Identification of single nucleotide variations in the AGPAT6 gene and its association with milk production traits in Murrah buffalo

Abstract

The present study investigated the association of genetic variations within the 5′UTR exons 1-1511, 3′UTR exons 1512-1723 of the sn-1-acylglycerol-3-phosphate-O-acyltransferase 6 (AGPAT6) gene of buffalo with milk production traits, using the PCR-SSCP and Sanger sequencing method. The study revealed two unique conformational patterns: ‘1’ and ‘2’ in 100 Murrah buffaloes. Ten primer pairs were used for amplification of the AGPAT6 gene and in total nine single nucleotide polymorphisms (SNPs) were identified: viz., two in Exon 4 and seven in Exon8. The frequency of SSCP pattern 1 was found to be consistently high in the buffalo population under study. The preliminary results showed substantial variations in the distribution of SSCP variant frequencies of pattern 1 and 2 within Murrah buffaloes. However, these variants of exon4 and exon 8 had non-significant association with milk yield, whereas the same variants in terms of SNPs in the coding region were found to have a significant (P≤0.01) association with fat percentage. This suggests that AGPAT6 affects the milk fat percentage, which is an economically important trait, and that further study of this gene is warranted in Murrah buffaloes. The polymorphisms observed can be used as molecular markers to assist selection.