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ARS Home » Midwest Area » Madison, Wisconsin » U.S. Dairy Forage Research Center » Cell Wall Biology and Utilization Research » Research » Publications at this Location » Publication #366280
Research Project: Investigating Microbial, Digestive, and Animal Factors to Increase Dairy Cow Performance and Nutrient Use Efficiency

Location: Cell Wall Biology and Utilization Research

Title: Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle

Author
item LOW, WAI YEE - UNIVERSITY OF ADELAIDE
item TEARLE, RICK - UNIVERSITY OF ADELAIDE
item LIU, CYNTHIA - UNIVERSITY OF ADELAIDE
item KOREN, SERGEY - NATIONAL INSTITUTES OF HEALTH (NIH)
item RHIE, ARANG - NATIONAL INSTITUTES OF HEALTH (NIH)
item BICKHART, DEREK
item Rosen, Benjamin - Ben
item KRONENBERG, ZEV - PHASE GENOMICS, INC
item KINGAN, SARAH - PACIFIC BIOSCIENCES INC.
item TSENG, ELIZABETH - PACIFIC BIOSCIENCES INC.
item THIBAUD-NISSEN, FRANCOISE - NATIONAL CENTER FOR BIOTECHNOLOGY INFORMATION (NCBI)
item MARTIN, FERGAL - EMBL-EBI
item BILLIS, KOSTAS - EMBL-EBI
item GHURYE, JAY - UNIVERSITY OF MARYLAND
item HASTIE, ALEX - BIONANO GENOMICS, INC.
item LEE, JOYCE - BIONANO GENOMICS, INC.
item PANG, ANDY - BIONANO GENOMICS, INC.
item Heaton, Michael - Mike
item PHILLIPPY, ADAM - NATIONAL INSTITUTES OF HEALTH (NIH)
item HIENDLEDER, STEFAN - UNIVERSITY OF ADELAIDE
item Smith, Timothy - Tim
item WILLIAMS, JOHN - UNIVERSITY OF ADELAIDE

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/27/2020
Publication Date: 4/29/2020
Citation: Low, W., Tearle, R., Liu, C., Koren, S., Rhie, A., Bickhart, D.M., Rosen, B.D., Kronenberg, Z.N., Kingan, S.B., Tseng, E., Thibaud-Nissen, F., Martin, F., Billis, K., Ghurye, J., Hastie, A.R., Lee, J., Pang, A., Heaton, M.P., Phillippy, A.M., Hiendleder, S., Smith, T.P., Williams, J.L. 2020. Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle. Nature Communications. 11:2071. https://doi.org/10.1038/s41467-020-15848-y.
DOI: https://doi.org/10.1038/s41467-020-15848-y

Interpretive Summary: Cattle were originally bred as livestock in the fertile crescent nearly 4000 years ago. Two unique types of cattle, Taurus and Indicus, arose from this event. One lineage, Indicus cattle, are better acclimated to heat and drought than the other lineage. Using new methods, we discover a genetic basis for this adaptation. We also provide a new reference genome for Indicus cattle that is similar in quality to the human reference genome. This reference genome will be used in the breeding of more efficient Indicus cattle for meat and milk production in warmer climates. It is likely to be used by geneticists and animal scientists in South America and India, particularly.

Technical Abstract: Inbred individuals were historically chosen to assemble genomes of livestock to circumvent assembly issue caused by haplotype variation. Here we report haplotype-aware assembly strategy from contig to final scaffolds using an Angus cross Brahman hybrid to produce chromosome-level genomes of two economically important cattle breeds. The assemblies enabled genome-wide selective sweep study, identification of structural variants and copy number variants differentiating taurine and indicine animals, and phasing of transcripts to detect allele-specific expression. We discovered an extra copy, positively selected indicus-specific fatty acid desaturase that may explain Bos Indicus adaptation to heat and drought. About 4000 years ago, humans probably interbred Indicus and Taurus cattle for the first time to cope with the multicentury drought. Now, our assemblies paved the way towards precise introduction of beneficial indicus genetic into taurine animals or vice versa and can contribute to the development of cattle that are able to survive climate change.