During evolution, organisms evolve mainly through natural and artificial selection, leaving distinctive signatures on genomic coordinates. Such genomic regions offer valuable insights into the molecular mechanisms that influence quantitative traits. India harbours a diverse buffalo population with Murrah breed exhibiting exceptional milk production and quality, notably a high fat and solids-not-fat content. Therefore, the present investigation focused on exploring selection signatures within the genome of the Murrah buffalo through whole-genome resequencing. A total of 17 472 799 SNPs were identified, which were further utilized for identification of selection signatures using site frequency spectrum-based Tajima’s D and Nucleotide Diversity; and linkage disequilibrium-based iHS approaches. A total of 248 regions under selection overlapped with 64 QTLs across various traits (milk, production, reproduction, meat and carcass, health, and exterior) on chromosomes 5, 9, and 17. A majority of the identified QTLs (39) were associated with milk-related traits, with 27 QTLs specifically linked to milk fat content. Notably, genes such as ARHGAP26, ADGRL3, and SUCLG2 mapped within the QTLs under selection are implicated in milk traits, while XPR1 is associated with growth. Hub genes included RPL23A, ADGRL3 (milk); AP3B1, TXN2 (reproduction); CDK6, IGF2R (body confirmation), and HSPA9 (heat tolerance). This study lays the groundwork for targeted breeding efforts aimed at enhancing milk production in buffalo.
Surati et al. (Thu,) studied this question.