Environmental Engineering Reference
In-Depth Information
a specific gene, several studies are underway that explore the identification of genes of value for
bioenergy for several hundred genes, targeting particularly those that code for enzymes of the lignin
and carbohydrate/cellulose pathways.
15.2.2.3 Future developments
Biotechnology and genomics research have allowed for achievements in the past few years that were
inconceivable at the beginning of the millennium. Procedures for genome sequencing, as well as
transcriptome, proteome, and metabolome characterization have all gained in efficiency by two to
three orders of magnitude within less than a decade. At the same time, the costs per data point have
been reduced by the same proportion. As a consequence of the decrease in cost, and the growing
interest of the U.S. Department of Energy (DOE) in bioenergy crops, an
Eucalyptus
genotype was
selected recently for sequencing by the Joint Genome Institute (JGI)/DOE, for completion in early
2010. The sequence will provide the foundation on which QTL cloning should become achievable.
The genome sequencing and the complete catalogue of genes will also allow for the development
of genomic tools such as whole-transcriptome microarrays, for characterization of gene expression
variation. The current sequence has coverage of 4 × (meaning that, on average, every nucleotide
has been sequenced 4 times) and is expected to reach 8 × by the summer of 2009. An assembly
based on the existing sequence data has already captured almost 80% of the genome sequence. This
suggests that—with the added sequencing to complete 8 ×—the final genome information will be
close to completion. The individual being sequenced is an elite
EG
genotype (Brasuz1). To support
the assembly and annotation of the genome sequence, two bacterial artificial chromosomes (BACs)
have been developed and over one hundred thousand BAC-ends have been sequenced. Furthermore,
a number of pedigrees are being genotyped with diversity array technology (DArT), microsatellite,
gene expression (GEM) and single-feature polymorphisms (SFP) markers, for the development of
hyper-saturated genetic maps that will be invaluable for the sequence assembly. To support the
annotation of the genome sequence (i.e., identification and definition of function for genes in the
genome), JGI is also sequencing a large number of random gene sequence fragments (expressed
sequence tags).
Perhaps even more exciting are the anticipated developments in the years ahead, particularly in
genome sequencing. Platforms in development have recently demonstrated the capacity to generate
sequencing data—although not yet fully interpretable—over 10-20 kilobases within a few hours
(Korlach et al. 2008). At the same time, miniaturization of devices and single molecule detec-
tion methods now permit sequencing of several million molecules in parallel (Eid et al. 2009). In
that scenario, sequencing a moderate size genome such as
Eucalyptus
(~500-600 Mbp) could be
achieved in less than one day. Ultra low sequencing reaction volumes also suggest that the costs of
such a task will be a few hundred U.S. dollars, rather than the current several hundred thousand.
In summary, in the next decade, genetic and genomics studies will likely discover the majority
of genes that regulate a significant part of the heritable variation of biomass productivity and wood
property traits in
Eucalyptus
and the most commercially important tree crops, such as
Populus
and
Pinus
. Consequently, it will be possible to identify superior genotypes based in large part on their
genotype across multiple critical loci. The challenge will be to develop genotyping assay meth-
ods that will be sufficiently cost effective to permit rapid screening of large progenies in breeding
programs. That will allow the development of genotypes that combine the optimal alleles for each
specific end-use purpose, including plants optimized for bioenergy purposes.
15.3 PIne
Worldwide,
Pinus
species are currently widely used for bioenergy and have considerable potential
for future use. The
Pinus
genus has over 100 species (Syring et al. 2005), and pines have high
genetic and phenotypic diversity that has bioenergy ramifications. Many pine species growing in
natural stands and/or established in plantations provide bioenergy opportunities.
