|LIU, MEI - Northwest Agricultural & Forestry University|
|FANG, LINGZHAO - University Of Maryland|
|LIU, SHULI - China Agricultural University|
|PAN, MICHAEL - Collaborator|
|SEROUSSI, EYAL - Collaborator|
|MA, LI - University Of Maryland|
|CHEN, HONG - Northwest Agricultural & Forestry University|
|Liu, Ge - George|
Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/21/2019
Publication Date: 3/7/2019
Citation: Liu, M., Fang, L., Liu, S., Pan, M.G., Seroussi, E., Cole, J.B., Ma, L., Chen, H., Liu, G. 2019. Array CGH-based detection of CNV regions and their potential association with reproduction and other economic traits in Holsteins. BMC Genomics. 20:181. https://doi.org/10.1186/s12864-019-5552-1.
Interpretive Summary: Copy number variation (CNV) represents a major source of genomic variation. By performing one of the first genome-wide association studies based on CNVs called by array CGH in Holstein cattle, we explored their relations with reproduction and other economic traits. These results fill our knowledge gaps and provide the foundation for incorporating CNV into the future dairy cattle 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: Background: Copy number variations (CNVs) are structural variants consisting of large-scale insertions and deletions of genomic fragments. Exploring CNVs and estimating their effects on phenotypes are useful for genome selection but remain challenging in the livestock. Results: We identified 1043 CNV regions (CNVRs) from array comparative genomic hybridization (CGH) data of 47 Holstein bulls. Using a probe-based CNV association approach, we detected 87 CNVRs significantly (Bonferroni-corrected P value < 0.05) associated with at least one out of 41 complex traits. Within them, 39 CNVRs are simultaneously associated with at least 2 complex traits. Notably, 24 CNVRs were markedly related to daughter pregnancy rate (DPR). For example, CNVR661 containing CYP4A11 and CNVR213 containing CTR9, respectively, were associated with DPR and other traits related to reproduction, production, and body conformation. CNVR758 was also significantly related to DPR, with a nearby gene CAPZA3, encoding one of F-actin-capping proteins which play a role in determining sperm architecture and male fertility. We corroborated these CNVRs by examining their overlapped quantitative trait loci and comparing with previously published CNV results. Conclusion: To our knowledge, this is one of the first genome-wide association studies based on CNVs called by array CGH in Holstein cattle. Our results contribute substantial information about the potential CNV impacts on reproduction, health, production, and body conformation traits, which lay the foundation for incorporating CNV into the future dairy cattle breeding program.