title: 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.
authors.affiliation: Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA.
authors.forename: Hyeonsoo
authors.initials: H
authors.lastname: Jeong
authors.affiliation: Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St. 599, Kwan-ak Gu, Seoul, South Korea 151-741, Republic of Korea.|C&K genomics, Main Bldg. #514, SNU Research Park, Seoul 151-919, Republic of Korea.
authors.forename: Kwondo
authors.initials: K
authors.lastname: Kim
authors.affiliation: Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.
authors.forename: Kelsey
authors.initials: K
authors.lastname: Caetano-Anollés
authors.affiliation: Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St. 599, Kwan-ak Gu, Seoul, South Korea 151-741, Republic of Korea.|Department of Agricultural Biotechnology, Seoul National University, Kwan-ak St. 599, Kwan-ak Gu, Seoul 151-742, Republic of Korea.
authors.forename: Heebal
authors.initials: H
authors.lastname: Kim
authors.affiliation: Gyeongsangbuk-do Livestock Research Institute, 186, Daeryongsan-ro, Anjung-myon, Yeoungju, Gyeongsangbuk-do, Republic of Korea.
authors.forename: Byung-Ki
authors.initials: BK
authors.lastname: Kim
authors.affiliation: Gyeongsangbuk-do Livestock Research Institute, 186, Daeryongsan-ro, Anjung-myon, Yeoungju, Gyeongsangbuk-do, Republic of Korea.
authors.forename: Jun-Koo
authors.initials: JK
authors.lastname: Yi
authors.affiliation: Gyeongsangbuk-do Livestock Research Institute, 186, Daeryongsan-ro, Anjung-myon, Yeoungju, Gyeongsangbuk-do, Republic of Korea.
authors.forename: Jae-Jung
authors.initials: JJ
authors.lastname: Ha
authors.affiliation: C&K genomics, Main Bldg. #514, SNU Research Park, Seoul 151-919, Republic of Korea.
authors.forename: Seoae
authors.initials: S
authors.lastname: Cho
authors.affiliation: Gyeongsangbuk-do Livestock Research Institute, 186, Daeryongsan-ro, Anjung-myon, Yeoungju, Gyeongsangbuk-do, Republic of Korea.
authors.forename: Dong Yep
authors.initials: DY
authors.lastname: Oh
mesh_terms: D000818:Animals; D049628:Body Size; D001947:Breeding; D002645:Chickens / Q000235:genetics* / Q000502:physiology; D004251:DNA Transposable Elements; D004528:Egg Shell; D054643:INDEL Mutation; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D000073336:Whole Genome Sequencing / Q000379:methods*
chemical_list: D004251:DNA Transposable Elements