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

Abstract

Gallus gallus (chicken) is phenotypically diverse, with over 60 recognized breeds, among the myriad species within the Aves lineage. Domestic chickens have been under artificial selection by humans for thousands of years for agricultural purposes. The North American Araucana (NAA) breed arose as a cross between the Chilean “Collonocas” that laid blue eggs and was rumpless and the “Quetros” that had unusual tufts but with tail. NAAs were introduced from South America in the 1940s and have been kept as show birds by enthusiasts since then due to several distinctive traits: laying eggs with blue eggshells, characteristic ear-tufts, a pea comb, and rumplessness. The population has maintained variants for clean-faced and tufted, as well as tailed and rumplessness traits making it advantageous for genetic studies. Genome resequencing of six NAA chickens with a mixture of these traits was done to 71-fold coverage using Illumina HiSeq 2000 paired-end reads. Trimmed and concordant reads were mapped to the Gallus_gallus-5.0 reference genome (galGal5), generated from a female Red Junglefowl (UCD001). To identify candidate genes that are associated with traits of the NAA, their genome was compared with the Korean Araucana, Korean Domestic and White Leghorn breeds. Genomic regions with significantly reduced levels of heterogeneity were detected on five different chromosomes in NAA. The sequence data generated confirm the identity of variants responsible for the blue eggshells, pea comb, and rumplessness traits of NAA and propose one for ear-tufts.

Mapping and Functional Dissection of the Rumpless Trait in Piao Chicken Identifies a Causal Loss of Function Mutation in the Novel Gene Rum

“…The region associated with the rumpless phenotype in the Piao breed was located on chromosome 2 and very close to the one earlier reported to be associated with the rumpless phenotype in an American chicken breed called Araucana ( Noorai et al 2012 ; Freese et al 2014 ; Noorai et al 2019 ). Population genomics analyses of Piao, Araucana, and multiple other populations with normal tail identify selection for both rumpless breeds in the same region of chromosome 2 ( Fig.…”

“…Both dominant and recessive inheritance has been reported ( Dunn 1925 ; Landauer 1945 ), often with variable extent of tail loss ( Dunn 1925 ; Dunn and Landauer 1936 ). More recently, researchers have utilized genome resequencing to characterize several rumpless stocks to study the molecular genetic basis of the trait ( Freese et al 2014 ; Jeong et al 2016 ; Wang et al 2017 ; Wang et al 2018 ; Noorai et al 2019 ). No causative mutations have been identified, but strong association signals have been reported on chromosome 2 in the Araucana breed ( Freese et al 2014 ; Noorai et al 2019 ).…”

Genetic effect on free amino acid contents of egg yolk and albumen using five different chicken genotypes under floor rearing system

“…Since higher and lower eggshell yellowness values (more and less than 0) indicate a higher degree of yellowness and blueness, respectively [34], the present ARA produced yellow eggshell color rather than blue. In general, it is well known that the pure breed of Araucana produces blue eggs [36][37][38]. Since the ARA egg in this study was close to green rather than blue, the ARA must be crossbred between purebred Araucana and brown layers.…”

The main genetic locus associated with the evolution of gamecocks is centered on ISPD

“…Additionally, we downloaded sequencing data of 32 individuals with >9× coverage from the Chicken SD database, http://bigd.big.ac.cn/chickensd/ . We also downloaded resequencing data of 300 samples with >8× coverage across all 4 Gallus species and 59 named chicken breeds from 12 NCBI BioProjects: PRJDB4092 ( Ulfah et al 2016 ), PRJEB39275 ( Gheyas et al 2021 ), PRJNA202483 ( Fan et al 2013 ), PRJNA232548 ( Ulfah et al 2016 ), PRJNA241474 ( Wang et al 2015 ), PRJNA306389 ( Li et al 2017 ), PRJNA432200 ( Lawal et al 2020 ), PRJNA482210 ( Huang et al 2020 ), PRJNA524911 ( Noorai et al 2019 ), PRJNA547951 ( Wang et al 2020a ), PRJNA552722 ( Guo et al 2019 ), PRJNA597842 ( Guo et al 2022a ), and PRJNA659069 ( Sun et al 2022 ).…”