Plant Improvement- Classical Breeding II Flashcards
What is marker assisted breeding?
Marker is anything that marks a particular living organism you are studying- Something you can see or record.
Markers act as surrogates for traits that are difficult to measure.
Markers can be scored sooner than traits that become visible at maturity (i.e. all yield-related traits). Can often score marker before scoring traits you are interested in- Plants take months to grow to maturity, but we can perform marker assays within days.
The easiest markers to work with are not influenced by the environment- Environment can affect some markers.
What are morphological markers?
Markers often detectable by eye, a physical feature of the plant.
What are protein electrophoresis markers?
First markers that were used.
These create banding patterns in electrophoresis, and banding pattern can correlate to a certain trait eg. Glutenin banding pattern used to predict baking quality.
What are DNA markers?
Mot common markers now, developed over the last 30-40 years.
RFLP- codominant- low polymorphism.
RAPD- dominant- low polymorphism.
AFLP- dominant- medium polymorphism.
SSR- codominant- medium polymorphism. (powerful, bit like mini satellite markers used for genetic fingerprinting in humans. Difficult to score.)
SNP- codominant- high polymorphism. (emerging as more important. Can score them singly, or in thousands or millions simultaneously in one sample.)
What is the KASP assay?
KBiosciences Allele Specific PCR.
Cheaper to score one single locus SNP marker, and sometimes only interested in one- might not want to score thousands at once.
All three allele-specific forward primers put in, but only one used at a time.
Sample will only prime with two of the three primers- will lead to a different colour signal. Fluorescence assay.
This is KASP assay- for up to 100s of samples, and low (1-20) markers. Assay of choice for this.
What is the Illumina assay?
This is the thousands or millions marker one- multi locus SNP markers.
Oligo pool assay-96 fibre optic bundles per matrix, 50,000 beads per bundle, 100,000s oligos per bead, 1536 SNPs per assay.
Each coloured dot is a single SNP assay- it is density that matters.
When are markers most useful?
Parent characterisation- Decisions can be made on the basis of the genotypes.
Early generation selection- Undesirable alleles can be excluded in large populations. Field trait scoring is slow and expensive.
Late generation selection- Purity of advanced lines is easily tested by genotyping.
Backcross introgression of novel alleles- Alleles for phenotypes masked in heterozygotes are almost impossible to follow in back-cross populations.
Following multiple loci or traits- A single experiment can yield thousands of genotype scores – very useful for background selection (= selecting against multiple loci in a single cross).
(Purity of lines easy to test with marker analysis.
Backcross programme- cross good line with bad line, get mixed line (F1). Cross mixed line with good parent several times while simultaneously selecting the good parts of bad parent.)
What is foreground marker assisted selection (MAS)?
The 2 closely linked markers that co-segregate with the trait can easily track the corresponding gene allele during crossing.
Selecting for presence of something- want to keep it in lines while they develop.
(Background looks to get rid of bad stuff).
In FMAS, is it better to select for a trait or a linked marker?
It depends:
- If the marker is tightly linked to the gene.
- If the QTL is ‘strong’ and well-defined positionally.
Then markers are intrinsically more accurate.
What is background selection?
Sometimes the breeder wants to introduce a useful gene from an otherwise poor parent (e.g. a wild ancestor or a landrace) into an elite cultivar. Often such genes encode useful new resistance to damaging pests of pathogens.
The desired outcome of such a breeding program is All of the genes from the good parent, except including the good gene from the poor parent, because it has the useful allele, together with minimal germplasm from the poor parent.
How is background selection done?
To remove the poor germplasm the F1 must be back-crossed with the elite parent.
Keep crossing to cultivar parent- keep reducing amount of poor parent DNA.
Backcrosses of 4 or 5 are typical.
Once happy, can self plant to get what you want.
Needed to also monitor every other chromosome pair-Don’t forget that each of these crosses produces multiple different genotypes and we must select the optimal plant each time.
Need to scan entire genome while doing this- need a lot of markers.
We use the marker scores to tell us which progeny has the best genetic background.
What is the linkage problem?
Markers are only perfect if the polymorphism causes the trait.
Markers show the scores of genetic change.
Recombination happens.
Have to check marker scores when dealing with new plants.
Describe the linkage problem using the markers linked to yellow rust R genes in wheat.
All crops are susceptible to microbial infections that can wipe out monocultures such as growing fields of wheat. Yellow rust is a Fungus that produces yellow spores, damages plant so damages yield. The only sources of resistance are wild or semi-wild lines.
This resistance gene was present in an old cultivar Lemhi-Yr5.
The molecular marker Sts7x8 maps very close to yellow rust resistance in a cross between Lemhi-Yr5 and a susceptible cultivar Chinese Spring.
Unfortunately, resistance breaks down very rapidly in crops. This can be inhibited by introducing multiple resistance genes instead of one.
We therefore wanted to move the Yr5 allele into 3 other cultivars which already had different yellow rust resistance genes
Markers developed, worked for 2 out of 3 plants.
This illustrates the serious problem that a marker can only be guaranteed to work in the line it was derived from (in this case Lemhi-Yr5 and Chinese Spring).
The best solution to this problem is to use genome sequencing to derive thousands of markers – these can then be tested in the lines you want to work with (again, NGS is the best way to do this) .
What is the “best with best” problem?
Crossing the best plants with the best plants- Reduces diversity of products.
Cultivars are better because most of the deleterious alleles have been taken away through thousands of years of selective breeding.
Pedigree breeding crosses elite cultivars with each other and looks through the progeny for better lines than the parents.
The consequence of this is ever-decreasing genetic diversity in the total cultivar gene pool as the ‘perfect’ combination of alleles is approached
But this implies that crop performance will plateau out – no more improvement.
(Possibilities- have improved as much as we could. Or- we have bottlenecked best alleles we could, but ancestors didn’t pick best alleles in first place.)
Develop lines to be perfect for time and place we’re in, but things change and turns out there is a better place to be.
Eg. if Scotland gets warmer, plants that are optimised now will no longer be optimised. Etc.
