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Tree Genetics and Molecular Breeding 2012, Vol.2, No.1, 1
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would be an important tool in the different research
fields for genotyping, genetic map building, QTL
mapping, as well conservation of genetic germplasm,
protection of endangered species, gene flow monitoring,
genetic drift research, gene mutation and systematic
analysis (Huang, 2002). The typical procedures for
development of microsatellite markers would be
including library construction, enrichment of microsatellite
sequences, sequencing, microsatellite searching and
primer designing that no doubt might be cumbersome
and expensive processes limiting the development
and application of microsatellite markers. Although
microsatellites can also mined by using the resourced
sequences in many different species, however, comparing
to the model animals and plants as well as important
crops, it is much more limited of genomic information
in most of forest tree species.
EST sequencing is an important means of functional
studies of genes. A large-scale EST sequencing of
trees have been done in the forest representatives of
pine, poplar and eucalyptus, there was an abundant
EST sequence information of these species deposited
in public databases (Sterky et al., 2004; Allona et al.,
1998; Keller et al., 2009), which provides important
sequence resources for developing the microsatellite
marker in these species. In fact, pine, eucalyptus and
poplar are known leading industrial timber species in
China and even in the world, developing the resources
of microsatellite markers would be an important to
strengthen the genetic studies of these species.
The characteristics of microsatellite sequences are
an important indicator to understand the genomic
differences of different species. Microsatellite is widely
distributed in the genome of eukaryote, exiting not
only in the region of introns and intervals of genes,
also presenting in the coding sequence of gene.
Because microsatellite sequences are prone to
variations, the genes containing the microsatellite
are more subjected to being mutations than that of
non-microsatellite.
A large number of studies have shown that microsatellite
instability is related to human cancer and neurological
diseases occurring (Lothe, 1997; Toth et al., 2000). In
the evolutionary process, the SSR within the gene
region will be influenced by the selection of
convergence.
The studies on the microsatellite in the exon
sequence of the poplar genome revealed that the
microsatellites with three-base repeat units in the
exons of poplar genome were far more than other
types of microsatellites (Li et al., 2009). Comparing
to microsatellites with other repeat types, the
microsatellite with three-base repeat unit had minimum
impacts on open reading frame of gene, enrichment of
three-base repeat microsatellite showed that microsatellite
in the exon region were influenced by the selection of
genetic code in the evolutionary process.
Currently, the studies of microsatellite in gene region
mostly focused on humans and model animals and
plants, especially in human cancer research (Lothe,
1997; Brinkmann et al., 1998; Toth et al., 2000). It
rarely reported on the research of microsatellite in
gene regions in forest tree species. Through comparison
of microsatellite in the gene region in different tree
species, it not only provides important parameters for
understanding the differentiation of the genomes of
different tree species, but also provides a reference of
bioinformatics for how to make use of these sequence
resources to develop microsatellite markers with high
polymorphism.
1 Results and analysis
1.1 Analysis of microsatellite abundance among the
expressed sequence pine, poplar and eucalyptus
There were 2,465, 4,599 and 5,612 of EST sequences
containing microsatellites with repeating units from 2
to 5 bp in length by using Sputnik software to search
each 30,000 EST sequences of pine, poplar and
eucalyptus, respectively. The frequency of microsatellite
occurring in EST sequences was 8.2% in pine, 15.3%
in poplar and 18.7% in eucalyptus respectively. The
results showed that the frequency of microsatellite
occurring in EST sequences was quite close between
eucalyptus and poplar, but EST-SSR abundance of the
pine was significantly lower than that of the poplar
and eucalyptus.
Analysis on repeat unit length of EST-SSR in three