Abstract

Ankamali pigs are a domesticated indigenous pig variety from Kerala, recognised for their resistance to diseases, production of lean meat and ability to thrive in tropical humid climates. However, there is still limited understanding of Ankamali pig genome variation, genetic relationships with other pig breeds and the process of domestication. Here, we focus on elucidating the genome-wide variants in Ankamali pig through whole genome sequencing. Whole genome sequencing of the Ankamali pig genome generated 205.66 Gb of raw data. By GATK Haplotype Caller algorithm we identified a total of 26.6 million single nucleotide variants (SNVs) including 21.3 million single nucleotide polymorphisms (SNPs) and 5.3 million InDels. Out of the total number of SNPs obtained, 69.59 per cent were transitions and 30.41 per cent were transversions. During functional annotation of SNVs, 66.19 per cent of the mutations were silent, 33.53 per cent were missense and 0.29 per cent were nonsense mutations. The potential variants identified in this study can facilitate future research into the positive attributes of Ankamali pigs, thereby aiding in the development of more effective conservation strategies.

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