Exome wide variant discovery by next generation dna sequencing in Vechur cattle of Kerala
2020
R. S. Reshma | T. V. Aravindakshan | G. Radhika | T. Naicy | K. Raji
Vechur, the native cattle breed of Kerala, India is well-known for economically valuable phenotypic traits like disease resistance, adaptability to hot and humid tropical climatic conditions, low feed requirements and high quality milk. However, genomic information underlying these traits is rare. In the present study, the whole exome sequencing of a Vechur cow using Illumina HiSeq 2500 platform is reported. Comparison of sequences with Bos taurus reference genome assembly (UMD 3.1) identified 1,716,847 variants including 1,578,749 Single Nucleotide Polymorphisms and 138,098 Insertion/Deletions, of which 359,034 variants (20.91%) were novel. Detailed annotation of the identified variants showed that majority were situated in the intergenic region. Out of the 724,808 variants found inside the gene region, 107,880 were exonic variants. In the exonic variant, substantial proportion of non-synonymous (34.83%), frameshift (12.47%), nonsense (0.3%), start loss (0.06%) and stop loss (0.0009%) variants were identified. This information will provide a better understanding of genetic differences responsible for the peculiar phenotypic traits inherent to Vechur cattle
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