Population genetic copy number variation of CHKB, KLF6, GPC1 and CHRM3 genes in Chinese domestic yak (Bos grunniens) breeds

Abstract

Single nucleotide polymorphisms (SNPs) are common markers used for population genetics studies. Recently, copy number variations (CNVs) have been used to study genetic and phenotypic diversity within and among populations. Therefore, studies of the genetics of CNVs are important in the context of understanding evolutionary changes and genomic selection based upon genetic and phenotypic variation. The aim of this study was to analyse the distribution of the choline kinase beta (CHKB), Krüpple-like factor 6 (KLF6), glypican 1(GPC1) and cholinergic receptor muscarinic 3 (CHRM3) genes in five representative Chinese domestic yak breeds. The data generated by qPCR was transformed into log₂ ratio and analysed using GraphPad (PRISM). The results show that the CNVs of CHKB, KLF6, and GPC1 genes presented more copy number losses in Tianzhu, Gannan and Plateau yak populations compared with the Datong and polled yak having relatively more copy number gains. However, the CHRM3 CNV showed more copy number gains in five yak populations. Therefore, these results indicate that there are relatively more copy number losses (deletion) in the yak populations; supporting the hypothesis that log₂ ratio is more powerful at detecting loss than gain in copy number types. Taken together, these data provide information on the application genome CNVs in population genetics and suggest that the CNVs of the genes could exert a significant effect on phenotypic differences in yak populations.

Keywords:

• CNVs
• population genetics
• genes
• domestic yak
• breeds

PUBLIC INTEREST STATEMENT

Copy number variations (CNVs) are useful in the study of genetic and phenotypic variation among individuals. Population genetics of the CNVs are useful in the understanding of evolutionary changes and genomic selection within a given population. Yak (Bos grunniens) breeding is an economically important sector and supports millions of people for milk and beef produce. In a previous study, the CNVs of CHKB, KLF6, GPC1 and CHRM3 gene were shown to reside within copy number variable regions of yak populations and overlapped with quantitative trait loci (QTLs). In this report, copy number gain events may be due to artificial insemination, hybridization, and introgression of yak breeds. The study has indicated that copy number losses (deletion) are more abundant in yak populations. The results obtained will be an essential step towards understanding the molecular mechanisms underlying phenotypic variation among domesticated yaks in Qinghai-Tibet Plateau (QTP) of China.

Acknowledgements

We thank Mr. Yong Feng Zhang for guidance and technical assistance during the laboratory work and Dr. Hong Bo Wang, Ms. Li Xiaoxiao and Mr. Peng Tang for blood sample collection.

Ethics  statement

The study was conducted between September 2016 and December 2017 at Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, the data obtained from yak breeding cooperatives of Gansu and Qinghai Province, China. All blood sample collection and body measurements were strict accordance of the guide for the Care and Use of Laboratory Animals, Lanzhou Institute of Husbandry Animal and Pharmaceutical Sciences, China. Also, all animals were slaughtered under anesthesia, and all necessary efforts were made to minimize risk of suffering. Thus, we agree to perform the research on the yak and the legal certificate number was SCXK (Gan) 2014-0002.

Competing interests

The authors declare no competing interests.

Author contributions

Habtamu Abera, data analysis, reviewed different journals and books in the line of this manuscript and Professor Ping Yan and Dr. Bao Pengjia, contributed to its supervisory and guiding. Dr. Wu Xiaoyun involved in drafting the manuscript and laboratory works. Habtamu made all writing and sketch of the manuscript.

Cover image

Source: Habtamu Abera Goshu (2017), Key Laboratory for Yak Genetics, Breeding & Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Science.

Additional information

Notes on contributors

Habtamu Abera Goshu

Ping Yan is a specialist in Genetics, Breeding & Reproduction. She has dedicated herself to the topics related to yak genetic resource and breeding. Her current research focuses primarily on evaluation and application of new developments and new technologies in sustainable yak breeding and reproduction, and marker-assisted selection (MAS) to increase disease resistance, productivity and product quality in economically important animals by adding information of DNA markers to phenotypes and genealogies for selection decisions. Currently, she is the deputy director of Lanzhou Institute of Husbandry and Pharmaceutical Sciences and director of Key Laboratory for Yak Genetics, Breeding & Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Science. She was successfully bred a new “strain” of Datong yak, which filled the blank in the history of the world 2019s domesticated animal breeding, therefore she has independent intellectual property right.