title: Multiple maternal origins of Indonesian crowing chickens revealed by mitochondrial DNA analysis.
abstract: The utilization of Indonesian crowing chickens is increasing; as such, assessing their genetic structures is important to support the conservation of their genetic resources. This study analyzes the matrilineal evolution of Indonesian crowing chickens based on the mtDNA displacement loop D-loop region to clarify their phylogenetic relationships, possible maternal origin, and possible routes of chicken dispersal. The neighbor-joining tree reveals that the majority of Indonesian crowing chickens belong to haplogroups B, D, and E, but haplogroup D harbored most of them. The Bayesian analysis also reveals that Indonesian crowing chickens derive from Bekisar chicken, a hybrid of the green junglefowl, suggesting the possible contribution of green junglefowl to chicken domestication. There appear at least three maternal lineages of Indonesian chicken origins indicated by the median network profile of mtDNA D-loop haplotypes, namely (1) Chinese; (2) Chinese, Indian, and other Southeast Asian chickens; and (3) Indian, Chinese, Southeast Asian, Japanese, and European chickens. Chicken domestication might be centered in China, India, Indonesia, and other Southeast Asian countries, supporting multiple maternal origins of Indonesian crowing chickens. A systematic breeding program of indigenous chickens will be very important to retain the genetic diversity for future use and conservation.
authors.affiliation: a Department of Animal Production and Technology, Faculty of Animal Science , Bogor Agricultural University , Bogor , West Java , Indonesia.|b Department of Biology, Faculty of Mathematics and Natural Science , Bogor Agricultural University , Bogor , West Java , Indonesia.
authors.forename: Maria
authors.initials: M
authors.lastname: Ulfah
authors.affiliation: b Department of Biology, Faculty of Mathematics and Natural Science , Bogor Agricultural University , Bogor , West Java , Indonesia.
authors.forename: Dyah
authors.initials: D
authors.lastname: Perwitasari
authors.affiliation: a Department of Animal Production and Technology, Faculty of Animal Science , Bogor Agricultural University , Bogor , West Java , Indonesia.
authors.forename: Jakaria
authors.initials: J
authors.lastname: Jakaria
authors.affiliation: a Department of Animal Production and Technology, Faculty of Animal Science , Bogor Agricultural University , Bogor , West Java , Indonesia.|c Directorate General of Livestock and Animal Health , Ministry of Agriculture of Republic Indonesia , South Jakarta , West Java , Indonesia.
authors.forename: Muhammad
authors.initials: M
authors.lastname: Muladno
authors.affiliation: b Department of Biology, Faculty of Mathematics and Natural Science , Bogor Agricultural University , Bogor , West Java , Indonesia.
authors.forename: Achmad
authors.initials: A
authors.lastname: Farajallah
mesh_terms: D063147:Animal Distribution; D000818:Animals; D001499:Bayes Theorem; D001947:Breeding; D002645:Chickens / Q000235:genetics*; D004272:DNA, Mitochondrial / Q000235:genetics*; D000071278:Domestication; D019143:Evolution, Molecular; D005260:Female; D006239:Haplotypes; D007214:Indonesia; D010802:Phylogeny
chemical_list: D004272:DNA, Mitochondrial
keywords: Indigenous crowing chicken; Indonesia; mtDNA D-loop region; origin