Whole genome sequencing of Gyeongbuk Araucana, a newly developed blue-egg laying chicken breed, reveals its origin and genetic characteristics

Abstract

Chicken, Gallus gallus, is a valuable species both as a food source and as a model organism for scientific research. Here, we sequenced the genome of Gyeongbuk Araucana, a rare chicken breed with unique phenotypic characteristics including flight ability, large body size, and laying blue-shelled eggs, to identify its genomic features. We generated genomes of Gyeongbuk Araucana, Leghorn, and Korean Native Chicken at a total of 33.5, 35.82, and 33.23 coverage depth, respectively. Along with the genomes of 12 Chinese breeds, we identified genomic variants of 16.3 million SNVs and 2.3 million InDels in mapped regions. Additionally, through assembly of unmapped reads and selective sweep, we identified candidate genes that fall into heart, vasculature and muscle development and body growth categories, which provided insight into Gyeongbuk Araucana’s phenotypic traits. Finally, genetic variation based on the transposable element insertion pattern was investigated to elucidate the features of transposable elements related to blue egg shell formation. This study presents results of the first genomic study on the Gyeongbuk Araucana breed; it has potential to serve as an invaluable resource for future research on the genomic characteristics of this chicken breed as well as others.

Discovery of genomic variations by whole-genome resequencing of the North American Araucana chicken

“…The NAA also had regions with ZH p ≤ -6, indicating strong selection. The KA, being more recently derived from a NAA (a Golden Duckwing Araucana) and WL [15], had ZH p values as low as -4.33, which indicate only the presence of moderate selection. One explanation for the discrepancy in the range of ZH p values between the two groups is the difference in the number of individuals; the NAA group has six chickens, whereas the KA group has only three chickens.…”

“…To examine the genetic architecture of the NAA genome, whole-genome resequencing of six Araucana birds was performed: one tailed and five rumpless, of which four had ear-tufts and two were clean-faced (Table 1). To identify breed specific NAA traits, alignments of the NAA Illumina HiSeq 2000 paired-end reads were compared to the Gyeongbuk/Korean Araucana (KA) and Korean Native Domestic (KD) breeds, as well as the highly inbred WL commercial line [15,16]. Results of the sequence comparison between KA, KD, and WL from PRJNA291174 have been described in Fig 2A and 2B of Jeong H, et al 2016 [15].…”

“…To identify breed specific NAA traits, alignments of the NAA Illumina HiSeq 2000 paired-end reads were compared to the Gyeongbuk/Korean Araucana (KA) and Korean Native Domestic (KD) breeds, as well as the highly inbred WL commercial line [15,16]. Results of the sequence comparison between KA, KD, and WL from PRJNA291174 have been described in Fig 2A and 2B of Jeong H, et al 2016 [15]. The relationship between these chickens seen in 2A and 2B are similar to what was found in our study.…”

Recent advances in avian egg science: A review

“…Jeong et al. ( 2016 ) extended investigations in the expression of this gene to alternative blue-egg layers, noticing that the SLCO1B3 gene was expressed similarly across the breeds. Moreover, the Araucana derivative breed considered by Jeong et al.…”

“…Moreover, the Araucana derivative breed considered by Jeong et al. ( 2016 ) displayed characteristics clearly removed from numerous popular breeds, physical size, flight ability, and egg production being a subset of these. Indeed, the origin of this breed suggests little crossing with other breeds within the investigation, such as Dongxiang from China.…”