Biology Reference
In-Depth Information
The early breeding stages are often devoted
to screening for CMD and CBSD (as in the case
of East Africa, for two to three years). If genes
at targeted loci for CMD are fixed, segregation
could be minimized or eliminated altogether, and
therefore preliminary MAS for CMD at early
stages could be avoided. This fast-tracking would
allow breeders the opportunity to rapidly gener-
ate planting material and start conducting trials
for yield and complex traits, thereby significantly
reducing the breeding cycle. The scheme pro-
posed in Nigeria gives preference in selection for
parents with fixed genes at targeted loci. MAS
for CMD would become necessary only where
heterozygous parents for the targeted CMD loci
are unavoidably used as donor parents for key
traits or to recombine complementary genes for
other traits being bred in combination with CMD
resistance.
MAB in cassava is currently based on the
SSR markers. Although SSRs, are generally
multi-allelic, that is, multiple alleles at a locus
(Syvanen 2001), and thus highly informative,
SNPs are better, because of their high den-
sity coverage in the genome and suitability
for ultra-high-throughput genotyping techniques
(Appleby et al. 2009; Rafalski 2002) required for
large scale MAB. The identification of high den-
sity of SNPs in cassava should lead to discovery
of genic SNPs that could be used to enhance trait
predictability in breeding programs. Recently,
the GCP converted 1,740 SNPs in cassava for
use on the KASPar platform. This system is
extremely flexible in terms of the combination
of numbers of markers and samples that can
be genotyped and, therefore, is particularly suit-
able for molecular breeding applications, such
as MAS or MARS (Morag et al. 2011). The
developed SNPs are being deployed in sev-
eral genetic mapping studies including those for
CBSD, CMD, and drought tolerance.
With genome sequencing initiatives in cas-
sava, the development of genomic resources and
breeding for cassava is expected to improve
rapidly in the years ahead. The first pilot project
produced a little less than 1x coverage from more
than 700,000 Sanger shotgun reads, using plas-
mid and fosmid libraries providing insights into
the overall characteristics of the cassava genome.
Much of the utility of the genome sequence
will come from the development of breeding
tools. Researchers at 454 LifeSciences and the
Joint Genome Institute (JGI) produced the first
draft of the cassava genome from a CIAT acces-
sion at the end of 2009. The assembly remains
highly fragmented (12,000 scaffolds) but is
believed to cover 69% of the predicted genome
size and to contain 97% of known coding loci
predicted 30,666 genes and 3,485 alternate
splice forms are supported by 1.4 M expressed
sequence tags (ESTs). Nearly 61 million 454
reads (single and paired-end) were generated and
combined with the Sanger data from the pilot
project as input for genome assembly. Plans are
underway to expand and improve upon the ini-
tial cassava genome sequence and to aid SNP
discovery via resequencing of many varieties of
cassava. These efforts should stimulate major
advance in applying modern genomics technol-
ogy and analytics for improving disease resis-
tance as well as for understanding the genetic
basis for disease resistance (Russell et al. 2011).
Having whole-genome sequences allows for
the exploration of genomic variations associ-
ated with traits of interest. A large number of
genomic sequences from a broad array of CMD-
resistant varieties of genotypes will enhance
marker-assisted CMD breeding in cassava. The
rapid advance of genomics, especially large-
scale genome resequencing technology, will
accelerate the improvement of cassava resistance
to pests and diseases and improve other key traits
such as yield and quality. These advances will
bring a much better understanding of the resis-
tance genes available from various sources and
how they can be best deployed in breeding and
will also address the methodologies for transfer-
ring high resistance to grower-accepted varieties.
Over the past 20 years we have witnessed
CMD pandemics in Africa where all the plants
already infected by a geminivirus have become
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