Analysis of genetic diversity and structure of endangered Dengchuan cattle population using a single-nucleotide polymorphism chip

Abstract

This study aimed to evaluate the genetic diversity and structure within the Dengchuan cattle population and effectively protect and utilize their germplasm resources. Herein, the single-nucleotide polymorphisms (SNPs) of 100 Dengchuan cattle (46 bulls and 54 cows) were determined using the GGP Bovine 100K SNP Beadchip. The results showed that among the Dengchuan cattle, a total of 101,220 SNPs were detected, and there were 83,534 SNPs that passed quality control, of which 85.7% were polymorphic. The average genetic distance based on identity-by-state (IBS) within the conservation population of Dengchuan cattle was 0.26 ± 0.02. A total of 3,999 genome-length runs of homozygosity (ROHs) were detected in the Dengchuan cattle, with ROH lengths primarily concentrated in the range of 1–5 Mb, accounting for 87.02% of the total. The average inbreeding coefficient based on ROHs was 4.6%, within the conservation population of Dengchuan cattle, whereas it was 4.9% for bulls, and the Wright inbreeding coefficient (F_IS) value was 2.4%, demonstrating a low level of inbreeding within the Dengchuan cattle population. Based on neighbor-joining tree analysis, the Dengchuan cattle could be divided into 16 families. In summary, the conservation population of Dengchuan cattle displays relatively abundant diversity and a moderate genetic relationship. Inbreeding was observed among a few individuals, but the overall inbreeding level of the population remained low. It is important to maintain this low level of inbreeding when introducing purebred bloodlines to expand the core group. This approach will ensure the long-term conservation of Dengchuan cattle germplasm resources and prevent loss of genetic diversity.

Keywords:

• Dengchuan cattle
• genetic diversity
• population structure
• ROH
• SNP chip

Acknowledgements

Thanks to all authors with the help of various aspects.

Author contribution

Conceived, drafted, and approved this research article: T.Z.Z. Conceptualization: P.P.W., G.Y.O. and T.Z.Z. Data curation: P.P.W., G.Y.O. and T.Z.Z. Formal analysis: P.P.W., G.Y.O. and T.Z.Z. Funding acquisition: T.Z.Z. Investigation: P.P.W., G.Y.O., H.Y.L., G.C.L. and T.Z.Z. Methodology: P.P.W., G.Y.O. and T.Z.Z. Project administration: T.Z.Z. Resources: T.Z.Z. and G.C.L. Visualization: P.P.W. and G.Y.O. Roles/Writing—original draft: P.P.W. and G.Y.O. Writing—review & editing: P.P.W., G.Y.O., H.Y.L. and T.Z.Z. All coauthors reviewed the final version and approved the manuscript before submission.

Ethics approval and consent to participate

All animal experiments were conducted according to the Regulations and Guidelines for Experimental Animals established by of Dali University.

Consent for publication

Not applicable.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Availability of data and materials

All data generated or analysed during this study are included in this published article.

Correction Statement

This article has been corrected with minor changes. These changes do not impact the academic content of the article.

Additional information

Funding

This research was supported by the Special Basic Cooperative Research Programs of Yunnan Provincial Undergraduate Universities (202301BA070001-033); Yunnan Provincial Key Laboratory of Entomological Biopharmaceutical R&D (AG2024003); Key projects of the Science and Technology Plan Doctoral Research Foundation Project of Dali University (KYBS2021072) and Basic Research of Dali Prefecture (2024).