Functional Genomics in Plants

Abstract

Abstract The first complete plant genome sequence to be determined was that of the model plant Arabidopsis thaliana , which was published in 2000. This was followed by the first drafts of the rice genome sequence in 2002. Since the publication of these landmark genomes, the development of high throughput sequencing technologies has reduced the time and cost of obtaining genome sequences to a fraction of that required a decade ago. This has enabled the sequencing of many plant genomes and thus a vast amount of genome sequence information is available to the researcher. The goal of functional genomics is to determine how these genome sequences generate plant phenotypes. The focus of most functional genomics research is to determine the function of all the genes involved in a particular process. To achieve this, functional genomics uses techniques and analyses that can survey the entire complement of genes in a genome. This chapter discusses the most commonly used functional genomics methods. Key Concepts: Advances in sequencing technologies are making entire genome sequences relatively easy to obtain. The goal of plant functional genomics is to understand how the genome generates the phenotype of the plant. Comparison to other gene sequences can often identify a likely function for a gene. Array and sequencing based methods can be used to show where and when all the genes in an organism are expressed. Gene function can be determined by knocking out or reducing gene function and can be achieved by insertion, chemical mutagenesis or RNAi. High throughput methods using recombination‐based cloning enable many tests of gene function to be applied on a genome‐wide scale.