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the last 20 years. Results of such studies have
demonstrated the limited use of QTL mapping
for breeding (Xu and Crouch 2008; Jannink et al.
2010). According to the recent review by Brum-
lop and Flinckh (2011), a total of 83 papers were
published between 1995 and 2009 concerning
the main areas of applicability for MAS in plant
breeding programs or in research projects. This
survey included very few studies (only 8 out of
83) that reported successful application of MAS
related to yield improvement. The main prob-
lems involved in using MAS for quantitative
traits are the difficulty of accurately determin-
ing the effects of the QTL, and of extrapolating
QTL expression from one genetic background
to another and from one environment to another.
This may explain why molecular markers are
not currently used in breeding schemes for the
improvement of sugarcane yield. New models
need to be developed that take the high com-
plexity of the sugarcane genome into account.
Effective incorporation of molecular genetics in
breeding programs will also depend on the avail-
ability of innovative genotyping technologies
yielding higher throughput markers to enable
more dense coverage of the large sugarcane
genome (10 Gb).
should also provide a valuable guide for prob-
able gene arrangements in sugarcane, both at
the global and local scales. This new resource
should facilitate strategies aimed at defining a
reference sequence of the sugarcane genome
based on bacterial artificial chromosome (BAC)
sequencing approaches. Regarding the complex-
ity and the size of the genome, Souza et al.
(2011) suggest focusing sequencing on 'euchro-
matin' BAC regions identified using the sorghum
sequence template. Euchromatin regions are
believed to be rich in genes and might include
most of the recombination scattered across the
genome. Conversely 'heterochromatin' is gene-
poor, repeat-rich, and recalcitrant to recombi-
nation. Therefore, sequencing at least the gene-
rich portions of the sugarcane genome should
provide a valuable resource for the develop-
ment of high throughput marker systems in
tight linkage disequilibrium with many QTLs
of agronomic interest. Souza and colleagues
(2011) predict that sequencing about 4,000-
5,000 sugarcane BACs could capture much of the
euchromatin.
To further develop high-throughput marker
systems from this draft sequence of euchromatin,
advantage should be taken of next-generation
sequencing (NGS) technologies. One of the first
investigations of the potential of NGS in sugar-
cane was conducted by Bundock and colleagues
in 2009, using 454 Genome Sequencer FLX.
These authors demonstrated that the discovery of
reliable single nucleotide polymorphism (SNP)
in sugarcane is feasible and would enable the
dosage of each allele to be measured. To envi-
sion a global NGS-based strategy for SNP detec-
tion, we need to improve our understanding of
genome organization and evolution linked to
polyploidization in order to assess the extent of
polymorphism existing among homo(eo)logous
loci. Two recent studies (Jannoo et al. 2007;
Le Cunff et al. 2008) based on the structural
analysis of two series of homo(eo)logous BACs
provided a first insight into genome dynamics
by revealing perfect colinearity as well as high
gene-structure conservation between sugarcane
Towards Increasing Throughput
Marker Systems
Efforts have to be invested in developing “uni-
versal” markers that would enable comparison
of the location of QTLs across sugarcane studies
and also between sugarcane and related species
(sorghum, miscanthus, maize). The achievement
of this objective should be supported by the
large scale development of markers based on
DNA sequences via high throughput genotyp-
ing facilities, such as microarray and sequenc-
ing technologies. The recent release of the refer-
ence sequence of the sorghum genome (Pater-
son et al. 2009) which has a large degree of
synteny with the sugarcane genome (Glaszmann
et al. 1997; Ming et al. 1998; Jannoo et al.
2007; Le Cunff et al. 2008; Wang et al. 2010)
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