Clemson University Genomics and Bioinformatics Facility, Clemson University, Clemson, South Carolina, United States of America.
Center for Human Genetics, Clemson University, Greenwood, South Carolina, United States of America.
PLoS One. 2019 Dec 10;14(12):e0225834. doi: 10.1371/journal.pone.0225834. eCollection 2019.
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.
鸡（Gallus gallus）是一个表型多样化的物种，在鸟类谱系中，有超过 60 种被认可的品种。几千年来，人类为了农业目的对家鸡进行了人工选择。北美阿劳卡纳（NAA）品种是由智利的“Collonocas”（下蓝色蛋且无尾椎骨）和“Quetros”（有奇特的簇羽但有尾）杂交而来。20 世纪 40 年代，NAA 从南美洲引入，此后，由于其具有几个独特的特征，如下蓝色蛋壳的蛋、特征性的耳簇、豌豆状的鸡冠和无尾椎骨，一直被爱好者作为观赏鸟饲养。该种群保持了无脸簇羽和有脸簇羽、有尾和无尾椎骨的变种，这使其成为遗传研究的优势。对具有这些特征混合的六只 NAA 鸡进行了基因组重测序，使用 Illumina HiSeq 2000 配对末端读取进行了 71 倍覆盖。使用 Trim 和一致的读数将其映射到 Gallus_gallus-5.0 参考基因组（galGal5），该基因组是由一只雌性红原鸡（UCD001）生成的。为了鉴定与 NAA 特征相关的候选基因，将其基因组与韩国阿劳卡纳、韩国国内鸡和白来亨鸡进行了比较。在 NAA 的五个不同染色体上检测到了显著降低异质性水平的基因组区域。生成的序列数据证实了导致 NAA 蓝色蛋壳、豌豆状鸡冠和无尾椎骨特征的变异的身份，并提出了一个导致耳簇羽的变异。
