Genetic basis of immunity in Indian cattle as revealed by comparative analysis of Bos genome.

Indicine cattle (Bos indicus) show notable resilience and disease resistance compared with taurine breeds, but the genomic basis of these traits remains largely unexplored. Identification of genomic elements for immunity will enable future controlled crossbreeding programs using molecular breeding methods. Therefore, we performed a genome-wide comparison among Nelore, Gir, and Hereford breeds using their whole-genome sequences, majorly focusing on immune-related structural and sequence variation. Our aims were to catalog insertions, deletions, and single nucleotide variants (SNVs) that intersect immune loci and known quantitative trait loci (QTLs), identify runs of homozygosity and selective-sweep signals, and prioritize candidate genes for follow-up functional studies. We retrieved whole-genome sequencing data for Nelore breed (n = 14) and Gir breed (n = 20) from NCBI using the SRA toolkit. Reads were checked with FastQC v0.12.1, filtered with Fastp 0.23.4 to remove low-quality bases and adaptors, and retained high-quality reads based on Q20 and Q30. The reads were mapped to the Bos taurus reference (ARS-UCD2.0) with Burrows-Wheeler Aligner - Maximal Exact Matches (BWA-MEM) v0.7.19-r1273; alignments were processed with Samtools 1.19.2 for sorting, duplicate marking, and MAPQ ≥ 20 filtering. Variants (insertions, deletions, SNVs) were called with GATK HaplotypeCaller (GATK v4.4.0.0), hard-filtered, normalized with Bcftools 1.19, and annotated with SnpEff 5.2b and SnpSift v5.2 f. Common variants were identified via in-house Python scripts; immune loci were detected from InnateDB and keyword searches; QTL overlaps were identified using Animal QTLdb; and DAVID was used for GO and KEGG enrichment (P < 0.05). ROH islands were defined in PLINK as regions shared by > 50% of individuals or samples, and selective sweeps were detected with RAiSD; genes overlapping ROH islands and RAiSD peaks were prioritized as candidate selection signatures. GATK v4.4.0.0 identified 1,884,058 indels and 13,997,533 SNVs in Nelore breed, and 1,457,337 indels and 11,627,881 SNVs in Gir breed, with Ti/Tv ratios of ~ 2.26 and ~ 2.25, respectively. Nelore breed has more number of variants than Gir. We observed frameshift insertions in TLR3 and LOC508441 (CD33) in both the breeds and frameshift deletions in JAM3 in Nelore breed and PAX5 in Gir breed. The variants were also identified in the regulatory regions of both breeds. The high-impact SNVs were in CD46 and IL26 genes in Nelore breed, and PLG gene in Gir breed. Genome-wide scans using RAiSD identified selective sweeps in 707 candidate genes in Nelore breed and 165 in Gir breed. Comparing the ROH and RAiSD results, we prioritized the genes ANKRD11, MAGI2, LOC132345096, FOXP2, TCF12, and ATP5PO in Nelore breed, and the genes MEFV and ORIF1 in Gir breed. These genes are found in QTLs linked to milk and health traits. Functional enrichment showed that the genes exhibiting all the three variants belong to immune pathways such as, NF-kappaB signaling, T-cell receptor signaling, and MAPK signaling in both breeds. These results reveal breed-specific genomic variation locating immune loci and its associated QTLs and provide a list of candidate genes and regions for experimental validation and marker development to improve disease resistance and productivity in Indicine cattle.