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United States Department of Agriculture

Agricultural Research Service

Research Project: Cloning, Characterization, and Validation of Altsb/a1 Tolerance in Rice

Location: Plant, Soil and Nutrition Research

2013 Annual Report


1a.Objectives (from AD-416):
The goal of this research is to identify the major genes involved in Al tolerance in rice and provide a better understanding of the physiological mechanisms of Al tolerance. Our preliminary work demonstrates that as a species, rice is capable of growing at Al3+ activities that are between 5-15 times higher than that for maize, sorghum, and wheat, leading us to hypothesize that rice may be a source of novel Al tolerance genes.


1b.Approach (from AD-416):
1. Characterize T-DNA knockouts for candidate AltSB MATE homologs in rice for physiological function and involvement in Al tolerance and quantification of the role of these candidate MATE genes in rice Al tolerance. 2. Fine map and/or clone the gene(s) underlying the novel major Al resistance QTL we recently identified on rice chr 12. 3. Complete the whole genome mapping for rice Al tolerance using the OryzaSNP II chip (44k SNP chip). 4) Initiate development of Al tolerance near isogenic lines (NILs) based on identified QTLs and also newly mapped loci from whole genome association mapping to quantify the contribution of individual loci to Al tolerance and as a resource for breeding for rice Al tolerance.


3.Progress Report:

In FY 2013 (no-cost extension and 4th year of this project), we completed work on the functional analysis of the rice aluminum (Al) tolerance gene, OsNrat1. This gene was previously identified and named Nrat1 (for Nramp aluminum transporter), an Al transporter localized to the plasma membrane of root cells, which when knocked out, enhances Al sensitivity. This is consistent with this transporter serving to mediate Al uptake by moving it directly into root cells, presumably into the vacuole, and away from the root cell wall. Based on DNA sequence analysis of this gene from a panel of Al sensitive and tolerant rice varieties, we found that there were putative sensitive and tolerant versions of the Nrat1 gene. We then identified several DNA sequence mutations that were specific to the Nrat1 gene in the Al sensitive rice accessions. We have shown that the tolerant version of this protein transports much more Al into the cell than does the sensitive version. We also discovered that Al sensitive rice lines that have the sensitive version of this gene have much higher concentrations of Al in the root cell wall than do the tolerant rice lines expressing the tolerant Nrat1 gene. These findings indicate this transporter is involved in a rice Al tolerance mechanism which maintains lower levels of Al in the cell wall (the subcellular region where most of the Al resides in the root) by transporting the Al into root cells where it is stored and detoxified in the cell vacuole (a large storage compartment in plant cells). We also found that when we express this transporter in transgenic Arabidopsis plants (Arabidopsis is a widely used model plant species), their Al tolerance is greatly increased. We are investigating the possibilities that other plant species may harbor superior variants of this protein which may enable us to enhance the Al tolerance of many plant species via marker-assisted plant breeding.


Last Modified: 10/1/2014
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