Tutorial Questions - Andy Flavell

Question 1

How big is the barley genome?

Answer 1

-5.1 gigabase

Question 2

name 3 model plant organisms?

Answer 2

• Arabidopsis - small flowering plant
• Maize - member of grass family
• Barley -versatile cereal grain

Question 3

Define the C-value concept ?

Answer 3

AMOUNT OF DNA ( in pictograms) contained in haploid nucleus

Question 4

What is meant by polyploidy and how can it occur?

Answer 4

Polyploidy is when the whole genome doubles , and organisms are produced with many sets of chromosomes ,This happens by spontaneous somatic duplication and non disjunction at meiosis, it can also occur through induction of artificial drugs ( which could affect cell division).

Question 5

Why is polyploidy important ?

Answer 5

it is an important driving factor of evolution, important for plant speciation, can impact the physical charachterisistics of a plant. Most of the important crops we rely on are polyploids.

Question 6

What is the essential difference between auto and allo-polyploidy?

Answer 6

Autopolyploidy comes from a single species , whereas allopolyploid come from two or more closely related species

Depending on what polyploidy class a specie falls into is important for how their chromosome pairing occurs.

Question 7

How is tandem gene duplication thought to occur?

Answer 7

Normal genetic recombination between chromatids occurs , however instead of the two strands lining up together , the two strands break and join together – however since the size of the chromosome stays the same and the break and joinage is the same for both strands – there is no effect on the actual order of the gene or the number of genes – since are identical on each chromatid.

Question 8

What is a pseudogene?

Answer 8

Non functional gene copies which have become inactivated , like a dead gene

Question 9

What type of plant genes are very numerous and often found in clusters in the genome?

Answer 9

( CHECK THIS ANSWER )

Tandem gene clusters ??? Retrotransponsons ( occur in large clusters??)

Question 10

What are two main classes of transposable elements in plants?

Answer 10

Class 1 = retrotransposons , class 2= DNA transposable elements

Question 11

Why are certain transposons so numerous in plant genomes?

Answer 11

Since they have very diverse sequences, as well as the plant genomes can be very large

Question 12

Essentially what steps are involved in physical mapping of plant genomes?

Answer 12

…. check !!!

Question 13

What are some of the main uses of Fluorescent in situ hybridization (FISH)?

Answer 13

Assigning a chromosome , as well as visualising the mapping out of DNA clones on chromosomes.

Question 14

Roughly how does BAC fingerprinting work?

Answer 14

This process works by using minimum tiling path –so if clones overlap they will have common restriction fragments. It works by using a restriction enzyme to cut a clone of the required DNA fragment , and then the fragments are purified and put on a gel to see the different Genes.

Question 15

Name two of the main ‘next generation sequencing’ methods?

Answer 15

Illumina , Roche 454 sequencing

Question 16

What is the main purpose of genome annotation?

Answer 16

To be able to understand and interpret the newly sequenced genome., very often using different software systems.

Question 17

Briefly define functional genomics?

Answer 17

The identification of the functions of all the genes within an organism

Question 18

18. Explain the main differences between forward and reverse genetics.

Answer 18

Forward genetics selects a specific phenotype (e.g. the height) , and then generates mutants and screens for that trait , whereas the reverse genetics selects a set of genes , generates mutants and then screens the mutants for a difference in gene sequence ( rather than look at the phenotype). Forward genetics uses naturally occurring phenotypes. Reverse genetics starts with a mutation

Question 19

19. Briefly explain how TILLING is performed.

Answer 19

A mutant population is made, DNA from these plants is isolated and then pooled together and then a gene is selected , PCR is then used to amplify these DNA pools and screened for mutations, then you select the plants which have mutated and analyse them.

Question 20

Name 3 different methods for performing gene knockouts.

Answer 20

…