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In elevated CO 2 conditions, the C4 grasses sugarcane [ 25 ], maize and sorghum [ 26 ] show better responses to drought stress than C3 grasses. Plants in the Saccharinae have some further advantages in comparison with other C4 grasses, such as maize. First, many routinely produce a 'ratoon' crop, regrowing after harvest and thus eliminating the need for replanting each year. Indeed, the Sorghum genus, with annual and perennial species that are genetically compatible, has become a botanical model for study of attributes related to perenniality [ 27 — 29 ].

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Third, some reports show better photosynthetic features of Saccharinae plants than other Andropogoneae. Light interception by the leaves is higher in Miscanthus than in maize [ 15 ] and Miscanthus can sustain higher levels of CO 2 assimilation than maize in lower temperatures [ 32 ]. Sugarcane photosynthesis is enhanced in elevated CO 2 in open-top chambers, increasing biomass productivity [ 33 ], which does not occur in maize grown in open-air elevation of CO 2 [ 34 ].

However, this finding is controversial since enclosure and open-air studies give different results for the same crop, and some authors argue that enclosed studies are not the best scenario to mimic future increases in CO 2 concentration [ 35 ]. Moreover, experiments with Miscanthus in ambient and open-air elevation of CO 2 show no differences in yield [ 36 ].

Since lignocellulosic biofuels use the plant cell wall as a source for fermentable sugars, it is important to understand the composition and architecture of the cell wall to develop strategies to degrade it efficiently. Grasses present a particular cell wall structure and composition Figure 2 , making a 'type II' cell wall that differs substantially from the 'type I' cell walls of other feedstocks, such as wood species [ 22 , 37 , 38 ].

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This also implies the evolution of different gene families involved in the synthesis of the cell wall [ 22 ]. Recently, a model for sugarcane cell wall architecture and for hierarchical enzymatic hydrolysis was proposed [ 39 ]. By understanding the structure of the cell wall, it is possible to choose the best method to improve hydrolysis yield, and design breeding strategies or develop improved procedures to recover the released carbohydrates.

Simplified schematic representation of the cell wall. The wall is shown as a transverse section. Grasses and non-grass angiosperms possess different types of cell wall. The text in red denotes the main differences. Surrounding the cellulose microfibrils, the inner and outer hemicellulose circles show tightly and loosely bound polysaccharides, respectively. Grasses have glucuronoarabinoxylans GAX as the main cross-linking hemicellulose and a primary wall matrix enriched in mixed-linkage glucans, with lower pectin content.

The thin red boundary in the primary wall of the grasses denotes the phenolic compounds, mainly ferulic acid, linked to GAX molecules. In grasses, seven cellulose microfibrils can be structured in a cellulose macrofibril. Typically, grasses have more lignin than other angiosperms. Non-grasses possess xyloglucan as the major cross-linking hemicellulose, a pectin-based matrix and structural proteins. In the secondary wall, note that pectins and mixed-linkage glucans are minor components.

Also, we can see lignin forming a structural barrier surrounding the carbohydrates.

Adapted from [ 39 ] and [ ] with permission. Improvements in sorghum are characteristic of many other major food and feed crops, and Miscanthus improvement is just beginning; examining sugarcane improvement therefore exemplifies the methods and approaches likely to be employed in biofuel grasses. Sugarcane improvement efforts follow both molecular-assisted breeding and transgenic routes [ 40 ]. Modern sugarcane cultivars derive from a few crosses between S. Breeding programs have been able to increase yield and sucrose content by crossing cultivars but gains are becoming slimmer.

To continue the improvement of yield it may be necessary to turn back to ancestral genotypes and broaden the genetic basis of crosses. World collections of Saccharum germplasm are held in Florida [ 42 ] and India [ 43 ], which keep ancestral genotypes and cultivars, and many private collections are also kept and used for crosses in specific breeding programs. Each world collection has over 1, accessions of ancestral genotypes, most of them S. Only a few small Miscanthus collections are held publicly, but several private collections associated with breeding programs are similar in size to the Saccharum collections.

Crosses between members of the Saccharinae are viable. In fact, sugarcane has been crossed to both Miscanthus and sorghum, generating viable progenies, and the strategy has been used to incorporate cold and drought resistance traits from Miscanthus into sugarcane [ 19 ]. The transformation of sugarcane is becoming an interesting and growing field. Methods for transformation are already established with efforts aimed mostly at sugar yield and quality [ 44 — 46 ], disease resistance [ 47 , 48 ], and the use of sugarcane as a biofactory to produce high-value bioproducts [ 49 , 50 ].

For biofuel production, some approaches show interesting results, with lower biomass recalcitrance [ 51 ] and expression and accumulation of microbial cellulolytic enzymes in sugarcane leaves [ 52 ] to improve biomass hydrolysis. The most widely used promoters are the constitutive CaMV 35S and maize ubi1 , but sugarcane promoters have already been used or characterized, including tissue-specific [ 46 , 47 ] and responsive promoters [ 53 ].

However, sugarcane transformation is not a trivial task since problems such as transgene silencing frequently occur [ 40 , 54 ] and references therein. Sorghum transformation is also routine although at lower efficiency than in some crops [ 55 ] , and Miscanthus transformation methods have been established [ 56 ].

For both molecular-assisted and transgenic strategies outlined above, the availability of a reference genome sequence is highly desirable, as well as the definition of the complete complement of genes and proteins. For the Saccharinae, the relatively small Mb and diploid genome of sorghum, which has not experienced genome duplication in about 70 million years [ 21 ], has become the best reference for genomics and transcriptomics in sugarcane [ 57 ]. Nonetheless, the sugarcane genome itself is being sequenced using a combination of approaches.

In a first phase, researchers are sequencing bacterial artificial chromosomes BACs combined with whole-genome shot-gun sequencing to produce a reference genome [ 58 ]. Currently, three sugarcane BAC libraries are available; from variety R [ 59 ], selfed progenies of R [ 60 ] and SP [ 61 ].

Biofuel and energy crops: high-yield Saccharinae take center stage in the post-genomics era

The two former libraries have , to , clones comprising about 12 times coverage of the basic genome complement but only about 1. The latter library has about 36, clones, and all three have inserts of about to kb. BAC sequencing has enabled research to deduce synteny and collinearity of much of the sugarcane genome with other grasses, especially sorghum, particularly in genic regions [ 61 — 63 ]. Unaligned regions between sorghum and sugarcane genomes are largely repetitive [ 62 ], enriched in transposon-related sequences [ 61 , 63 ].

Groups from Australia, Brazil, France, South Africa and the USA are advancing these efforts in genome sequencing, increasing the number of BACs sequenced and producing shot-gun data of several cultivars. It is expected that reference genome sequences will be made available for both cultivars and ancestral genotypes [ 65 ] and, to that end, researchers are developing statistical models using SNPs where homology groups with any ploidy level may be estimated [ 66 ]. This will be essential to obtain a saturated genetic map of the sugarcane genome that may aid genome assembly.

The greatest challenge that distinguishes the sequencing of Saccharum and Miscanthus from the more tractable genomes of sorghum and other cereal models is large physical size approximately 10 Gb and large copy numbers of even 'low-copy' elements 8 to 12 in sugarcane; 4 to 6 in Miscanthus.

Crop Science Abstract - Conversion of Alien Sorghums to Early Combine Genotypes1 | Digital Library

Linkage maps based on molecular markers have shown synteny and collinearity of sorghum and sugarcane genomes, but are complicated to make in sugarcane due to the polyploidy and absence of inbred lines [ 69 ] and references therein. A recent development that may help breeders in marker-assisted selection efforts has been the development of an algorithm and software ONEMAP for constructing linkage maps of outcrossing plant species that has been successfully applied to sugarcane [ 73 ].

Enriched mapping of DNA polymorphisms that also provide for deconvolution of closely related sequences may also aid in assembly of such highly polyploid genomes. Changes in gene expression associated with allopolyploidy are well known, but sugarcane functional genomics is a challenge due the complexity of its largely autopolyploid and aneuploid genome and the absence of a reference sequence. Again, the sorghum genome has been serving as a reference to define putative transcripts. Deep RNA sequencing methods have overcome many limitations of microarray technologies and have allowed recent studies to reveal sorghum genes, gene networks, and a strong interplay among various metabolic pathways in different treatments [ 75 ], as well as the identification of particular paralogs that putatively encode enzymes involved in specific metabolic networks [ 76 ].

Despite the absence of a sequenced genome and the complexities associated with the presence of about 8 to 12 copies of each gene, functional genomics has made considerable progress towards understanding unique biological attributes of sugarcane. These studies assist in the development of new applications for bioenergy, biomaterial industries and improved 'energy' cultivars [ 57 ]. The fundamental databases and resources for studies of functional genomics in sugarcane have been reviewed recently [ 57 , 77 , 78 ] and a sugarcane computational environment SUCEST-FUN Database has been developed for storage, retrieval and integration of genome sequencing, transcriptome, expression profiling, gene catalogs, physiology measures and transgenic plant data [ 79 ].

Studies on sugarcane gene expression have been based mainly on EST information from different tissues, treatments and genotypes.


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A total of 39, sugarcane proteins were predicted from 43, clusters [ 67 ] using ESTScan [ 82 ] and the Oryza sativa matrix Table 5. Putative orthologs and paralogs were identified by pairwise proteome comparisons with InParanoid software [ 83 ]. With the aid of MultiParanoid software [ 84 ], we found orthology relationships among multiple proteomes Table 6. The analysis encompassed a comparison among five species: Saccharum sp. Proteins were grouped into 18, orthologous clusters. The sugarcane transcriptome has been studied using technologies, including cDNA macroarrays nylon membranes , cDNA microarrays spotted onto glass slides, and oligonucleotide arrays either spotted or synthesized in situ.

A summary of the available platforms, samples and related works for sugarcane and sorghum using array technologies is shown in Table 3 and has been reviewed recently [ 57 , 68 , 78 , 85 ]. Sugarcane transcriptomics has identified genes associated with sucrose content, biotic and abiotic stresses, photosynthesis, carbon partitioning and roles of phytohormones and signaling pathways in adaptive responses. These studies also allowed for the identification of promoters that can be used to drive transgene components in a tissue-specific or controlled manner. Several other methods to study sugarcane expression profiles at a moderate scale have been used to confirm the expression patterns observed in large-scale transcript studies [ 57 ].

More recently, the use of oligoarrays has included studies on the regulation of antisense gene expression in sugarcane, pointing to a role for these transcripts in drought responses [ 86 ].

Biofuel and energy crops: high-yield Saccharinae take center stage in the post-genomics era

Some years ago, serial analysis of gene expression SAGE in sugarcane revealed an unexpectedly high proportion of antisense transcripts and chimeric SAGE [ 87 ]. High-throughput sequencing Table 4 is useful for assessing transcriptomes, providing detailed information for transcript variants, particularly SNPs, assessment of the expression of hom oe ologous alleles in the polyploid genome, spliced isoforms and so on [ 88 ].

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Google Adsense. Indeed, the Sorghum genus, with annual and perennial species that are genetically compatible, has become a botanical model for study of attributes related to perenniality [ 27 — 29 ]. Third, some reports show better photosynthetic features of Saccharinae plants than other Andropogoneae. Light interception by the leaves is higher in Miscanthus than in maize [ 15 ] and Miscanthus can sustain higher levels of CO 2 assimilation than maize in lower temperatures [ 32 ]. Sugarcane photosynthesis is enhanced in elevated CO 2 in open-top chambers, increasing biomass productivity [ 33 ], which does not occur in maize grown in open-air elevation of CO 2 [ 34 ].

However, this finding is controversial since enclosure and open-air studies give different results for the same crop, and some authors argue that enclosed studies are not the best scenario to mimic future increases in CO 2 concentration [ 35 ]. Moreover, experiments with Miscanthus in ambient and open-air elevation of CO 2 show no differences in yield [ 36 ]. Since lignocellulosic biofuels use the plant cell wall as a source for fermentable sugars, it is important to understand the composition and architecture of the cell wall to develop strategies to degrade it efficiently.

What is Genomic Sequencing?

Grasses present a particular cell wall structure and composition Figure 2 , making a 'type II' cell wall that differs substantially from the 'type I' cell walls of other feedstocks, such as wood species [ 22 , 37 , 38 ]. This also implies the evolution of different gene families involved in the synthesis of the cell wall [ 22 ].

Recently, a model for sugarcane cell wall architecture and for hierarchical enzymatic hydrolysis was proposed [ 39 ]. By understanding the structure of the cell wall, it is possible to choose the best method to improve hydrolysis yield, and design breeding strategies or develop improved procedures to recover the released carbohydrates. Simplified schematic representation of the cell wall. The wall is shown as a transverse section. Grasses and non-grass angiosperms possess different types of cell wall.