Identification and characterization of SNP in 5’UTR of MLPH gene for goats with different coat colours
Journal Title: Animal Science Papers and Reports - Year 2014, Vol 32, Issue 1
Abstract
Melanophilin (MLPH) gene has been characterized as one of the candidate genes for coat colour dilution in human, mice and dog, but little is known about it in goat. Part of the 5’UTR (650bp, JQ743911) was sequenced leading to identify four polymorphic loci (g.G426A, g.A570G, g.G592T and g.612-614insCTC). The genetic diversity was analysed in 120 individuals of four breeds of goat. The possible transcription factors in the four loci were mined by online tools. The results show that the four loci were in Hardy-Weinberg equilibrium (P>0.05) and there was a significant difference in gene sequence between Jining Grey (JN) and Leizhou Black (LZ) breeds (P < 0.05). JN has the highest allele frequency of A, A, G and insertion CTC at the four loci; and LZ has the highest allele frequency of G, G, T and deletion CTC. JN has the lowest effective allele number and the lowest value of Shannon I at the four polymorphic loci. LZ has the highest effective allele number and the highest Shannon I at the four polymorphic loci. Moreover, JN has the highest Fst and Gst (0.08 and 0.12, respectively) and the lowest Nm (2.80) compared to LZ. In silico analysis showed that the possible transcription factors having a potential binding site in the sequence consisting of A, A and G and insertion CTC in the four polymorphic loci of 5’UTR of MLPH gene were BRN2, CCAT, P, STAT and USF. The sequence consisting of G, G, T and deletion CTC in the 5’UTR region of MLPH formed the possible binding sites of MyoD, c-Myb, v-Myb, AP-1, USF and NKX25. It could be concluded that JN has different gene sequence in the four mutation sites of 5’UTR of MLPH compared to LZ and the mutation caused the variation of possible transcription factors that may play a role in the MLPH gene expression regulation; so JN has dilute, ashen and grey coat colours and LZ is of solid black colour.
Authors and Affiliations
Lanhui Li, Qiang Fu, Xianglong Li, Rongyan Zhou, Yuhong Ren
Keywords
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