Plant Model Systems

Question 1

What model systems have been historically focused on?

Answer 1

Historically focused on angiosperms,
Such as:
- Solanum lycopersicum
- Petunia hybrida
- Triticum aestivum (green revolution)
Many of these are large plants with complex genomes

Question 2

How do model systems develop?

Answer 2

• Intrinsic properties: (immediate) Commercial importance or practical qualities
• Derived properties: (immediate / over time) Laboratory methods / tools
• Community properties: (over time) Availability of seed lines, shared resources

Question 3

What is Arabidopsis thaliana and why is it a good model system?

Answer 3

• Small annual pioneer plant from the Brassicaceae family, eudicot, angiosperm
• Small, simple growth requirements
• Short life cycle (~8 wks)
• Self fertilising (maintains genetic lines)
• Large number of seeds (20,000 pp)
• Diploid, small genome, low abundance of transposons (125 Mbp)
• Easily transformed by Agrobacterium floral dip, no need for tissue culture / regeneration

Question 4

What is The Arabidopsis Information Resource (TAIR)?

Answer 4

• Project funded in 1999
• Searches for genes of interest in Arabidopsis
• JBrowser provides info on: locus description, chromosome sequence, RNA expression data, protein data, phylogenetic trees, polymorphisms etc.

Question 5

How can gene expression and protein data be researched?

Answer 5

• Botany Array Resource (BAR)
• Electronic Fluorescent Pictograph (eFP) browsers
  Produced by research community
  Microarray data from chips measuring ~28,000 genes
  RNA sequencing of whole samples

Question 6

When was the Arabidopsis proteome released?

Answer 6

Proteome - The complete set of proteins expressed
- Released in 2020
- 30 tissues, >18,000 genes
- Separated by HPLC and measured via mass spectrometry

Question 7

What are some of the global seed stock centres?

Answer 7

• Nottingham Arabidopsis stock centre
• Arabidopsis biological resource centre
• 1,000,000+ seed stocks

Question 8

What are the types of stocks available?

Answer 8

• Variation (natural accessions)
• Mapping tools; Recombinant inbred lines, Near-Isogenic Lines (RILs, NILs)

Question 9

What TDNA lines are available?

Answer 9

• Random mutagenesis
• Over 250,000 TDNA insertions and their genome locations now available
• Can order seeds of one or more mutant allele in almost any gene (~£10 each)
• Enables you to study the function of a gene of interest

Question 10

What are some of the impacts of Arabidopsis research?

Answer 10

• Plant genome sequencing
• Genome wide TDNA collections
• Live cell imaging of cellulose synthesis
• Idea of ‘basal defence’
• Rewriting of lignin biosynthesis is pathway
• …

Question 11

What are some examples of the choice of model depending on the scientific question?

Answer 11

• Grasses and cereals: Brachypodium distachyon
• C4 photosynthesis: (maize and sugarcane), Setaria vividis

Question 12

How are model plants being redefined now?

Answer 12

• Sometimes need to work directly in the crop of interest
• Possible because we can now generate high quality genome assemblies even for large and complex plant genomes