Whole-genome selective sweeps analysis in Pakistani Kamori goat

Natural and artificial selection fix certain genomic regions of reduced heterozygosity which is an initial process in breed development. The primary goal of the current study is to identify the genomic selection signatures under positive selection and underlying genes in the Pakistani Kamori goat breed. High throughput whole-genome pooled-seq of Kamori (n = 12) and Bezoar (n = 8) was carried out. Raw fastq files underwent quality checks, trimming, mapping against reference genome, SNPs calling against Bezoar goat and allele frequency calculation. Selection sweeps were identified by applying pooled heterozygosity (Hp) and Tajima's D (TD) on Kamori while regions under divergent selection between Kamori & Bezoar were observed by Fixation Index (FST) analysis. Genome sequencing yielded 619,031,812 reads of which, 616,624,284 were successfully mapped. A total of 98,574 autosomal selection signals were detected; 32,838 from Hp and 32,868 from each FST & TD statistics. Annotation of the regions (with threshold −ZHp > 5, −ZTD > 2.5 & -ZFST < −4.5) detected 92 candidate genes. The top hits harbor Chr.6, 8, 12 & 26 having genes associated with body weight (GLIS3), coat color (DOCK8) and multidrug resistance-associated protein 4-like (LOC102179751 & LOC102180583). Other significant windows harbor milk production, immunity, adaptation and reproduction trait related genes. Current findings highlighted the genomic regions under-selection in Kamori breed which are likely to be associated with its vested traits that can be ameliorated further, by exploring the full genetic potential of this valued species. These may also be propagated to other undefined goat breeds by adopting targeted breeding policies. •Blood sampling, genomic DNA extraction and pooled-sequencing of Pakistani Kamori goat was carried out.•Three statistical methods Hp, TD and, FST were used to detect the genomic selective sweeps in Kamori vs. Bezoar goat.•Total 98,574 autosomal selection signals were detected; 32,838 from Hp and 32,868 from each FST & TD statistics.•Annotation of the regions with threshold (−ZHp > 5, −ZTD > 2.5 & -ZFST < -4.5) detected 92 candidate genes.•The top hits harbor Chr.6, 8, 12 & 26 having genes associated with GLIS3, DOCK8, LOC102179751 and LOC102180583.•Under-selection genes were associated with body mass/height, color, milk, reproduction, immunity, adaptation to environment.