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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #364425
Research Project: Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

Title: Probe-based association analysis identifies several deletions associated with average daily gain in beef cattle

Author
item XU, LINGYANG - Chinese Academy Of Agricultural Sciences
item YANG, LIU - Chinese Academy Of Agricultural Sciences
item WANG, LEI - Collaborator
item ZHU, BO - Chinese Academy Of Agricultural Sciences
item CHEN, YAN - Chinese Academy Of Agricultural Sciences
item GAO, HUIJIANG - Chinese Academy Of Agricultural Sciences
item GAO, XUE - Chinese Academy Of Agricultural Sciences
item ZHANG, LUPEI - Chinese Academy Of Agricultural Sciences
item Liu, Ge - George
item LI, JUNYA - Chinese Academy Of Agricultural Sciences

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/20/2018
Publication Date: 1/10/2019
Citation: Xu, L., Yang, L., Wang, L., Zhu, B., Chen, Y., Gao, H., Gao, X., Zhang, L., Liu, G., Li, J. 2019. Probe-based association analysis identifies several deletions associated with average daily gain in beef cattle. BMC Genomics. 20(1):31. https://doi.org/10.1186/s12864-018-5403-5.
DOI: https://doi.org/10.1186/s12864-018-5403-5

Interpretive Summary: Copy number variation (CNV) represents a major source of genomic variation. By studying CNVs in Chinese Simmental beef cattle, we identified their significant assocaitions with a meat growth trait. These results fill our knowledge gaps and provide the foundation for incorporating CNV into the future genetic breeding program. Farmers, scientist, and policy planners who need improve animal health and production based on genome-enable animal selection will benefit from this study.

Technical Abstract: Average daily gain (ADG) is an important trait that contributes to the production efficiency and economic benefits in the beef industry. The molecular mechanisms of ADG have not yet been fully explored because most recent association studies for ADG are based on SNPs or haplotypes. We reported a systematic CNV discovery and association analysis for ADG in Chinese Simmental beef cattle. Our study identified 4,912 nonredundant CNVRs with a total length of ~'248.7 Mb, corresponding to ~8.9% of the cattle genome. Using probe-based CNV association, we identified 24 and 14 significant SNP probes within four deletions and three duplications for ADG, respectively. Among them, we found one common CNV deletion with 89 kb imbedded in LHFPL Tetraspan Subfamily Member 6 (LHFPL6) at 22.9 Mb on BTA12, which has high frequency (12.9%) dispersing across population. CNV selection test using VST statistic suggested this common deletion may be under positive selection in Chinese Simmental cattle. Moreover, this deletion was not overlapped with any candidate SNP for ADG compared with previous SNPs-based association studies, suggesting its important role for ADG. In addition, we identified one rare deletion near gene Growth Factor Receptor-bound Protein 10 (GRB10) at 5.1 Mb on BTA4 for ADG using both probe-based association and region-based approaches. Our results provided some valuable insights to elucidate the genetic basis of ADG in beef cattle, and these findings offer an alternative perspective to understand the genetic mechanism of complex traits in terms of copy number variations in farm animals.