Environmental Engineering Reference
In-Depth Information
circumference at breast height in a large half-sib population of
EG
. Similarly, other studies have also
typically reported few QTL with moderate to high effect in growth and biomass traits, suggesting
an immediate value of this information for marker-assisted selection. QTL analysis of chemical and
physical property traits (e.g., lignin and cellulose content, wood specific gravity), which are critical
for efficient biomass conversion to biofuels, was initially severely hampered by the cost, labor and
time required for sample analysis. However, the development of novel methods for high-throughput
phenotyping, such as near-infrared spectrometry, SilviScan (x-ray densitometry combined with
automated scanning x-ray diffraction and image analysis) and mass spectrometry, computer tomog-
raphy x-ray densitometry (CT scan) and pyrolysis molecular beam mass spectrometry (pyMBMS)
has modified that scenario drastically in the past decade, and analysis of these traits is now com-
monplace. For example, the application of indirect, high throughput phenotyping of wood quality
traits by NIR was demonstrated in
Eucalyptus
, and the information used for QTL mapping in a
pseudo-backcross of
EG
and
E. globulus
(Myburg 2001). Approximately 300 individuals that had
been previously genotyped with AFLP markers were analyzed by NIR, and predictions were made
for pulp yield, alkali consumption, basic density, fiber length and coarseness, and several wood
chemical properties (lignin, cellulose and extractives).
In summary, efforts to identify regions of the genome that regulate biomass growth and wood
quality in
Eucalyptus
have been largely successful. However, the use of this information in breeding
programs was rapidly shown to be unreliable because of two main factors: (1) rapid linkage disequi-
librium (LD) decay among unrelated individuals and (2) the extensive level of genetic heterogeneity
in diverse populations, as previously predicted (Strauss et al. 1992). The low extent of LD meant that
significant marker-trait associations detected in specific segregating populations were not detect-
able when unrelated genotypes were considered. The genetic heterogeneity of existing populations,
where multiple alleles at a large number of loci may contribute to trait variation, signified that
marker-trait associations detected in one pedigree were not relevant in all backgrounds. Therefore,
it became clear that the identification of makers associated with traits in one or few segregating
populations was not sufficient, but that the causative polymorphisms, or at least knowledge of the
specific gene that regulated trait variation, was necessary. However, success in positionally cloning
QTL in forest tree species (Stirling et al. 2001), as it had been done in some agricultural crops like
tomato (Paterson et al. 1988; Martin et al. 1993), was not immediately achieved.
15.2.2.2 Genomics and the Identification of Genes regulating Bioenergy traits
Identification of genes that regulate quantitative variation in plants, animals and humans, went
through significant advances in large part because of the development of genomic technologies. The
high-throughput sequencing of expressed genes initiated in the beginning of the decade, with the
release of the first ESTs of
Eucalyptus
species (Kirst et al. 2004b). This initial effort was rapidly
followed by more extensive EST sequencing projects, which surveyed the pool of genes expressed
in several
Eucalyptus
tissues, and identified putative orthologs for the suite of genes involved in
metabolic and regulatory pathways associated with biomass growth and wood quality (Kirst et al.
2004b). The sequencing of expressed genes lead to the development of the first studies that char-
acterized the expression of large number of genes (i.e., transcriptomics) in
Eucalyptus
and hybrid
populations (Voiblet et al. 2001; Kirst et al. 2004b). A genetic genomics study, which combined the
information from QTL of biomass growth and sequence and expression of genes in differentiating
xylem suggested that the genetic elements that regulated traits related to bioenergy and other prop-
erties could be rapidly unraveled (Kirst et al. 2004b, 2005). Similarly, novel approaches to identify
polymorphisms that regulate complex traits were also developing rapidly in
Eucalyptus
. Thumma
and colleagues were the first to demonstrate the power of association genetics in a tree species
(Thumma et al. 2005), which relies on the detection of polymorphisms associated with quantitative
variation in populations of unknown ancestry, in a woody species. Specifically, the study identi-
fied cinnamoyl CoA-reductase (CCR), a known gene in the phenylpropanoid pathway, as being a
significant determinant of fiber properties in
Eucalyptus
. Although this first study was focused on
