Research Article

Molecular cloning, polymorphisms, and association analysis of the promoter region of the STAM2 gene in Wuchuan Black cattle

Published: September 13, 2013
Genet. Mol. Res. 12 (3) : 3651-3661 DOI: https://doi.org/10.4238/2013.September.13.9
Cite this Article:
(2013). Molecular cloning, polymorphisms, and association analysis of the promoter region of the STAM2 gene in Wuchuan Black cattle. Genet. Mol. Res. 12(3): gmr3114. https://doi.org/10.4238/2013.September.13.9
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Abstract

The STAM protein plays an important role in the cytokine-related JAK/STAT pathway. We selected the STAM2 gene as a candidate gene that could be linked to growth performance in analysis of a Chinese cattle breed (Wuchuan Black cattle). We examined genetic variants in the promoter region of the STAM2 gene and their associations with eight growth traits in 159 individuals. Seven SNPs, which included six new SNPs for the SNP database, were found. The core promoter region was identified with a bioinformatic software. This analysis also showed that the SNPs have a significant influence on the function and structure of the STAM2 promoter in terms of RNA secondary structure, CpG island, and transcription factor binding sites. Association analysis demonstrated that G-102A is significantly associated with withers height, heart girth, cannon circumference, chest width, and hip height in this population, which leads us to suggest that G-102A is a useful SNP marker for cattle growth performance. Animals with the genotype AA had higher mean values for withers height, cannon circumference, chest width, and hip height than those with GG and AG genotypes. This SNP of the STAM2 gene could be applied in marker-assisted selection for improving growth performance in cattle.

The STAM protein plays an important role in the cytokine-related JAK/STAT pathway. We selected the STAM2 gene as a candidate gene that could be linked to growth performance in analysis of a Chinese cattle breed (Wuchuan Black cattle). We examined genetic variants in the promoter region of the STAM2 gene and their associations with eight growth traits in 159 individuals. Seven SNPs, which included six new SNPs for the SNP database, were found. The core promoter region was identified with a bioinformatic software. This analysis also showed that the SNPs have a significant influence on the function and structure of the STAM2 promoter in terms of RNA secondary structure, CpG island, and transcription factor binding sites. Association analysis demonstrated that G-102A is significantly associated with withers height, heart girth, cannon circumference, chest width, and hip height in this population, which leads us to suggest that G-102A is a useful SNP marker for cattle growth performance. Animals with the genotype AA had higher mean values for withers height, cannon circumference, chest width, and hip height than those with GG and AG genotypes. This SNP of the STAM2 gene could be applied in marker-assisted selection for improving growth performance in cattle.