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Dyah Maharani,Simon P. Ginting,Simon Elieser,Andi Tarigan,I Gede Saputra Budisatria,Antonius,Dwi Nur Happy Hariyono,Aprilianna Putri Zahara Nafsina Luvita Sari 한국동물유전육종학회 2021 한국동물유전육종학회지 Vol.5 No.1
Calpastatin (CAST) gene has been considered as a candidate gene for meat quality traits in livestock animals. In this study, single nucleotide polymorphisms (SNPs) of the CAST gene were evaluated for determination of haplotype block pattern and linkage disequilibrium in 21 Boer × Kacang (Boerka) crossbred goats. Five SNPs: g.146C>A (SNP1), g.224A>G (SNP2), g.281G>A (SNP3), g.373C>T (SNP4) and g.431G>A (SNP5) were found in CAST gene (620 bp) using direct sequencing. Based on these SNPs, four haplotype block patterns (A, B, C and D) with different SNPs combination were performed. All blocks had high D’prime equal to 1.0. The highest LOD (1.75), r2 (1.00) and haplotype frequency (97.6%) were observed in block A (SNP1&2, SNP1&5 and SNP2&5). The lowest LOD (0.01) and r2 (0.0010) were found in block A (SNP1&4, SNP2&4 and SNP4&5). Block B, C and D had only 3, 2 and 1 SNPs combination, respectively, with a medium haplotype frequency (57.1%) each. Our study demonstrated that the SNPs and their haplotype combinations in the CAST gene could be useful for association studies with meat quality traits.