Model plants and their Role in genetic manipulation

Mitesh Shrestha

Definition of Model Organism

• Specific species or organism

• Extensively studied in research laboratories

• Advance our understanding of – Cellular function

– Development

– Disease

• Ability to apply new knowledge to other organisms

Current Models

• Drosophila

• Xenopus

• Zebrafish

• Mouse

• C. elegans

• Yeast

• E. coli

• Arabidopsis

Arabidopsis thaliana

Arabidopsis thaliana • Small flowering plant native to Eurasia.

• Considered a weed

• Found by roadsides and in disturbed lands.

• A winter annual with a relatively short life cycle,

• Popular model organism in plant biology and genetics.

• Relatively small genome of approximately 125 megabase pairs (Mbp).

• It was the first plant to have its genome sequenced, and is a popular tool for

understanding the molecular biology of many plant traits, including flower development and light sensing.

• In 2016, it was named as one of the organisms that would be involved in CRISPR-based genetic engineering.

Arabidopsis thaliana

• Dicotyledonous angisoperm • The model Plant for Genetic

Engineering of Plants • Member of Mustard Family • Belongs to Brassicaceae Family • Discovered by botanist Johannes Thal

in the 1500s • First mutant reported in 1873 • Chromosome number discovered in

1907 by Friedrich Laibach in 1907 • Entire genome sequenced in 2000

Arabidopsis thaliana

• Tens of thousands of the plant can be grown at a time

• Commonly known as “mouse ear cress”

• Grows luxuriantly in temperate regions of the world

• More than 750 natural varieties seen around the world

Arabidopsis thaliana

Arabidopsis thaliana

• A single Plant produces around 6,000 seeds /germination- massive production

• This enables geneticists to screen large population of seedlings for specific phenotypes

• Because it has very short life cycle; takes only six weeks from germination to mature seeds

• Easy to grow- even in small spaces or indoor areas

• Only requires water, soil and light to reach maturity

• Also found to be capable of growing in hydroponic system

Arabidopsis thaliana

• Generally self-fertilizes, but selective breeding is possible by fertilizing flowers with pollen from another plant

• Can be easily transformed with Agrobacterium or any standard chemical mutagens

• Although closely related to such economically important crop plants as turnip, cabbage, broccoli and canola not a economically important plant

• Lay the groundwork for studying the biology of all other plant species.

Genome of Arabidopsis thaliana

• First Plant genome to be sequenced, sequencing completed in 2000 by an organsation international collaboration “Arabidopsis Genome Initiave (AGI)”- started in 1996 and now readily available to the scientific community

• Nuclear DNA of Arabidopsis carried by five pairs of small chromosomes with well defined banding patterns

• Contains about 125 megabase sequences • Encode approximately 25,500 genes • Arabidopsis has many gene families common to plants and

animals which have been greatly expanded in plants – for instance, Arabidopsis contains 10- fold as many aquaporin (water channel) proteins than any other sequenced organism

Arabidopsis Genome • 5 chromosomes; 25,498 genes, and 125 million

bases – Smallest genome of any plant

• First complete genome sequence of a plant

• Useful plant-specific gene functions for crop enhancement

– Grow crops in salty or metallic soils or in very cold or hot climates

Arabidopsis Genome

Sequence

• Sequenced by Arabidopsis Genome Initiative (AGI)

• Started in 1996, planned to finish by 2004, but actually finished in 2000

• Current and future research done by The Arabidopsis Information Resource (TAIR)

• 8,811 articles on Arabidopsis

Arabidopsis Genome Initiative (AGI) comprises six main groups

The Institute of Genomic Research (TIGR)

SPP Consortium (Stanford University, Plant Gene Expression Center, and University of Pennsylvania)

The CSHL Consortium (Cold Spring Harbor Laboratory, Washington University at St. Louis and Applied Biosystems, Inc.)

The European Union’s European Scientist Sequencing Arabidopsis (ESSA) network of laboratories

The Centre National de Sequencage (CNS), Frances

Kazusa DNA Research Institute, (Japan)

Features of Arabidopsis genome

• Each chromosome contains a limited amount of repetitive DNA

• Unlike the genes of other plants, the Arabidopsis genes are more tightly packed and contain only small introns- much higher percentage of the genome is associated with coding and genetic function

• Many crop species have large genomes often as a result of polyploidization events and accumulation of non-coding sequences during their evolution.

• Maize has a genome of approximately 2400 Megabase pairs (Mbp) – around 19 times the size of the Arabidopsis genome – with probably no more than double the number of genes, most of which occur in duplicate within the genome.

• The wheat genome is 16000 Mbp – 128 times larger than Arabidopsis and 5 times larger than Homo sapiens – and it has three copies of many of its genes.

• The large crop genomes pose challenges to the researcher, including difficulty in sequencing as well as in isolation and cloning of mutant loci.

• Evidence from the rice genome project suggests that the Arabidopsis genome may be missing some homologs of genes present in the rice genome.

• Despite this, most of the difference in gene number between Arabidopsis and crop species appears to result from polyploidy of crop species’ genomes, rather than from large classes of genes present in crop species that are not present in Arabidopsis.

• Therefore, the genes present in Arabidopsis represent a reasonable model for the plant kingdom.

• However, it is clear that Arabidopsis represents a starting point rather than the finish line for utilizing the full power of genomics for crop improvement.

Significance of Arabidopsis in Plant Genetics

Basic life processes similar to those of more complex

crop plants such as corn, soybean, and wheat It can be assumed that the basic set of genes that

control these processes are the same, making findings applicable to other species

Focus of intense genetic, biochemical and physiological study

Relatively small, genetically tractable genome that can be manipulated through genetic engineering more easily and rapidly

What makes Arabidopsis thaliana a model organism??

• Small (20 cm),unremarkable spindly weed, with tiny, white, four-

petalled flowers

• Rapid growth (takes 48 days from germination to mature seed

development- Many offsprings)

• Small nuclear genome and therefore relative genetic simplicity

• Convenience and abundance

• Susceptibility to T-DNA insertions

• Basic similarities to other crops

• A large number of mutant lines and genomic resources

Convenience

Easy to grow

Small plant size means tens of thousands can be grown at a time

6-8 weeks from seeds to seeds

Massive seed production (potential up to 10,000 seeds per plant)

Ability of Arabidopsis thaliana to self-fertilize

Easy to Grow Arabidopsis can be grown in small spaces or indoors. They only require water, soil, and light to reach maturity.

Short Life Cycle •48 days from germination to mature seed development.

Making Knockout Plants

Easily susceptible to Agrobacterium which contain Ti plasmids, the vehicles for T-DNA insertion

Easy to establish many knockout lines in short amount of time

Significance of Arabidopsis in Plant Genetics

Basic life processes similar to those of more complex crop plants such as corn, soybean, and wheat

It can be assumed that the basic set of genes that control these processes are the same, making findings applicable to other species

Disadvantages of Arabidopsis

• Since the genotypes are so similar, it is hard to distinguish the phenotypes

unrecognizable mutations

• Pests are attracted to these plants

• Agar can get very contaminated by Fungi

Assignment

• What are the desired characteristics of a model organism? [3]

• Give brief description about the plant Model Organism.[3]

• What are the advantages of having Arabidopsis as a model organism? [3]

• What are the disadvantages of having Arabidopsis as a model organism? [3]