Genome-wide detection of copy number variations in indigenous Red Sindhi cattle using ddRAD sequencing

In livestock, copy number variations (CNVs) are important structural differences that affect phenotypic variety and adaptation. The genome-wide CNVs in 72 Red Sindhi cattle, an indigenous breed prized for its disease resistance and heat tolerance, were characterised in this study using double-digest restriction-site associated DNA sequencing (ddRAD-seq). The Illumina Novaseq platform was used to sequence the genomic DNA, and CNVs were identified using CNVnator with a 1000 bp bin size. PANTHER and Animal QTLdb were then utilized for functional annotation. A total of 3,269 high-confidence CNVs were found, mostly on autosomes. The highest number of CNVs (205) was detected on chromosome 1. Duplications mainly occurred in larger size classes (100 kb-1 Mb), while deletions were frequent in the 10-100 kb range. All regions contained 253 CNV regions (CNVRs), and 46% of individuals had a significant duplication on chromosome 18 (1-4.43 Mb). These CNVs overlapped with 2,593 genes associated with 112 quantitative trait loci (QTLs) that affected environmental adaptability, immunology, milk production, and reproduction. Znrf1, Snca, and Bola loci are important genes that have been linked to immune response and stress tolerance, underscoring their importance in the robustness of the breed. This study presents the first comprehensive CNV map for Red Sindhi cattle, highlighting the affordability of ddRAD-seq as a native breed genomic research tool. These findings support the use of marker-assisted selection and conservation techniques to produce climate-smart tropical animals.