Genomic Analysis of a Nematode-plant Interaction: A Tool to Study Plant Biology

植物寄生线虫使美国每年的农业产量减少了50多亿美元。最重要的一类是根结线虫（RKN: Meloidogyne spp.），它们是粮食和纤维作物的破坏性病原体。由于健康和环境方面的原因，化学控制剂的减少，在世界范围内RKN的经济重要性日益增加。开发任何新的、环境安全和负担得起的控制策略的先决条件是彻底了解植物-线虫相互作用的生物学。基因组技术的最新进展使这种以前难以处理的宿主-寄生虫系统易于研究。由于这种相互作用的密切性，以及线虫对寄主的明显发育和生理扰动，了解这种联系的生物学将为植物的基本过程提供新的视角。RKN非常广泛的寄主范围（超过2000种植物）意味着这种寄生虫能够调节宿主生物学的一些非常基本和广泛保守的方面。RKN在土壤中孵化为发育受阻的幼虫，然后侵入根部，与宿主建立亲密关系。一个精心制作的永久取食场所，其特点是在宿主胆内形成“巨细胞”，由线虫诱导。巨细胞为发育中的线虫提供必需的营养来源，使其变得静止不动。功能基因组学方法将被应用于分析这种相互作用。这种方法是可行的，因为已经建立了完善的宿主和寄生虫模型（拟南芥和秀丽隐杆线虫分别），包括完整的基因组序列。线虫和植物的基因套件，确定途径的寄生虫相互作用的建立将被确定，并量化他们的表达。寄主在摄食点形成过程中的反应，以及与寄主耦合的线虫的生物学转变（例如，在摄食开始时从发育停滞中退出）尤其有趣。组织学表明，植物激素水平在受感染的根中发生改变，拟南芥基因集的表达将被量化，重点是激素反应基因（预计将发现这类新成员），以及先前确定的特异性线虫反应基因。本项目解决了三个普遍且相互关联的科学问题：1)寄主是如何被识别的，寄生物是如何将其生物学和发育与寄主的线索结合起来的；2)寄主体内寄生虫诱导的变化是什么，特别是植物激素的来源和作用是什么；3)寄主是如何进化的，水平基因转移的作用是什么，这是否反映在寄主基因的组织中？RKN有大量的描述性信息，一个重要的目标是将基因组研究结果与这些生物学数据结合起来。rkn -植物相互作用的许多特征（例如，胆形成）对于涉及多种生物（包括昆虫）的广泛宿主-寄生虫关联来说是典型的，并且也代表了一个可处理的模型来研究正常植物发育的各个方面，包括植物激素的生物合成/调节。更好地了解宿主-寄生虫的相互作用将揭示新的线虫管理策略的关键所在。此外，由于这项研究将在研究生和本科教育的框架内进行，它将为学生提供重要的专业发展机会。

Plant-parasitic nematodes reduce annual US agricultural production by more than $5 billion. The most important group are the root-knot nematodes (RKN: Meloidogyne spp.), which are devastating pathogens of food and fiber crops. With the loss of chemical control agents for health and environmental reasons, the economic importance of RKN is increasing world-wide. A prerequisite to developing any new, environmentally-safe and affordable control strategy is a thorough understanding of the biology of the plant-nematode interaction. Recent advances in genomic techniques make this previously intractable host-parasite system amenable to study. Because of the intimate nature of the interaction, and the obvious developmental and physiological perturbations to the host induced by the nematode, understanding the biology of this association will shed new light on basic plant processes. The very broad host range of RKN (excess of 2,000 plant species) implies that this parasite is able to modulate some very fundamental and widely conserved aspect of host biology.RKN hatch in the soil as developmentally-arrested larvae prior to invading a root, where the parasite establishes an intimate relationship with its host. An elaborate permanent feeding site, characterized by the formation in the host of "giant cells" within a gall, is induced by the nematode. Giant cells serve as the obligate nutritive source for the developing nematode, which becomes sedentary. Functional genomic approaches will be applied to analyze this interaction. This approach is feasible because well developed models of the host and parasite (Arabidopsis and C. elegans respectively) have been established, including complete genomic sequences.Suites of nematode and plant genes that define pathways for establishment of the parasitic interaction will be identified, and their expression quantified. Host responses during feeding-site formation, and the biological transitions in the nematode that are coupled to the host (e.g., exit from developmental-arrest at the onset of feeding) are especially interesting. The histology suggests that phyto-hormone levels are altered in infected roots, and expression of Arabidopsis gene sets, with an emphasis on hormone-responsive genes (new members of this class are anticipated to be identified) will be quantified, as well as genes previously identified as being specifically nematode-responsive. This project addresses three general and inter-related scientific questions: 1) how is the host recognized, and how does the parasite couple its biology and development to host cues, 2) what are the parasite-induced changes in the host, and in particular what is the source and role of phyto-hormones, 3) how has parasitism evolved, what has been the role of horizontal gene transfer, and is this reflected in the organization of parasitism genes?A large body of mostly descriptive information exists for RKN and an important goal will be to couple the genomic findings with this biological data. Many features of the RKN-plant interaction (e.g., gall formation) appear canonical for a broad range of host-parasite associations involving diverse organism (including insects), and also represents a tractable model to study aspects of normal plant development, including phyto-hormone biosynthesis/regulation. Better understanding the host-parasite interaction will reveal the linch-pins from which novel nematode-management strategies can be derived. Furthermore, because this research will be performed within a framework of graduate and undergraduate education, it will provide students with significant opportunities for professional development.