NUCLEOTIDE SEQUENCING AND DETECTION OF MUTATION IN CARCASS ASSOCIATED CANDIDATE GENES IN INDIGENOUS CATTLE OF BANGLADESH

Abstract

Carcass related traits are very complex and difficult to measure phenotypically, they are not usually included in selection programs. Several studies have indicated associations between genes associated with carcass traits and the genetic polymorphisms in these genes. However, genetic research on indigenous cattle carcass traits in Bangladesh is scanty. Therefore, this study was carried out to screen polymorphisms of the CACNA2D1 gene for carcass weight, dressing percentage, meat percentage, and backfat thickness and MYF5 for live weight, loin eye height, loin eye area and water holding capacity. To identify and assess the association between polymorphisms and carcass traits a total of 80 animals were randomly selected. Genomic DNA was extracted from collected blood samples using a commercial DNA extraction kit for amplification of the fragments of exon 25 of CACNA2D1 gene and exon 2 of MYF5 gene using Polymerase Chain Reaction (PCR). PCR products were sequenced using DNA sequencing. Phylogenetic analysis was also performed to explore the genetic diversity of different cattle. This preliminary research on polymorphism of the CACNA2D1 gene exon 25 in cattle revealed C1993A, T2058A, C2068A might be helpful as genetic markers in Red Chittagong Cattle (RCC) and Crossbred (RCC × Local) cattle. According to the score in Polyphen2, it can be confidently predicted to be deleterious. The SNP C1993A resulted in a missense mutation leading Leu (L) to 658 Ile (I) amino acid substitution, which may cause possible damage due to the less significant effect of isoleucine in protein synthesis. This detrimental effect may cause a reduction in muscle mass along with body weight. The absence of this mutation in the RCC population may have a positive effect, and carcass quality may be better in RCC than crossbreed as those mutations may negatively impact the cattle population. In case of MYF5 the mutation at the 1795C˃T position, which is intronic, does not cause an amino acid substitution but several recent investigations revealed that SNPs in the intron region had significant associations with carcass and meat quality traits. Results from this study indicate that the CACNA2D1 gene and MYF5 have potential effects on carcass and meat quality traits, opening up possibilities for cattle breeding and improvement in gene-assisted selection and future research is necessary to evaluate other candidate genes. Moreover, the results for cattle carcass traits would be a scientific basis for the conservation and utilization of cattle genetic resources