Principles of Plant Genetics and Breeding

250 CHAPTER 14
genetic mapping. As previously discussed, the recombination
frequency between genes is a function of the
distance between them. Consequently, a map distance
is a function of the recombination that occurs during
meiosis. Genetic maps are more useful in plant breeding
if they are dense (i.e., the entire genome is covered with
closely spaced markers). There are certain basic steps in
mapping.
Select parents and screen for polymorphism
The first step in mapping is to select parents that are
genetically divergent at many loci, and where desirable
agronomic traits are segregating. It is important that
useful polymorphisms be present in each pair of parents
used for mapping traits of interest. The basic steps in the
screening process are DNA extraction → restriction
enzyme digestion → electrophoresis → Southern blotting
→ clone hybridization → RFLP detection. The probe
and enzyme combination used for RFLP detection
between the parents is used again on the F2 population.
The frequency of polymorphisms depends on the nature
of the population. Usually, polymorphism frequency
between parents may be about 80% per restriction
enzyme for species that are cross-compatible, and about
20% per enzyme between varieties that are genetically
distinct. Polymorphism between backcross varieties may
be 0–1%. The researcher’s goal is to find as many useful
probes as possible (probes that can be used to distinguish
among genotypes). Some probes detect RFLPs
more frequently than others. About 5–10 restriction
enzymes are used to screen about 500 parents to find
about 100 useful probes.
Generate a mapping population
From the results of the parental screening, desirable
parents are crossed to produce F1 and F2 plants. BC1 populations may be generated, but F2 populations give
more information per sample. More advanced generations
(F3 –Fx ) may be used if agronomic traits are scored
over different environments and over years. About
50–100 plants are mapped, more plants giving closer
map distances.
Score RFLPs
DNA extracted from P1 , P2 , F1 , and a random sample of
F2 plants are digested with a set of restriction enzymes.
Several filters are obtained for each enzyme (following
electrophoresis and blotting). A filter may be probed
several to many times (10 times or more) with different
probes (washing between probes). About 100 or more
probes may be made.
Linkage analysis
Segregation of RFLP markers in F2 plants is used in
constructing the linkage map. The markers are arranged
in linkage groups (the linkage of markers to chromosomes
is established). These analyses are made possible
by using statistical packages and computer mapping
software (MapMaker, Map Manager XP). Linkage relationship
among markers with a recombination frequency
of less than 50% LOD (logarithm of the odds, or LOD
score) of 3 or greater indicates that a gene and an RFLP
marker are linked. LOD is the ratio of two probabilities:
no linkage/a certain degree of linkage. The gene and
RFLP marker are first assumed to be unlinked. Then,
the probability that the observed pattern of inheritance
of the gene and the marker have a certain degree of
linkage is calculated.
QTLs in plant breeding
Quantitative traits are of a major concern to plant breeders
because most of the traits of economic importance to
breeders and consumers are quantitative traits.
What are quantitative traits?
These traits, as previously indicated, are controlled by
polygenes or QTLs. QTLs are genetic factors that are
responsible for a part of the observed phenotypic variation
for a quantitative trait (polygenic trait). A QTL is
similar to a gene, but in actuality, it merely indicates a
region on the genome that may comprise one or more
functional genes. QTL mapping entails an analysis of
the association between observed trait values and the
presence or absence of alleles of markers that have been
mapped onto a linkage map. A QTL is declared to exist
when it is determined that the association did not occur
by some random process.
QTLs have come a long way from being statistical
abstractions that breeders used to explain the performance
of traits, to their current status where they
are being isolated and cloned as DNA fragments,
sequenced, and attempts are being made to use their
allelic variation to elucidate them. A lot remains to be
known about QTLs. It is not generally known if they
are structural or regulatory genes or how many there
are. Researchers are working to better understand the
precise nature of the allelic variation, their genomic