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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 #380741

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

Location: Animal Genomics and Improvement Laboratory

Title: Comparative transcriptome in large-scale human and cattle populations

Author
item YAO, YUELIN - University Of Edinburgh
item LIU, SHULI - China Agricultural University
item XIA, CHARLEY - University Of Edinburgh
item GAO, YUHUI - University Of Maryland
item PAN, ZHANGYUAN - University Of California, Davis
item CANELA-XANDRI, ORIOL - University Of Edinburgh
item KHAMESH, AVA - University Of Edinburgh
item RAWLIK, KONRAD - University Of Edinburgh
item WANG, SHENG - Chinese Academy Of Sciences
item LI, BINGJIE - Sruc-Scotland'S Rural College
item ZHANG, YI - China Agricultural University
item PAIRO-CASTINEIRA, EROLA - University Of Edinburgh
item D'MELLOW, KENTON - University Of Edinburgh
item LI, XIUJIN - Zhongkai University
item YAN, ZE - China Agricultural University
item Li, Congjun - Cj
item YU, YING - China Agricultural University
item ZHANG, SHENGLI - China Agricultural University
item MA, LI - University Of Maryland
item Cole, John
item ROSS, PABLO - University Of California, Davis
item ZHOU, HUAIJUN - University Of California, Davis
item HALEY, CHRIS - University Of Edinburgh
item Liu, Ge - George
item FANG, LINGZHAO - University Of Edinburgh
item TENESA, ALBERT - University Of Edinburgh

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/9/2022
Publication Date: 8/22/2022
Citation: Yao, Y., Liu, S., Xia, C., Gao, Y., Pan, Z., Canela-Xandri, O., Khamesh, A., Rawlik, K., Wang, S., Li, B., Zhang, Y., Pairo-Castineira, E., D'Mellow, K., Li, X., Yan, Z., Li, C., Yu, Y., Zhang, S., Ma, L., Cole, J.B., Ross, P.J., Zhou, H., Haley, C., Liu, G., Fang, L., Tenesa, A. 2022. Comparative transcriptome in large-scale human and cattle populations. Nature Genetics. 23:176. https://doi.org/10.1186/s13059-022-02745-4.
DOI: https://doi.org/10.1186/s13059-022-02745-4

Interpretive Summary: Comprehensive analyses of trsnacriptiomes will benefit our understanding of genetic bases for complex traits. We provided the first cattle-human tissue RNA expression patterns. These results fill our knowledge gaps and will benefit both human biomedicine and livestock genetic improvement. 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: Cross-species comparison of the transcriptome is important for elucidating evolutionary molecular mechanisms underpinning phenotypic variation between and within species, yet to date it has been essentially limited to model organisms with relatively small sample sizes. Here, we systematically analyse and compare 10,830 and 4,866 publicly available RNA-seq samples in humans and cattle, respectively, representing 20 common tissues. We demonstrate that the degree of average gene expression, inter-individual variation of expression, genes with expression quantitative trait loci (eQTLs) and gene co-expression networks is generally conserved in humans and cattle. By examining large-scale genome-wide association studies (GWAS) for 46 human traits and 45 cattle traits, we reveal that heritability of complex traits in both species is significantly enriched in transcriptionally conserved rather than diverged genes across tissues. These findings will benefit both human biomedicine and livestock genetic improvement.