Copy number variation of the CCDC39 gene is associated with growth traits in Chinese cattle

Linyong Hu; Junjian Yu; Rong Huang; Peng Yang; Zijing Zhang; Yanan Chai; Qiaoting Shi; Fuying Chen; Xian Liu; Zhiming Li; Baorui Ru; Eryao Wang; Chuzhao Lei; Wei Peng; Yongzhen Huang

doi:10.1002/vms3.712

Copy number variation of the CCDC39 gene is associated with growth traits in Chinese cattle

Vet Med Sci. 2022 Mar;8(2):917-924. doi: 10.1002/vms3.712. Epub 2022 Mar 2.

Authors

Linyong Hu¹, Junjian Yu², Rong Huang³, Peng Yang², Zijing Zhang⁴, Yanan Chai⁴, Qiaoting Shi⁴, Fuying Chen⁴, Xian Liu⁵, Zhiming Li⁵, Baorui Ru⁵, Eryao Wang⁴, Chuzhao Lei¹, Wei Peng³, Yongzhen Huang²

Affiliations

¹ Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, People's Republic of China.
² College of Animal Science and Technology, Northwest A&F University, Yangling, Qinghai, People's Republic of China.
³ Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, Qinghai, People's Republic of China.
⁴ Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, People's Republic of China.
⁵ Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan, People's Republic of China.

Abstract

Background: Copy number variation (CNV) has become an essential part of genetic structural variation. Coiled-coil domain containing 39 (CCDC39) is a gene that related to the growth and development of organs and tissues. It is identified that it has a CNV region by animal genome resequencing.

Objective: In this study, we detected the phenotypic traits and different distributions of CCDC39 gene copy numbers in five Chinese cattle breeds (Qinchuan (QC) cattle, Yunling (YL) cattle, Xianan (XN) cattle, Pinan (PN) cattle and Jiaxian (JX) cattle).

Methods: Five hundred and six cattle were randomly selected for CNV distribution detection. Blood samples were taken and genomic DNA was extracted. Different tissues were obtained from adult (n = 3) XN cattle, including heart, liver, kidney, skeletal muscle and lung. The genome qPCR experiment was performed with SYBR Green in triplicate. CDNA qPCR was used to detect the expression level of CCDC39 in different tissues and varieties. Using SPSS v20.0 software, the relationship between CCDC39 CNV and the growth traits of PN, XN, QC, NY and YL cattle breeds was analyzed by one-way analysis of variance (ANOVA).

Results: The results showed that the expression of CCDC39 in lung was higher than that in other tissues. The expression in liver and kidney was similar, but the expression in heart and muscle was less. It can be seen that the duplication type of QC cattle CCDC39 CNV is higher than the deletion or normal in the height at hip cross. The normal type of PN cattle in body length and hip width was better than duplication and deletion (p < 0.05). In XN cattle, the deletion type of CNV had superior growth characteristics in heart girth and cannon bone circumference compared with the duplication type and the normal type (p < 0.05).

Conclusion: The study revealed a significant association between CNV of CCDC39 gene and growth traits in different Chinese cattle breeds.

Keywords: CCDC39 gene; Chinese beef cattle; association; copy number variations (CNV); growth trait; mRNA expression.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Body Weight / genetics
Cattle / genetics
China
DNA Copy Number Variations*
Phenotype
Sequence Analysis, DNA / veterinary