Genomic scans for diversity and selection signatures in Indian Red Sindhi cattle

Red Sindhi cattle, a distinguished dairy breed from India, are famous for their resilience in tropical climates and exceptional milk yield. This study utilized double digest restriction site-associated DNA sequencing (ddRADseq) across 96 individuals to explore genome-wide diversity and uncover signatures of selection. The analysis revealed a high proportion of polymorphic SNPs (0.956), moderate nucleotide diversity (π = 0.215 ± 0.114), and a low minor allele frequency (MAF = 0.149 ± 0.128). The analysis of Red Sindhi data showed a steep decline in effective population size (Ne) from 2387 to 125.9 over 13 generations, implying potential bottlenecks and underscoring the urgency of conservation efforts. Employing Tajima's D, composite likelihood ratio (CLR), integrated haplotype score (iHS), and runs of homozygosity (ROH) methods, we identified 490 genomic regions under positive selection, encompassing 1282 genes and aligning with 574 quantitative trait loci (QTLs). Functional annotations highlighted several genes linked to reproduction (RHOU, MND1), production (DOK6, NPFFR2), immune response (BOLA-DYA and BOLA-DMB), and environmental adaptation (HSPA14, NOD2, GCLC, and RPS19BP1). Several MHC class II genes under selection pressure indicate robust immune competence, while stress-response genes supported Red Sindhi's remarkable tolerance to extreme heat. These findings show the breed's strong adaptability and disease resilience, underlining its importance as a valuable genetic resource for improving livestock in challenging environments.