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（新墨西哥州州立大学-拉斯克鲁塞斯）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已经集中在最重要的全球粮食作物的产量提高上（例如，玉米、小麦、水稻和大豆）。 然而，热带系统中鲜为人知的作物也具有巨大的意义，但这些作物受到的研究关注相对较少。若干这类植物群被广泛称为“多用途作物”，往往代表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。一个这样的鲜为人知的系统包括银合欢属的成员，其中包括24种固氮的小乔木和灌木。银合欢叶蛋白质含量异常高，特别是银合欢。leucocephala）帮助获得了“奇迹树”和“热带苜蓿”的称号，到1980年代末，小规模和大规模种植达到了500万低地热带公顷。这些引入的种植园提供：1）独特的富含蛋白质的叶子，用于牲畜生产系统中的动物饲料，2）绿色肥料，用作作物的富氮肥料和用于小巷种植系统中的土壤稳定，以及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的生物燃料。 该项目的目标是研究植物转录组如何随着时间的推移而变化，并与物种的多样化有关。 具体而言，将使用具有成本效益和遗传学信息的方法对来自银合欢属所有物种的表达基因（转录组）进行测序、组装和比较。昆虫饲养试验将用于确定与木虱昆虫抗性相关的基因和广泛的代谢途径，并在不同种类的银合欢中易感。 此外，该项目将使用生成的数据来调查转录组大小变异的广泛模式，并确定与地理隔离物种形成相关的一些特定变化，与基因组复制（异源多倍体）相关的杂交物种形成进行比较。 最后，产生的数据将用于开发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广泛使用至关重要，有助于世界贫困热带地区的可持续农业。NMSU是一所少数民族服务的大学，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本科生实验室，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。 对该MCA-PGR项目的支持将为PI，相关博士后研究员和研究生提供广泛的培训和指导，他们将与应用新基因组学技术的主要研究者密切合作，以解决这些研究问题。 从该项目中获得的序列数据将通过项目网站提供，并通过NCBI的Short Read Archive长期提供。 具体数据源的链接将在http://biology-web.nmsu.edu/bailey/上开发和发布时提供。

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/.