The Decoding of Gene Functions—Transcriptomics Tools Toward Molecular Physiology and Breeding
For the last decade plant functional genomics was developed based on model organisms such as Arabidopsis thaliana and more recently Oryza sativa. The knowledge gathered is now extensively used to study other plants including Brassica crop species. Brassica species have been studied in many aspects: seed growth, development, disease resistance and abiotic stress tolerance (van Poecke and Dicke 2002; Tuberosa and Salvi 2006; Broekgaarden et al. 2007, 2008). Vegetable Brassicas are recognized as a valuable source of vitamins, nutrients and anticancer compounds (Paterson et al. 2001). The large effort to bridge the gap between model plants and crop species functional genomics studies leveraged the development of manygenomics resources for Brassica. Several tools were established to decipher gene functions (van Poecke and Dicke 2002; Tuberosa and Salvi 2006; Broekgaarden et al. 2007, 2008). These include expressed sequence tag (EST) collections, cDNA libraries, comprehensive mutant collections and DNA microarrays (Lim et al. 1996; Kwak et al. 1997). Special attention has been given to the generation of transcriptomic platforms, which are now released to the community and well supported. So far the Brassica transcriptome has been analyzed to address both agricultural and fundamental biological questions (Paterson et al. 2001; Kwun et al. 2004; Li et al. 2005; Soeda et al. 2005; Joosen et al. 2007; Kang et al. 2008; Lee et al. 2008; Xiang et al. 2008; Sarosh et al. 2009). The available microarray experiments uncovered genes with diverse functions that may act in regulation of embryogenesis and seed development (Lim et al. 1996; Soeda et al. 2005; Li et al. 2005; Kang et al. 2008; Xiang et al. 2008), stress response, and stress tolerance (Hammond et al. 2005; Vanderauwera et al. 2007; Zhou et al. 2007; Broekgaarden et al. 2008; Lee et al. 2008). Various analytical approaches were employed to facilitate the identifi cation of new Brassica specifi c genes that respond to biotic and abiotic stimuli (Hammond et al. 2005; Broekgaarden et al. 2008; Lee et al. 2008). The available microarray studies revealed a large variety of functional assignments based on the conserved expression patterns of othologous genes. The microarray approach also has the potential to elucidate regulatory pathways controlling important traits, thereby increasing the effectiveness of plant breeding. This chapter presents the current status of transcriptomic resources and efforts in determining the functions of genes in Brassica species.