Genomics and Arabidopsis

What is ‘genomics’? Study of an organism’s entire genome –All the DNA encoded in the organism –Nucleus, mitochondria, chloroplasts –Genes & the stuff in between them What made genomics possible? –High throughput sequencing technology –Availability of many “landmarks” –Bioinformatic techniques to assemble sequences

Genome sizes Amoeba – 670 Gb (billion base pairs) Humans – 3 Gb Corn – 2.5 Gb Honey Bee – 1.8 Gb Soybean – 1.4 Mb (million base pairs) Arabidopsis – 135 Mb Fruit fly – 130 MB (60% of fruit fly genes conserved with human) Yeast – 20 Mb E. coli bacterium – 4 Mb Viruses – 10 3 – 10 5 bps

What are the functions of all the genes? Functional genomics – uses high throughput/global methods to simultaneously study the functions of large numbers or all the genes of an organism Transcriptomics – study the collection of all the gene transcripts in a cell/tissue/organism. DNA microarrays. Proteomics – study the collection of all proteins in a cell/tissue/organism. Rely heavily on computational biology, bioinformatics, and statistics to analyze and manage data sets. Model organisms are also important

Arabidopsis is a model for the study of plant gene functions

Why Arabidopsis????? It is a good laboratory model (like a fruit fly or mouse) Small size Rapid life cycle – for a plant Diploid genetics 5 relatively small chromosomes = small genome Large amount of natural diversity within the species Extremely easy to make transgenic plants

What can you study with Arabidopsis??? Most of the major questions in fundamental plant biology Plant growth and development Photosynthesis Hormone functions Mechanisms of gene regulation Plant reproduction Responses to abiotic stress Responses to pathogens Plant genome structure and function etc. etc. etc.

The Arabidopsis thaliana genome (March 2007) Approximate total chromosome length: 134,634,692 bp (for comparison corn ~2.5 billion bp, soybean ~1.4 billion bp)

Program Title: 2010 Project To determine the function of all genes in Arabidopsis thaliana by the year 2010 Synopsis of Program: The Directorate for Biological Sciences (BIO) of the National Science Foundation (NSF) announces its intention to continue support of research to determine the function of all genes in the model plant Arabidopsis thaliana by the year Individual investigators or groups of investigators will be supported to conduct creative and innovative, genome- wide or systems-level research designed to determine, using all available means, the functions of Arabidopsis genes. This year, the Program will focus on: (1) projects that include genome-wide analyses for benchmarking the function of all genes in the genome; (2) projects that will develop experimental and computational methods, tools, and resources for enabling a broad community of scientists to conduct functional genomics research on Arabidopsis; and (3) research on exemplary networks that use high throughput methods and integrate modeling with experimental data to understand the gene circuitry underlying basic plant processes. What do all those genes do???

Reverse genetics Old paradigm – “forward genetics”, trait (phenotype)  inheritance, gene (but still good) New paradigm – “reverse genetics”, gene  trait (phenotype) Must know the genes Required new tools for plant molecular biologists/geneticists - Knock out genes (loss of function mutations) - Knock in genes (gain of function over expression) Study function of any gene of interest

Reverse genetics in Arabidopsis Collections of mutations that reside in almost every gene & Methods to rapidly knock out or knock in genes of interest Enabling tools for reverse genetics How to choose a gene Your favorite gene family or gene function Candidate genes from other genomics approaches associated with your favorite biological process Candidate genes from other organisms associated with your favorite biological process

Are studies in Arabidopsis relevant??? CO/FT regulatory module controls timing of flowering and seasonal growth cessation in trees Published May 19, 2006 in Science.

Questions???