Gene expression divergence and nucleotide differentiation between males of different color morphs and mating strategies in the ruff
Gene expression divergence and nucleotide differentiation between males of different color morphs and mating strategies in the ruff
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DOI：
10.1002/ece3.370
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发表时间：
2012-10-01
影响因子：
2.6
通讯作者：
Burke, Terry
中科院分区：
文献类型：
--
作者：
Ekblom, Robert;Farrell, Lindsay L.;Burke, Terry
通过下一代转录组测序，可以获得核苷酸序列变异和基因表达的数据。我们使用这种方法 (RNA-Seq) 来研究非模式鸟类鹬 (Philomachus pugnax) 羽毛颜色和交配策略差异的遗传基础。雄性颈毛鸟的装饰羽毛颜色存在巨大差异，用于个体识别。这种多态性与繁殖策略有关，深色雄性（独立者）在 leks 上保卫领土，对抗其他独立者，而白色变异者（卫星）则共同占领独立者的法庭，没有竞争性互动。之前的工作发现了交配策略的强大遗传成分，但所涉及的基因尚未确定。我们提供了 6,000 多个从头测序的 ruff 基因的羽毛转录组数据（尽管其中许多基因的覆盖范围有限）。所鉴定的基因均未显示出雄性之间显着的表达差异，但许多遗传标记显示出不同颜色形态和交配策略之间的核苷酸差异。其中包括一些羽毛角蛋白基因、剪接因子和 Xg 血型基因。许多在交配策略之间具有显着遗传结构的基因尚未被注释，其功能仍有待阐明。我们还对28个预先确定的显色候选基因进行了深入研究。其中两个（EDNRB 和 TYR）分别在黑色和铁锈色雄性中特异表达。我们已经证明了下一代转录组测序在没有先前基因组资源的非模型物种中识别和基因分型大量遗传标记的实用性，并强调了这种方法在解决生态重要变异的遗传基础方面的潜力。
By next generation transcriptome sequencing, it is possible to obtain data on both nucleotide sequence variation and gene expression. We have used this approach (RNA-Seq) to investigate the genetic basis for differences in plumage coloration and mating strategies in a non-model bird species, the ruff (Philomachus pugnax). Ruff males show enormous variation in the coloration of ornamental feathers, used for individual recognition. This polymorphism is linked to reproductive strategies, with dark males (Independents) defending territories on leks against other Independents, whereas white morphs (Satellites) co-occupy Independent's courts without agonistic interactions. Previous work found a strong genetic component for mating strategy, but the genes involved were not identified. We present feather transcriptome data of more than 6,000 de-novo sequenced ruff genes (although with limited coverage for many of them). None of the identified genes showed significant expression divergence between males, but many genetic markers showed nucleotide differentiation between different color morphs and mating strategies. These include several feather keratin genes, splicing factors, and the Xg blood-group gene. Many of the genes with significant genetic structure between mating strategies have not yet been annotated and their functions remain to be elucidated. We also conducted in-depth investigations of 28 pre-identified coloration candidate genes. Two of these (EDNRB and TYR) were specifically expressed in black-and rust-colored males, respectively. We have demonstrated the utility of next generation transcriptome sequencing for identifying and genotyping large number of genetic markers in a non-model species without previous genomic resources, and highlight the potential of this approach for addressing the genetic basis of ecologically important variation.