Detection of InDel and CNV of SPAG17 gene and their associations with bovine growth traits

Abstract

Sperm-associated antigen 17 (SPAG17) gene encodes a central pair protein, which is involved in flagellar motility, male fertility and skeletal growth in ruminants. The insertions/deletions (indels) and copy number variations (CNVs) influence phenotypic traits by altering the sequences and copy numbers of functional genes, respectively. This study identified a novel 8-bp indel of SPAG17 gene in 1520 individuals from eight different cattle breeds, as well as a novel CNV region in 355 animals. The correlation analysis of indel showed that the individuals of ID genotype had superior performance traits such as body height (p = 0.038) and body slanting length (p = 0.041) as compared to other genotypes in Xianan cattle. For the CNV, different copy numbers were closely related to the body height in Qinchuan (p = 0.045) and body weight in Xianan (p = 0.036) breeds. Importantly, significant difference was observed between the 8-bp indel and the copy number loss in Xianan breed (p < 0.01). These findings indicated that the variations within the bovine SPAG17 gene can be considered as an effective DNA molecular marker for beef cattle breeding.

Keywords:

• Cattle
• SPAG17
• insertions/deletions (indels)
• copy number variations (CNVs)
• growth traits

Authors’ contributions

conceptualization, Ping Yan and Xianyong Lan; methodology, Xian Guo; software, Jie Pei and Xuezhi Ding; validation, Pengjia Bao and Lin Xiong; formal analysis, Min Chu and Xiaoyun Wu; investigation, Xian Guo and Jie Pei; resources, Guo Xian, Ping Yan and Xianyong Lan; data curation, Jie Pei, Lin Xiong and Xiaoyun Wu; writing-original draft preparation, Xian Guo and Xianyong Lan; writing—review and editing, Ping Yan and Xianyong Lan; visualization, Xian Guo; supervision, Ping Yan and Xianyong Lan; project administration, Xian Guo, Ping Yan and Xianyong Lan; funding acquisition, Xian Guo, Ping Yan and Xianyong Lan.

Acknowledgments

The authors thank M.D. Jin YY for her help in doing some experiments and preparing a part of the draft. The authors also thank the graduates from Prof. Chen Hong’s lab for extracting the genomic DNA and the staff of the different cattle farms for collecting the samples.

Disclosure statement

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

Additional information

Funding

This research was funded by the China Agriculture Research System [CARS-37], the Innovation Project of Chinese Academy of Agricultural Sciences [CAAS-ASTIP-2014-LIHPS-01], the National Natural Science Foundation of China [31672400] and the Central Public-interest Scientific Institution Basal Research Fund [1610322016006].