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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 #379540

Research Project: Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

Title: A comprehensive catalogue of regulatory variants in the cattle transcriptome

Author
item LIU, SHULI - China Agricultural University
item GAO, YAHUI - University Of Maryland
item CANELA-XANDRI, ORIOL - University Of Edinburgh
item WANG, SHENG - Chinese Academy Of Sciences
item YU, YANG - China Agricultural University
item CAI, WENTAO - Chinese Academy Of Agricultural Sciences
item LI, BINGJIE - Sruc-Scotland'S Rural College
item PAIRO-CASTINEIRA, EROLA - University Of Edinburgh
item D'MELLOW, KENTON - University Of Edinburgh
item RAWLIK, KONRAD - University Of Edinburgh
item XIA, CHARLEY - University Of Edinburgh
item YAO, YEULIN - University Of Edinburgh
item LI, XIUJIN - Zhongkai University
item YAN, ZE - University Of Edinburgh
item Li, Congjun - Cj
item Rosen, Benjamin - Ben
item Van Tassell, Curtis - Curt
item Vanraden, Paul
item ZHANG, SHENGLI - China Agricultural University
item MA, LI - University Of Maryland
item Cole, John
item Liu, Ge - George
item TENESA, ALBERT - University Of Edinburgh
item FANG, LINGZHAO - University Of Edinburgh

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/7/2022
Publication Date: 8/11/2022
Citation: Liu, S., Gao, Y., Canela-Xandri, O., Wang, S., Yu, Y., Cai, W., Li, B., Pairo-Castineira, E., D'Mellow, K., Rawlik, K., Xia, C., Yao, Y., Li, X., Yan, Z., Li, C., Rosen, B.D., Van Tassell, C.P., Van Raden, P.M., Zhang, S., Ma, L., Cole, J.B., Liu, G., Tenesa, A., Fang, L. 2022. A comprehensive catalogue of regulatory variants in the cattle transcriptome. Nature Genetics. 54(9):1438-1447. https://doi.org/10.1038/s41588-022-01153-5.
DOI: https://doi.org/10.1038/s41588-022-01153-5

Interpretive Summary: Comprehensive analyses of genetic regulatory variants will benefit our understanding of genetic bases for complex traits. We provided the first cattle Genotype-Tissue Expression atlas. These results fill our knowledge gaps and provide the foundation for incorporating new transcriptome insights into the future animal breeding program. Farmers, scientist, and policy planners who need improve animal health and production based on genome-enabled animal selection will benefit from this study.

Technical Abstract: The characterization of genetic regulatory variants on the transcriptome of livestock is essential for interpreting the molecular mechanisms underlying traits of economic value, and to increase the rate of genetic gain through artificial selection. Here, we build a cattle Genotype-Tissue Expression atlas (cGTEx, http://cgtex.roslin.ed.ac.uk/) for the research community based on 11,642 RNA-seq publicly available datasets from over 100 cattle tissues. We describe the landscape of transcriptome across tissues and report thousands of cis and trans genetic variants associated with gene expression and alternative splicing for 24 tissues. We evaluate the specificity/similarity of these genetic regulatory effects across tissues, and functionally annotate them using a combination of multi-omics data. Finally, we link gene expression in different tissues to 43 economically important traits using a large transcriptome-wide association (TWAS) study to provide novel biological insights into the molecular regulatory mechanisms underpinning agronomic traits in cattle.