Sugarcane - Bioenergy Crop Plants - page 532

sugarcane cultivars are complex interspecific hybrids with a chromosome number ranging from
100 to 130, of which 15-25% comes from S. spontaneum . Considering monoploid genomes, the
DNA content is ~930 Mb for S. officinarum, ~750 Mb for S. spontaneum and approximately 1000
Mb for sugarcane hybirds (D'Hont 2005). At Clemson University Genomic Resources a BAC
library prepared from the R570 sugarcane cultivar is available and is represented by 103,296 BAC
clones with an average size of 130 kbp (CUGI 2009). This library has been screened for resis-
tance gene analogs (A. D'Hont, personal communication), adh locus (Janoo et al. 2007), sorghum
euchromatic regions (A. Paterson, personal communication), transposable elements and genes
associated to sucrose content and drought responses. These trends render it feasible to undertake a
pilot project to sequence the sugarcane genome and address questions related to gene allelic varia-
tion and regulatory regions.
A combined approach of new sequencing technologies such as 454 pyrosequencing and Sanger
reads will give access to the sugarcane genome sequence uncovering the genetic basis structure
sustaining the biological processes. Not only will regulatory regions associated to specific genes
of interest be discovered but also gene prediction models compared to sorghum, rice and maize.
Breeding strategies can benefit from the comparative genome sequence of homologous regions
between R570 and SP80-3280 (the cultivar most represented in the EST collections), thereby allow-
ing for rapid translation of the sequence data into genetic markers. Regulatory sequence variation
is also to be uncovered through this comparative approach and, in combination with the expression
profile analysis, relevant insights on the evolution of these regions and the contribution of transpos-
able elements will come to light. In a broader view, BAC sequencing will add to the understanding
of chromosomal differentiation among Poaceae.
A long-standing goal in polyploid genomes is to understand the relative contribution of each
allele to a particular phenotype in a given cultivar. The key problem in achieving this goal is iden-
tifying allelic variation and subsidizing breeding programs to quickly select it from among a seg-
regating population. Also, accumulating multiple genes into plant varieties is not yet widely used
for polyploid plants. Because of the lack of understanding of the genetic basis of heterozis, genome
sequencing of “gene of interest” containing regions will advance knowledge on genome structure
creating the molecular basis to explore the genetic diversity among cultivars and breeding popula-
tions segregating for characters of interest.
One innovative approach is to understand the relative contribution of TEs to genetic variation
in the sugarcane polyploid genome. These mobile elements are ubiquitous among living organisms
and constitute intermediate-repeat DNA long considered as selfish (or junk) DNA (Doolittle and
Sapienza 1980; Orgell and Crick 1980). Contrary to that, and as previously proposed by McClintock
(1984), a new biological concept is arising for transposable elements where, despite their mutagenic
capacity, they actively contribute to changes in the gene expression profile and may ultimately result
in species divergence (Cordaux et al. 2006; Jordan 2006; Cropley and Martin 2007; Xiao et al.
2008). Their contribution to eukaryotic genome structure is usually associated with gains of nuclear
interspersed sequences such as noncoding repetitive DNA between and sometimes within coding
units. One means of understanding the contribution of a particular class of TE to the genome is
to first identify the gene pool present, its relative amplification across contrasting varieties and its
expression pattern. Much of the initial work will be to create a ground basis for identifying TE fami-
lies associated to particular traits (brix, drought, high CO 2 environment, and regeneration capabil-
ity). This recognition will impact on balancing selection for (or against) the presence of a given
TE family. Clearly, a prerequisite in sequencing polyploid genomes is to be familiarized with its
repetitive DNA elements. For sugarcane, 21 families have been identified and further studies were
carried out on two retrotransposons ( Hopscotch -like and SURE) and two transposons ( Mutator -
like and hAT-like). Hopscotch -like and Mutator -like elements contain lineages that are represented
by highly repeated unit spread along the chromosomes with no particular clustering evidenced at
telomeric or centromeric regions. Independent of their amplification profiles both high and low copy
number elements are expressed in different tissues of sugarcane.