Karakterisasi Genome Mitokondria dan Analisis Filogenetik Ayam Hitam di Indonesia

Abstract

Indonesian black chickens, including Cemani, Kedu, and Sumatera chickens, represent important local genetic resources with significant value for national livestock development as well as cultural heritage. Despite their biological and cultural importance, information regarding the phylogenetic relationships of Indonesian black chickens, particularly Cemani, Kedu, and Sumatera breeds, remains limited. This study aims to provide a fundamental reference for identifying genetic characteristics associated with specific traits, assigning functional roles to particular genes, and examining phylogenetic relationships to support conservation studies on the origin of Indonesian black chickens. One approach to understanding genetic characteristics associated with specific traits in chickens, particularly black chickens, is through mitochondrial genome analysis. Data collection was conducted from August 2023 to March 2024. The research was carried out at the Genomics and Environment Laboratory, National Research and Innovation Agency (BRIN), Cibinong, Bogor, West Java, Indonesia. The materials used in this study included blood samples from three purebred Cemani chickens, which are part of the genetic collection of the Museum Zoologicum Bogoriense (MZB), BRIN. Samples of Kedu, Sumatera, Javanese black chicken, Sumateran black chicken, as well as Red and Green Junglefowl were obtained from the DNA Data Bank of Japan (DDBJ) under accession number PRJNA306389. Complete mitochondrial genome sequences of other chicken breeds were retrieved from the GenBank database of NCBI, and analyzed with NGS methods. The complete mitochondrial genomes of Cemani and Sumatera black chickens were found to be 16,784 bp in length, while the mitochondrial genome of Kedu chicken was 16,785 bp. The mitochondrial genome annotation of Cemani, Kedu, and Sumatera black chickens revealed a total of 38 genes, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and one non-coding control region. The nucleotide composition of Cemani, Kedu, and Sumatera black chickens showed similar ATCG base patterns, indicating close genetic relationships and a possible common ancestral origin. Phylogenetic analysis of Indonesian black chickens was conducted using a phylogenetic tree. The phylogenetic tree demonstrated that Cemani, Kedu, and Sumatera black chickens exhibit phenotypic variation within the same genetic group. These three breeds showed a high level of genetic similarity and formed a major cluster with strong bootstrap support. The conclusions are Indonesian black chicken populations appear to originate from a common genetic ancestor while still maintaining genetic diversity. These findings provide important information to support breeding programs and conservation efforts for Indonesian black chicken genetic resources.

Keywords: Indonesian Black Chickens, Mitochondrial genome; NGS; phylogenetics, Sumatera chicken