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Genetic variation analysis of Guanling cattle based on whole-genome resequencing |
Longxin Xu1 
, Xin Wang1
, Junda Wu1
, Hua Wang1
, Wenzhang Zhou1
, Jing Liu1
, Mengmeng Ni2,3
, Kaikai Zhang1
, Bo Yu1,*
, Ruiyi Lin4,*
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1Institute of Animal Husbandry and Veterinary Science, Guizhou Academy of Agricultural Sciences, Guiyang 550005, China
2College of Animal Sciences, Guizhou University, Guiyang 550000, China
3Guizhou Yellow Cattle Industry Group Co., Ltd, Guiyang 550001, China
4College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China |
Correspondence:
Bo Yu, Tel: +86-15085916661, Email: yuboky@163.com
Ruiyi Lin, Tel: +86-14759103866, Email: linruiyi@fafu.edu.
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Received: 26 March 2024 • Revised: 12 May 2024 • Accepted: 18 June 2024 |
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| Abstract |
Objective
The objective of this study was to unravel the genetic traits of Guanling cattle, pinpoint genes advantageous for muscle growth, and lay a foundation for the preservation of genetic diversity and further analysis of regulation mechanism of important economic traits in local cattle breed.
Methods
In this study, we sequenced the whole genome of 3 Guanling cattle in Guizhou province using the Illumina HiSeq cBo sequencing platform. And, high- multiplex polymerase chain reaction technology was employed to detect high-quality single nucleotide polymorphism (SNP) sites of other 55 Guanling cattle.
Results
Our study identified 166,411 non-synonymous SNPs (nsSNPs) and 42,423 insertions and deletions (indels). Through SNP annotation, gene function enrichment analysis, and comparing with Simmental, Angus, and Limousin cattle, we identified six genes (LEPR, AKAP9, SIX4, SPIDR, PRG4, FASN) which are potentially influential on meat quality traits, playing crucial roles in muscle growth, fat metabolism, and bodily support. We also examined polymorphisms at seven SNP sites in Guanling cattle and found that all seven were in Hardy–Weinberg equilibrium.
Conclusion
These findings suggested that these gene sites are stable and widespread in the Guanling cattle population. Our research lays the groundwork for future genetic enhancement and variety identification of Guanling cattle. |
| Keywords:
Gene Screening; Guanling Cattle; Resequencing; Single Nucleotide Polymorphism (SNP) |
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