RESEARCH-PGR: Systems Genomics of Rice Stress Adaptation

水稻等作物适应环境压力是确保在这些条件下高产的基本要求。盐碱化是农作物面临的主要环境压力之一，由于土地压力增加和气候变化，它目前正威胁着水稻种植，这将农业推向边缘土地。水稻是一种主要的世界作物，包括两个物种：一个来自亚洲（Oryza sativa），一个来自非洲（O. glaberrima）。该项目旨在通过对两个物种内部和物种之间对盐胁迫具有不同适应性的水稻品种的比较分析，确定与适应盐碱地有关的基因。不止一种适应性策略的发现将增加水稻育种者在他们的项目中可以实施的选择。该项目将使用几种方法来识别当植物暴露于高盐环境时具有独特协调表达模式的基因，同时这些基因与旺盛的生长和生产力相关。该项目还将利用纽约市生物巴士开展公共宣传活动。这是一辆配备了移动教育实验室的公共汽车，已经在420多所学校和社区为11.5万人提供服务。植物生物学实验室模块将在BioBus上开发，部署在整个纽约市。这些模块将主要针对服务不足社区的学童，以及街头集市上的公众。盐度是作物面临的生长胁迫挑战之一。在这个系统基因组学提案中，我们将剖析O. sativa（亚洲水稻）和O. glaberrima（非洲水稻）对盐胁迫的适应性反应。首先，我们将利用时间序列转录组和染色质可及性数据，结合最先进的网络推断方法，推断亚洲和非洲水稻盐胁迫的基因调控相互作用网络。其次，我们将利用基因表达水平的表型选择分析来确定胁迫反应基因的选择强度和模式。最后，我们将绘制盐胁迫下伴随基因表达变化的全基因组关联（GWAS）位点的表达图谱，重点关注在表型选择分析中被鉴定为正选择、稳定选择或破坏性选择的基因。此外，我们还将在这两种水稻物种中识别生理盐水条件下植物适应性和适应性相关性状的GWAS位点，并将这些定位分析和表型选择分析的结果与亚洲和非洲水稻全基因组序列数据的选择性扫描证据相结合。我们的工作将确定在环境扰动（盐胁迫）下影响关键位点基因表达差异的基因、遗传网络和基因组变异，并明确地将基因调控变异与植物适应性联系起来。

Adaptation of crop plants like rice to environmental stress is an essential requirement to ensure high yields under those conditions. Salinity is among the major environmental stresses that crop plants face, and it is currently threatening rice cultivation due to increasing land pressure and climate change, which are pushing agriculture to marginal lands. Rice is a major world crop comprising two species: one from Asia (Oryza sativa), and one from Africa (O. glaberrima). This project aims to identify genes associated with adaptation to saline soils through comparative analyses of rice varieties that have contrasting adaptation to salt stress, within and between the two species. The discovery of more than one adaptive strategy will increase the options rice breeders could implement in their programs. This project will use several approaches to identify genes that have a uniquely coordinated pattern of expression when the plant is exposed to elevated salt, and at the same time are correlated with vigorous growth and productivity. This project will also undertake public outreach programs using the New York City BioBus. This is a transit bus equipped as a mobile educational laboratory that has been on the road reaching 115,000 people at more than 420 schools and communities. Plant biology laboratory modules will be developed for deployment across New York City on the BioBus. These modules will primarily target schoolchildren in underserved communities, and also the general public in street fairs.Salinity is one of the growing stress challenges crop plants face. In this systems genomics proposal, we will dissect the adaptive response of O. sativa (Asian rice) and O. glaberrima (African rice) to salt stress. First, we will infer the gene regulatory interaction network for salt stress in Asian and African rice using time-series transcriptome and chromatin accessibility data, coupled with state-of-the-art network inference methods. Second, we will use phenotypic selection analysis on gene expression levels to determine the strength and pattern of selection on stress response genes. Finally, we will map expression genome-wide association (GWAS) loci accompanying gene expression variation under salt stress, focusing on the genes that have been identified in phenotypic selection analysis as undergoing positive, stabilizing or disruptive selection. Moreover, we will also identity GWAS loci for plant fitness and fitness-related traits under saline conditions in both rice species, and integrate the results of these mapping analyses and phenotypic selection analyses with evidence for selective sweeps in whole genome sequence data from Asian and African rice. Our work will identify genes, genetic networks and genomic variants that affect gene expression differences in key loci in response to an environmental perturbation - salt stress -and explicitly connect gene regulatory variation to plant fitness.