Functional genomics: Probing plant gene function and expression with transposons

Abstract

Transposable elements provide a convenient and f lexible means to disrupt plant genes, so allowing their function to be assessed. By engineering transposons to carry reporter genes and regulatory signals, the expression of target genes can be monitored and to some extent manipulated. Two strategies for using transposons to assess gene function are outlined here: First, the PCR can be used to identify plants that carry insertions into specific genes from among pools of heavily mutagenized individuals (site-selected transposon mutagenesis). This method requires that high copy transposons be used and that a relatively large number of reactions be performed to identify insertions into genes of interest. Second, a large library of plants, each carrying a unique insertion, can be generated. Each insertion site then can be amplified and sequenced systematically. These two methods have been demonstrated in maize, Arabidopsis, and other plant species, and the relative merits of each are discussed in the context of plant genome research.

Molecular characterization, expression pattern, and function analysis of the OsBC1L family in rice

“…Completion of the rice genome sequence has enabled gene identification and functional analysis on a large scale. In order to elucidate the gene function in rice genome, a global effort to generate insertional mutants, mainly by T-DNA and transposable elements insertion, has been carried out and a large number of mutants has been collected in the last few years (Hirochika et al 2004;Jeon et al 2000;Martienssen 1998;Osborne and Baker 1995;Wu et al 2003). Further, additional research tools of functional genomics in rice, such as full-length cDNA collection and whole genome expression profiling, have been established and have enhanced the pace for elucidating gene function throughout the genome .…”

Deletion-Based Reverse Genetics in Medicago truncatula

“…Systematic reverse genetic platforms, allowing researchers to obtain plants mutated at any identified locus, have streamlined functional genomics in well-resourced model species. These platforms are generally based on insertional mutagenesis using T-DNA (Azpiroz-Leehan and Feldmann, 1997; Krysan et al, 1999;Sussman et al, 2000;Sessions et al, 2002;Alonso et al, 2003) or transposon tagging (Martienssen, 1998;Parinov et al, 1999;Speulman et al, 1999;Parinov and Sundaresan, 2000;Tadege et al, 2008), which, through the introduction of known sequences, greatly facilitates gene cloning and allows the high-throughput characterization of insertion sites. However, these approaches are not feasible in the majority of species where, although genomic sequence information may be extensive, transformation and tissue culture-based methods are not practical.…”

Isolation and characterization of rice mutants compromised in Xa21-mediated resistance to X. oryzae pv. oryzae

“…Mutants produced by deletion or insertion mutagenesis will play an important role in assigning function to the large amount of new sequence information. The most commonly used insertional mutagenesis systems in plants are transposon and T-DNA tagging (Martienssen 1998). Although many genes have been identified using both strategies, these two systems have their limitations in gene function analysis.…”