Identification of genetic variants by whole genome sequencing in Ankamali pigs of Kerala

Abstract

Ankamali pig is a domesticated native variety of Kerala which is well known for its disease resistance, lean meat and adaptability to hot tropical environments. Recent breakthrough in genome sequencing technologies have created unparalleled prospects to characterize individual genomic landscapes and identifying mutations between and within populations. The current study aims to determine the genetic variations in Ankamali pigs using whole genome sequencing. The GATK HaplotypeCaller was used to identify the variants. There were over 26 million (26,604,589) single nucleotide variants (SNVs), including more than 21 million SNPs and over 5 million indels. In Ankamali pigs, the total genome length obtained was more than 2.5 billion with an average variant rate of one variant in every 94 bases. The significance of different variant rate on 18 chromosomes were analysed using the chi-square statistics. The variant rates in Sus scrofa chromosomes10 and 13 were significantly different (p<0.01%) in Ankamali pigs. The significantly higher variable rate on chromosome 10 was observed with one variant per 64 bases. Whereas, significantly lower variable rate was observed on chromosome 13, with one variant in every 122 bases. The variant rate reported on Sus scrofa chromosome 12 (SSC12) was also significantly higher (p<0.05%), having one variant per 72 bases. The variability of many genes and QTLs associated with several haematological traits and meat quality traits located on these chromosomes may contribute the phenotypic and genetic uniqueness of Ankamali animals.

Keywords

• gatk haplotype caller
• single nucleotide variants
• indels
• haematological traits
• missense
• quantitative trait loci (qtl)