Partial sequence analysis of mitochondrial D-loop gene in tukong chicken

Tukong chicken is called the rumples (no tailbone) chicken in Indonesia. This research was done to determine whether the D-loop in mitochondrial DNA might be used to distinguish between the Tukong chicken and other local chickens. The D-loop region's first 630 base pairs were amplified and successfully sequenced. Our research displayed 34 nucleotide variants based on the alignment between the Tukong and GenBank of Gallus (25 accession number) sequences of Indonesian local chicken and several exotic chicken breeds. However, there were no specific mutations for Tukong chicken. The Tajima's neutrality test showed that from 31 sequences and 34 total sites, the nucleotide diversity (π) was 0.013. The phylogenetic analysis by the maximum-likelihood method revealed that the Tukong chicken was in a different clade from the Araucana, Nunukan, and Piao chickens, which have similar rumples phenotypes. Meanwhile, the local chicken of Indonesia (Kampung Sumatera, Pelung, Cemani, and Bekikuk) and the Tukong chicken are closely related. It can be concluded that based on the partial D-loop sequences, the Tukong chicken is more closely related to Indonesian local chicken despite its different morphological appearance.