Abstract
With the development of high-throughput
sequencing techniques, transcriptome sequencing
projects which provide valuable resources for designing
simple sequence repeat (SSR) primers have been
carried out for many plants. However, the utility of
SSRs for molecular breeding depends on genomewide
distribution and coverage, as well as moderately
high allelic variability, in the available SSR library. In
this study, we characterized the exonic SSRs developed
from the publicly available Populus genome as a
case study to determine their value for molecular
breeding. As expected, our results confirmed that
microsatellites occurred approximately three times
less often in coding regions than in non-coding
regions. Mutability test also showed that exonic SSRs
contained less allelic variability than intronic SSRs.
More importantly, exonic SSRs were unevenly distributed
both among and within chromosomes. Large
exonic SSRs deserts were observed on several chromosomes.
Differential selection between paralogous
chromosomes, at the gene level, appears to be
responsible for these SSR deserts, though the mechanisms
that cause chromosome-specific SSR deserts
are not known. This work provides ample evidence
that the candidate gene approach based on unigenes
identified from transcribed sequences may not be the
best strategy to identify highly polymorphic SSRs.
