DNA Barcode of Red Junglefowl Gallus gallus L, 1958 (Aves: Phasianidae) of Sumatra Based on Mitochondrial COI DNA Gene

Jarulis Jarulis(1), Nurmeiliasari Nurmeiliasari(2), Hery Haryanto(3), Iqwati Vilanda(4),

DOI: https://doi.org/10.15294/biosaintifika.v14i2.36530


(1) Department of Biology, Faculty of Mathematics and Natural Sciences, ¬University of Bengkulu, Jalan W. R. Supratman, Kandang Limun, Bengkulu, Indonesia
(2) Department of Animal Science, Faculty of Agriculture, ¬University of Bengkulu, Jalan W. R. Supratman, Kandang Limun, Bengkulu, Indonesia.
(3) Department of Biology, Faculty of Mathematics and Natural Sciences, ¬University of Bengkulu, Jalan W. R. Supratman, Kandang Limun, Bengkulu, Indonesia.
(4) Department of Biology, Faculty of Mathematics and Natural Sciences, ¬University of Bengkulu, Jalan W. R. Supratman, Kandang Limun, Bengkulu, Indonesia.

Abstract

Genetic data of red junglefowl (Gallus gallus) from southern Sumatra is valuable for conservation efforts in Indonesia. A mitochondrial COI DNA gene sequencing was performed to elucidate its genetic character, single nucleotide polymorphism, genetic distance, and phylogeny. Blood samples (±0.5 ml) from 20 individuals of Gallus gallus were taken from the living collections of the people of Bengkulu Province (Central Bengkulu Regency and Seluma Regency) and South Sumatra Province (North Musi Rawas Regency) from May to November 2021. Total DNA isolation followed the procedure of The Spin-Column Protocol Kit uses the Dneasy® Blood and Tissue Kit, Qiagen. DNA replication using the Polymerase Chain Reaction technique with primers (COIGG_F and COIGG_R) using MEGA 10.0 software and Bioedit for data analysis. The results revealed716 conserved sites, 16 variable sites, 9 parsimony sites, and 6 singleton sites from the 732 bp nucleotide sequence. Six specific sites (SNPs) as barcodes for Sumatran Junglefowl were found at sequences 51, 273, 327, 721, 729, and 732. The mean genetic distance between individuals was 0.1%, between populations was 0.8%, between species was 7.4%, and between genera was 15.5%. The red junglefowlof South Sumatra Province and Bengkulu Province are closely related with 98% bootstrapping and separated from other Gallus in the same group (ingroup) with 100% bootstrap. The Gallus-gallus group is quite far apart from the outgroup species in the Phasianidae family with 47-100% bootstrap. Red junglefowl from southern Sumatra has genetic differences from other chickens in the world and these differences can be used as a species barcode and as origin identification the widely traded red jungle fowl.

Keywords

barcoding; deforestation; genetic conservation; illegal trading; Phasianidae

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References

Abinawanto, Zulistiana, T., Lestari, R., Dwiranti, A., Bowolaksono, A. (2022). The genetic diversity of ayam ketawa (Gallus gallus domesticus, Linneaus, 1758) in Bangkalan District, Madura Island, Indonesia. Biodiversitas, 22 (6): 3145-3155.

Ashari, H., & Astuti, D. (2017). Study on Phylogenetic Status of Javan Plover Bird (Charadrius, Charadriidae, Charadriiformes) through DNA Barcoding Analysis. Biosaintifika: Journal of Biology & Biology Education, 9 (1), 49-57.

Astuti, D., & Prijono, S. N. (2018). Diversity of The Ornate Lorikeet (Trichoglossus ornatus) Birds Based on Mitochondrial DNA Protein Coding Gene. Biosaintifika: Journal of Biology & Biology Education, 10(2), 465-471.

Bondoc, O. L. & Santiago, R. C. (2012). The use of DNA barcodes in the evolutionary analysis of domestic breeds and strains of chicken (Gallus gallus domesticus) in the Philippines. Philip Agric Sci, 95 (4): 358-369.

Brisson, J. A., Nuzhdin, S. V., Stern, D. L. (2009). Similar Patterns of Linkage Disequilibrium and Nucleotide Diversity in Native and Introduced Populations of the Pea Aphid Acyrthosiphon pisum. BMC Genetics, 10 (22):1-10.

Dharmayanti, N. L. P. I. (2011). Molecular Phylogenetic; organism taxonomic methods base on evolution history. Wartazoa, 21:1-10. [Indonesian).

Dorji, N., Duangjinda, M., Phasuk, Y. (2012). Genetic characterization of Bhutanese native chickens based on an analysis of Red Junglefowl (Gallus gallus gallus and Gallus gallus spadecieus), domestic Southeast Asian and commercial chicken lines (Gallus gallus domesticus). Genetics and Molecular Biology,35 (3): 603-609.

Eaton, J. A., Balen, B. V., Brickle, N. W., Rheindt, F. E. (2016). Birds of the Indonesian Archipelago. Greater Sundas and Wallace. Lynx Editions. Barcelona.

Ghaheri, M., Kahrizi, D., Yari, K., Babaie, A., Suthar, R. S., Kazemi, E. 2016. A comparative evaluation of four DNA extraction protocols from whole blood sample. Cell. Mol. Biol, 62 (3): 120-124.

Gonçalves, P. F. M., Marques, A. R. O., Matsumoto, T. E., Miyaki, C. Y. (2015). DNA barcoding identifies illegal parrot trade. Journal of Heredity, 106:560-564.

Graur, D. & Li, W. H. (2010). Fundamental of Molecular Evolution Second Edition. Sunderland: Sinauer Associates Inc. pp. 481.

Hall, T. 2011. BioEdit: An important software for molecular biology. GERF Bulletin of Biosciences, 2 (1):60-61.

Hariyanto, S., Adro’i, H., Ali, M., & Irawan, B. (2019). DNA Barcoding: A Study of Guppy Fish (Poecilia reticulata) in East Java, Indonesia. Biosaintifika: Journal of Biology & Biology Education, 11(2), 272-278.

Hata, A., Nunome, M., Suwanasopee, T., Duengkae, P., Chaiwatana, S., Chamchum roon, W., Suzuki, T., Koonawootrittriron, S., Matsuda, Y., Srikulnath K. (2021). Origin and evolutionary history of domestic chickens inferred from a large population study of Thai red junglefowl and indigenous chickens. Scientific Reports, 11:2035.

Huang, Z. & Tu, F. (2016). DNA barcoding and phylogeny of Calidris and Tringa (Aves: Scolopacidae). Mitochondrial DNA, http://dx .doi.org/10.3109/24701394.2016.1155121.1-4.

Huang, Z. & Ruan, R. (2017). DNA barcodes and insights into the phylogenetic relationships of Corvidae (Aves: Passeriformes). Mitochondri al DNA Part A, 15 (44): 1-6.

Jarulis, Solihin, D. D., Mardiastuti, A., Prasetyo, L. B. (2018). DNA barcode of seven Indonesian hornbills species (Aves: Bucerotidae) based on mitochondrial DNA cytochrome oxidase subunit I. HAYATI Journal of Bioscience, 25 (4): 178-187.

Kamagi, D. D. W. (2017). Isolation and Amplification of mtDNA of Red Jungle Fowl and North Sulawesi Lokal Chicken (Gallus gallus). Sains Journal, Mathematics & Education, 5 (2): 162-167. [Indonesian].

Kress, W. J., Robledo, C. G., Uriarte, M., Erickson, D. L. 2014. DNA barcodes for ecology, evolution, and conservation. Trends in Ecology & Evolution, xxx (x): 1-11.

Kumar, S., Stecher, G., Li, M., Knyaz, C., Tamura, K. (2018). MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol, 35:1547-1549. DOI: 10.1093/molbev/msy096.

Lawal, R. A., Al-Atiyat, R. M., Aljumaah, R. S., Silva, P., Mwacharo, J. M., Hanotte, O. (2018). Whole Genome Resequencing of Red Junglefowl and Indigenous Village Chicken Reveal New Insights on the Genome Dynamics of the Species. Frontiers in Genetics, 9: 264.

Li, X., Huang, Y., Lei, F. 2015. Comparative mitochondrial genomics and phylogenetic relationships of the Crossoptilon species (Phasianidae, Galliformes). BMC Genomics, 16 (42): 1-12.

Natalia, R. A., Naharuddin, Rosyid, A. (2020). Population of Red Jungle Fowl (Gallus Gallus) in the Forest Area of Tonusuke Village, Pamona Pusalemba District, Poso Regency. Warta Rimba Journal, 8 (1): 64-68. [Indonesian].

Nei, M. & Kumar, S. (2000). Molecular Evolution and Phylogenetics. Oxford University Press. United Kingdom.

Phuc, H. N. & Berres, M. E. (2018). Genetic structure in Red Junglefowl (Gallus gallus) populations: Strong spatial patterns in the wild ancestors of domestic chickens in a core distribution range. Ecology and Evolution, 8: 6575-6588.

Putranto, H. D., Hasibuan, G. P., Yumiati, Y., Setianto, J., Brata, B., Kurniati, N., Hakiki, F. F. (2017). The estimation of dynamical distribution of domesticated Burgo chicken population in Bengkulu coastal area, Indonesia. Biodiversitas, 8 (2): 458-464.

Rangkuti, N. A., Hamdan, Daulay, A. H. (2016). Identification of morphometrics and genetic distance of Kampung chickens in South Labuhanbatu. J Integrated Anim Husb, 3 (1): 96-119.

Riztyan, Kawabe, K., Shimogiri, Kawamoto, Y., Rerkamnuaychoke, Nishida, T., Okamoto, S. (2014). Genetic Diversity and Ancestral Relationships of Red Junglefowls and Domestic Chickens in Southeast Asia. J. Poult. Sci., 51: 369-374.

Setianto, J., Sutriyono, Prakoso, H., Zain, B. (2016). Identification of the origins of the Red Jungle Fowl raised by the community in Seluma District. Journal of Farm Science Indonesia, 11 (2): 141-152. [Indonesian].

Setianto, J., Zain, B., Sutriyono, Prakoso, H. (2017). Domestication of red jungle fowl: A case study of the red jungle fowl chicks procurement by the communities in Central Bengkulu, Indonesia. Biodiversitas, 18 (1): 183-189.

Suhadi, M. (2019). Study on catching Red Jungle Fowl in Kaur Regency, Bengkulu. Wahana Farm Journal, 3 (2): 9-13. [Indonesian].

Sulandari, S. & Zein, M. S. A. (2009). Mitochondria DNA D-loop analysis for positioning Red Jungle Fowl in chicken domestication in Indonesia. Farm Media, 32 (1): 31-39. [Indonesian].

Sulandari, S., Zein, M. S. A, Sartika, T. (2008). Molecular characterization of Indonesian indigenous chickens based on mitochondrial DNA displacement (D)-loop sequences. Hayati Journal of Biosciences, 15 (4): 145-154.

Susanti, R., Iswari, R. S., Fibriana, F., Indriawati. (2018). The duck cytochrome oxidase I (COI) gene: Sequence and patterns analysis for potential barcoding tool. Biodiversitas, 19 (3): 997-1003. DOI: 10.13057/biodiv/d1903 31.

Susanti, R., Fibriana, F., Yuniastuti, A. (2017). PCR-RFLP Analysis of D-Loop mtDNA in Indonesian Domestic Waterfowl. Biosaintifika: Journal of Biology & Biology Education, 9(3), 537-544.

Wang, N., Kimball, R. T., Braun, E. L., Liang, B., Zhang, Z. (2013). Assessing Phylogenetic Relationships among Galliformes: A Multigene Phylogeny with Expanded Taxon Sampling in Phasianidae. PLoS ONE 8 (5): e64312.

Waugh, J. (2007). DNA barcoding in animal species: progress, potential and pitfalls. Bioessays, 29: 188-197. DOI:10.1002/bies.20 529.

Zein, M. S. A. (2018). DNA barcode of eagle (Accipitridae) in Indonesia. Ber Biol, 17 (2): 165-173. [Indonesian].

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