Genetic diversity analysis of the thyroglobulin gene promoter in buffalo and other bovines

Abstract

In total 937bp of the thyroglobulin (TG) gene, including promoter, exon1 and partial intron1 were characterized and compared across four livestock species, cattle, buffalo, yak and mithun. Identity was more than 98% and transcription factor binding sites analysis revealed the presence of variable numbers of potential binding sites in cattle, riverine buffalo, swamp buffalo, yak and mithun. The putative TTF-1 binding sites appeared to be conserved across all the investigated species except for a single C>T variation observed in TG promoter of Indicus cattle. A total of 15 polymorphic sites were observed in cattle and 8 in buffalo, out of which 2 were already reported in cattle and 4 polymorphic sites were common among cattle and buffaloes. The Principal component analysis results based on identified SNPs, revealed a close relationship between Crossbred and Indian Tharparkar breed of cattle as well as between Murrah and Banni breeds of buffalo. Analysis of the previously reported SNP, PsuI (g.−422C>T) marker (378C>T in our studies), associated with low marbling trait of meat in cattle, revealed an average frequency of 95% for the favourable C allele in Indian cattle, while it was fixed in the Indian swamp and riverine buffalo breeds. The study indicates, identification of genetic variation in the promoter region that could potentially affect the TG expression however, the association of the T allele with the fat deposition in Indian cattle and buffalo breeds needs to be verified.