Identification and population genetic analyses of copy number variations in six domestic goat breeds and Bezoar ibexes using next-generation sequencing

Authors: GUO, JIAZHONG - Sichuan Agricultural University; ZHONG, JIE - Sichuan Agricultural University; Liu, Ge - George; YANG, LIU - Sichuan Agricultural University; LI, LI - Sichuan Agricultural University; CHEN, GUANGLING - Sichuan Agricultural University; SONG, TIANZENG - Sichuan Agricultural University; ZHENG, HONGPING - Sichuan Agricultural University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/23/2020
Publication Date: 11/27/2020
Citation: Guo, J., Zhong, J., Liu, G., Yang, L., Li, L., Chen, G., Song, T., Zheng, H. 2020. Identification and population genetic analyses of copy number variations in six domestic goat breeds and Bezoar ibexes using next-generation sequencing. BMC Genomics. 21(1):840. https://doi.org/10.1186/s12864-020-07267-6.
DOI: https://doi.org/10.1186/s12864-020-07267-6

Interpretive Summary: Copy number variation (CNV) represents a major source of genomic variation. We performed CNV detectyion and population genetic analyses in goat. These results fill our knowledge gaps and provide the foundation for incorporating CNV into the future goat breeding program. Farmers, scientist, and policy planners who need improve animal health and production based on genome-enable animal selection will benefit from this study.

Technical Abstract: Background: Copy number variations (CNVs) are a major form of genetic variations and are involved in animal domestication and genetic adaptation to local environments. However, little is known about genome-wide characteristics and population genetic properties of CNVs in domestic goats. Results: Here, we aimed to investigate them using the 38 goat sequence data of three Chinese breeds (Chengdu Brown, Jintang Black, and Tibetan Cashmere) from our lab and 26 public goat sequence data from three other breeds (two Moroccan and one Chinese), as well as 21 Bezoar ibexes. We obtained a total of 2394 CNV regions (CNVRs) by merging 208,649 high-confidence CNVs, which spanned ~267 Mb of total length and accounted for 10.80% of the goat autosomal genome. Functional analyses showed that 2322 genes overlapping with the CNVRs were significantly enriched in 57 functional GO and KEGG terms, most related to the nervous system, metabolic process, and reproduction system. Clustering patterns of all 85 samples generated separately from duplications and deletions were generally consistent with the geographical origins of these goats and the results from SNPs, suggesting the usefulness of CNVs for the population structure analyses. Besides a white breed, we found a duplication encompassing the ASIP gene in some individuals from a black breed, indicating that there was no clear association of CNV of ASIP in this study with coat color variation. Based on genome-wide FST at each CNV locus, some genes overlapping with the highly divergent CNVs between domestic and wild goats were mainly enriched for the reproduction and immune related functions. Furthermore, a 507-bp deletion at ~14 kb downstream of FGF5 on chromosome 6 showed highly divergent (FST = 0.983) between highland and lowland goats. Together with an enhancer activity of this sequence shown previously, the function of this duplication in regulating fiber growth deserved to be further investigated in detail. Conclusion: We generated a comprehensive map of CNVs in goats, and these deletions and duplications are useful genetic markers for the population structure analyses. Many genetically differentiated CNVs among various goat populations might be associated with the population characteristics of domestic goat breeds.