A novel genetic variant of the goat Six6 gene and its association with production traits in Chinese goat breeds

Abstract

We looked for novel genetic variations within the Six6 gene by PCR-SSCP, DNA sequencing and forced RFLP-PCR and estimated their associations with production traits in 2132 goats of eight indigenous Chinese breeds. A novel single nucleotide polymorphism (NM_001104993.1: g.232T>C) within the goat Six6 gene was identified. The frequencies of allele "C" varied from 0.8621 to 1.000, which were in Hardy-Weinberg equilibrium. Genotype and allele frequencies were found to be significantly different in the breeds. Association analysis revealed a significant relationship between genotypes and cannon circumference in Hainan black goats (P = 0.047); adult individuals with genotype CT showed higher cannon circumference than those with genotype CC. Another significant association of genotypes with five-year-old fiber length was found in Inner Mongolia white cashmere goats (P = 0.002). In addition, individuals with genotype CT had longer fiber length than those with genotype CC. The data revealed that the Six6 gene positively affects growth traits and cashmere traits. Polymorphism of Six6-PstI could be useful as a DNA marker for goat breeding and genetics via marker-assisted selection.