Two novel SNPs identified in STAT1 gene adjoining a QTL for milk production in Holstein Friesian crossbreds of Kerala

We analyzed the effect of a single nucleotide polymorphism, g. C3141T in the 3 & PRIME; UTR of Signal transducer and activator of transcription-1 gene (STAT1) on milk production traits in the Holstein Friesian crossbred cattle of Kerala (n = 144) by association analysis and expression study. The population was genotyped by restriction fragment length polymorphism using Pag1. Association study using the General Linear Model-Analysis of Variance revealed that none of the yield or composition traits analyzed were significantly differed. The expression profile of STAT1 gene in leucocytes of animals bearing homozygous genotypes was compared by quantitative real time PCR using SYBR green chemistry with and relative expression was not found to be significantly differed. The second stage of the study, the STAT1 mRNA spanning 3213 bp was amplified from leucocytes and sequenced (GenBank: MT459802.1). Two novel SNPs were identified; one synonymous mutation in the coding region (g.A1212G) and the other in the 3'UTR (g.T3042C). The novel SNPs might contribute to STAT1 gene regulation mediated by alternate spicing or binding sites for regulatory molecules. The results reiterate the importance of extensive studies of STAT1 gene variants to substantiate the presence of a quantitative trait loci for dairy traits in the vicinity of STAT1 gene.