Genome Wide Genetic Variation Analysis of a Brown Leghorn Layer Chicken Line

Genetic variation in livestock is of great importance for future genetic improvement and breeding programs. Genetic variants take many forms, ranging from single base to whole chromosome changes and are categorized as simple (single nucleotide polymorphisms, SNPs and small insertion/deletion, Indels) to complex variants (copy number and structural variations). Advancements in sequencing technologies has enabled the detection of thousands of SNPs and Indels simultaneously from sequenced data. Using a whole genome re-sequencing approach, we studied the genomic regions and genetic variations in a closed population of Brown Leghorn layer chickens. A total of nine chickens were individually sequenced on the Illumina platform. Mapping of pair-end sequence reads to reference genome (Galgal4) were performed with the Burrows-Wheeler Aligner and variant calling was performed using SAMtools. This work will facilitate the genome wide characterization of the genetic variants, identification of potentially functional mutations and their influence on traits of interest. Furthermore, this work will contribute towards comparative genomics analysis between different selected chicken lines.