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correspond to monomorphic loci in another
subgenome. For example, 18,066 out of 23,037
SNPs on two genetic maps in B. napus were poly-
morphic in one subgenome and monomorphic in
another one, and these molecular markers were
identified as hemi-SNPs (Bancroft et al. 2011).
Although hemi-SNPs can be detected through
next-generation sequencing, it is not practical
to directly sequence hemi-SNPs for marker-
assisted selection in crop breeding, where thou-
sands of individuals are commonly included. To
deal with hemi-SNPs, a strategy for developing
genome-specific molecular markers as was done
for the FAE1.1 gene for marker-assisted selec-
tion of the erucic acid trait in crosses of rapeseed
and canola might be used (Rahman et al. 2008).
In this case, genome-specific primers flanking
allelic variants are used to amplify the targeted
allelic variants in one subgenome and then PCR
products containing the targeted SNPs can be
detected with all the commonly used SNP detec-
tion methods.
Marker-assisted selection is very useful for
eliminating linkage drag in introgression of
disease-resistance genes from related species or
wild species in Brassica. In general, most agro-
nomic traits in wild species are not as good
as those in cultivated species. Moreover, most
agronomic traits in Brassica vegetables are quite
different from those in Brassica oilseed crops.
When disease-resistance genes are introgressed
from wild species to cultivated species, or from
Brassica vegetables to oilseed species or vice
versa, linkage drag may occur if the genes under-
lying important agronomic traits are flanking
these disease resistance genes. For example, two
blackleg-resistance genes on chromosome N10
in B. napus were introgressed from wild species
B. rapa subsp. sylvestris L. with a genetic dis-
tance of 20 cM between these two resistance
genes (Long et al. 2011). In canola breeding,
these two genes from wild B. rapa and the
genes in the middle between these two blackleg-
resistance genes is retained in genotypes when
a high level of blackleg resistance is selected.
Recently, new canola lines, in which the wild
Marker-Assisted Selection for Disease
Resistance in Brassica Crop Breeding
Mapping and cloning of disease-resistance
genes will facilitate the practical use of
molecular markers in Brassica crop breeding
through marker-assisted selection. Currently,
major blackleg- and clubroot-resistance genes
are commonly used in canola, Chinese cabbage,
and other Brassica vegetable crops, and MAS is
successfully integrated with conventional breed-
ing selection at many breeding organizations.
However, most major blackleg- and clubroot-
resistance genes have not been cloned yet, pyra-
miding of multiple resistance genes is randomly
performed, and the results are quite elusive. After
resistance genes are cloned, resistance gene-
specific molecular markers will be developed
easily which will facilitate the pyramiding of
different race-specific resistance genes. Multiple
race-specific dominant resistance genes are com-
bined with quantitative resistance genes, which
may result in stronger and longer lasting blackleg
and clubroot resistance.
Genome-specific molecular markers are pre-
requisite for efficient and effective MAS
in allotetraploid Brassica crop species. As
described in the triangle of U, Brassica species
are genetically classified into diploid and allote-
traploid groups. In general, development and
detection of molecular markers in diploid species
is relatively easier than that in allotetraploid
species. In the diploid Brassica species, most
allelic variants can be used to develop high
quality molecular markers, although sequence
similarity of homologs in gene and segmental
duplications in the genome may interfere with
the detection of a few allelic variants. In the
allotetraploid species, intrasubgenome and inter-
subgenome polymorphism co-exist, whereas
only allelic variants in intrasubgenomes are
useful for the development of genome-specific
molecular markers. Since there is a high level
of sequence similarity between the A, B, and
C subgenomes of the allotetraploid Brassica
species, most allelic variants in one subgenome
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