Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University Norbyvägen 18 D, SE-75236, Uppsala, Sweden ; Department of Animal and Plant Sciences, University of Sheffield Sheffield, S10 2TN, UK.
Ecol Evol. 2012 Oct;2(10):2485-505. doi: 10.1002/ece3.370. Epub 2012 Aug 31.
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.
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。我们已经使用这种方法（RNA-Seq）来研究非模型鸟类物种——黑腹滨鹬（Philomachus pugnax）的羽毛颜色和交配策略差异的遗传基础。黑腹滨鹬雄鸟的饰羽颜色存在巨大的变异，用于个体识别。这种多态性与繁殖策略有关，深色雄鸟（独立雄鸟）在求偶场中捍卫领地，抵御其他独立雄鸟的入侵，而白色雄鸟（卫星雄鸟）则在不发生争斗的情况下共同占据独立雄鸟的领地。之前的研究发现，交配策略有很强的遗传成分，但参与其中的基因尚未确定。我们展示了超过 6000 个从头测序的黑腹滨鹬基因的羽毛转录组数据（尽管其中许多基因的覆盖度有限）。没有发现雄性之间存在显著表达差异的基因，但许多遗传标记显示了不同颜色形态和交配策略之间的核苷酸分化。这些标记包括几个羽毛角蛋白基因、剪接因子和 Xg 血型基因。许多在交配策略之间具有显著遗传结构的基因尚未被注释，它们的功能仍有待阐明。我们还对 28 个预先确定的候选颜色基因进行了深入研究。其中两个基因（EDNRB 和 TYR）分别在黑色和锈色雄鸟中特异性表达。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情况下，用于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具有重要生态意义的变异的遗传基础方面的潜力。
