Phylogenetic perspectives of rare Tukong rumpless chickens in Indonesia based on complete mitochondrial DNA D-loop sequences

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.