TY - JOUR
T1 - Comparative transcriptome in large-scale human and cattle populations
T2 - Comparative transcriptome in humans and cattle
AU - Yao, Yuelin
AU - Liu, Shuli
AU - Xia, Charley
AU - Gao, Yahui
AU - Pan, Zhangyuan
AU - Canela-Xandri, Oriol
AU - Khamseh, Ava
AU - Rawlik, Konrad
AU - Wang, ShengLi
AU - Li, Bingjie
AU - Zhang, Yi
AU - Pairo-Castineira, Erola
AU - D'Mellow, Kenton
AU - Li, Xiujin
AU - Yan, Ze
AU - Li, Cong-jun
AU - Yu, Ying
AU - Zhang, Shengli
AU - Ma, Li
AU - Cole, John B.
AU - Ross, Pablo J.
AU - Zhou, Huaijun
AU - Haley, Chris S
AU - Liu, George
AU - Fang, Lingzhao
AU - Tenesa, Albert
N1 - Funding Information:
This work was supported in part by AFRI grant numbers 2013-67015-20951, 2016-67015-24886, and 2019-67015-29321, 2020-67015-31398, and 2021-67015-33409 from the USDA National Institute of Food and Agriculture (NIFA) and BARD grant number US-4997-17 from the US-Israel Binational Agricultural Research and Development (BARD) Fund. G.E.L. and C.P.V.T. were supported by appropriated project 8042-31000-001-00-D, “Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection” of the Agricultural Research Service (ARS) of the United States Department of Agriculture (USDA). C.-J.L. was supported by appropriated project 8042-31310-078-00-D, “Improving Feed Efficiency and Environmental Sustainability of Dairy Cattle through Genomics and Novel Technologies” of ARS-USDA. J.B.C. was supported by appropriated project 8042-31000-002-00-D, “Improving Dairy Animals by Increasing Accuracy of Genomic Prediction, Evaluating New Traits, and Redefining Selection Goals” of ARS-USDA. This research used resources provided by the SCINet project of the USDA ARS project number 0500-00093-001-00-D. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. The USDA is an equal opportunity provider and employer. For the purpose of open access, the author has applied a Creative Commons Attribution (CC BY) licence to any Author Accepted Manuscript version arising from this submission.
Funding Information:
We thank Professor Chris Ponting (MRC Human Genetic Unit, The University of Edinburgh) and Dr. Paul M. Vanraden (ARS, USDA) for the valuable comments and suggestions. We thank US dairy producers for providing phenotypic, genomic, and pedigree data through the Council on Dairy Cattle Breeding under ARS-USDA Material Transfer Research Agreement 58-8042-8-007. Access to 1000 Bull Genomes Project data was provided under ARS-USDA Data Transfer Agreement 15443. International genetic evaluations were calculated by the International Bull Evaluation Service (Interbull; Uppsala, Sweden). The review history is available as Additional file 12. Tim Sands was the primary editor of this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.
Funding Information:
A. Khamseh was supported by the XDF program from the University of Edinburgh and Medical Research Council (MC_UU_00009/2). A. Tenesa acknowledged funding from the BBSRC through program grants BBS/E/D/10002070 and BBS/E/D/30002275, MRC research grant MR/P015514/1, and HDR-UK award HDR-9004. O. Canela-Xandri was supported by MR/R025851/1. L. Fang. was partially funded through HDR-UK award HDR-9004 and the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No 801215. This project was partially supported by Agriculture and Food Research Initiative Competitive Grant no. 2020-67015-31398 and 2021-67015-33409 from the USDA National Institute of Food and Agriculture. Y. Zhang. was supported by the earmarked fund for CARS36.
Publisher Copyright:
© 2022, The Author(s).
PY - 2022/8/22
Y1 - 2022/8/22
N2 - BACKGROUND: Cross-species comparison of transcriptomes 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.RESULTS: Here, we systematically analyze and compare 10,830 and 4866 publicly available RNA-seq samples in humans and cattle, respectively, representing 20 common tissues. Focusing on 17,315 orthologous genes, we demonstrate that mean/median gene expression, inter-individual variation of expression, expression quantitative trait loci, and gene co-expression networks are generally conserved between humans and cattle. By examining large-scale genome-wide association studies for 46 human traits (average n = 327,973) and 45 cattle traits (average n = 24,635), we reveal that the heritability of complex traits in both species is significantly more enriched in transcriptionally conserved than diverged genes across tissues.CONCLUSIONS: In summary, our study provides a comprehensive comparison of transcriptomes between humans and cattle, which might help decipher the genetic and evolutionary basis of complex traits in both species.
AB - BACKGROUND: Cross-species comparison of transcriptomes 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.RESULTS: Here, we systematically analyze and compare 10,830 and 4866 publicly available RNA-seq samples in humans and cattle, respectively, representing 20 common tissues. Focusing on 17,315 orthologous genes, we demonstrate that mean/median gene expression, inter-individual variation of expression, expression quantitative trait loci, and gene co-expression networks are generally conserved between humans and cattle. By examining large-scale genome-wide association studies for 46 human traits (average n = 327,973) and 45 cattle traits (average n = 24,635), we reveal that the heritability of complex traits in both species is significantly more enriched in transcriptionally conserved than diverged genes across tissues.CONCLUSIONS: In summary, our study provides a comprehensive comparison of transcriptomes between humans and cattle, which might help decipher the genetic and evolutionary basis of complex traits in both species.
KW - Comparative transcriptome
KW - Gene co-expression
KW - Heritability enrichment
KW - Inter-individual variability
KW - RNA-seq
U2 - 10.1186/s13059-022-02745-4
DO - 10.1186/s13059-022-02745-4
M3 - Article
C2 - 35996157
SN - 1465-6906
VL - 23
SP - 1
EP - 24
JO - Genome Biology
JF - Genome Biology
IS - 1
M1 - 176
ER -