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Adaptive divergence in the bovine genome

William Barendse, Sean McWilliam, Rowan J. Bunch, Blair E. Harrison
doi: https://doi.org/10.1101/022764
William Barendse
aCommonwealth Scientific and Industrial Research Organization, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, Queensland 4067, Australia
bSchool of Veterinary Science, University of Queensland, Gatton, Queensland, 4343, Australia
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Sean McWilliam
aCommonwealth Scientific and Industrial Research Organization, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, Queensland 4067, Australia
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Rowan J. Bunch
aCommonwealth Scientific and Industrial Research Organization, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, Queensland 4067, Australia
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Blair E. Harrison
aCommonwealth Scientific and Industrial Research Organization, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, Queensland 4067, Australia
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Abstract

Cattle diverged during the Pleistocene into two subspecies, one in temperate and one in tropical environments. Here we have used next generation sequencing of the indicine subspecies of cattle and compared it to the taurine subspecies. Although 23.8 million single nucleotide polymorphisms (SNP) were found, the number of fixed amino acid substitutions between the taurine and indicine subspecies was low and consistent with the Haldane predictions for adaptive selection rather than with Neutral Theory. We noted 33 regions of enhanced divergence of nonsynonymous SNP between the subspecies, which included an increased rate of deleterious variants. Signals of positive selection were found for genes associated with immunity, including the Bovine Major Histocompatibility Complex, which also showed an increased rate of deleterious amino acid variants. The genes important in sensing the environment, especially the olfactory system, showed a network wide signal of positive selection.

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Posted July 17, 2015.
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Adaptive divergence in the bovine genome
William Barendse, Sean McWilliam, Rowan J. Bunch, Blair E. Harrison
bioRxiv 022764; doi: https://doi.org/10.1101/022764
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Adaptive divergence in the bovine genome
William Barendse, Sean McWilliam, Rowan J. Bunch, Blair E. Harrison
bioRxiv 022764; doi: https://doi.org/10.1101/022764

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