Genetic features of red and green junglefowls and relationship with Indonesian native chickens Sumatera and Kedu Hitam

Abstract

Background: More than 2,500 breeds of chicken are reared throughout the world as a source of eggs or meat and as pets. The primary ancestor of the present domestic chicken is widely believed to be the red junglefowl, although genetic contributions from other junglefowls cannot be excluded entirely. The reference genome for chicken was obtained from a red junglefowl, the genetic purity of which has been debated. There is, at present, insufficient data to resolve these interesting issues.

Results: In this study, we performed whole-genome sequencing to compare various species and breeds of chicken, including wild red and green junglefowl, as well as the Indonesian native chickens Sumatera and Kedu Hitam and their respective descendants, the American Black Sumatra and Black Java. The data indicate that wild junglefowls have retained their genetic identity, but the Indonesian and American breeds have not. The Black Sumatra and Black Java are now closely related to each other, suggesting loss of genetic identity after export to the United States. In addition, the results indicate that the red junglefowl used as reference genome is more closely related to domestic chickens and apparently different from other wild red junglefowls.

Conclusions: This study illuminates the genetic and phylogenetic relationships among these species. It provides a framework for genetic studies in wild junglefowls and native and domestic chicken breeds.

Keywords: Green junglefowl; Indonesian native chicken; Mitochondrial DNA; Phylogeny; Red junglefowl; SNP; Whole-genome sequencing.

Fig. 1

Chicken populations compared by whole-genome sequencing. a-b: American Black Sumatra (a) and Black Java (c). c: Sumatera chickens from three different geographical regions including Riau, north, and west Sumatra, Indonesia. d: Red junglefowl from west and south Sumatra, Indonesia. e: Kedu Hitam chickens from central Java, Indonesia. f: Red junglefowl from Java, Indonesia. g: Green junglefowl from Madura and east Java, Indonesia. Photos by Jeannette Beranger (a, b), Marka Hidayat (c), M. Fatchur Rohim (d), Maria Ulfah (e), Rahman Hidayat (f), and Reza Aulia Ahmadi (g). Map was retrieved from Wikimedia Commons [https://commons.wikimedia.org/wiki/File:Location_Southeast_Asia.svg]

Fig. 2

Histogram of SNPs (blue), insertions (yellow), deletions (green), and total (red). The number of SNPs and indels were averaged from individuals in each breed, except for Rhode Island Red and White Plymouth Rock. RedJunglefowlS, red junglefowl from Sumatra; RedJunglefowlJ, red junglefowl from Java; GreenJunglefowlM, green junglefowl from Madura; GreenJunglefowlJ, green junglefowl from Java

Fig. 3

Neighbor-joining tree based on 14,554,492 SNPs. Bootstrap values from 100 replicates are shown on internal branches. Abbreviations are defined in Fig. 2. Numbers after the name of a breed are the sample numbers. Colors on labels are colored by breeds. Red junglefowl are in red, green junglefowl are in green, Black Sumatra in blue, Black Java in purple, Sumatera in pink, Kedu Hitam in yellow, and Rhode Island Red, White Plymouth Rock, and White Leghorn are in gray

Fig. 4

Bayesian consensus tree based on mitochondrial genome. Numbers beside internal branches indicate bootstrap values >50 % from 100 replicates (left) and Bayesian posterior probabilities (right). (-) indicates a node not recovered in the maximum-likelihood analysis or bootstrap values <50 %. Abbreviations are defined in Fig. 2. Numbers after the name breed are the sample numbers. Colors on labels are defined in Fig. 3