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Tree Genetics and Molecular Breeding 2012, Vol.2, No.1, 1
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unit of microsatellite in gene region might affect the
gene expressed products, mutations in repeat unit of
microsatellite might lead to gene silencing or the
occurrence of selective removing. Therefore, analysis
of base compositions of the dominant repeat unit
could help to understand the gene of which the
nucleotide composition of the repeat unit had a higher
mutation receptivity.
Table 2 The nucleotide compositions and frequency of the dominant repeat units of microsatellites in pine, poplar and eucalyptus
The type of repeats
The composition and proportion of nucleotides in dominant repeat units
Pinus
Poplar
Eucalyptus
Di-nucleotide
TA/AT (38.6%)
AG/TC (37.5%)
AG/TC (48.8%)
Tri-nucleotide
AAG/TTC (9.8%)
AAG/TTC (11.8%)
AAG/TTC (11.1%)
Tetra-nucleotide
AAAG/TTTC (6.7%)
AAAG/TTTC (14.8%)
AGTG/TCAC (26.4%)
Penta-nucleotide
CTGCG (6.3%)
AAAAG/TTTTC (12.7%)
CAAAG (8.5%)
Note: The percentage values in this table are the ratio of the listed dominant repeat units in different lengths of repeat units
1.3 Length variations of microsatellites with different
length of repeat units in pine, poplar and eucalyptus
The length variations of microsatellites containing
repeat unit of two bases, three bases, four and five
bases were shown in figure for pine, poplar and
eucalyptus (Figure 1). A different part of each pie
chart (Figure 1) represented the repeating numbers of
different length of each repeat unit, more repetitions
showed greater differentiation. Overall, the longer of
the length of repeat unit of microsatellite in the EST
sequences was, the less variation of repetitions of
repeat was in pine, eucalyptus and poplar trees. However,
in three species, the rate of repeat unit losing or
gaining was not significantly difference in five
nucleotide repeat unit microsatellites as well as in four
repeat unit microsatellites. As the differentiation of
the sequence length has been exhibited the rate of
repeat unit losing or gaining of microsatellite, this
feature close associated with the polymorphisms of
microsatellite sites. The results of the figure showed
that there was higher polymorphism in microsatellites
containing short repeat unit than in microsatellites
containing long repeat unit in the three species. This
would be a kind of reference for developing highly
polymorphic microsatellite markers.
We had the searched microsatellites divided into two
categories, the first class included the SSRs with 20
bp or more in length, the second class including
these SSRs with 12 bp more in and 20 bp less
(Temnykh et al., 2001). The first class SSRs had a
higher polymorphism than the second class SSRs, of
which the law that Weber (1990) firstly discovered in
experimental data of microsatellite in human had been
confirmed in many organisms. The second class
generated less mismatching sites in slipping chain
matching because of the short fragment length of SSR,
so the polymorphism of the second class SSRs was
not as the first class. Mutation rate of SSR sequences
with less than 12 bp fragment length was no any
difference with other sequences, which would have a
random variation in trend. In this study, the 33.3% of
EST-SSRs in eucalyptus belonged to in the first
category and 18.9% in poplar but only 8.1% in the
pine. As mentioned above data, the largest proportion
of Eucalyptus EST containing high polymorphic SSRs
was eucalyptus, followed by poplar and pine trees.
And the number of first class SSR in eucalyptus and
pine both were higher than in poplar (Figure 1).
Above mentioned results showed that the abundance
of pine SSR in gene region was significantly lower
than that in poplar and eucalyptus, while enrichment
of three-base repeat microsatellites was also significantly
higher than that of pine and poplar, these results might
be connected to codon selection, which indicated that
microsatellite in gene region of pine should be
accumulated with very strong selection pressure.
Microsatellite length variations also showed that the
content of microsatellites with high polymorphism in
the pine trees was significantly lower, which might
also be due to codon selection. If the microsatellites in
gene region had some strong cumulative selection
pressure in pine in the evolutionary process, the content
of microsatellites in gene region and enrichment of