Genetic diversity and phylogenetic analysis of Indonesian local and commercial rabbit breeds based on mitochondrial D-loop
This study aimed to evaluate the genetic diversity and phylogenetic relationships among four rabbit breeds raised in Central Java, namely Indonesian Local rabbit (LC), Hycole (HC), Hyla (HL), and New Zealand White (NZ), using mitochondrial D-loop region sequences. A total of 40 blood samples were co...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Diponegoro University
2025
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| Online Access: | http://psasir.upm.edu.my/id/eprint/121061/ http://psasir.upm.edu.my/id/eprint/121061/1/121061.pdf |
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| author | Lestari, D. A. Latifa, A. P. Sutopo, S. Kurnianto, E. Setiatin, E. T. Agustine, A. D. Nabilah, Z. Kamila, F. T. Prahara, P. G. Kamalludin, M. H. Setiaji, A. |
| author_facet | Lestari, D. A. Latifa, A. P. Sutopo, S. Kurnianto, E. Setiatin, E. T. Agustine, A. D. Nabilah, Z. Kamila, F. T. Prahara, P. G. Kamalludin, M. H. Setiaji, A. |
| author_sort | Lestari, D. A. |
| building | UPM Institutional Repository |
| collection | Online Access |
| description | This study aimed to evaluate the genetic diversity and phylogenetic relationships among four rabbit breeds raised in Central Java, namely Indonesian Local rabbit (LC), Hycole (HC), Hyla (HL), and New Zealand White (NZ), using mitochondrial D-loop region sequences. A total of 40 blood samples were collected from rabbits in three regencies in Central Java. DNA was extracted from each sample, followed by gene amplification, Sanger sequencing, and sequence analysis. A 906 bp fragment of the mitochondrial D-loop region was successfully amplified from all individuals. The overall genetic diversity was found to be low, with mean values of k = 4.615, nucleotide diversity (π) = 0.00509 ± 0.00092, and haplotype diversity (Hd) = 0.385 ± 0.070. Genetic distance analysis showed a close relationship among the breeds, ranging from 0.00349 to 0.00610. Two haplotypes (A and B) were identified, and both were shared across all breeds, indicating limited genetic differentiation. Phylogenetic tree reconstruction further demonstrated that the four breeds clustered closely together and were most likely derived from European lineages rather than distinct indigenous origins. In conclusion, rabbits raised in Central Java represent a genetically homogenous group with low diversity, highlighting the need for broader genetic resource management and conservation strategies to ensure long-term population sustainability. |
| first_indexed | 2025-11-15T14:49:58Z |
| format | Article |
| id | upm-121061 |
| institution | Universiti Putra Malaysia |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-15T14:49:58Z |
| publishDate | 2025 |
| publisher | Diponegoro University |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | upm-1210612025-10-24T02:09:05Z http://psasir.upm.edu.my/id/eprint/121061/ Genetic diversity and phylogenetic analysis of Indonesian local and commercial rabbit breeds based on mitochondrial D-loop Lestari, D. A. Latifa, A. P. Sutopo, S. Kurnianto, E. Setiatin, E. T. Agustine, A. D. Nabilah, Z. Kamila, F. T. Prahara, P. G. Kamalludin, M. H. Setiaji, A. This study aimed to evaluate the genetic diversity and phylogenetic relationships among four rabbit breeds raised in Central Java, namely Indonesian Local rabbit (LC), Hycole (HC), Hyla (HL), and New Zealand White (NZ), using mitochondrial D-loop region sequences. A total of 40 blood samples were collected from rabbits in three regencies in Central Java. DNA was extracted from each sample, followed by gene amplification, Sanger sequencing, and sequence analysis. A 906 bp fragment of the mitochondrial D-loop region was successfully amplified from all individuals. The overall genetic diversity was found to be low, with mean values of k = 4.615, nucleotide diversity (π) = 0.00509 ± 0.00092, and haplotype diversity (Hd) = 0.385 ± 0.070. Genetic distance analysis showed a close relationship among the breeds, ranging from 0.00349 to 0.00610. Two haplotypes (A and B) were identified, and both were shared across all breeds, indicating limited genetic differentiation. Phylogenetic tree reconstruction further demonstrated that the four breeds clustered closely together and were most likely derived from European lineages rather than distinct indigenous origins. In conclusion, rabbits raised in Central Java represent a genetically homogenous group with low diversity, highlighting the need for broader genetic resource management and conservation strategies to ensure long-term population sustainability. Diponegoro University 2025 Article PeerReviewed text en cc_by_sa_4 http://psasir.upm.edu.my/id/eprint/121061/1/121061.pdf Lestari, D. A. and Latifa, A. P. and Sutopo, S. and Kurnianto, E. and Setiatin, E. T. and Agustine, A. D. and Nabilah, Z. and Kamila, F. T. and Prahara, P. G. and Kamalludin, M. H. and Setiaji, A. (2025) Genetic diversity and phylogenetic analysis of Indonesian local and commercial rabbit breeds based on mitochondrial D-loop. Journal of the Indonesian Tropical Animal Agriculture, 50 (3). pp. 189-198. ISSN 2087-8273; eISSN: 2460-6278 https://ejournal.undip.ac.id/index.php/jitaa/article/view/76174 10.14710/jitaa.50.3.189-198 |
| spellingShingle | Lestari, D. A. Latifa, A. P. Sutopo, S. Kurnianto, E. Setiatin, E. T. Agustine, A. D. Nabilah, Z. Kamila, F. T. Prahara, P. G. Kamalludin, M. H. Setiaji, A. Genetic diversity and phylogenetic analysis of Indonesian local and commercial rabbit breeds based on mitochondrial D-loop |
| title | Genetic diversity and phylogenetic analysis of Indonesian local and commercial rabbit breeds based on mitochondrial D-loop |
| title_full | Genetic diversity and phylogenetic analysis of Indonesian local and commercial rabbit breeds based on mitochondrial D-loop |
| title_fullStr | Genetic diversity and phylogenetic analysis of Indonesian local and commercial rabbit breeds based on mitochondrial D-loop |
| title_full_unstemmed | Genetic diversity and phylogenetic analysis of Indonesian local and commercial rabbit breeds based on mitochondrial D-loop |
| title_short | Genetic diversity and phylogenetic analysis of Indonesian local and commercial rabbit breeds based on mitochondrial D-loop |
| title_sort | genetic diversity and phylogenetic analysis of indonesian local and commercial rabbit breeds based on mitochondrial d-loop |
| url | http://psasir.upm.edu.my/id/eprint/121061/ http://psasir.upm.edu.my/id/eprint/121061/ http://psasir.upm.edu.my/id/eprint/121061/ http://psasir.upm.edu.my/id/eprint/121061/1/121061.pdf |