Evaluation of Lipin 1 polymorphisms for genetic markers in association with performance traits in Azikheli buffalo

Abstract

Lipin 1 regulates lipid metabolism in mammary glands. Genetic variation in lipin 1 gene is thought to effect milk production in dairy animals. This study aimed to investigate the association of SNPs in the exon 6 and 8 of the lipin 1 gene with milk yield in Azikheli buffalo from Swat, Pakistan. Azikheli buffaloes raised in a farm were selected based on their milk yield records. Three buffaloes were selected from the high milk yielding group with an average production of 12.96 ± 0.83 liters per day, and three from low yielding group producing 6.12 ± 0.28 liters of milk per day. Genomic DNA was extracted from the blood samples of these buffaloes, which were used to amplify exon 6, 8 the adjacent introns (6, 7 and 8) of the lipin 1 gene. The PCR products was sequenced through sanger sequencing. A total of 45 SNPs were found in the targeted regions of the lipin 1 gene in both high and low yielding buffaloes. Overall, four missense variants (g.62048T>C; Met399Thr and g.62069C>A; Pro406His) were found in the exon 8 of lipin 1 gene in Azikheli buffalo. Milk yield was positive correlated with SNP g.62048T>C; Met399Thr that was more frequent (0.83 vs 0.33) in high milk yielding buffaloes compared to the low yielding group. SNP g.62069C>A; Pro406His was unique to low milk yielding buffaloes suggesting its negative association with milk yield. Moreover, the visualization of 3D structure of the lipin I protein constructed using Phyr2 web server and the Missense 3D analysis identified no structural damages caused by the reported SNPs on the target protein. In conclusion, SNPs g.62048T>C; Met399Thr and g.62069C>A; Pro406His could serve as potential genetic markers for increasing milk productivity in buffaloes.