Genetic characterization and phylogenetic study of Lakor goat from Southwest Maluku Regency based on mitochondrial COI gene
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Published:2020
Issue:6
Volume:13
Page:1209-1220
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ISSN:2231-0916
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Container-title:June-2020
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language:en
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Short-container-title:Vet World
Author:
Rumanta Maman1, Kunda Rony Marsyal2, Volkandari Slamet Diah3, Indriawati Indriawati3, Kakisina Pieter2
Affiliation:
1. Department of Biology Education, Study Program, Faculty of Education and Teacher Training, Universitas Terbuka, Jakarta, Indonesia. 2. Department of Biology, Faculty of Mathematics and Natural Science, Universitas Pattimura, Ambon, Indonesia. 3. Research Center for Biotechnology, Indonesian Institute of Sciences, Jakarta, Indonesia.
Abstract
Aim: This study is aimed at characterizing the genetic and phylogenetic structure of Lakor goats as indigenous livestock from the Southwest Maluku Regency based on mitochondrial COI gene sequences.
Materials and Methods: The genomes of 103 follicle samples from Lakor goats, collected from Lakor Island, were analyzed. The polymerase chain reaction was used to amplify 1548 bp of the mitochondrial COI gene using two primer pairs (COIA and COIB). Following sequencing, genetic variation and phylogenetic relationship were established using MEGA version X software.
Results: The results of multiple COI gene alignment of the total sequences identified four polymorphic nucleotides that function as genetic markers between individual animals within the Lakor goat population. These correspond to positions 228 (A-G), 519 (G-A), 900 (C-T), and 1266 (T-C). Phylogenetic signals based on the COI gene showed that Lakor goat breed is a monophyletic group or single clade with a bootstrap value of 100% by the neighbor-joining (NJ) and maximum likelihood (ML) evolutionary models. This data indicated that evolutionarily, the Lakor goat breed has a very close kinship with three goat breeds from China: The Meigu goat (KM 244714.1), Chinese Tibet (Capra hircus) (KJ 940969.1), and C. hircus (KP 677510.1). Phylogenetic information based on the cladistics system classified the Lakor goat as a single clade (monophyletic group). The low-genetic diversity within populations indicates that there has been an inbreeding depression occurring at a very high frequency.
Conclusion: We conclude that the Lakor goat may be divided into a single clade or monophyletic group based on the COI gene sequence. Four nucleotides were identified that can be used as genetic markers among individual animals within the Lakor goat population, as well as C. hircus and others as derived from GenBank data. The Lakor goat population has a high level of inbreeding depression as a result of geographical isolation, which supports the formation of a monophyletic group with different genetic characteristics, and does not allow the introduction of males from other breeds. Phylogenetic signals indicated that Capra aegagrus (bezoar) is the ancestor of the native goats in Indonesia, including the Lakor goats.
Funder
Lembaga Penelitian dan Pengabdian Kepada Masyarakat
Publisher
Veterinary World
Subject
General Veterinary
Reference56 articles.
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