Transcript Document Here - Genomics and Arabidopsis

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 – 103 – 105 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)
What do all those genes do???
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 2010. Individual investigators
or groups of investigators will be supported to conduct creative and innovative, genomewide 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.
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
Enabling tools for reverse genetics
Collections of mutations that reside in almost every gene &
Methods to rapidly knock out or knock in genes of interest
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???
http://www.entm.purdue.edu/extensiongenomics/GAME/default.html
http://www.prep.biotech.vt.edu/index.html
http://www.genome.gov