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Chapter 7: Molecular markers in breeding
Why use molecular markers in breeding?
For which type of applications? Where?
Which type of molecular markers? How?
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Chapter 7: Molecular markers in breeding
With many thanks to Isabel Roldán-Ruiz 1
for allowing me to use information and
pictures from the slides of her course ()
Institute for Agricultural and Fisheries
Research ILVO (Research institute of
Ministry of the Flemish Community)
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2

Why?
The phenotype is an imperfect predictor of the genotype:
possibly unobservable before the time selection must be made
the phenotype of a plant is always the expression of its
genotype, but with a relatively big influence of the environment
The phenotype is not effective in resolving negative associations
between genes (linkage, epistasis)
Genotype
Environment
Breeder’s black box:
• Number of genetic factors
The breeder works with
• Relative importance of each factor for
‘phenotypes’, and makes
the determination of the phenotype
inferences about ‘genotypes’
• Interactions among factors
(pleiotropism, epistasis, linkage,
association)
Phenotype
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
Why? DNA markers = direct reflection of genotype
• Two plants can display similar phenotypes, but be very
different from a genetic point of view
e.g. Lolium perenne genotypes with similar yield. In each
genotype different genomic regions can be responsible
for the high yield potential
Genotype A
Genotype B
same phenotype
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
Why? DNA markers = direct reflection of genotype
• Two plants can display different phenotypes, but be
very similar from a genetic point of view
e.g. Mutant genotypes in edible apple (Malus domestica).
Columnar phenotype in cv. Telamon (carrier of a
spontaneous mutation original found in cv. McIntosh) is
caused by mutation at one single locus
Wild type
Mutant
Short inter-nodes
Reduced plant height
Different branching
….
Different phenotype
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Why?
• A molecular marker is a DNA sequence which can be
readily detected and whose inheritance can be monitored.
For example in the case of pathogen resistance, a good
marker avoids elaborate infection tests for the selection
of resistant plants.
• DNA-markers allow the breeder to introduce into their
cultivated plant only the gene(s) of interest from a related
species. While conventional breeding methods rely on the
transfer of the whole genome (along the gene of interest,
undesirable characters are also co-inherited and have to
be eliminated through back crossing followed by
selection) DNA-markers allow to eliminate in a few
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generations ‘undesired’ genome regions.

Why?
• The introgression of recessive alleles through
classical back cross breeding is even more
lengthy as this requires additional generations of
selfing (to identify the homozygous recessive)
after every back-crossing
• Some characters like complex disease resistance
reaction or biotic stresses (QTLs) that show
continuous variation and do not fit into Mendelian
ratios are most difficult to detect and transfer
through conventional plant breeding, due to
interactions with the environment
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
Why?
How can molecular markers help?
Molecular markers allow working with genotype information
directly
Analyze the effect of the genotype on the phenotype
Provide the breeder a tool to look into the ‘black box’ of the
genotype
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Genes and genomes
Eukaryotic genomes contain much DNA outside the genes
Human
Yeast
Z. mays
E. coli
Genomes 2
T.A. Brown, Bios
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
Which? Two basic types of DNA-markers
Causal mutations: the mutation is responsible for the change in
the color of the flower
Mutation
= Marker
- The most useful
- Difficult to find
- Difficult to prove
- Less often used
Presumed non-functional DNA-markers, in the gene (but not the causal
mutations) or linked to the gene
Mutation
M
m Marker
- In some cases enough
- Easier to find
- Easier to prove
- Frequently used
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
Where?
•
•
•
•
Fields of application
Cultivar identification
Specific markers
Understanding relationships
Analysis of diversity
 Chapter 8
• Construction of genetic linkage maps and tagging
economically important genes
• Marker assisted selection
e.g. Introgression, QTL-analysis
 Chapter 9, applications based on genetic maps
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
Where?
Cultivar identification (fingerprint)
– Useful to control the identity of
reproductive material (seeds, grafts,
bulbs…)
– Useful to control the non-authorized use of
cultivars from other breeders
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
Where? Understanding germplasm relationships
Markers are useful in four types of
measurements needed in this field:
• Identity: correct label of plants?
• Similarity: degree of relatedness
among plants?
• Structure: is possible to identify
groups of related plants?
• Detection: posses some plants
of the collection a particular
allele of a gene?
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
Where?
Construction of genetic linkage maps and tagging economically
important genes
– Segregating population constructed using plants with contrasting
characteristics
– Through linkage analysis (analysis of the co-segregation of marker
alleles) a genetic map is constructed
– By combining phenotypic data with genetic-map information, identify
markers which are linked to the gene(s) responsible of the trait
m-
Position of gene(s)
responsible for the trait
m-
m-
m-
mmmmmmmX m- mmmmm- mmmmmm-
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
Where?
Marker Assisted Selection and
introgression through back-crossing
– Use markers linked to agronomic traits to
select the best plants to cross
– In most cases, selection has to be performed
for more than one trait simultaneously
– In some cases we are interested in the
introgression of a specific genome region
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Where?
Quantitative trait
– Multiple genes affect the expression of the trait
– The expression in the population is a ‘bell-shaped’ curve: there are many
genotypes and there are no clear phenotypic differences among them:
If we want to find DNAmarkers that can help us to
predict this phenotype, we
are searching for several
genetic loci simultaneously
Frequency distribution

Height
There exist standard
experimental approaches
for this (e.g. QTL analysis)
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
How?
DNA markers: desired properties
• Highly polymorphic: able to detect many different alleles
• Highly informative; if one individual carries two different
alleles we can visualize both (co-dominant)
• Occurrence throughout the studied genome, at high
densities but not clustered
• Easy, fast and inexpensive to screen
• Reproducible within and between laboratories
 No single technique fulfills all these criteria
 Choice of DNA analysis technique depends upon the
infrastructure, technical expertise and operational funds
available as well as requirements of the experiment
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How?
• Identification individual: multilocus STR (of AFLP)
• Analysis relationship:
- Sequence if different species
- AFLP within genus or species
- Multilocus STR within species
• Specific marker for diagnosis or marker assisted
breeding PCR-RFLP or SCAR or SNP or STR
• Overview whole genome (breeding, diversity):
AFLP, multilocus STR or SNP
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