Environmental Engineering Reference
In-Depth Information
The advent of microarrays increased significantly the number of studies on gene expression
profiling. Carbohydrate metabolism has been extensively studied in sugarcane using cDNA micro-
arrays to define gene expression associated with sucrose content. Microarrays were used to profile
the developing culm (Casu et al. 2003, 2004) leading to the identification of sugar transporters
highly expressed in the maturing stem and the coordinated expression of enzymes involved in
sucrose synthesis and cleavage. Transcripts associated with fiber metabolism and defense and stress
mechanisms were the most highly expressed transcripts in maturing stem. Stress responses were
also defined in roots (Bower et al. 2005) using the same arrays. Customized microarrays contain-
ing signal transduction components were used to profile the individual variation of plants culti-
vated in the field and transcript abundance in six plant organs (flowers, roots, leaves, lateral buds,
and 1st and 4th internodes) leading to the identification of genes ubiquitously expressed or tissue-
enriched (Papini-Terzi et al. 2005). The same arrays were also used to study signal transduction-
related responses to phytohormones and environmental challenges in sugarcane (Rocha et al. 2007)
including drought, methyl jasmonate, abscisic acid, insect ( Diatraea saccharalis ) , and endophytic
bacteria ( Gluconacetobacter and Herbaspirillum ) elicited responses. Thirty genotypes contrasting
for sucrose content were profiled and over 300 genes associated to sucrose content were discovered
(Papini-Terzi et al. 2009). In parallel, sugarcane plantlets were treated with sucrose to define genes
directly responsive to this sugar. Interestingly, a large overlap was observed between gene expres-
sion responsive to drought and sucrose indicating a common controlling mechanism behind these
processes that may rely on protein kinases of the SnRK/SNF1 family. Hormonal regulation associ-
ated to sucrose content was also revealed that included ethylene, auxins, jasmonates, absicic, and
salycilic acid. Additionally, sugarcane has been expression-profiled under the effect of elevated CO 2
(de Souza et al. 2008). This is an important issue related with sugarcane physiological responses to
the global climatic changes (GCC). GCC can be characterized by an elevation of the atmospheric
CO 2 concentration (because of fossil fuel usage), which leads to the elevation of temperature and
consequently changes in the climate. An experiment performed with sugarcane plants growing in
elevated CO 2 showed that they respond by increasing photosynthesis (CO 2 assimilation) and growth
(50% more biomass). This culminated with the production of more sucrose and fiber (ca. 29% each).
The authors evaluated the gene expression changes associated with the treatment and found car-
bon metabolism to be affected. Genes related to electron transport in the chloroplasts were more
expressed. On the other hand, no effects on CO 2 assimilation were observed, suggesting that sugar-
cane leaves will respond to the elevation of CO 2 by improving their light harvesting system to use
the excess of CO 2 (de Souza et al. 2008).
A large part of the gene expression data is publicly available. Most published sugarcane micro-
arrays were catalogued on public repositories such as Gene Expression Omnibus (GEO-NCBI),
Center for Information Biology Gene Expression Database (CIBEX), Microarray Gene Expression
Data Society (MGED), and ArrayExpress (Tables 21.3 and 21.4).
taBle 21.3
summary of sugarcane microarray data
total
sucest-Fun
others
Number of platforms
6
3
3
Number of series
17
12
5
Number of samples
226
182
44
Source:
Gene Expression Omnibus database, www.ncbi.nlm.nih.gov/geo/
 
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