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

Area of Science:

• Genomics
• Livestock Genetics
• Bioinformatics

Background:

• Copy number variations (CNVs) are crucial structural genomic differences influencing livestock traits.
• Red Sindhi cattle are indigenous, valued for disease resistance and heat tolerance.
• Understanding CNVs in this breed can enhance adaptation and productivity.

Purpose of the Study:

• To characterize genome-wide CNVs in Red Sindhi cattle.
• To identify genes and quantitative trait loci (QTLs) associated with adaptive traits.
• To establish a comprehensive CNV map for this indigenous breed.

Main Methods:

• Double-digest restriction-site associated DNA sequencing (ddRAD-seq) was employed for genome-wide analysis.
• CNV identification was performed using CNVnator with a 1000 bp bin size.
• Functional annotation utilized PANTHER and Animal QTLdb for gene and QTL association.

Main Results:

• A total of 3,269 high-confidence CNVs were identified, predominantly on autosomes.
• Significant CNVs were found on chromosomes 1 and 18, including duplications and deletions.
• CNVs overlapped with 2,593 genes linked to 112 QTLs affecting adaptability, immunity, milk production, and reproduction.

Conclusions:

• This study provides the first comprehensive CNV map for Red Sindhi cattle.
• ddRAD-seq is an affordable tool for genomic research in native breeds.
• Findings support marker-assisted selection and conservation for climate-smart tropical livestock.