Abstract: India, home to a significant portion of the world's cattle population, boasts a diverse range of Bos indicus cattle breeds. Among them, Sahiwal cattle play a pivotal role, contributing substantially to India's milk production. To enhance genetic improvement and conservation strategies, this study utilized a cost-effective reduced representation next-generation sequencing technique known as Double-digest RAD (ddRAD) sequencing to identify genome-wide single nucleotide polymorphisms (SNPs) and indels in the Sahiwal cattle genome.
A total of 12 unrelated Sahiwal cattle provided blood samples, and genomic DNA was extracted and sequenced following the RAD sequencing protocol. The bioinformatic analysis pipeline included FastQC for quality assessment, PRINSEQ for trimming adapters and barcodes, STACKS for sequence filtering, Bowtie2 for alignment to the Bos indicus reference genome, and Vcftools for variant calling. SNPs were annotated using SnpEff and Ensembl Variant Effect Predictor.
The study generated 94.61 million raw reads, of which 96.28% passed quality control, resulting in 181,975 SNPs identified at a read depth of 10. Genome-wide annotation revealed 1545 SNPs mapped to transcripts, 139,715 in introns, and 111,963 in intergenic regions. The transition/transversion (Ts/Tv) ratio was 2.4682, suggesting potential genomic stability.
Further exploration focused on candidate genes associated with milk yield and fat percentage. A total of 1447 high-quality variants were annotated in 69 genes affecting these traits. Noteworthy genes such as SP110, IFIH1, ITPR2, GHR, LEP, and TRAPPC9 exhibited multiple SNPs, with ITPR2 having the highest count at 157 SNPs, indicating its potential significance in milk production.
