Genetic distance analysis of Lingnan, Arab, and Kedu chicken as parental lines based on mitochondrial DNA

Abstract

Abstract Lingnan, Arab, and Kedu chickens are the main breeds used as parental lines to develop Maron chickens. The genetic distance between Maron chicken parental lines is critical to achieving heterosis. D-Loop Mitochondria’s Hypervariable 1 (HV1) region is a genetic distance marker. This study aims to determine the genetic distance between the Maron chicken parental lines using the mitochondria HV1 marker. A total of 73 blood samples were collected from Lingnan, Arab, and Kedu chicken. In this study, Polymerase Chain Reaction was employed to amplify D-loop HV1 region in mitochondria, followed by DNA sequencing. A maximum likelihood (ML) analysis then used to generate phylogenetic reconstruction. As a result, eight haplotypes were identified, 21 being the highest, and 1 belonging to the lowest. All pairwise comparisons reveal significant population differences (Fst = 0.67 - 0.962). PCA analysis revealed that Lingnan, Arab, and Kedu populations are different from one to another. Then it is concluded that Lingnan, Arab, and Kedu chickens have a significant genetic distance, which can be used to guide the breeding process of Maron chicken.