Detection of Polymorphisms in , , and Genes and Their Association with Milk Yield and Composition Traits in River Buffalo of Bangladesh.

This study aimed to identify SNPs in the intron, exon, and UTR regions of the , , and genes and to investigate their possible association with milk yield and composition traits in the riverine buffalo of Bangladesh. A total of 150 DNA samples from riverine buffalo were used for PCR amplification with five pairs of primers, followed by association studies using a generalized linear model in R. SNP genotyping was performed by direct sequencing of the respective amplicon. Traits analyzed included DMY, fat%, protein%, and SNF%. This study identified 8 SNPs in (g.7163G>A and g.7271C>T), (g.7809C>T and g.8525C>T) and (g.387642C>T, g.387758A>G, g.409354A>G, and g.409452G>A). Genotypic and allelic frequencies differed significantly for each SNP genotype and did not follow the Hardy-Weinberg principle ( 0.01 or 0.001) in most cases. The g.7163G>A and g.7271C>T SNP genotypes of the gene were significantly associated with milk fat%, with the latter also significantly associated with SNF%. The g.8525C>T polymorphism of the gene significantly affected protein% ( 0.01). Additionally, gene polymorphisms showed significant associations: g.387642C>T with fat% ( 0.05); g.387758A>G and g.409354A>G with protein% ( 0.001) and SNF% ( 0.01); and g.409452G>A with DMY ( 0.001), fat% ( 0.05), and protein% ( 0.01). Reconstructed haplotypes of the gene were significantly associated ( 0.01) with all traits except SNF%. These findings suggest that polymorphisms in these three candidate genes have the potential as molecular markers for improving milk yield and composition traits in the riverine buffalo of Bangladesh.