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


Autoři: Rooksana E. Noorai aff001;  Vijay Shankar aff002;  Nowlan H. Freese aff003;  Christopher M. Gregorski aff004;  Susan C. Chapman aff004
Působiště autorů: Clemson University Genomics and Bioinformatics Facility, Clemson University, Clemson, South Carolina, United States of America aff001;  Center for Human Genetics, Clemson University, Greenwood, South Carolina, United States of America aff002;  Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America aff003;  Department of Biological Sciences, College of Science, Clemson University, Clemson, South Carolina, United States of America aff004
Vyšlo v časopise: PLoS ONE 14(12)
Kategorie: Research Article
doi: 10.1371/journal.pone.0225834

Souhrn

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.

Klíčová slova:

Animal sexual behavior – Bird genetics – Bird genomics – Birds – Chickens – Introns – Peas – Sequence alignment


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