Skip to main content
ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Publications at this Location » Publication #380749
Research Project: Developing a Systems Biology Approach to Enhance Efficiency and Sustainability of Beef and Lamb Production

Location: Genetics and Animal Breeding

Title: Adaptive selection signatures in river buffalo with emphasis on immune and major histocompatibility complex genes

Author
item REN, YAN - University Of Adelaide
item MACPHILLAMY, CALLUM - University Of Adelaide
item TO, THU-HIEN - Norwegian University Of Life Sciences
item Smith, Timothy - Tim
item WILLIAMS, JOHN - Università Cattolica Del Sacro Cuore
item LOW, WAI YEE - University Of Adelaide

Submitted to: Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/23/2021
Publication Date: 11/1/2021
Citation: Ren, Y., MacPhillamy, C., To, T., Smith, T.P.L., Williams, J.L., Low, W.Y. 2021. Adaptive selection signatures in river buffalo with emphasis on immune and major histocompatibility complex genes. Genomics. 113(6):3599-3609. https://doi.org/10.1016/j.ygeno.2021.08.021.
DOI: https://doi.org/10.1016/j.ygeno.2021.08.021

Interpretive Summary: The development of high quality reference genomes of mammalian species enables comparative analyses that were previously difficult. In order to identify gene gains and losses during evolution that distinguish species, the genome of the river buffalo was aligned with those of goat, pig, human, and cattle. This identified 194 gene families that were expanded specifically in buffalo and 132 that had contracted since the evolutionary divergence of buffalo from cattle. Some of these genes play important roles in protein degradation, the olfactory receptor system, detoxification processes, and the immune system, and may help to explain differences between cattle and buffalo in traits such as disease resistance, heat tolerance, and meat quality. An insertion of a sequence that appears to come from a pathogenic protozoa named Babesia ovata was found in an immunity-related gene in buffalo. The functional consequences of this insertion are not known but provide information to investigate its effects.

Technical Abstract: River buffalo is an agriculturally important species with many traits, such as disease tolerance, which promote its use worldwide. Highly contiguous genome assemblies of the river buffalo, goat, pig, human and two cattle subspecies were aligned to study gene gains and losses and signs of positive selection. The gene families that have changed significantly in river buffalo since divergence from cattle play important roles in protein degradation, the olfactory receptor system, detoxification and the immune system. We used the branch site model in PAML to analyse single-copy orthologs to identify positively selected genes that may be involved in skin differentiation, mammary development and bone formation in the river buffalo branch. The high contiguity of the genomes enabled evaluation of differences among species in the major histocompatibility complex. We identified a Babesia-like L1 LINE insertion in the DRB1-like gene in the river buffalo and discuss the implication of this finding.