Journal of Animal Breeding and Genomics (J Anim Breed Genom)
Dyah Maharani1*, Simon P. Ginting2, Simon Elieser2, Andi Tarigan2, I Gede Saputra Budisatria1, Antonius2, Dwi Nur Happy Hariyono3, Aprilianna Putri Zahara Nafsina Luvita Sari1
1Faculty of Animal Science, Universitas Gadjah Mada, Jl. Fauna 3, Bulaksumur, Yogyakarta 55281, Indonesia
2Indonesian Goat Research Institute Sei Putih, Galang 20585, North Sumatera, Indonesia
3Department of Animal Science, Faculty of Agriculture, Universitas Khairun, Ternate 97719, Indonesia
Correspondence to Dyah Maharani, E-mail: d.maharani@ugm.ac.id
Volume 5, Number 1, Pages 11-17, March 2021.
Journal of Animal Breeding and Genomics 2021, 5(1), 11-17. https://doi.org/10.12972/jabng.20210002
Received on 22 February, 2021, Revised on 22 February, 2021, Accepted on 31 March, 2021, Published on 31 March, 2021.
Copyright © 2021 Korean Society of Animal Breeding and Genetics.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0).
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.
Boerka goat, CAST gene, Haplotype, Linkage disequilibrium, Single nucleotide polymorphism
This study was conducted in collaboration between the Faculty of Animal Science, Universitas Gadjah Mada and Indonesia Goat Research Center, and funded by the Indonesian Ministry of Research, Technology and Higher Education (No.1713/UN1/DIT-LIT/DIT/LT/2018).