Genome-wide profiling to identify unique immune markers in Indigenous cattle (Kangayam, Gir, Tharparkar, Sahiwal) vs. exotic (Holstein Friesian), and crossbred cattle (Karan Fries)

This study aims to identify immune signatures in Indigenous cattle breeds (Kangayam, Gir, Tharparkar, and Sahiwal) compared to exotic (Holstein Friesian) and crossbred (Karan Fries) cattle. A total of 6 samples were collected for three different location of each breed, resulting 108 samples (6 breeds x 6 samples x 3 locations) and these samples were pooled into 18 samples (6 breeds x 1 pooled sample x 3 locations) based on locations for whole genome sequencing. Sequencing was performed using an Illumina short-read platform NovoSeq 6000, with quality assessment and preprocessing conducted using FASTQC and Trimmomatic. Reads were mapped to the Bos taurus reference genome (ARS-UCD2.0) using BWA-Mem, and variants were identified using DELLY (structural variants) and FreeBayes (SNPs, MNPs, and indels). The study focuses on detecting common immune-related genomic variations across breeds.