Genome-wide Scan for Selection Signatures Using Tajima’s D and Pooled Heterozygosity in Ankamali Pigs of Kerala State, India

Abstract

Abstract Ankamali pig, a domesticated native variety is found in several parts of Kerala. They are well known for their disease resistance, lean meat and adaptability to hot and humid environmental conditions. Natural and artificial selection over a period of time left unique footprints (selection signatures) in genome resulting in dramatic changes in the phenotype of animals. Detection of artificial selection footprints in genomic regions can provide insights for understanding the function of specific phenotypic traits and better guide animal breeding. The present study is aimed to explore, genome-wide scanning using whole genome sequencing to detect selection signatures and enrichment analysis of selective sweep regions. Genomic DNA was isolated from 12 pigs and pooled after quality checks for WGS. Selective sweep regions were identified by using Tajima’s D (TD) and pooled heterozygosity (Hp) statistics. A total of 437 and 484 selective signals were obtained (with a threshold of –ZTD < -2.32 and -ZHp < -2.32) and more than 600 potential genes were annotated. Several candidate genes associated with body size (PKPD1, MSTN), fertility (INHBB, CSMD1), erythrocyte stability (GYPC) and lipid metabolism (REPIN1) were identified. Gene ontology (GO) terms, including biological process (BP), cellular component and molecular function and KEGG pathway enrichment analyses were conducted. Two hundred sixty-eight enriched GO terms were found in the present study. In KEGG analysis, nine and more than 30 enriched pathways were found using Tajima’s D and pooled Heterozygosity respectively, with herpes simplex infection being the most enriched, followed by Neurotrophin signalling pathway, m TOR signalling pathway etc.