional enrichment analyses,CNVs were mainly related to nervous system,sensory perception of smell,metabolism,reproduction,and immune system(P_adj<0.05).As above,280(F_ST>0.27)CNVs were identified between highland goats（TC）and lowland goats（lowland:CB+JT+SC+MD+MN）.These CNVs were mainly involved in olfactory,nervous system,immune system,and even reproduction(P_adj<0.05).In this study,87.78%（68.23%–97.56%）of CNVs detected above can be identified from the high-depth resequencing data of the same goats（n=9）,which prove that the detection results of CNVs in this study are reliable.In conclusion,we have completed a high-quality whole-genome CNVR genetic map of goat,CNVs are distributed widely in the goat genome.Our study demonstrates the utility of CNVs in the population structure analyses.There are many differentiated CNVs between domestic goat populations and Bezoar ibexes,and between highland and lowland goat populations.It is suggested that CNVs play an important role in goat domestication and adaptation to highland environments.