MCA-PGR: Genetic and Genomic Approaches to Understanding Low-K Tolerance in Rice

University Of California-Berkeley, Berkeley CA

Investigators

Abstract

PI: Sheng Luan (University of California, Berkeley) CoPI: Peggy Lemaux (University of California, Berkeley) Key Collaborators: Rod Wing (University of Arizona)and Bin Han (National Center for Gene Research, Chinese Academy of Sciences) Plant growth minimally requires sunlight, CO2, water, and minerals. While sunlight and CO2 are abundant, water and minerals are major limiting factors for crop production. Although extensive research effort has been directed to studying water use efficiency and drought tolerance, much less effort has been expended on understanding the mechanisms of plant nutrient use efficiency and tolerance to low-nutrient status in the soil. Not knowing how to increase nutrient use efficiency in crops resorts to heavy use of fertilizers, a practice that endangers environment and sustainable agriculture. The overall goal of this project is to provide a comprehensive understanding of the gene networks responsible for high potassium (K)-use efficiency in cereal crops using genome-wide approaches. Rice is chosen as a model because of its rich genetic and genomic resources and its ease of transformation. The specific objectives are as follows: (1) to characterize the biological roles of all K-transporters encoded in the rice genome. As K+ is not metabolized, effective uptake and distribution of K+ hold the key for high K+ use efficiency in plants. Dissecting the roles of all K-transporters in rice will generate a "road map" of K+ movement throughout a cereal crop and provide possible ways to improve efficiency; (2) to identify genetic loci and individual genes associated with low-K tolerance in rice. Rice landraces display dramatic natural variations in low-K tolerance and such variations can be linked to genes using sequencing-based association mapping that would speed up the identifications of QTLs; (3) to conduct RNA-seq-based comparative transcriptome analysis and identify genes involved in low-K response and adaptation. By comparing transcriptomes of "highly tolerant" and "highly sensitive" landraces to the low-K condition, differentially expressed genes between the two phenotypic groups will be identified and their relevance to phenotypic variations will be scored; and (4) to integrate the datasets from Objectives 1-3 to assemble a gene regulatory network. This transformative knowledge will lay the foundation for marker-assisted classical breeding as well as genetic engineering approaches to improve K-use efficiency in cereal crops and reduce the use of fertilizers in crop production. A number of broader impacts to society and education will be achieved. Rice is one of the most important food crops, feeding more than half of the world's population. Understanding the mechanisms of low-K tolerance in rice will provide a knowledge base for breeding rice varieties (and other cereals) that produce high yield with minimal fertilizer use, protecting environment and contributing to sustainability of agriculture. This project integrates undergraduate and graduate education into all aspects of the research. Outreach activities will be undertaken that include training of underserved high school and community college students through collaboration with Biotech Partners and STEM program to introduce these students to modern biology techniques and knowledge with the goal of increasing their interest in science careers. All sequence data and annotations will be accessible through the Rice Genome Annotation Project (http://rice.plantbiology.msu.edu/). All sequences generated from expression profiling will be deposited at GenBank, the Plant Expression Database (http://www.plexdb.org/) and PlantGDB (http://www.plantgdb.org/).