Rice Genetics IV - IRRI books - International Rice Research Institute

Transposons and functionalgenomics in riceR. Greco, P.B.F. Ouwerkerk, C. Sallaud, A. Kohli, C. Favalli, T. Beguiristain,L. Colombo, E. Pè, P. Puigdomènech, E. Guiderdoni, P. Christou, J.H.C. Hoge,and A. PereiraGenome and expressed sequence tag sequencing in rice provides a vastresource of gene sequences whose functions need to be determined by reversegenetics methods for expression and mutational analysis. To developinsertional mutagenesis strategies in rice, we transformed japonica and indicacultivars with maize transposon constructs, for knockout and gene detectioninsertions. A green fluorescent protein (GFP) excision assay developedenabled the visualization of transposon excision in a variety of tissues.Surprisingly, early Ac excision was observed directly after transformation froma construct containing the strong double CaMV enhancer element adjacentto the Ac promoter. We identified genotypes with Ac amplification events andwith a forward transposition rate of 15–50% that are useful for generatinglines containing multiple transposons. The sequence of DNA flanking transposedAc provided a resource of Ac-tagged sites, which represented about50% in the target region, indicating insertional specificity appropriate for theidentification of mutants of sequenced genes. Clustered Ac transpositionwas revealed by six insertions in 70 kb of chromosome 6. Gene detection Ac-Ds enhancer trap and activation tag transformants revealed active transpositionin about half the lines. These resources for functional genomics aredeveloped by an EU-funded consortium and will be made available to riceresearchers worldwide.Genomic technologies and DNA sequence information have become important inunderstanding the genetics of plants. This is particularly true for model organismssuch as rice, in which the availability of vast amounts of genome information encouragesbiologists to ask questions in genetics, biochemistry, physiology, and molecularbiology in a genomic perspective. Arabidopsis genomics and functional genomicshave led the way and will provide the blueprint for the structure and function of manyplant genes. Some of the remarkable insights emerging from whole-genome analysis(Lin et al 1999, Mayer et al 1999) are the number of gene clusters, large-scale duplicationsof chromosome segments, as well as a surprisingly high frequency (40%) ofnewly discovered genes of unknown function.Transposons and functional genomics in rice 263