Forest Trees - Bioenergy Crop Plants - page 364

emissions while enhancing local economies. The Brazilian experience can also be transferred to
other developing countries, thus enabling locally produced bioenergy worldwide.
15.2.2 e ucAlyptus B ioEnErgy E nhancEmEnt through B iotEchnology and g EnomicS
As the main SRWCs in the southern hemisphere, several Eucalyptus species have been the subject
of studies in genomics and biotechnology, targeted at improving wood and growth properties for
bioenergy, or related applications. The most significant developments for enhancement of wood and
productivity properties began almost two decades ago, with the production of the first dense genetic
maps. Before that, the available tools were severely restricted to the analysis of few genetic loci.
Since then, most research efforts in Eucalyptus genomics have been dedicated to the discovery of
polymorphisms that confer superior phenotype to elite trees. The expectation is that these polymor-
phisms identify genetic markers for indirect selection in breeding programs, but may also define a
gene for modification using transgenic approaches.
As a first step in the establishment of the tools necessary to identify genes of economic value
for selection, the first high-density Eucalyptus genetic maps were established in the mid-1990's
(Grattapaglia and Sederoff 1994). Development of genetic maps was soon followed by the mapping
of genomic regions, of quantitative trait loci (QTL) that regulate a portion of the phenotypic varia-
tion for wood quality and growth (Grattapaglia et al. 1995, 1996). These early developments were
highly restricted because of the lack of sequence information for Eucalyptus , and most other woody
species. This deficiency started to diminish in the past decade, initially with the high-throughput
sequencing of fragments of expressed genes (expressed sequence tags, or ESTs) ( Paux et al. 2004;
Vicentini et al. 2005; Novaes et al. 2008), and more recently with the perspective of the availability
of the first Eucalyptus genome. Here we review the developments in the use of biotechnology and
genomics, aimed at improving bioenergy traits in Eucalyptus . For general reviews about Eucalyptus
genomics and its applications to breeding, the readers are directed to other recent publications (Poke
et al. 2005; Myburg et al. 2007; Grattapaglia and Kirst 2008).
15.2.2.1 Genetic mapping and quantitative traits loci analysis
Most mapping studies in agricultural crops or model plants have relied on the analysis of inbred
lines, near-isogenic lines or backcross progenies. In outbred tree species like Eucalyptus , the long-
generation time and high genetic load have limited the development of these types of segregating
populations (Kirst et al. 2004a). To address these limitations, new mapping strategies that use
half-sib, full-sib and pseudo-backcross populations were developed and successfully implemented
(Grattapaglia and Sederoff 1994; Myburg et al. 2003). Isozyme markers were first applied to
genetic mapping of Eucalyptus (Moran and Bell 1983) but were of limited use for genetic studies
that require high-density, saturated maps. Restriction fragment polymorphism markers were also
used for the development of second-generation genetic maps (Byrne et al. 1995; Thamarus et al.
2002). However, the most significant advances came with the development of PCR-based markers
such as random amplified polymorphic DNA (RAPD) markers (Grattapaglia and Sederoff 1994;
Verhaegen and Plomion 1996; Bundock et al. 2000; Gan et al. 2003), amplified fragments length
polymorphism (AFLP) and microsatellite markers (Brondani et al. 1998, 2002; Marques et al.
1998, 2002; Bundock et al. 2000; Gion et al. 2000; Thamarus et al. 2002; Gibbs et al. 2003). A few
genes have also been added to existing maps (Bundock et al. 2000; Gion et al. 2000; Thamarus
et al. 2002).
Development of high-coverage genetic maps established the foundation for the quantitative
genetic analysis of bioenergy traits in Eucalyptus and identification of genes that regulate them.
QTL analyses for traits associated with biomass growth have been numerous in Eucalyptus ,
including in pure EG crosses (Grattapaglia et al. 1996), E. nitens (Byrne et al. 1997), EG and EU
hybrids (Verhaegen et al. 1997) and EG and E. globulus crosses (Kirst et al. 2004b). The first report
(Grattapaglia et al. 1996) identified three QTL, explaining 13.7% of the phenotypic variation for