Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of domestication

Prasun Dutta; Andrea Talenti; Rachel Young; Siddharth Jayaraman; Rebecca Callaby; Santosh Kumar Jadhav; Velu Dhanikachalam; Mayakannan  Manikandan; Bhim B.  Biswa; Wai Y. Low; John L. Williams; Elizabeth Cook; Phil Toye; Eileen Wall; Appolinaire Djikeng; Karen Marshall; Alan Archibald; Suresh Gokhale; David Hume; James Prendergast

doi:10.1038/s41467-020-18550-1

Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of domestication

Prasun Dutta, Andrea Talenti, Rachel Young, Siddharth Jayaraman, Rebecca Callaby, Santosh Kumar Jadhav, Velu Dhanikachalam, Mayakannan Manikandan, Bhim B. Biswa, Wai Y. Low, John L. Williams, Elizabeth Cook , Phil Toye , Eileen Wall, Appolinaire Djikeng, Karen Marshall, Alan Archibald, Suresh Gokhale, David Hume, James Prendergast

Research output: Contribution to journal › Article › peer-review

Abstract / Description of output

More people globally depend on the water buffalo than any other domesticated species, and as the most closely related domesticated species to cattle they can provide important insights into the shared evolutionary basis of domestication. Here we sequence the genomes of 79 water buffalo across seven breeds and compare patterns of between breed selective sweeps with those seen for 294 cattle genomes representing 13 global breeds. The genomic regions under selection between cattle breeds significantly overlap regions linked to stature in human genetic studies, with a disproportionate number of these loci also shown to be under selection between water buffalo breeds. Investigation of potential functional variants in the water buffalo genome identifies a rare example of convergent domestication down to the same mutation having independently occurred and been selected for across domesticated species. Cross-species comparisons of recent selective sweeps can consequently help identify and refine important loci linked to domestication.

Original language	English
Article number	4739 (2020)
Number of pages	13
Journal	Nature Communications
Volume	11
Early online date	21 Sept 2020
DOIs	https://doi.org/10.1038/s41467-020-18550-1
Publication status	E-pub ahead of print - 21 Sept 2020

Access to Document

10.1038/s41467-020-18550-1

s41467-020-18550-1 (1)Final published version, 5.2 MBLicence: Creative Commons: Attribution (CC-BY)

XP-EHH and XP-CLR scores across water buffalo and cattle breeds
Prendergast, J. (Creator), Dutta, P. (Creator) & Talenti, A. (Creator), Edinburgh DataShare, 1 Jun 2020
DOI: 10.7488/ds/2849, https://www.bomabrowser.com
Dataset

James Prendergast
- James.Prendergastroslin.ed.acuk
- Royal (Dick) School of Veterinary Studies - Personal Chair of Bioinformatics
Person: Academic: Research Active

Cite this

Dutta, P., Talenti, A., Young, R., Jayaraman, S., Callaby, R., Jadhav, S. K., Dhanikachalam, V., Manikandan, M., Biswa, B. B., Low, W. Y., Williams, J. L., Cook , E., Toye , P., Wall, E., Djikeng, A., Marshall, K., Archibald, A., Gokhale, S., Hume, D., & Prendergast, J. (2020). Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of domestication. Nature Communications, 11, Article 4739 (2020). Advance online publication. https://doi.org/10.1038/s41467-020-18550-1

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title = "Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of domestication",

abstract = "More people globally depend on the water buffalo than any other domesticated species, and as the most closely related domesticated species to cattle they can provide important insights into the shared evolutionary basis of domestication. Here we sequence the genomes of 79 water buffalo across seven breeds and compare patterns of between breed selective sweeps with those seen for 294 cattle genomes representing 13 global breeds. The genomic regions under selection between cattle breeds significantly overlap regions linked to stature in human genetic studies, with a disproportionate number of these loci also shown to be under selection between water buffalo breeds. Investigation of potential functional variants in the water buffalo genome identifies a rare example of convergent domestication down to the same mutation having independently occurred and been selected for across domesticated species. Cross-species comparisons of recent selective sweeps can consequently help identify and refine important loci linked to domestication.",

author = "Prasun Dutta and Andrea Talenti and Rachel Young and Siddharth Jayaraman and Rebecca Callaby and Jadhav, {Santosh Kumar} and Velu Dhanikachalam and Mayakannan Manikandan and Biswa, {Bhim B.} and Low, {Wai Y.} and Williams, {John L.} and Elizabeth Cook and Phil Toye and Eileen Wall and Appolinaire Djikeng and Karen Marshall and Alan Archibald and Suresh Gokhale and David Hume and James Prendergast",

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Dutta, P, Talenti, A, Young, R , Jayaraman, S, Callaby, R, Jadhav, SK, Dhanikachalam, V, Manikandan, M, Biswa, BB, Low, WY, Williams, JL, Cook , E, Toye , P, Wall, E , Djikeng, A, Marshall, K, Archibald, A, Gokhale, S, Hume, D & Prendergast, J 2020, 'Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of domestication', Nature Communications, vol. 11, 4739 (2020). https://doi.org/10.1038/s41467-020-18550-1

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T1 - Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of domestication

AU - Dutta, Prasun

AU - Talenti, Andrea

AU - Young, Rachel

AU - Jayaraman, Siddharth

AU - Callaby, Rebecca

AU - Jadhav, Santosh Kumar

AU - Dhanikachalam, Velu

AU - Manikandan, Mayakannan

AU - Biswa, Bhim B.

AU - Low, Wai Y.

AU - Williams, John L.

AU - Cook , Elizabeth

AU - Toye , Phil

AU - Wall, Eileen

AU - Djikeng, Appolinaire

AU - Marshall, Karen

AU - Archibald, Alan

AU - Gokhale, Suresh

AU - Hume, David

AU - Prendergast, James

PY - 2020/9/21

Y1 - 2020/9/21

N2 - More people globally depend on the water buffalo than any other domesticated species, and as the most closely related domesticated species to cattle they can provide important insights into the shared evolutionary basis of domestication. Here we sequence the genomes of 79 water buffalo across seven breeds and compare patterns of between breed selective sweeps with those seen for 294 cattle genomes representing 13 global breeds. The genomic regions under selection between cattle breeds significantly overlap regions linked to stature in human genetic studies, with a disproportionate number of these loci also shown to be under selection between water buffalo breeds. Investigation of potential functional variants in the water buffalo genome identifies a rare example of convergent domestication down to the same mutation having independently occurred and been selected for across domesticated species. Cross-species comparisons of recent selective sweeps can consequently help identify and refine important loci linked to domestication.

AB - More people globally depend on the water buffalo than any other domesticated species, and as the most closely related domesticated species to cattle they can provide important insights into the shared evolutionary basis of domestication. Here we sequence the genomes of 79 water buffalo across seven breeds and compare patterns of between breed selective sweeps with those seen for 294 cattle genomes representing 13 global breeds. The genomic regions under selection between cattle breeds significantly overlap regions linked to stature in human genetic studies, with a disproportionate number of these loci also shown to be under selection between water buffalo breeds. Investigation of potential functional variants in the water buffalo genome identifies a rare example of convergent domestication down to the same mutation having independently occurred and been selected for across domesticated species. Cross-species comparisons of recent selective sweeps can consequently help identify and refine important loci linked to domestication.

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DO - 10.1038/s41467-020-18550-1

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SN - 2041-1723

VL - 11

JO - Nature Communications

JF - Nature Communications

M1 - 4739 (2020)

ER -

Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of domestication

Abstract / Description of output

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Datasets

XP-EHH and XP-CLR scores across water buffalo and cattle breeds

Profiles

James Prendergast

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