The genetics and evolution of eye color in domestic pigeons (Columba livia).
The genetics and evolution of eye color in domestic pigeons (Columba livia).
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DOI：
10.1371/journal.pgen.1009770
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发表时间：
2021-08
期刊：
影响因子：
4.5
通讯作者：
Luo SJ
中科院分区：
文献类型：
--
作者：
Si S;Xu X;Zhuang Y;Gao X;Zhang H;Zou Z;Luo SJ
鸟类眼睛的颜色，通常指虹膜的颜色，是由色素沉着和结构着色引起的。鸟类虹膜颜色表现出惊人的种间和种内变化，对应于独特的进化和生态历史。在这里，我们确定了珍珠（白色）虹膜颜色的家鸽（鸽）的遗传基础，探索在很大程度上未知的遗传机制，鸟类虹膜颜色的演变。使用全基因组关联研究（GWAS）的方法，在92鸽子，我们映射珍珠虹膜性状的9 kb的区域含有促进葡萄糖转运蛋白基因SLC2A11B。一个无义突变（W49X）导致SLC2A11B提前终止密码子被确定为致病变异。转录组分析表明，SLC2A11B功能的丧失可能下调了黄色素细胞分化基因CSF1R和蝶啶生物合成关键基因GCH 1，从而导致珍珠鸢尾表型。聚合和系统发育分析表明，突变起源于大约5,400年前，与鸽子驯化的开始相吻合，而正选择可能与人工繁殖有关。在鸟类中，潜在受损的SLC2A11B被发现在来自六个不同谱系的六个物种中，其中四个与它们的标志性棕色或蓝色眼睛和缺乏蝶啶有关。脊椎动物SLC2A11B直系同源物的分析显示，在鸟类进化枝宽松的选择，与鸟类从爬行动物祖先的分歧，SLC2A11B涉及的皮肤色素细胞的发展可能退化的羽毛覆盖的存在下，期间和之后的情况是一致的。我们的研究结果提供了新的见解鸟类虹膜颜色变化的机制和色素在脊椎动物的进化。鸟类眼睛颜色的差异很大，为了解鸟类进化提供了一个独特的角度。本研究通过全基因组测序和全基因组关联分析（GWAS）方法，将家鸽（Columba livia）珍珠色（白色）虹膜的遗传基础与SLC2A11 B的无义突变W49 X相关联。SLC2A11B是一个已知在鱼类色素细胞分化中起作用的基因，转录组分析表明，SLC2A11B功能缺失可能下调了黄色素细胞分化基因CSF1R和蝶啶生物合成关键基因GCH 1，导致鸽子的珍珠虹膜表型。据估计，SLC2A11B变体起源于大约5,400年前，与鸽子驯化的开始相吻合，然后受到可能与人工育种有关的积极选择。潜在受损的SLC2A11B也被发现在六个物种从六个不同的鸟类谱系。脊椎动物SLC2A11B直系同源物的分析显示，在鸟类进化枝宽松的选择，与SLC2A11B涉及的皮肤色素细胞的发展可能在羽毛覆盖的存在下退化的情况相一致。我们的研究揭示了鸟类虹膜颜色变化进化的基本未知的遗传机制。
The eye color of birds, generally referring to the color of the iris, results from both pigmentation and structural coloration. Avian iris colors exhibit striking interspecific and intraspecific variations that correspond to unique evolutionary and ecological histories. Here, we identified the genetic basis of pearl (white) iris color in domestic pigeons (Columba livia) to explore the largely unknown genetic mechanism underlying the evolution of avian iris coloration. Using a genome-wide association study (GWAS) approach in 92 pigeons, we mapped the pearl iris trait to a 9 kb region containing the facilitative glucose transporter gene SLC2A11B. A nonsense mutation (W49X) leading to a premature stop codon in SLC2A11B was identified as the causal variant. Transcriptome analysis suggested that SLC2A11B loss of function may downregulate the xanthophore-differentiation gene CSF1R and the key pteridine biosynthesis gene GCH1, thus resulting in the pearl iris phenotype. Coalescence and phylogenetic analyses indicated that the mutation originated approximately 5,400 years ago, coinciding with the onset of pigeon domestication, while positive selection was likely associated with artificial breeding. Within Aves, potentially impaired SLC2A11B was found in six species from six distinct lineages, four of which associated with their signature brown or blue eyes and lack of pteridine. Analysis of vertebrate SLC2A11B orthologs revealed relaxed selection in the avian clade, consistent with the scenario that during and after avian divergence from the reptilian ancestor, the SLC2A11B-involved development of dermal chromatophores likely degenerated in the presence of feather coverage. Our findings provide new insight into the mechanism of avian iris color variations and the evolution of pigmentation in vertebrates. Birds exhibit striking eye color variations, providing a unique angle for understanding avian evolution. Here we identified the genetic basis of the pearl (white) iris color in domestic pigeons (Columba livia) to a nonsense mutation W49X in SLC2A11B via whole genome sequencing and genome-wide association study (GWAS) approaches. SLC2A11B is a gene with known roles in fish pigment cells differentiation and transcriptome analysis indicated that SLC2A11B loss of function may downregulate the xanthophore-differentiation gene CSF1R and the key pteridine biosynthesis gene GCH1, resulting in the pigeon’s pearl iris phenotype. The SLC2A11B variant was estimated to have originated at approximately 5,400 years ago coinciding with the onset of pigeon domestication and was then under positive selection likely associated with artificial breeding. Potentially impaired SLC2A11B was also found in six species from six distinct avian lineages. Analysis of vertebrate SLC2A11B orthologs revealed relaxed selection in the avian clade, consistent with the scenario that the SLC2A11B-involved development of dermal pigment cells likely degenerated in the presence of feather coverage. Our study sheds new light on the largely unknown genetic mechanism underlying the evolution of avian iris color variations.
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DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
9.2
作者：
Domyan, Eric T.;Guernsey, Michael W.;Kronenberg, Zev;Krishnan, Shreyas;Boissy, Raymond E.;Vickrey, Anna I.;Rodgers, Clifford;Cassidy, Pamela;Leachman, Sancy A.;Fondon, John W., III;Yandell, Mark;Shapiro, Michael D.
通讯作者：
Shapiro, Michael D.
DOI：
10.18632/aging.100927
发表时间：
2016-04
期刊：
Aging
影响因子：
--
作者：
Ding D;Jiang H;Chen GD;Longo-Guess C;Muthaiah VP;Tian C;Sheppard A;Salvi R;Johnson KR
通讯作者：
Johnson KR
影响因子：
5.8
作者：
Bradbury, Peter J.;Zhang, Zhiwu;Buckler, Edward S.
通讯作者：
Buckler, Edward S.
影响因子：
4.5
作者：
Bruders, Rebecca;Van Hollebeke, Hannah;Shapiro, Michael D.
通讯作者：
Shapiro, Michael D.