Variants, population structure and signatures of selection in Sri Lankan village chicken (Gallus gallus domesticus) and Sri Lankan junglefowl (Gallus lafayettii) as revealed by whole-genome analysis.

In Sri Lanka, village chicken can be identified in household backyard systems and Sri Lankan junglefowl which is endemic for the country can be identified in isolated wild areas. Both two species are categorized under genus Gallus and well adapted to harsh tropical environments. Identification of the unique genomic variants of these environmentally adapted species is an important step for developing country specific commercial poultry lines which can survive under harsh conditions while maintaining high productivity. Hence, this study was conducted to identify the whole genome variants of Sri Lankan village chicken and Sri Lankan junglefowl. 16 local chickens (eleven Sri Lankan village chickens and five Sri Lankan junglefowls) were investigated in this study. Genome sequencing was performed on the Illumina HiSeq 2000/2500/X platforms and the resulted quality-controlled short-read sequences (FASTQ reads) had more than 98% mapping rate with mean sequencing depth of 14.9× ±1 bases against the reference genome: GCF_016699485.2. Over 26.1 million single nucleotide polymorphisms and over 3.3 million Insertions and Deletions were identified for two species with the joint variant calling. Principal Component analyses and the phylogenetic analysis confirmed the distinct genetic differentiation between the two species. Fst and Runs of Homozygosity based selection signatures analysis revealed 432 unique genomic regions under selection for junglefowl and 58 unique genomic regions under selection for village chicken. These findings will contribute to identify genomic linkages between different chicken populations and pave the way of applying those in the development of novel commercial poultry lines.