Vol. 7, Issue 10 (2018)

Author(s):
Anu Bosewell, TV Aravindakshan, Radhika G and Jinty Sukumaran

Abstract:
Indigenous cattle play an important role in the sustenance and welfare of traditional rural farmers. The indicine cattle genetic groups of Kerala, (the southernmost state in India) namely Kasargod dwarf and Vadakara dwarf cattle are believed to possess numerous attributes such as very short stature, disease resistance, heat tolerance, less susceptibility to ticks and lower feed consumption. A detailed genetic study regarding the variations would reveal unique features responsible for its rare phenotypes. The aim of the present study was to perform the whole exome analysis of these native cattle of Kerala using Bovine All Exon capture kit (Agilent Sure Select) followed by sequencing on Illumina HiSeq 2500 platform. We successfully identified a total of 1578008 and 1425816 variants including 1453933 (92.13%) and 1314506 (92.19%) Single Nucleotide Polymorphisms (SNPs) and 124075 (7.86%) and 111310 (7.80%) In Dels (Insertions/Deletions) in Kasargod dwarf and Vadakara dwarf cattle, respectively. Out of the total variants 1245431 and 1134579 were found to be novel in Kasargod dwarf and Vadakara dwarf cattle, respectively. Detailed variant annotation revealed that the majority of the SNPs were located in the intergenic region of the genome. Furthermore the exonic variants were distributed as 63002 and 57516 non synonymous SNPs, 37773 and 35021 missense mutations, 324 and 323 nonsense mutations and 73 and 64 start loss mutations in Kasargod dwarf and Vadakara dwarf cattle, respectively. These findings are particularly interesting because presence of these SNPs might be the probable reason for the peculiar characteristics of these indicine cattle and therefore efforts have to be made to conserve and develop these indigenous cattle resources.