Principles of Plant Genetics and Breeding

252 CHAPTER 14
selection in a breeding program hinges on the availability
of useful molecular markers. Fortunately, this resource
is becoming increasingly available to many species,
thanks to the advances in biotechnology. This breeding
approach is applicable to improving both simple and
complex traits, as a means of evaluation of a trait that
is difficult or expensive to evaluate by conventional
methods. The basic requirement is to identify a marker
that co-segregates with a major gene of the target trait.
MAS is more beneficial to breeding quantitative traits
with low heritability.
The key steps in the implementation of MAS in
breeding QTLs are summarized by D. W. Podlich and
his colleagues as follows:
1 Creation of a dense genetic map of molecular markers.
2 Detection of QTLs based on statistical association
between markers and phenotypic variability.
3 Definition of a set of desirable marker alleles based on
the results of the QTL analysis.
4 The use and/or extrapolation of this information
to the current set of breeding germplasm to enable
marker-based selection decisions to be made.
However, as these researchers noted, MAS for more
complex traits is still challenging, partly because of the
difficulty of effective detection, estimation, and utility of
QTLs and their effects. The problem is more significant
with more complex traits (such as grain yield) that are
controlled by many genes under the influence of epistasis
(gene-by-gene interaction) and gene-by-environment
(G × E) interaction effects. On the contrary, most
researchers engaged in evaluations of mapping and MAS
tend to assume that QTLs act independently (i.e., no
interaction with other genes and/or environment).
To overcome this problem, Podlich and colleagues
proposed a new approach to MAS from the conventional
one, which assumes that desirable QTL alleles,
once identified, will remain relevant throughout many
cycles of selection during plant breeding. In the conventional
procedure, researchers tend to estimate QTL
effects at the beginning of the project and continue to
apply the estimates to new germplasm created during
the breeding process (i.e., mapping start only). The
assumption of fixed QTL values is appropriate if the
traits are controlled by additive genes. This will allow
MAS to be conducted by independently assembling
or stacking desirable alleles. This assumption is not
applicable to situations in which context dependencies
(changes in genetic background) occur. On such occasions,
the value of QTL alleles can change depending on
the genetic structure of the current set of germplasm in
the breeding program. In other words, QTL values will
change over the cycles of selection, as the background
effects change. These progressive changes in genetic
structure may make the initial combinations of alleles no
longer the best target or no longer significant in increasing
the trait performance in future breeding cycles.
Podlich and colleagues proposed the “mapping as
you go” approach to MAS of complex traits. QTL
effects are cyclically re-estimated each time a new set of
germplasm is created. This ensures that the basis of MAS
remains relevant to the current set of germplasm.
S. D. Tanksley and T. C. Nelson developed a procedure,
advanced backcross breeding, for the simultaneous
discovery and transfer of desirable QTLs from
unadapted germplasm into elite lines. Basically, this procedure
postpones QTL mapping until the BC 2 or BC 3 ,
applying negative selection during these generations to
reduce the occurrence of undesirable alleles from the
donor (unadapted genotype). The advantage of this
strategy is that BC 2 /BC 3 provides adequate statistical
power for QTL identification, while at the same time
being sufficiently similar to the recurrent parent to allow
selection for QTL-NIL (near-isogenic line) in a short
time (1–2 years). The QTL discovered can be verified
and the NILs used directly as improved cultivars or as
parents for hybrid breeding.
Important applications of molecular
markers in plant breeding
Molecular markers may be used by breeders to increase
the rate of genetic gain, verification or identification
of parentage, characterization of germplasm, and
quantification of genetic variability.
1 Screening single traits. Molecular markers associated
with many agronomic traits of importance (e.g.,
nematode resistance in sugar beet, blast resistance in
rice) have been discovered and used for screening for
these traits in breeding. MAS is useful for simple
traits, or those for which genetic gain per unit time
(rate of genetic gain) is of high economic return.
2 Speeding up breeding programs. Markers add
speed and precision to backcross breeding programs.
They help to identify the gene of interest to be transferred
and facilitate the elimination of the undesirable
genome in the donor parent (reduces linkage drag).
A fewer number of backcrosses are needed to recover
the genotype of the adapted parent.