RESEARCH-PGR: Genomic Basis of Rice Ecosystem Adaptation

New York University, New York NY

Investigators

Abstract

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.