RESEARCH-PGR: Genomic Basis of Rice Ecosystem Adaptation

生物种群适应环境的变化，而局部适应确保种群在其居住的地点具有高度的适合度。作物品种也可以在当地适应不同温度、水分供应和土壤类型的特定农业环境的生长。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不清楚。水稻(Oryza sativa SSP.)亚洲水稻是世界上最重要的粮食作物之一，品种适合在灌溉(按面积50%)、雨养低地(25%)和雨养旱地(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，使我们能够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异，并使我们能够研究形成局部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。这项工作还将通过识别其表达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努力。此外，田间水稻基因表达的数据有助于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门化是进化变化的一个关键方面，被认为在物种形成和对不断变化的环境的进化中发挥作用。生物学上的一个重大挑战--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、生物表型和生态学之间的因果关系。水稻的适应性和基因组反应。将在涵盖植物系统生物学、进化生态学、数量基因组学和种群基因组学的系统基因组学框架内，研究从亚洲水稻到灌溉、旱地和旱地的环境。首先，将利用大规模的基因-生态系统和基因-环境关联作图来确定可能构成环境适应和最近的自然定向选择的基因组区域。其次，将使用全基因组关联研究(GWAS)来研究不同水稻生态系统中适应性特征的遗传结构。最后，表型/基因选择分析将被用来确定这三个关键生态系统中水稻基因表达水平上的自然选择的类型和强度。最后，联合作图和群体基因组分析的结果将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。这项拟议的研究将从跨学科和多尺度的角度研究作物生态系统适应的基因组基础--从基因组到基因表达，从组织特征(适合度)到生态系统。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势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.