Title: Revealing gene function and genetic diversity in plants and animals via TILLING and EcoTILLING Authors
Submitted to: Advances in Genome Science
Publication Type: Book / Chapter
Publication Acceptance Date: February 12, 2013
Publication Date: April 4, 2013
Citation: Barkley, N.L., Wang, M.L. 2013. Revealing gene function and genetic diversity in plants and animals via TILLING and EcoTILLING.In: Neri, C. of Advances in Genome Science Changing Views on Living Organisms. Volume 1. Oak Park, IL: Bentham Science Publishers. p.316-351. Interpretive Summary: In the last 13 years, the technology for obtaining the basic chemical components or building blocks of DNA has rapidly improved so that researchers can quickly unravel the underlying genetic code. The building blocks (A, C, G, and T) or sequence of bases in genes are currently publicly available for many model plant and animal species. Therefore, the focus has now shifted from determining the sequence of a gene to evaluating the function of each gene. Understanding the role of each gene in a genome can allow scientists to pinpoint disease and improve germplasm. Determining the function of a gene requires collecting empirical data from the species of interest. TILLING (Target Induced Local Lesions in Genomes) is a method to facilitate a scientist’s task of elucidating gene function. In this method, one would induce mutations in a species of interest using a chemical mutagen, identify samples that have an induced mutation in a gene of interest in a high throughput manner, and subsequently, use the mutants discovered from the technique to ultimately gain insight on the role of a gene. EcoTILLING is similar to TILLING; however, the focus of this method is to identify naturally occurring variants in a gene of interest instead of induced mutations. Both of these methods have proven to be highly effective in plant and animals species. This review details how to perform TILLING and EcoTILLING, provides an overview of the current literature, advantages and disadvantages of these methods, and discusses technological challenges.
Technical Abstract: With the fairly recent advent of inexpensive, rapid sequencing technologies that continues to improve sequencing efficiency and accuracy, many species of animals, plants, and microbes have complete annotated genome information publicly available. The focus on genomics has thus been shifting from the collection of whole sequenced genomes to the study of functional genomics. Reverse genetic approaches have been used for many years to elucidate the gene function and resulting phenotype from DNA sequence content. Many of the currently used approaches (RNAi, gene knockout, site-directed mutagenesis, transposon tagging) rely on the creation of transgenic material, the development of which is not always feasible for many plant or animal species. TILLING is a non-transgenic reverse genetics approach that is applicable to all animal and plant species which can be mutagenized, regardless of its mating / pollinating system, ploidy level, or genome size. This approach, however, does require prior DNA sequence information. TILLING can ultimately provide an allelic series of silent, missense, nonsense, and splice site mutations to examine the effect of various mutations in a gene and their link to a particular phenotype. TILLING has proven to be a practical, efficient, and an effective approach for functional genomic studies in numerous plant and animal species. EcoTILLING, which is a variant of TILLING, examines natural genetic variation in populations and has been successfully utilized in animals and plants to reveal genetic diversity. In this review, TILLING and EcoTILLING techniques are described and reviewed, as well as, their beneficial applications and limitations.