Fine mapping and candidate gene analysis for root traits in rice (Oryza sativa L.).
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Rice is a major staple food for more than 30% of the world's population with 85% of its production devoted to human consumption (IRRl, 1997). Rice is grown in diverse agro-ecological conditions, ranging from deepwater lowland areas to high altitude upland areas. Nearly half of the areas planted in rice are in rainfed ecosystems. Drought is one of the main abiotic constraints in rice, causing huge yield losses each year. A thick and deep root system is considered a favorable component allowing rice crops to maintain their water status under conditions in which there is water available at deep soil layers (Nguyen et al., 1997). The presence of sub-soil compaction layers in many rainfed lowland areas impedes optimal growth in rice cultivars without these characters. To fully understand biological processes underlying rice root growth, it is important to isolate and characterize the genes involved in these processes. In the present study, two approaches were employed in order to identify genes involved in rice root growth, a Differential Display Reverse Transcription (DDRT) analysis and a "map-based cloning" strategy. In the DDRT analysis, 2 candidate cDNA clones putatively involved in rice root penetration ability (CR19C1 and CR23A1) were identified. Results from sequence homology searches indicated that the DD fragment CR19C1 has some similarity to the locus AT1G72960 on chromosome 1 of the Arabidopsis genome. This locus is a putative gene conferring root hair defects in Arabidopsis thaliana. The DD fragment CR23A1 was similar to the locus AT1G76490 on chromosome 1 of Arabidopsis thaliana. This locus is a putative gene coding for 3-hydroxy-3-methylglutaryl CoA reductase (HMGR), the enzyme involved in cell division in many species. These findings give us some ideas about the functions of candidate genes involved in root growth mechanisms in rice. In a map-based cloning strategy, 1,037 NILs derived from the BC4F2 population were used for fine mapping of the BRT QTL on rice chromosome 4. So far, the marker R1408B has been mapped in the target QTL between the flanking markers RG939 and RZ905, leading to the dissection of the target QTL into 2 smaller segments with a genetic distance of 2.3 and 2.8 cM, respectively. More RFLP markers are being screened with the aim of narrowing the genetic distance of the target QTL down to 1 cM or less. Chromosome substitution lines have been selected for further root characteristic evaluation in the greenhouse. Results from this experiment will facilitate fine mapping of the target QTL.