FUNCTIONAL GENOMICS IN CLOSE WILD RELATIVES OF ARABIDOPSIS THALIANA

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 现在已经对几种模式生物的整个基因组进行了测序，下一个挑战是识别基因并了解它们在生物学意义上的功能(Jackson等人)。2002年)。例如，拟南芥2010年项目现在寻求在十年内了解所有25000个拟南芥基因的功能，但要做到这一点，我们必须了解自然环境在决定基因功能方面的作用。 为了更好地了解基因的功能和调控，可以跨重要的生态梯度来研究基因的表达。例如，昆虫食草动物的取食在植物中引起信号转导和防御反应(Karban和Baldwin 1997)，然而，对参与这些反应的基因或它们在其他生态环境中的表达模式知之甚少。尽管利用拟南芥进行实验室实验的研究人员开始了解硫代葡萄糖苷基因在植物对草食动物抗性中的作用(例如，Jander等人)。2001年；Lambrix等人。2001年)，需要对野生近亲进行生态基因组研究，以更好地了解这些基因和许多其他基因的功能(Mitchell-olds 2001)。Arabis属，最近(Al-Shehbaz 2003)被分裂为Arabis，Boechera和Arabitopsis，包含了一些与拟南芥最接近的野生近亲(Koch等人。2000)。由于Boechera的多样性中心在北美(Rollins 1993)，我们已经开始对Boechera的物种进行研究，以检验防御进化的一般理论(例如Jones等人)。提交手稿；西门子等人。2003年；西门子和罗伊，2005年；Steffes等人。在准备中)。我们从这些研究和其他研究中得出的结果(西门子等人，2002)表明，抗性和耐性防御基因可能还具有其他生态功能，如提高植物的竞争能力，必须调节防御反应，以优化多种功能。在这里，我们使用拟南芥的分子工具(微阵列)来识别和理解可能的防御基因的功能及其调控。 防御进化的最优化理论(哈密尔顿等人)2001)，这是我们目前所拥有的理解植物防御和竞争能力同时进化的最佳框架，它预测了防御和竞争之间的权衡，因为国防生产被认为从竞争增长中分流了有限的资源(Herms和Mattson 1992)。我们通过(1)研究防御中的遗传或环境变异对竞争生长的影响，以及(2)研究竞争中的遗传变异对防御表达的影响，对这种进化权衡进行了测试。尽管我们检测到防御成本在没有食草动物的情况下表现为增长放缓，但在竞争环境中没有检测到这些成本(Siemens等人。2002年；西门子等人。2003年)。也就是说，国防生产影响了增长，但不影响竞争力。我们还发现证据表明，防御措施，如硫代葡萄糖苷浓度，有时在更好的竞争对手中更高或更具竞争性地诱导。防御基因的竞争功能可以解释这些结果中的许多。拟南芥的基因组工具使我们能够确定竞争对手是否诱导防御基因，正如人们所预期的那样，防御系统也在竞争中发挥作用。基因组方法还允许对预测的防御和竞争能力之间的权衡进行测试，这可能会加深我们对基因调控的理解(Stearns和Magwene 2003)。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Now that the entire genome has been sequenced for several model organisms, the next challenge is to identify genes and understand their functions in biologically meaningful contexts (Jackson et al. 2002). The Arabidopsis 2010 project, for example, now seeks to understand the functions of all 25000 Arabidopsis genes within a decade, but to do so, we must understand the role of the natural environment in determining gene function. To better understand gene function and regulation, gene expression can be studied across important ecological gradients. Feeding by insect herbivores, for example, elicits signal transduction and defense responses in plants (Karban and Baldwin 1997), however, relatively little is known about the genes involved in these responses or their expression patterns in other ecological contexts. Although researchers conducting laboratory experiments using Arabidopsis are beginning to understand the role of glucosinolate genes in plant resistance against herbivores (e.g., Jander et al. 2001; Lambrix et al. 2001), ecological genomic studies with close wild relative are needed to better understand the function of these and many other genes (Mitchell-Olds 2001). The genus Arabis, which has recently been split (Al-Shehbaz 2003) into Arabis, Boechera, and Arabidopsis, contains some of the closest wild relatives of Arabidopsis thaliana (Koch et al. 2000). Since the center of diversity of Boechera is in North America (Rollins 1993), we have begun studies on species of Boechera to test general theory on defense evolution (e.g. Jones et al. submitted manuscript; Siemens et al. 2003; Siemens and Roy 2005; Steffes et al. in prep). Our results from these and other studies (Siemens et al. 2002) suggest that resistance and tolerance defensive genes may have other ecological functions, such as increasing plant competitive ability, and that defense responses must be regulated to optimize multiple functions. Here we used the molecular tools of Arabidopsis (microarrays) to identify and understand the function of putative defensive genes and their regulation. Optimality theory for defense evolution (Hamilton et al. 2001 for overview), currently the best framework we have to understand the simultaneous evolution of defense and competitive ability in plants, predicts a tradeoff between defense and competitiveness because defense production is thought to divert limited resources away from competitive growth (Herms and Mattson 1992). We have tested for this evolutionary tradeoff by (1) studying the effects of genetic or environmental variation in defenses on competitive growth, and by (2) studying the effects of genetic variation in competitiveness on defense expression. Although we have detected costs of defenses manifest as reduced growth in the absence of herbivores, these costs were not detected in competitive environments (Siemens et al. 2002; Siemens et al. 2003). That is, defense production affected growth, but not competitive ability. We have also found evidence that measures of defense, such as glucosinolate concentration, were sometimes higher or competitively induced in better competitors. A competitive function for defensive genes would explain many of these results. The genomic tools of Arabidopsis allow us to determine whether competitors induce defensive genes, as one would expect for defenses that also function in competition. A genomic approach also allows a test for the predicted tradeoff between defense and competitive ability, which may further our understanding of gene regulation (Stearns and Magwene 2003).