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Identification of novel SNPs and evaluation of allelic frequencies of Myo D gene in Pakistani cattle breeds

Research Paper | December 1, 2017

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Javed Ahmed Ujan, OM Parkash, Shahnawaz Ujjan, Abdul Hameed

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Int. J. Biosci.11( 6), 248-254, December 2017

DOI: http://dx.doi.org/10.12692/ijb/11.6.248-254


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Research on association of candidate genes and their associations with meat characteristics involves many cattle breeds for improving the quality of meat. Present research was performed to identify the Novel SNPs and evaluation of Allelic frequencies of MyoD gene in coding and non-coding regions of the 04 Pakistani cattle breeds. PCR –SSCP technique was employed for the screening of novel SNPs and Genotyping of the bovine samples. The PCR product were separated on agarose gel and photographed under UV-illumination. Hereafter, the PCR product were purified and sequenced on ABI310 genetic analyzer. The sequence was aligned by using MEGA software. We have sequence selected samples of each breed, which include 04 samples of Red Sindhi (RDS), 05 samples of Dhani (DH), 02 samples of Cholistani (CH) and 02, samples of Thari (TH) breed. Overall four sequence variants were observed, one in the coding (exon 2) region (which not only caused the change of Nucleotide c.679G>A and codon GAC>AAC but also altered the amino acid sequence as p.Asp227Asn) and the other three variants were in non-coding (intronic) region (Intronic region T>A, Intronic C>G and Intronic T>A that only altered the Nucleotide but did not cause any change in the codon sequence). In addition, X2 test showed that genotypes in three cattle breeds (RDS, DH, CH is not in Hardy – Weinberg equilibrium (P> 0.05), while, TH breeds were in Hardy-Weinberg equilibrium (P> 0.05), which may be due to the long process of intensive commercial breeding selection.


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Identification of novel SNPs and evaluation of allelic frequencies of Myo D gene in Pakistani cattle breeds

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