Genetic characterization and phylogenetic study of Lakor goat from Southwest Maluku Regency based on mitochondrial COI gene

Abstract

<jats:p>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.</jats:p>

Polymorphism of Growth Hormone (GH) Gene in Lakor Goat from Lakor Island of Southwest Maluku Regency

“…Research by Volkandari et al (2019) and Rumanta et al (2020) reported that there is low genetic variation within the Lakor goat population after few generations of selection and domestication. This condition is due to improper breeding mechanisms and broodstock management.…”

“…Currently, the policy being socialized related to the use of genetic information from the GH gene to farmers on Lakor island is controlling breeding mechanisms and broodstock management may be done by selecting buck from neighboring villages and not from the same village as doe. Rumanta et al (2020), reported that on Lakor Island, respective villages have a permanent fence composed of rocks (local name is Lutur) to protect the mixing of livestock between villages. We assume that, in this way, the rate of genetic loss in the Lakor goat population can be reduced.…”

“…Goat is one of the livestock of the principal meat producing animals in Indonesia and has immense contribution to the resource poor section of society for their livelihood. Several goat breeds that have adapted to the environment and geography in the territory of Indonesia, they are Marica, Bengal, Etawah, Kosta, Kacang, Gembrong, Muara, Samosir (Batubara et al, 2013), and Lakor goats (Volkandari et al 2019;Rumanta et al 2020). Budisatria et al (2008), stated that goats are known as livestock that produce meat, milk, and fur, but are also used in traditional and religious ceremonies.…”

Kajian Molekuler Ikan Oreochromis spp. dari Perairan Daratan Merauke-Papua, Berdasarkan DNA Mitokondria Fragmen Gen Sitokrom Oksidase Subunit I

“…Data genetik dapat memberikan kontribusi penting dalam pemahaman konektivitas populasi, strategi konservasi dan pengelolaan, termasuk di dalamnya penentuan daerah konservasi (Díaz-Ferguson et al, 2010). Analisis kekerabatan, sejarah evolusi maupun dinamika evolusi dapat dipelajari melalui rekonstruksi filogenetik (Sohpal, 2013;Rumanta et al, 2020). Pendekatan filogenetik molekuler telah banyak dilakukan dalam mengidentifikasi spesies ikan (Jefri et al, 2015;Saleky et al, 2020;Dailami et al, 2021).…”

“…Rekonstruksi pohon filogenetik Pendekatan filogenetik molekuler dapat digunakan untuk membedakan dan mengidentifikasi spesimen yang sulit diidentifikasi (Jefri et al, 2015). Rekonstruksi pohon filogenetik molekuler memanfaatkan data biomolekuler struktural atau fungsional yang dapat digunakan untuk konstruksi pohon filogenetik (Pardi et al, 2016;Rumanta et al, 2020 filogenetik dan keragaman genetik seluruh sampel yang dianalissi memiliki 1 haplotipe dengan jarak genetik 0,000 -0,0032 pada ikan nila sedangkan pada ikan mujair seluruh sampel memiliki jarak genetik 0,000. DNA barcode dapat digunakan dalam mengidentifikasi dan konfirmasi spesies dalam pengelolaan dan konservasi spesies.…”