MCA-PGR: A Phylogenetically Informed Investigation of Transcriptome Evolution and Transcriptome Response of the Tropical Crop Genus Leucaena (Leguminosae) to Psyllid Herbivores

PI: C. Donovan Bailey（新墨西哥州立大学- Las Cruces）高级合作者- Colin Hughes（苏黎世植物园）下一代测序在农业研究中的广泛应用集中在最重要的全球粮食作物（如玉米，小麦，水稻和大豆）的产量提高上。然而，热带系统中不太为人所知的作物也具有巨大的意义；然而，这些问题得到的研究关注相对较少。有几种这样的植物群被广泛地称为“多用途作物”，它们往往是可持续农业的关键要素，对贫困地区种植的主流作物的产量增长至关重要。其中一个不太为人所知的系统包括青绿属的成员，它由24种固氮的小树和灌木组成。Leucaena（尤其是L. leucocephala）异常高的叶片蛋白质含量有助于获得“奇迹树”和“热带苜蓿”的称号，并导致到20世纪80年代末，热带低地的小型和大规模种植面积达到500万公顷。这些引进的人工林提供：1)独特的富含蛋白质的树叶，用于牲畜生产系统中的动物饲料；2)绿肥，用于作物的富氮肥料和谷地种植系统中的土壤稳定；3)快速可再生的木质生物质，用于建筑、薪材，甚至通过木质纤维素前体提供生物燃料。该项目的目标是研究植物转录组如何随时间变化以及与物种多样化的关系。具体地说，将采用一种成本效益高、系统发育知情的方法对所有青合欢种的表达基因（转录组）进行测序、组装和比较。昆虫摄食试验将用于鉴定不同种类银合欢木虱抗性和易感性相关的基因和广泛的代谢途径。此外，该项目将利用生成的数据调查转录组大小变化的广泛模式，并通过与基因组复制相关的杂交物种形成（异源多倍体）相比，通过地理隔离确定与物种形成相关的一些特定变化。最后，所产生的数据将用于开发用于植物育种和其他研究的分子标记。新开发的热带木本物种育种工具对于未来在世界贫穷的热带地区广泛使用并促进可持续农业至关重要。新密西根州立大学是一所少数族裔大学，现有的项目成功地吸引了代表性不足的个人从事科学研究。此外，该项目还包括实施一门新课程和开发的本科实验室，以提高西班牙裔服务机构学生对植物基因组研究的兴趣和理解，该机构使用对中美洲文化和遗产感兴趣的植物系统。对MCA-PGR项目的支持将为PI、相关博士后和研究生提供广泛的培训和指导，他们将与一名主要研究者密切合作，应用新的基因组学技术来解决这些研究问题。从该项目中获得的序列数据将通过项目网站提供，并长期通过NCBI的短读档案提供。在开发和发布特定数据源时，将在http://biology-web.nmsu.edu/bailey/提供这些数据源的链接。

PI: C. Donovan Bailey (New Mexico State University - Las Cruces)Senior Collaborator - Colin Hughes (Zurich Botanical Garden)The extensive application of next generation sequencing in agricultural research has focused on yield improvements in the most important global food crops (e.g., corn, wheat, rice, and soybean). However, lesser-known crops in tropical systems are also of tremendous significance; yet these receive comparatively little research attention. Several such plant groups are broadly known as "multipurpose crops", often representing key elements in sustainable agriculture that are fundamental to production gains in mainstream crops grown in impoverished regions. One such lesser-known system includes members of the genus Leucaena, which comprises 24 nitrogen-fixing species of small trees and shrubs. The unusually high leaf protein content of Leucaena (particularly L. leucocephala) helped to garner the titles "miracle tree" and "alfalfa of the tropics" and resulted in small- and large-scale plantings reaching 5 million lowland tropical hectares by the late 1980s. These introduced plantations provide: 1) unique protein-rich leaves for animal feed in livestock production systems, 2) green manure used as nitrogen-rich fertilizer for crops and for soil stabilization in alley-cropping systems, and 3) rapidly renewable woody biomass for construction, fuelwood, and even biofuels through lignocellulosic precursors. The goal of this project is to investigate how plant transcriptomes change through time and in association with diversification of species. Specifically, a cost- effective and phylogenetically informed approach will be used to sequence, assemble, and compare sets of expressed genes (transcriptomes) from all species of Leucaena. Insect feeding trials will be used to identify genes and broad metabolic pathways associated with psyllid insect resistance and susceptibility among different species of Leucaena. In addition, the project will use the data generated to investigate broad patterns of transcriptome size variation and identify some of the specific changes that have been associated with speciation through geographic isolation in comparison to hybrid speciation associated with genome duplication (allopolyploidy). Finally the data generated will be used to develop molecular markers for plant breeding and other studies.Newly developed breeding tools for tropical woody species are critical for future widespread use as contributors to sustainable agriculture in poor tropical regions of the world. NMSU is a minority serving university with existing programs successfully attracting underrepresented individuals to careers in scientific research. Furthermore, this project includes the implementation of a new course and undergraduate laboratories developed to advance interest and the understanding of plant genome research among students at a Hispanic Serving Institution using a plant system of interest to Mesoamerican culture and heritage. Support of this MCA-PGR project will provide extensive training and mentoring for the PI, associated postdoctoral fellow and graduate student who will work closely with a primary investigator applying new genomics technologies to address these research questions. Sequence data derived from this project will be made available through a project website and long-term through the NCBI's Short Read Archive. Links to specific data sources will be provided as they are developed and released at http://biology-web.nmsu.edu/bailey/.