Biology Reference
In-Depth Information
maturity, and desirable seed quality. Now, dif-
ferent cultivars and advanced breeding lines are
available with desirable traits, such as resis-
tance to cowpea weevil, cowpea aphid, and
Striga, along with resistances to bacterial blight,
CABMV, and other pathogens. The challenge is
to incorporate suites of these desirable traits into
individual cultivars with acceptable grain qual-
ity and adaptation to a diverse array of farming
systems and environments. The array of mark-
ers now available for biotic stress resistance and
other traits will be very useful in expediting this
process.
version from the Illumina platform. Genotypic
information was received from the genotyping
provider in about two weeks, which is considered
normal turnaround time. Since we had genotyped
the same lines with the same SNPs using Illumina
GoldenGate Assay, we compared the genotyping
results from the two assays and found identical
genotype calls for all alleles of all individuals.
The Illumina GoldenGate Assay platform is
a fixed array assay for 1,536 SNPs. This fea-
ture presents advantages in that data handling
can be standardized and time and effort are not
needed to choose subsets of markers for individ-
ual populations. However, the fixed array design
means paying for assays on a large number of
markers that are not informative between a given
pair of parent genotypes. As a general rule, the
fixed array sets will be less expensive on larger
numbers of markers, but more expensive when
fewer markers are being used, which is typically
the case for genotyping a breeding population.
However, in these calculations, the informatics
costs related to choosing and analyzing specific
marker sets for specific populations also must be
considered.
In order to make an SNP genotyping plat-
form more available, flexible, and affordable to
the broader cowpea breeding community, the
CGIAR Integrated Breeding Platform has con-
tracted with KBiosciences (LGC Genomics) in
the United Kingdom to convert a subset of
∼
Outsourced Genotyping
A limitation of high-throughput genotyping sys-
tems has been the initial investment required for
platform development, especially the sequenc-
ing costs related to SNP discovery. However, as
sequencing costs have fallen dramatically over
the last several years, this is becoming less an
issue. Another consideration is the high cost of
genotyping equipment and locating dedicated
bench space and lab personnel for genotyping
operations. On the positive side, several pub-
lic and private 'fee-for-service' SNP genotyping
providers are now available using a range of SNP
genotyping platforms, so there is little need for
cowpea breeding programs to invest in in-house
genotyping infrastructure. In developing coun-
tries, issues related to availability and high costs
of imported consumables and repairs make the
case for out-sourced genotyping even more com-
pelling. In our marker-assisted recurrent selec-
tion (MARS) breeding projects, genotyping was
done via outsourcing from two African loca-
tions. Fresh leaf tissue disks from 6 plants per
line were bulked, placed in 96-well plates pro-
vided by the genotyping service company, the
plates were enclosed with silica gel packs (to
dehydrate the tissue) inside a plastic bag, and
mailed via a courier service to the genotyping
provider. The samples were genotyped for a sub-
set of markers polymorphic in each parental pair
using the Sequenom platform after marker con-
1,000 of the mapped SNPs from the Illumina
GoldenGate Assay Platform for use with the
single-plex KBiosciences KASP (Kompetitive
Allele Specific PCR) genotyping platform. This
platform allows users to choose customized sub-
sets of SNPs for genotyping on particular sets
of germplasm. Hence a breeder can choose a
suite of trait-linked polymorphic SNPs and well-
distributed 'background' SNPs for genotyping,
with the number chosen partially determined by
budget considerations and the trade-off between
numbers of markers and numbers of genotypes.
For example, assume the breeder is working to
pyramid four resistance traits for which SNP
markers have been identified and which are
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