RESEARCH-PGR: Genomic Basis of Rice Ecosystem Adaptation

生物种群适应环境的变化，局部适应确保种群在其居住的地点具有高适应性。作物品种也可以在当地适应不同的温度，水的可用性和土壤类型的特定农业环境中生长。然而，植物适应特定生态系统和生境的基因组基础在很大程度上仍然未知。稻籼稻（亚洲稻）是世界上最重要的粮食作物之一，并且品种适于在灌溉（50%面积）、灌溉低地（25%）和灌溉高地（13%）生态系统中生长。水稻对这些特定生态系统的适应性和基因组反应，允许识别影响与生态系统适应相关的基因表达差异的基因和基因组变体，并使我们能够调查形成当地适应的进化和生态力量以及导致作物多样化的基因组变化。这项工作还将通过鉴定与适应特定水稻生态系统相关的基因来影响未来的作物育种工作。此外，水稻基因在田间表达的数据可以帮助提供基因功能的关键信息，有助于推进植物遗传学研究。 通过局部适应的生态专业化是进化变化的一个关键方面，并被认为在物种形成和进化中发挥作用，以改变环境。生物学的一个重大挑战-了解生物对栖息地环境的适应，并提供基因组变异，基因表达，生物表型和生态之间的因果关系。水稻的适应性和基因组反应。将在一个系统基因组学框架内，包括植物系统生物学、进化生态学、数量和群体基因组学，研究从亚洲水稻到灌溉、灌溉的低地和高地环境的变化。首先，大规模的基因生态系统和基因环境关联映射将被用来确定基因组区域，可能是环境适应和最近的自然定向选择的基础。第二，将使用全基因组关联研究（GWAS）检查不同水稻生态系统中适合度性状的遗传结构。最后，表型/基因型选择分析将被用来确定在这三个关键生态系统的水稻基因表达水平的自然选择的类型和强度。最后，将关联作图和群体基因组分析的结果与基因表达选择分析相结合，剖析水稻基因组中的适应性生态型分化。这项研究将从跨学科和多尺度的角度研究作物适应生态系统的基因组基础--从基因组到基因表达，再到生物体性状（适应性），再到生态系统。该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Populations of organisms are adapted to variations in environments, and local adaptation ensures a population has high fitness in the site where it resides. Crop varieties can also be locally adapted to growth in specific agricultural environments that differ in temperature, water availability, and soil types. The genomic basis of plant adaptation to specific ecosystems and habitats, however, remain largely unknown. Oryza sativa ssp. indica (Asian rice), is one of the most important food crops in the world, and varieties are adapted for growth in irrigated (50% by area), rainfed lowland (25%) and rainfed upland (13%) ecosystems. The adaptive and genomic response of rice to these specific ecosystems, allowing the identification of genes and genomic variants that affect gene expression differences associated with ecosystem adaptation, and allow us to investigate the evolutionary and ecological forces that shape local adaptation and the genomic changes that lead to crop diversification. This work will also impact future crop breeding efforts by identifying genes whose expression is associated with adaptation to specific rice ecosystems. Moreover, the data on rice gene expression in the field can help provide key information on gene function which can help advance plant genetics research. Ecological specialization through local adaptation is a key aspect of evolutionary change, and is thought to play a role in speciation and evolution to changing environments. A grand challenge in biology – to understand organismal adaptation to habitat environments, and to provide causal connections between genomic variation, gene expression, organismal phenotype and ecology. The adaptive and genomic response of Oryza sativa ssp. indica (Asian rice) to irrigated, rainfed lowland and upland environments will be investigated within a systems genomics framework that encompasses plant systems biology, evolutionary ecology, quantitative and population genomics. First, large-scale gene-ecosystem and gene-environment association mapping will be employed to identify genomic regions that may underlie environmental adaptation and recent natural directional selection. Second, the genetic architecture of fitness traits across different rice ecosystems will be examined using genome-wide association studies (GWAS). Finally, phenotypic/genotypic selection analysis will be used to determine the type and strength of natural selection on levels of gene expression in rice in these three key ecosystems. In the end, the results from the association mapping and population genomic analyses will be integrated with gene expression selection analyses to dissect adaptive ecotype differentiation in the rice genome. The proposed research will examine the genomic basis of ecosystem adaptation in crop plants with an interdisciplinary and multi-scale perspective – from genome to gene expression to organismal traits (fitness) to ecosystems.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.