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United States Department of Agriculture

Agricultural Research Service

Research Project: Dissecting the Genetic, Molecular and Physiological Basis of Aluminum Tolerance in Rice: Implications for Cereal Improvement

Location: Plant, Soil and Nutrition Research

Project Number: 8062-21000-036-17-I
Project Type: Interagency Reimbursable Agreement

Start Date: Sep 1, 2013
End Date: Aug 31, 2018

This is a renewal proposal for a current and finishing NIFA grant on rice aluminum (Al) tolerance. We will build upon the progress we have made in identifying novel Al tolerance QTL from joint genome-wide association (GWA) and linkage mapping, From this analysis, we have finescale mapped a major Al tolerance QTL and shown it is due to ART1, a transcription factor that controls the Al-induced increase in expression of a number of other Al tolerance genes. We also found from our GWA studies a QTL that explains 40% of the variation in the aus subpopulation of rice and is due to the action of Nrat1, and Al uptake transporter in the plasma membrane of root cells. We have identified two different Nrat1 haplotypes that exhibit 4 amino acid changes which result in less Al uptake via the al sensitive Nrat1 haplotype. In the new proposal, we will focus on 3 objectives. 1) Characterize natural variation in the Al tolerance gene ART1, and how it can be exploited to improve rice Al tolerance; 2) Investigate the transferability of the rice Al tolerance mechanism conferred by Nrat1 into other cereal crops; and 3) Identify novel rice Al tolerance genes and their corresponding physiological mechanisms. This third objective will focus on the role of cell wall carbohydrates and proteins in rice Al tolerance. Part of this research will focus on a very significant QTL on chr 7 identified from our GWA studies where a number of genes encoding cell wall xyloglucan endotransglucosylases reside. A second subobjective will focus on the role of cell wall loosening proteins, expansins, in Al toxicity and tolerance.

Objective1: A. Complete fine-mapping of a major Al tolerance QTL on chr 12 (co-localized with ART1) and obtain reciprocal NILs for field evaluation of QTL effects. B. Perform RNA-seq on reciprocal NILs and parental lines to quantify the effect of QTL (ART1) alleles on genome-wide gene expression in an indica and a tropical japonica genetic background. C. Evaluate diversity of ART1 alleles in the rice diversity panel; characterize structural and expression differences; clarify relationship between ART1 and the QTL on chr. 12. D. Evaluate the phenotypic impact of different ART1 alleles via rice transformation. E. Perform yeast-two-hybrid screening to identify ART1-interacting proteins. Objective 2: A. Analyze Nrat1 allelic variation and expression levels in a diverse set of rice lines, to determine how allelic variation in Nrat1 affects Al tolerance in rice. B. Identify and characterize Nrat1 homologs in maize, sorghum, and wheat. C. Introduce the tolerant rice Nrat1 allele into sensitive transgenic rice, maize and wheat. Objective 3: A. Characterize cell wall carbohydrate modifying candidate genes underlying major GWAS peak on chr. 7 with strong statistical association with Al tolerance. B. Investigate the role of the cell wall proteins with a focus on expansins in Al toxicity to identify novel candidate tolerance proteins.

Last Modified: 10/18/2017
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