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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

2011 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 the second year of this project, “association genetics” analysis of rice Al tolerance which involves phenotyping of a panel of 400 different rice lines for Al tolerance, were conducted. This diversity panel has been genotyped with over 44,000 unique molecular markers. Association genetics involved using a novel statistical program to identify molecular markers that associate with rice Al tolerance. Using this approach, we have identified a number of novel regions of the rice genome where Al tolerance genes reside and are in the process of cloning and evaluating candidate Al tolerance genes.


Last Modified: 4/21/2014
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