Biology Reference
In-Depth Information
progress can be hampered by misclassified indi-
viduals. This is in contrast to single nucleotide
polymorphisms, or SNPs, which show very high
fidelity of allele calling in repeated rounds of
genotyping.
breeding. First among these is high-throughput
genotyping capability, for rapid and dense fin-
gerprinting of parents and breeding progenies at
a reasonable cost. This multiplexing approach is
a critical advance over low-throughput systems
where genotyping is conducted on a marker-
by-marker, individual-by-individual basis. For
cowpea, a high-throughput genotyping platform
was developed between 2007 and 2009 as an
important outcome of a 'Tropical Legumes I'
project based at the University of California,
Riverside, and funded by the Consultative
Group on International Agricultural Research
(CGIAR) Generation Challenge Programme
(GCP). The genotyping platform was developed
as an Illumina GoldenGate Assay for 1536 SNP
loci. This platform can genotype simultaneously
96 DNA samples at 1,536 SNP loci. The
genotypic information is provided to users with
specialized 'Illumina GenomeStudio' software,
which allows rapid visual inspection and data
summarization. The development and technical
details of this platform were presented in detail
in the work of Muchero and colleagues (2009).
Briefly, this platform consists of 1,536 EST-
derived SNPs chosen from a selected subset of
about 10,000 SNPs identified from comparisons
of 183,000 EST sequences from 13 cowpea
genotypes. Of these, 1,375 SNPs performed
technically well in the assay. Among the several
technical considerations in choosing the 1,536
SNP subset, high polymorphic information
content among African germplasm was primary,
in order to ensure that the chosen SNPs were
highly polymorphic in African breeding mate-
rials. Examples of the numbers of polymorphic
markers observed in crosses between breeding
lines both within and between several African
breeding programs following genotyping with
this platform are shown in Table 10.1. These
results show a high average level of polymorphic
markers between any two parents, ranging from
134 to 391 and indicating that the SNPs selected
for inclusion on the current 1,536 Illumina
GoldenGate platform represent an effective set
for MAS in West African breeding programs.
SNPs in Cowpea Breeding for
BioticStress Resistance
Genotyping platforms based on SNPs are pre-
ferred over other marker types in plant breed-
ing applications because they are amenable
to high-throughput yet highly precise assays
(Rafalski 2002). SNPs derived from expressed
sequence tags (ESTs) are especially useful
because they are derived ultimately from mRNA
transcripts and thereby reflect allelic differ-
ences between individuals and present oppor-
tunities for cloning genes through comparisons
with annotated genome sequences of other plant
species. SNP genotyping is highly developed
from a technical and equipment perspective
because of the large investments made in this
area in human and animal genetics that are being
leveraged for crop improvement. The private
crop breeding sector was quick to grasp this
opportunity and develop these systems for major
crop plants such as maize and soybean, hav-
ing employed them in breeding programs for
more than a decade (Eathington et al. 2007). It
appears that the private sector has found marker-
assisted breeding (MAB) with SNPs to be an
effective approach, as evidenced by the fact
that SNP genotyping platforms continue to be
developed for more and more crops bred in this
sector. In cowpea, a 1536-Illumina GoldenGate
SNP genotyping platform was developed in 2009
(Muchero et al. 2009) and is described briefly
below.
High-Throughput SNP Genotyping
Platform for Cowpea Breeding
Several key resources are needed for the com-
prehensive implementation of modern cowpea
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