Genetic variability analysis of indigenous Indonesian chickens and Hy-Line Brown using mitochondrial DNA D-Loop HV1 region
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Abstract. Albani OP, Ismoyowati, Widodo HS, Rahayu S, Purwantini DD. 2025. Genetic variability analysis of indigenous Indonesian chickens and Hy-Line Brown using mitochondrial DNA D-Loop HV1 region. Biodiversitas 26: 2540-2547. Genetic diversity plays a very significant role in the context of sustainable farming and food security. Indonesia is known for its diverse local chicken populations, whose genetic profile reflects their adaptation to the environments in which they live, as well as the various natural selection and breeding factors that differ from one region to another. Therefore, this research was carried out with the aim of knowing the genetic diversity and evolutionary origin of three Indonesian native chickens, namely Kedu Merah, Kampung, and Sentul chicken, based on mtDNA D-Loop sequences and compared it with a commercial stock of Hy-Line Brown laying hens. A total of 160 chickens, consisting of 40 chickens from each population, are analyzed using the PCR-SSCP technique, with the polymorphic results further sequenced. The result showed there are 9 haplotypes distributed across populations, with the Kedu Merah being the most diverse population (He = 0.624) and Hy-Line Brown being the least diverse (He = 0.219). Sequencing revealed that there are at least 19 polymorphic sites distributed along 167 bp of the HV1 region of the D-loop mtDNA sequence. Evolutionary analysis was performed by comparing the sequenced DNA with references from each chicken clade, and the result showed that Kedu Merah, Kampung, and Sentul chicken has a single maternal origin and belong to clade E, which can be traced back to the Indian subcontinent.
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References
Alexander M, Ho SYW, Molak M, Barnett R, Carlborg Ö, Dorshorst B, Honaker C, Besnier F, Wahlberg P, Dobney K, Siegel P, Andersson L, Larson G. 2015. Mitogenomic analysis of a 50-generation chicken pedigree reveals a rapid rate of mitochondrial evolution and evidence for paternal mtDNA inheritance. Biol Lett 11 (10): 20150561. DOI: 10.1098/rsbl.2015.0561.
Al-Jumaili AS, Hanotte O. 2023. The usefulness of maternally inherited genetic markers for phylogeographic studies in village chicken. Anim Biotechnol 34 (4): 863-881. DOI: 10.1080/10495398.2021.2000429.
Antikasari RR, Iskandar R, Subagja H. 2023. Analisis keberlanjutan pada usaha ayam Kampung Unggul Balitnak (KUB) di Kabupaten Cianjur. Jurnal Ilmiah Inovasi 23 (2): 127-136. DOI: 10.25047/jii.v23i2.4033. [Indonesian]
Booker TR, Keightley PD. 2018. Understanding the factors that shape patterns of nucleotide diversity in the house mouse genome. Mol Biol Evol 35 (12): 2971-2988. DOI: 10.1093/molbev/msy188.
Boudali SF, Al-Jumaili AS, Bouandas A, Mahammi FZ, Aoul NT, Hanotte O, Gaouar SBS. 2022. Maternal origin and genetic diversity of Algerian domestic chicken (Gallus gallus domesticus) from North-Western Africa based on mitochondrial DNA analysis. Anim Biotechnol 33 (3): 457-467. DOI: 10.1080/10495398.2020.1803892.
Carvalho G, Repolês BM, Mendes I, Wanrooij PH. 2022. Mitochondrial DNA instability in mammalian cells. Antioxid Redox Signal 36 (13-15): 885-905. DOI: 10.1089/ars.2021.0091.
DeWoody JA, Harder AM, Mathur S, Willoughby JR. 2021. The long?standing significance of genetic diversity in conservation. Mol Ecol 30 (17): 4147-4154. DOI: 10.1111/mec.16051.
Eda M. 2021. Origin of the domestic chicken from modern biological and zooarchaeological approaches. Anim Front 11 (3): 52-61. DOI: 10.1093/af/vfab016.
Elferink MG, Megens H-J, Vereijken A, Hu X, Crooijmans RPMA, Groenen MAM. 2012. Signatures of selection in the genomes of commercial and non-commercial chicken breeds. PLoS One 7 (2): e32720. DOI: 10.1371/journal.pone.0032720.
Febrianto F, Ismoyowati, Mufti M, Prayitno P, Purwantini D. 2018. Polymorphisme gene GH and morphological characteristic of Anas platyrhynchos and Cairina moschata. Anim Prod 20 (1): 17-27. DOI: 10.20884/1.jap.2018.20.1.665.
Garcia E, Wright D, Gatins R, Roberts MB, Pinheiro HT, Salas E, Chen J-Y, Winnikoff JR, Bernardi G. 2021. Haplotype network branch diversity, a new metric combining genetic and topological diversity to compare the complexity of haplotype networks. PLoS One 16 (6): e0251878. DOI: 10.1371/journal.pone.0251878.
Gjøen J, Jensen P. 2024. Social preferences in chickens-Effects of domestication and tameness. Front Anim Sci 5: 1487688. DOI: 10.3389/fanim.2024.1487688.
Godinez CJP, Nishibori M, Matsunaga M, Espina DM. 2019. Phylogenetic studies on Red Junglefowl (Gallus gallus) and native chicken (Gallus gallus domesticus) in Samar Island, Philippines using the mitochondrial DNA D-loop region. J Poult Sci 56 (4): 237-244. DOI: 10.2141/ jpsa.0180131.
Guo X, Xu W, Zhang W, Pan C, Thalacker-Mercer AE, Zheng H, Gu Z. 2023. High-frequency and functional mitochondrial DNA mutations at the single-cell level. Proc Natl Acad Sci USA 120 (1): e2201518120. DOI: 10.1073/pnas.2201518120.
Hata A, Nunome M, Suwanasopee T, Duengkae P, Chaiwatana S, Chamchumroon 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. Sci Rep 11 (1): 2035. DOI: 10.1038/s41598-021-81589-7.
Ibrahim A, Baliarti E, Budisatria IGS, Artama WT, Widayanti R, Maharani D, Tavares L, Margawati ET. 2023. Genetic diversity and relationship among Indonesian local sheep breeds on Java Island based on mitochondrial cytochrome b gene sequences. J Genet Eng Biotechnol 21: 34. DOI: 10.1186/s43141-023-00491-z.
Irwanto R, Marinah, Awanni SRA, Gusnia TM. 2023. Keanekaragaman fenotipe dan daya dukung lingkungan pada ayam lokal di Kecamatan Merawang Kabupaten Bangka. Pendipa J Sci Educ 7 (2): 158-167. DOI: 10.33369/pendipa.7.2.158-167. [Indonesian]
Ismoyowati, Darmanto A, Tugiyanti E, Suhartati FM, Suryapratama W, Sodiq A, Saleh DM, Sumaryadi MY. 2022. The effects of native chicken strains and feed additives on immunity, kidney functions, and blood protein. J Indones Trop Anim Agric 47 (4): 277-289. DOI: 10.14710/jitaa.47.4.277-289.
Ismoyowati, Saleh DM, Rosidi. 2010. Egg production and quality of Kedu chicken based on plumage color reared intensively. In: The 5 th International Seminar on Tropical Animal Production: Community Empowerment and Tropical Animal Industry. Yogyakarta, 19-22 October 2010.
Ismoyowati, Sukardi, Susanto A. 2012. Genetic diversity of Kedu chicken based on phenotypic characteristics and microsatellite loci. Intl J Poult Sci 11 (9): 605-610. DOI: 10.3923/ijps.2012.605.610.
Jeedigunta SP, Minenkova AV, Palozzi JM, Hurd TR. 2021. Avoiding extinction: Recent advances in understanding mechanisms of mitochondrial DNA purifying selection in the germLine. Ann Rev Genomics Hum Genet 22: 55-80. DOI: 10.1146/annurev-genom-121420-081805.
Kanaka KK, Sukhija N, Goli RC, Singh S, Ganguly I, Dixit SP, Dash A, Malik AA. 2023. On the concepts and measures of diversity in the genomics era. Curr Plant Biol 33: 100278. DOI: 10.1016/j.cpb.2023.100278.
Kawabe K, Worawut R, Taura S, Shimogiri T, Nishida T, Okamoto S. 2014. Genetic diversity of mtDNA D-loop polymorphisms in Laotian native fowl populations. Asian-Australas J Anim Sci 27 (1): 19-23. DOI: 10.5713/ajas.2013.13443.
Komiyama T, Ikeo K, Gojobori T. 2003. Where is the origin of the Japanese gamecocks? Gene 317 (1-2): 195-202. DOI: 10.1016/S0378-1119(03)00703-0.
Kossoga KA, Dayo G-K, Bilalissi A, N’nanle O, Oke EO, Tete-Benissan KA. 2023. Genetic diversity and structure of local chicken populations raised in five agroecological zones of Togo. J World's Poult Res 13 (3): 352-363. DOI: 10.36380/jwpr.2023.38.
Liu Y-P, Wu G-S, Yao Y-G, Miao Y-W, Luikart G, Baig M, Beja-Pereira A, Ding Z-L, Palanichamy MG, Zhang Y-P. 2006. Multiple maternal origins of chickens: Out of the Asian jungles. Mol Phylogenet Evol 38 (1): 12-19. DOI: 10.1016/j.ympev.2005.09.014.
Mengistie D, Edea Z, Tesema TS, Dejene G, Dessie T, Jema J, Asefa E, Kim KS, Samuel B, Dadi H. 2022. Genome-wide signature of positive selection in Ethiopian indigenous and European beef cattle breeds. Res Sq 2022: 1-14. DOI: 10.21203/RS.3.RS-2226293/V1.
Nayak SS, Panigrahi M, Rajawat D, Jain K, Sharma A, Bhushan B, Dutt T. 2024. Unique footprints of balancing selection in bovine genome. 3 Biotech 14 (2): 55. DOI: 10.1007/s13205-024-03914-x.
Nguyen TTB, Duc NH, Khoa DVA, Tuong NH, Reyer H, Wimmers K, Thuy DTN, Thuy NTD. 2022. Genetic diversity of Vietnamese native chicken breeds based on mitochondrial DNA D-loop sequence. J Anim Plant Sci 32 (3): 653-662. DOI: 10.36899/JAPS.2022.3.0466.
Noni? M, Šija?i?-Nikoli? M. 2021. Genetic diversity: Sources, threats, and conservation. In: Leal Filho W, Azul AM, Brandli L, Lange Salvia A, Wall T (eds). Life on Land. Encyclopedia of the UN Sustainable Development Goals. Springer, Cham. DOI: 10.1007/978-3-319-95981-8_53.
Oka T, Ino Y, Nomura K, Kawashima S, Kuwayama T, Hanada H, Amano T, Takada M, Takahata N, Hayashi Y, Akishinonomiya F. 2007. Analysis of mtDNA sequences shows Japanese native chickens have multiple origins. Anim Genet 38 (3): 287-293. DOI: 10.1111/j.1365-2052.2007.01604. x.
Okani-Onyejiaka MC, Ogundu UE, Boudali SF, Bamidele O, Ogbuewu IP, Aladi NO. 2022. Genetic diversity of mitochondrial DNA (mtDNA) D-loop sequences in six improved tropically adapted chicken breeds (iTABs) in Imo State, Nigeria. Genet Biodivers J 6 (2): 199-219. DOI: 10.46325/gabj. v6i2.289.
Pathak S. 2024. Influence of Indian culture on Indonesia. Siginjai: Jurnal Sejarah 4 (2): 175-189. DOI: 10.22437/js. v4i2.38730.
Peters J, Lebrasseur O, Irving-Pease EK, Paxinos PD, Best J, Smallman R, Callou C, Gardeisen A, Trixl S, Frantz L, Sykes N, Fuller DQ, Larson G. 2022. The biocultural origins and dispersal of domestic chickens. Proc Natl Acad Sci USA 119 (24): e2121978119. DOI: 10.1073/pnas.2121978119.
Pham LD, Giang TTN, Nguyen VB, Pham TPM, Tran TTT, Nguyen TQC, Van Nguyen K, Do DN. 2023. The complete mitochondrial genome and phylogenetic analyses of to chicken in Vietnam. Genes 14 (5): 1088. DOI: 10.3390/genes14051088.
Ran B, Zhu W, Zhao X, Li L, Yi Z, Li M, Wang T, Li D. 2023. Studying genetic diversity and relationships between Mountainous Meihua chickens using mitochondrial DNA control region. Genes 14 (5): 998. DOI: 10.3390/genes14050998.
Ren T, Nunome M, Suzuki T, Matsuda Y. 2023. Genetic diversity and population genetic structure of Cambodian indigenous chickens. Anim Biosci 35 (6): 826. DOI: 10.3390/genes14050998.
Saelao P, Simone-Finstrom M, Avalos A, Bilodeau L, Danka R, De Guzman L, Rinkevich F, Tokarz P. 2020. Genome-wide patterns of differentiation within and among US commercial honeybee stocks. BMC Genomics 21 (1): 704. DOI: 10.1186/s12864-020-07111-x.
Saha SK, Al Saba A, Hasib M, Al Rimon R, Hasan I, Alam MS, Mahmud I, Nabi AHMN. 2021. Evaluation of D-loop hypervariable region I variations, haplogroups and copy number of mitochondrial DNA in Bangladeshi population with type 2 diabetes. Heliyon 7 (7): e07573. DOI: 10.1016/j.heliyon. 2021.e07573.
Shi X, Ma C, Chen N, Xu M-M, Kambal S, Cai Z-F, Yang Q, Adeola AC, Liu L-S, Wang J, Lu W-F, Li Y, Msalya GM, Lei C, Mwacharo JM, Han J-L, Hanotte O, Zhang Y-P, Peng M-S. 2025. Selection increases mitonuclear DNA discordance but reconciles incompatibility in African cattle. Mol Biol Evol 42 (2): msaf039. DOI: 10.1093/molbev/msaf039.
Sulandari S, Zein MSA, Sartika T. 2008. Molecular characterization of Indonesian indigenous chickens based on mitochondrial DNA displacement (D)-loop sequences. Hayati J Biosci 15 (4): 145. DOI: 10.4308/hjb.15.4.145.
Teinlek P, Siripattarapravat K, Tirawattanawanich C. 2018. Genetic diversity analysis of Thai indigenous chickens based on complete sequences of mitochondrial DNA D-loop region. Asian-Australas J Anim Sci 31 (6): 804-811. DOI: 10.5713/ajas.17.0611.
Zhao X, Wen J, Zhang X, Zhang J, Zhu T, Wang H, Yang W, Cao G, Xiong W, Liu Y, Qu C, Ning Z, Qu L. 2024. Significant genomic introgression from grey junglefowl (Gallus sonneratii) to domestic chickens (Gallus gallus domesticus). J Anim Sci Biotechnol 15 (1): 45. DOI: 10.1186/s40104-024-01006-7.