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

Association analysis of polymorphism in thyroglobulin gene promoter with milk production traits in riverine buffalo (Bubalus bubalis)

“…This is an important finding, since in India riverine buffalo is a major dairy animal, contributing more than 50% of the total milk produced, mainly due to more liking of buffalo milk taste, having higher fat and protein percentage compared to cattle. Earlier reports have also indicated existence of substantial variation in the TG gene promoter region, across bovine species with some of the changes present within the important putative transcription factor binding sites and fixation of favourable allele for marbling at 422C > T locus in buffalo ( Dubey et al, 2014 ). Taking lead from these earlier findings, the region further − 423 nucleotides upstream was targeted in the present study.…”

“…Overall riverine buffalo sequence exhibited maximum homology with cattle and having similar transcription factors binding sites (Supplementary Table 1). However, deletion of single nucleotide A at the upstream position of 671 nucleotides from exon1 in buffalo ( Dubey et al, 2014 ) as compared to cattle leads to generation of an important transcription factor binding site, SREBP1, reported to be playing an important role in lipid metabolism ( Zhou et al, 2012 ). Further studies are also required to establish the impact of deletion within putative transcription factor SREBP1 binding site, on thyroglobulin gene expression in cattle and buffalo, two important dairy species of India, differing in the fat quality as well as fat contents in meat as well as milk.…”

“…But Holstein sire family in another study did not show significant association between TG variants and milk production traits ( Khatib et al, 2007 ). Previous studies in buffalo, whereas have shown fixation of favourable C allele at 422 locus ( Dubey et al, 2014 ), indicating the need for novel efforts to assess the variability among the genes regulating important production traits in buffalo.…”

“…A set of oligonucleotide primers (forward: 5′-AGAGGGGAAAGGGGGATGACT-3′ and reverse: 5′-GGGGGTGTGGCTTCATAATTC-3′) was designed from the cattle thyroglobulin gene promoter sequence using PrimerSelect program of Lasergene software (DNASTAR Inc., Madison, WI, USA), to amplified 300 bp region, comprising part of promoter region, − 423 bp upstream to exon 1 start site ( Dubey et al, 2014 ). Polymerase chain reaction was performed in a final reaction volume of 25 μL, containing ~ 100 ng of genomic DNA, 5 pmole of each primer, 200 μM of each dNTPs, 2.5 μL of 10 × buffer with 15 mM MgCl 2 and one unit of Taq DNA polymerase (Bangalore Genei, India).…”

“…Each of the identified SSCP variants was sequenced from both ends using both forward and reverse primers and submitted to NCBI, GenBank ( Table 2 ). Multiple sequence alignment of the buffalo sequences along with cattle sequence was carried out using MegAlign program of Lasergene software (DNASTAR, Inc., Madison, WI, USA) and different transcription binding factors were analyzed and compared using GPMiner and p-Match software ( http://gpminer.mbc.nctu.edu.tw/ , http://www.gene-regulation.com/pub/programs.html ), as described previously for buffalo ( Dubey et al, 2014 ).…”