Phenome Analysis in Plant Species Using Loss-of-Function and Gain-of-Function Mutants

Abstract

Analysis of genetic mutations is one of the most effective ways to investigate gene function. We now have methods that allow for mass production of mutant lines and cells in a variety of model species. Recently, large numbers of mutant lines have been generated by both 'loss-of-function' and 'gain-of-function' techniques. In parallel, phenotypic information covering various mutant resources has been acquired and released in web-based databases. As a result, significant progress in comprehensive phenotype analysis is being made through the use of these tools. Arabidopsis and rice are two major model plant species in which genome sequencing projects have been completed. Arabidopsis is the most widely used experimental plant, with a large number of mutant resources and several examples of systematic phenotype analysis. Rice is a major crop species and is used as a model plant, with an increasing number of mutant resources. Other plant species are also being employed in functional genetics research. In this review, the present status of mutant resources for large-scale studies of gene function in plant research and the current perspective on using loss-of-function and gain-of-function mutants in phenome research will be discussed.

Production and characterization of a large population of cDNA-overexpressing transgenic rice plants using Gateway-based full-length cDNA expression libraries

“…Furthermore, it is impossible to detect the mutant phenotypes that correspond to the mutated genes when gene knockouts lead to embryonic lethality or severe defects in plant growth and development. Activation tagging is the most common gain-of-function strategy for the large-scale identification of gene function and uses the random insertion of a transcriptional enhancer into plant chromosomes to activate the gene(s) near the enhancer (Hsing et al 2007, Jeong et al 2002, Kuromori et al 2009, Mori et al 2007, Nakazawa et al 2003, Wan et al 2009). Further, activation tagging is applicable for the identification of functions of genes with and without annotation.…”

A Comprehensive Dataset of Genes with a Loss-of-Function Mutant Phenotype in Arabidopsis

“…This deficiency will only become more severe as global approaches to plant phenotyping are expanded in the future (Sozzani and Benfey, 2011). Attempts to document plant phenotypes on a large scale have been described before (Kuromori et al, 2009). But finding a simple, comprehensive dataset of cloned genes with mutant phenotypes in a reference plant remains elusive.…”

Achievement of genetics in plant reproduction research: the past decade for the coming decade

“…In addition, numerical-based and phenotype-based databases are becoming more established (Kuromori et al, 2009;Kojima et al, 2009;Mano et al, 2009;Ogata et al, 2009). This situation indicates the necessity of an integrated database among various types of omics data (Swarbreck et al, 2008;Rice Annotation Project, 2008; also reviewed in Shinozaki and Sakakibara, 2009).…”