Agriculture Reference
In-Depth Information
established, robust QTLs that were detected
over multiple environments for enrichment of
favorable alleles in populations. The alternative
includes testing populations over multiple envi-
ronments, which can take years.
complete, the possibility of cloning a gene or
mapping a candidate gene that controls a specifi c
trait is very real. Gene cloning can be done via
positional cloning and the use of large insert
libraries of wheat, of which several are available.
The gene sequence is used to develop a perfect
marker in the sense that there is no recombination
between the trait measured and the gene-based
marker.
It has been demonstrated that the success of
MAS is related to linkage distance between the
marker and the actual trait (Kuchel et al., 2005).
Thus, MAS applications would ideally be con-
ducted using perfect markers which are those that
have been developed from the sequence of the
cloned genes. Genes have been cloned for numer-
ous high-molecular-weight (HMW) and low-
molecular-weight (LMW) glutenin genes as well
as genes coding for gliadin proteins (Cloutier
et al., 2001; de Bustos et al., 2001; Radovanovic
and Cloutier 2003). Robust molecular markers
have been developed for specifi c HMW glutenin
alleles. For example, a PCR-based marker for the
Bx7 allele from the cultivar Glenlea was devel-
oped, because it was shown that the Glenlea Bx7
allele was required for the “extra-strong” dough
strength of this wheat cultivar (Radovanovic
et al., 2002). Grain hardness genes, or the
puroindoline genes, have been cloned and
perfect markers for
Pina-D1
and
Pinb-D1
are
available (Giroux et al., 2000; Limello and
Morris 2000).
Ellis et al. (2002) reported perfect markers for
the
Rht-B1b
and
Rht-D1b
dwarfi ng genes. These
markers were found to be quite robust since they
correctly categorized 19 wheat cultivars from 5
countries of known
Rht
type. The
Rht
markers
were deemed perfect because they are designed to
detect the base-pair change responsible for the
semidwarf phenotype. Recent cloning of
Lr
genes
(Feuillet et al., 2003 [
Lr10
]; Huang et al., 2003
[
Lr21
]; Cloutier et al., 2007 [
Lr1
]) will permit the
development of robust markers for important
wheat diseases such as leaf rust. Sherman et al.
(2004) reported the development of
VRN-A1
-
specifi c markers developed with the aid of the
cloned gene sequence. PCR-based primers were
developed that amplifi ed a 810-bp segment con-
Haplotype analysis
Haplotype analysis includes genotyping a collec-
tion of lines over a defi ned genetic or physical
DNA interval and representing each line as a
multilocus genotype. This can be at the level of a
gene sequence (Jung et al., 2004), depicting SNPs
within a few hundred nucleotides, or at the genetic
level depicting SSR alleles present over centim-
organ distances (McCartney et al., 2004). It is
now becoming routine to perform a haplotype
analysis in multiple regions of the genome where
desirable QTLs have been discovered and
mapped.
In wheat, haplotype analysis is best performed
with multiallelic markers fl anking and within the
signifi cance interval of the QTL. Wheat lines car-
rying the desired phenotype, and thus alleles, are
compared to lines carrying undesirable pheno-
types by collecting genotypic data across the
interval on a set of germplasm. In some cases, the
desired phenotype can be associated with a spe-
cifi c haplotype consisting of a few genetic loci.
This strategy may also help to position the con-
tributing gene to a smaller interval.
There are good examples of successful haplo-
type analysis for leaf rust (
Lr16
) resistance
(McCartney et al., 2005b) and FHB resistance
(Liu and Anderson, 2003; McCartney et al.,
2004). For example, the haplotype surrounding
Lr16
on 2BS is unique to the donor source line.
No other susceptible line tested carried this hap-
lotype and thus deployment of markers is facili-
tated. Likewise, the haplotype at FHB resistance
loci derived from Sumai 3 is quite unique at
FHB1
on 3BS and
FHB2
on 6BS (Cuthbert
et al., 2006a,b). The haplotype approach is easily
extended to include any mapped QTL.
Gene cloning and perfect markers
Once genetic mapping or QTL analysis is
