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Plant sciences > Lecture 3 - Plant Genome Plasticity - Polyploidy > Flashcards

Lecture 3 - Plant Genome Plasticity - Polyploidy Flashcards

1
Q

What are two types of Polyploidy?

A
  • Autopolyploidy

- Allopolyploidy

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2
Q

What is Polyploidy?

A
  • Whole genome doubling
  • Produces organisms with multiple sets of chromosomes
  • can arise spontaneously or through non disjunction at meiosis
  • can be artificially induced with drugs (e.g. colchine)
  • can be limited to certain tissues - endopolyploidy
    MUCH MORE COMMON IN PLANTS THAN ANIMALS!
  • can drive plant speciation
  • have multiple sets of chromosomes
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3
Q

Why is polyploidy more common in plants ?

A

…

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4
Q

Why are many crop plants are polyploid?

A

…

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5
Q

Many diploid plant genomes derive from ancient polyploid species - where have these genes gone ?

A

…alot of diploids are actually polyploid

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6
Q

what are autopolyploids?

A
  • they derive from a single species

- same chromosomes doubling from 2 - 4

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7
Q

What are allopolyploids ?

A

they derive from 2 or more closely related species

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8
Q

What are some possible paths to polyploidy ?

A

(slide 8 - lecture 3)

-speciation ?

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9
Q

Why is polyploidy important?

A
  • major force in plant evolution ( especially ferns and flowering plants )
  • directly effects the physical properties of plants (e.g. size of seeds, life cycle)
  • many important crop plants are polyploids
  • most plants retain the vestiges of ancient polyploidization events
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10
Q

Polyploidy and evolution - speciation in vascular plants

A

polyploidy results in irreversible evolutionary changes - changes to the characteristics.

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11
Q

roughly how many flowering plants arose through polyploidization?

A
  • 35%

e. g. wheat , petunia

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12
Q

What are some effects of polyploidy on the plant?

A
  • increased size of some cells and some organs ( immediate response in cell nulceus need to double in size for all the chromosomes )
  • changes in shape and texture of organs ( we know this because we can create polyploids by crossing plants)
  • differing ability to colonize new habitats n(e.g. different growth properties of an organism to their parent )
  • reduction in fertility and seed production ( because of changes in size/shape)
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13
Q

How are polyploids recognised ?

A
  • count chromosomes using cytogenetics ( if a species has pairs of closely related chromosomes - it is probably polyploid) - chromosomes will have doubled !
    also if they fall into pairs - they are polyploid and can be stained.
  • increased organ size (e.g. stomatal cells will increase in size under polyploid conditions)
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14
Q

The effects of Polyploidy - Brassica Napus?

A
  • Brassica Napus is a tetraploid that shows ‘ hybrid vigour’ over its two diploid progenitors
  • Brassica Napus - was created in the Lab - and you can see the different properties relative to its parents - its interesting as you can cross two small plants to create a double sized one - its called heterosis / hybrid vigour
  • Brassica has many cases of Allotetraploidy , and its easy to create brand new ones
    (e. g. different types may have different combinations , chromosome numbers , )

note. half the things we buy that are green are hybrids!

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15
Q

What is hybrid vigour?

A

the tendency of a cross-bred individual to show qualities superior to those of both parents.

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16
Q

What is Heterosis?

A

Heterosis refers to the phenomenon that progeny of diverse varieties of a species or crosses between species exhibit greater biomass, speed of development, and fertility than both parents.

17
Q

How do we distinguish between Auto and Allopolyploidy?

A

What happens to chromosome pairing - depends on whether they are auto or allopolploidy

  • Allopolyploids- are variable - multivalent pairing when closely related
  • autropolyploids - typically have multivalent pairing - chromosomes are more or less identical
18
Q

How can we identify something as allopolyploidy?

A
  • using In situ hybridisation ( probes from paternal species)
  • another way to identify allopolyploidy is by looking at chromosomes (in particular parinting the chromosomes with probes that derive from the paternal species )
19
Q

What is in situ Hybridisation?

A

…

20
Q

Potential causes of Novel Variation in polyploids

A
  • increased variation for dosage regulated genes ( have potential for lot of variation)
  • altered regulatory interaction
  • genetic changes ( long term effect of polyploidy)
  • epi-genetic changes ( dont need too much detail on this for exam….)
21
Q

What happens after polyploid formation ( autopolyploids) ?

A

Autopolyploids
-Genomes recombine freely – no chance for individual chromosome evolution
-Gene expression -
Dosage effect (linear relationship between gene expression and number of gene copies).
-Autopolyploids have 4 copies of chromosomes
- They are capable of assorting together freely – nothing will change – because every chromosome will be joining to one another – there is no possibility for one chromosome for divergeing from one another !

22
Q

What happens after polyploid formation ( allopolyploids) ?

A
  • Genomic changes
  • Diploidization
  • Genome structural evolution

-Alloploids - different ( e.g one pair will never interact with the other pair ) – so will evolve independently – the chromosomes will diverge – and so events like genetic changes over millions of years ( that can NEVER HAPPen in AUTOPLOIDY !!!)

23
Q

What happens after polyploid formation?

A
  • after polyploidisation - it is possible for gene division)

diploidization

24
Q

What is Diploidzation?

A
  • shortly after a genome duplication event, genes begin to be deleted at a rapid rate
  • this happens more or less randomly between the duplicated chromosomes - ( though there is some evidence for selective loss)
  • after about 50 million years - theres only a few % of the duplicated genes left ( and they are of course diverging from each other)
  • In the long term allopolyploids do not actually need all these copies.
25
Q

The story of cotton?

A

cotton is a tetraploid
parental genome - came from different continents - africa and the new world
- although at the beginning when the tetraploid was formed - it must have been together - otherwise it would have occured naturally

(slide 28-30,LT3)

26
Q

What do you know about genomic interactions in cotton?

A
  • intergenomic colonisation - repetitive sequences specific from A - genome are found in the G- genome in gossypium polyploids
    ( probably transposable elements)

they can be observed using colonisation of one allogenome by the other - the repetitive sequences specific from the A plant are found in the D genome – using this ‘painting technique’ so tracing the transposable elements – so oer millions of years will jump between the genomes

27
Q

What is the story of Wheat?

A

1 mya – spontaneous hybridization – to a wild hetroploud AB ( emmer wheat ) – which is the direct ancestor of the Durum wheat – which is a heterploid

Bread wheat arose by AB genome mix , so mix with heteroploid and diploid to make a hexioploid ….

During this time farming was starting in middle east – they collected big seeds compared to the normal – and ended up producing plants – that have been sown and harvested ever since that day

Because its 3 genomes are very similar, wheat can tolerate loss of one copy of any chromosome

Each plant has 7 chromosomes ( all cereals related to wheat have 7 chromosome pairs )
Wheat can tolerate the loss of one of these pairs – so if it happens they can still be a viable plant – because they have back u genes
Chromosomes of 1 A will not interact with chromosome 1 D ( they are separated by millions of years !)

This is a useful breeding tool!

28
Q

What do you know about Potatoes?

A

All 4 chromosome sets’ are the same – All can pair at meiosis
This makes breeding/genetics difficult.

Potato is an autopolyploid – 4 copies of every chromosome – so every chromosome goes with each other – so difficult to produce plants with different things..

29
Q

What is ancient polyploidy?

A
  • much more complicated
  • much more difficult to detect
  • chromosomes become scrambled by rearrangements
  • divergence or loss of duplicate genes
  • Bits of chromosomes / fusions of chromosomes , a big mix of chromosomes ….
30
Q

What methods are used with ancient polyploidy?

A

Detection is now quite easy because of sequenced genomes
Dating (or at least relative dating) of the events can be achieved if sequences are available from many taxa
The mode of polyploid formation (allo- or autopolyploidy?) is often unclear

In some ways this is difficult and easy … now we can sequence everything !!!!

By comparison of the sequences , and looking at diveregnce of base pairs you can figure out the timings ….

In the ancient past its hard to work out if allo or autoploidy actually happened

31
Q

How did arabidopsis arise?

A

Arabidopsis – we think has arisen because of two separate polyploidy events…
A lot of duplicated genes were removed and only remnents were seen after it … the genome decided to simplify right down..

This can be detected by comparing the entire genomes , and line up the sequences of each of the 5 chromosmes , and look for diagonals – which would show whether they are similar or not…

The outcomes of ancient polyploidization can be seen by comparing a genome sequence against itself,

32
Q

what do we know about ancient polyploidy - in cereal grasses?

A

Since the duplication event rice has been affected much less than barley by subsequent rearrangement

Common events are insertions of whole chromosomes or chromosome arms into centromeric regions and telomere-telomere fusions

33
Q

What are important polyploidy in crop improvement ?

A

-Gene buffering
Slower response to selection but more adaptive potential.

-Dosage effect
Additive effect of the alleles increases the number of phenotypes.

-Increased allele diversity and heterozygosis
More possible allele combinations and opportunities for breeding.

-Novel phenotypic variation
Genome interactions and changes in gene expression

notes:
Gene buffering: multiple copies of a gene would retard the response to natural/artifitial selection due to mutation or recombination. Buffering effect even when genes are mutated.
multiple copies of gene, some are mutated to null allele. Presented simple segregation ratios and linear expression instead of segregate as quantitative traits.
Allele dosage: some key regulator genes preserved their function. All copies operate in the same manner.
Increase diversity: intergenomic heterozygosity has positive effects. More seed yielding in brassica, longer and stronger fiber in cotton.
New phenotypes in synthetic allopolyploids that stabilized over generations. Man different mechanisms explain novel variation

Plant sciences (15 decks)

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