Environmental Engineering Reference
In-Depth Information
its existing importance as an energy crop. The eucalypt, the most widely planted forest species
in tropical and subtropical parts of the world, is being sequenced because of its energy potential.
This, combined with the available poplar genome sequence, will provide a foundation for genomics
approaches in woody biomass crops.
2.5 analysIs oF Genome varIatIon
Genotyping an entire genome allows association genetics to be applied to the discovery of the
genetic basis of important traits. Analysis of variation in plant genomes can now be considered
an analysis of all of the single-feature polymorphisms. This includes all of the insets and dele-
tions (indels) and the single nucleotide polymorphisms (SNPs). Analytically indels can usually be
detected or assayed as SNPs. SNP discovery and analysis in plants has recently been reviewed
(Henry and Edwards 2009). SNP discovery even in complex plant genomes is now facilitated
by advancing DNA sequencing technologies (Bundock et al. 2009; Trick et al. 2009). Efficient
targeted mutagenesis techniques have been developed for the discovery of naturally occurring or
induced mutations (Cross et al. 2008). Analysis of variation in known SNPs in a plant population
is now possible with very high-throughput techniques (Edwards et al. 2009; Masouleh et al. 2009)
and is being advanced by the application of nanotechnology (Pattemore et al. 2008). Association
genetics has often considered only a few candidate genes. The identification of the genetic basis
of gelatinization temperature in plant starches is a good example of this because this trait may
be important in determining the energy required to gelatinize starch for conversion to sugars and
subsequently into a biofuel. Starch biosynthesis genes were the obvious candidates, and analysis
revealed that SNPs altering key amino acid residues in the soluble starch synthases of rice could
individually be responsible for an 8°C reduction in gelatinization temperature (Waters et al. 2007).
This alters the structure of the amylopectin, allowing water to penetrate the starch granule more
easily. This approach would complement the expression of thermostable amylases in plants to digest
the starch during processing to biofuels (Wolt and Kraman 2007). Genomics tools are making the
consideration of all options possible, and these developments are important when candidate genes
are not readily identifiable for the trait of interest.
2.6 transcrIPtome analysIs
The same tools that have revolutionized DNA sequencing have the potential to allow detailed
analyses of genes expressed in different plants or tissues at different times. Transcriptome analysis
allows the identification of genes controlling key traits for selection in plant domestication and
improvement for human use. This approach involves the identification of candidate genes by deter-
mining their differential expression in association with the trait of interest. Candidate genes are
then usually screened to determine function and to confirm association with the trait. Microarray
analysis has been widely applied to transcript analysis in gene discovery. Early complementary
DNA (cDNA)-based arrays were replaced by oligonucleotide arrays as the availability of more gene
sequence data for more species made this possible. Advances in DNA sequencing technology offer
techniques for comprehensive transcript profiling by sequencing, even in species without well-
characterized genomes.
2.7 ProteomIcs oF BIoenerGy croPs
In some cases, the plant proteome will be the key area for analysis, although for bioenergy traits
associated with carbohydrate composition this is probably less likely. However, proteins (for ani-
mal feed or other higher value applications) may be an important co-product in the energy crop.
Proteomics is likely to make important contributions to understanding of the regulation of genes
determining bioenergy traits.
