Joint NSF/ERA-CAPS: Collaborative Research: BEAN-ADAPT - Genetic Architecture of Rapid Evolutionary Adaptation to Changing Environments in Domesticated Phaseolus Bean Species

pi: Paul L. Gepts（加州大学戴维斯分校）和Scott A. Jackson（佐治亚大学）Roberto Papa（意大利马尔奇理工大学）、Alisdair R. Fernie（德国马克斯-普朗克分子植物生理学研究所）和Andreas Graner（德国莱布尼茨植物遗传学和作物研究所）在世界范围内，豆类作为蛋白质、矿物质、维生素和膳食纤维的来源，发挥着重要的营养作用。它们固定氮的能力（即将大气中的氮转化为植物可以利用的形式）使豆科植物成为可持续农业的天然贡献者。作为驯化作物，豆科植物已经适应了许多不同环境的生长，但这种适应的遗传基础在很大程度上是未知的。该项目将利用两种豆科植物（普通豆和毛豆）的大型基因库集合来发现负责适应新的、变化的和可变的环境的基因。研究结果将为更好地利用这些基因库所代表的遗传资源进行豆科作物改良提供依据。该项目将包括来自美国、哥伦比亚、意大利和德国的合作者。参与研究小组之间的学生交流将提供学习新技术的机会，并在协调研究工作中整合信息。此外，向来自美国西南部的本科生提供接触植物基因组学的实践研究经验。在本项目中，将结合高通量基因组工具，对大型基因库收集物进行多地点、多年的实地评估，以了解豆科植物（Phaseolus vulgaris）和芸豆（P. coccineus）的适应遗传基础。将使用DNA测序方法对大约10,000个普通豆和1,000个跑腿豆进行基因分型，并在欧洲（高纬度）和南美洲（赤道附近）的不同环境和条件下进行测试，以将基因与适应环境变量（如白天长度、温度、海拔和降雨量）联系起来。两种Phaseolus物种具有截然不同的生活史、生殖系统和种群结构，为比较不同的适应路径提供了机会。序列信息将与精选子集的转录组学和代谢组学分析相补充，以产生数据集，用于建立模型，研究普通豆从中美洲和南安第斯山脉的两个驯化中心扩散后如何适应新环境。展望未来，这些信息将有助于开发适应变化或可变环境的新作物品种。

PIs: Paul L. Gepts (University of California-Davis) and Scott A. Jackson (University of Georgia)ERA-CAPS Collaborators: Roberto Papa (Universita Politecnica delle Marche, Italy), Alisdair R. Fernie (Max-Planck-Institute of Molecular Plant Physiology, Germany), and Andreas Graner (Leibniz Institute of Plant Genetics and Crop Plant Research, Germany)Worldwide, legumes serve an important nutritional role as a source of protein, minerals, vitamins, and dietary fibers, and their ability to fix nitrogen (i.e. convert nitrogen in the atmosphere into a form that can be used by the plant) makes legumes natural contributors to sustainable agriculture. As domesticated crops, legumes have adapted to growth in many different environments, but the genetic basis for such adaptation is largely unknown. This project will take advantage of large gene bank collections of two legume species, common bean and runner bean, to discover the genes responsible for adaptation to new, changing, and variable environments. The results will allow better use of the genetic resources represented by these gene banks for improvement of legume crops. The project will include collaborators in the U.S., Colombia, Italy and Germany. Exchanges of students among the participating research groups will offer opportunities to learn new techniques and integrate information across the coordinating research efforts. In addition, outreach to undergraduates from the Southwest U.S. will provide exposure to hands-on research experiences in plant genomics. In this project, multi-location, multi-year field evaluations of large gene bank collections will be combined with high-throughput genomic tools to understand the genetic basis of adaptation in the legumes common bean (Phaseolus vulgaris) and runner bean (P. coccineus). Approximately 10,000 common bean and 1,000 runner bean accessions will be genotyped using a DNA sequencing approach and tested in contrasting environments and conditions in Europe (higher latitude) and South America (near the Equator) to associate genes with adaptation to environmental variables, such as day length, temperature, altitude, and rainfall. The two Phaseolus species have contrasting life histories, reproductive systems, and population structures, providing an opportunity to compare different adaptation paths. Sequence information will be complemented with transcriptomic and metabolomics profiling on a select subset of accessions to produce datasets that will be used to build models of how common bean adapted to new environments after its dispersal from two domestication centers in Mesoamerica and the Southern Andes. Prospectively, this information will be useful for developing new crop varieties adapted to changing or variable environments.