Y.A. Tribudi, V.M.A. Nurgiartiningsih, M. Ulfah, M.H. Natsir, D. Maharani, A.P.Z.N.L. Sari, D.N.H. Hariyono, R. Crooijmans, I. Lovadi, D.A. Lestari, A. Ibrahim
1. This study investigated the maternal lineage and genetic diversity of indigenous Indonesian chickens using mitochondrial DNA (mtDNA) D-loop sequences to assess population structure and maternal origins. 2. Fifty-two samples from eight chicken populations were sequenced for the 1231 bp mtDNA D-loop region. A total of 26 haplotypes were identified, with high diversity observed across all populations (Hd = 0.700–0.933). Most chickens, including Tukong, clustered in haplogroup D1, which suggested a shared maternal lineage common to Southeast Asian domesticated chickens. Two individuals (KUB2 and TK2) were positioned in sub-haplogroup D2, indicating sequence divergence. Merawang and Nunukan chickens were grouped into haplogroups A and B, respectively, consistent with haplotypes shared with Chinese and Japanese chickens, pointing to historical maternal introgression, likely via trade or migration. Analysis of molecular variance (AMOVA) revealed that 28.45% of genetic variation existed among populations (Fst = 0.284, p < 0.001), which indicated a moderate but statistically significant population structure. 3. Multiple haplogroups in Indonesian chickens reflect complex maternal origins and past gene flow from outside populations. These findings highlighted the importance of understanding genetic structure to inform the management and characterisation of native breeds. The distinct maternal lineages in Merawang and Nunukan showed historical introductions, while the close relationship among Tukong and Kampung chickens implied interbreeding under extensive rearing systems. © 2026 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
Department of Animal Science, Faculty of Agriculture, Universitas Tanjungpura, Pontianak, Indonesia; Department of Reproduction and Animal Breeding, Faculty of Animal Science, Universitas Brawijaya, Malang, Indonesia; Department of Animal Production and Technology, Faculty of Animal Science, IPB University, Bogor, Indonesia; Department of Feed and Animal Nutrition, Faculty of Animal Science, Universitas Brawijaya, Malang, Indonesia; Department of Animal Breeding and Reproduction, Faculty of Animal Science, Universitas Gadjah Mada, Yogyakarta, Indonesia; Department of Animal Production, Faculty of Animal Husbandry, Universitas Padjadjaran, Sumedang, Indonesia; Department of Animal Science, Faculty of Agriculture, Universitas Khairun, Ternate, Indonesia; Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands; Department of Biology, Faculty of Mathematics and Natural Science, Universitas Tanjungpura, Pontianak, Indonesia; Department of Animal Science, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, Indonesia; Research Centre for Animal Husbandry, Research Organisation of Agriculture and Food, National Research and Innovation Agency (BRIN), Bogor, Indonesia
