A single nucleotide polymorphism of CAPN1 gene region 3'UTR in Bali cattle

Abstract

Bali cattle (Bos javanicus), as Indonesian origin genetic resources, is domesticated from banteng (Bibos banteng). Bali cattle have the potential to be developed as producer of premium beef. Genes that have important role in meat quality are calcium-activated neutral protease genes, as known as calpains (CAPN). Calpains are classified as Ca2+ dependent intracellular cysteine proteases, including the ubiquitously expressed μ-calpain (CAPN1) and m-calpain (CAPN2). The purpose of this study was to analyze single nucleotide polymorphism (SNP) region 3'UTR CAPN1 gene in beef cattle. Polymorphism of CAPN1 gene was analyzed by direct DNA sequencing method in 42 Bali cattle that compared with 11 Belgian Blue, 7 Limousine, 12 Pasundan, and 12 Katingan. The result showed that CAPN1 gene has 7 polymorphic SNPs (g.15284 C>T, g.15347 T>G, g.15525 G>A, g.15674 C>T, g. 15853 G>A, g.15905 G>A and g.15915 G>A) in Bali cattle. These SNPs that polymorphic in Bali cattle were monomorphics in Belgian Blue, Limousine, Pasundan and Katingan cattle. Only one SNP g.15853 G>A in Bali cattle was polymophics in Belgian Blue. Deletion was detected that 8 nucleotides deletion (CTCCCTCC) occurred in Bali, Pasundan, and Katingan cattle at position g.15795 - g.15802, while Belgian Blue and Limousine cattle the deletion was not found.