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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

2012 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 2012 (the third year of this project), we conducted research to clone, and characterize the gene(s) underlying a major and novel rice Al tolerance quantitative trait loci (QTL) we had previously identified. In order to positionally clone the Alt12.1 QTL on chromosome 12, that explained ~19% of the variation in Al tolerance identified from a RIL population between the tolerant parent Azucena (O. sativa tropical japonica) and the susceptible parent, IR64 (O. sativa indica), (Famoso et al, 2010, Plant Physiol.153: 1678–1691), a fine mapping strategy was carried out that narrowed the region of the rice genome where the gene responsible for this Al tolerance QTL to a region spanning 30,000 DNA nucleotide bases. This region includes 6 putative genes. One of the genes is a transcription factor, ART1 (for Al resistance transcription factor.
1)that was recently identified by other researchers as a protein that controls the expression of a number of possible rice Al tolerance genes. We now will use molecular breeding and biotechnology approaches to express a tolerant version of ART1 as an Al sensitive rice line to verify it is the Al tolerance gene responsible for this QTL.


Last Modified: 8/21/2014
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