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Genome. 2013 Oct;56(10):592-8. doi: 10.1139/gen-2013-0082. Epub 2013 Aug 2.

Whole genome sequencing of Gir cattle for identifying polymorphisms and loci under selection.

Author information

1
a Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G2P5, Canada.

Abstract

Genetic variation in Gir cattle (Bos indicus) has so far not been well characterized. In this study, we used whole genome sequencing of three Gir bulls and a pooled sample from another 11 bulls to identify polymorphisms and loci under selection. A total of 9 990 733 single nucleotide polymorphisms (SNPs) and 604 308 insertion/deletions (indels) were discovered in Gir samples, of which 62.34% and 83.62%, respectively, are previously unknown. Moreover, we detected 79 putative selective sweeps using the sequence data of the pooled sample. One of the most striking sweeps harbours several genes belonging to the cathelicidin gene family, such as CAMP, CATHL1, CATHL2, and CATHL3, which are related to pathogen- and parasite-resistance. Another interesting region harbours genes encoding mitogen-activated protein kinases, which are involved in directing cellular responses to a variety of stimuli, such as osmotic stress and heat shock. These findings are particularly interesting because Gir is resistant to hot temperatures and tropical diseases. This initial selective sweep analysis of Gir cattle has revealed a number of loci that could be important for their adaptation to tropical climates.

PMID:
24237340
DOI:
10.1139/gen-2013-0082
[Indexed for MEDLINE]
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