ABSTRACT
<p><b>OBJECTIVE</b>The SSR information in the transcriptome of Erigeron breviscapus was analyzed in this study, in order to further develop new functional genes SSR markers laid a solid foundation.</p><p><b>METHOD</b>SSR loci were searched in all of 52,060 unigenes by using est_timmer. Perl program and SSR primers were designed by Primer3. Furthermore, 36 pairs of primers were randomly selected for the polymorphism analysis on 13 Erigeron breviscapus plants collected from different places.</p><p><b>RESULT</b>A total of 3639 SSRs were found in the transcriptome of Erigeron breviscapus, distributed in 3260 unigenes with the distribution frequency of 6.99%. Di-nucleotide repeat was the main type, account for as much as 34.41% of all SSRs, followed by mono-nucleotide (31.41%) and tri-nucleotide repeat motif (28.08%). The di-nucleotide repeat motifs of AT/AT and AC/GT were the predominant repeat types (28.71%). The tri-nucleotide repeat motifs of AAT/AT was the predominant repeat types (7.94%). For validation the availability of those SSR primers, we randomly selected 36 pairs of primers for PCR amplification. Among them, 34 pair primers (94.44%) produced clear and reproductive bands, 19 pair primers showed polymorphism (52.78%), and 13 Erigeron breviscapus plants were divided into 2 groups.</p><p><b>CONCLUSION</b>There are numerous SSRs in Erigeron breviscapus transcriptome with high frequency and various types, this will provide abundant candidate molecular markers for genetic diversity study and genetic map in this plant.</p>
Subject(s)
China , DNA Primers , Genetics , Erigeron , Classification , Genetics , Genetic Variation , Microsatellite Repeats , Phylogeny , Polymorphism, Genetic , TranscriptomeABSTRACT
Objective: The SSR loci information in the transcriptome of Panax vietnamensis var. fuscidiscus (PVF) was analyzed in this study to provide more powerful tools for molecular marker-assisted breeding in this plant. Methods: Simple sequence repeats (SSR) loci were searched in all 126 758 unigenes by using MISA. SSR loci information was analized and SSR primers were designed by Primer3. Furthermore, 30 pairs of primers were randomly selected for the polymorphic analysis on 13 PVF plants collected from different habitats. Results: A total of 21 320 SSRs were found in the transcriptome of PVF, distributed in 17 780 unigenes with the distribution frequency of 16.82%. Di-nucleotide repeat was the main type, accounted for as much as 52.52% of all SSRs, followed by tri-nucleotide repeat motif (28.08%). The dinucleotide repeat motifs of AG/CT and AT/AT were the predominant repeat types (46.25%). Using Primer3, a total of 39 336 pairs of SSR primers were designed. For validating the availability of those SSR primers, we randomly selected 30 pairs of primers for PCR amplification. Among them, 29 pairs of primers (96.67%) produced clear and reproductive bands, 15 pairs of primers (50.00%) showed polymorphism, and 13 PVF plants were divided into two groups by UPGMA. Conclusion: There are numerous SSRs in PVF transcriptome with high frequency and various types, this will provide the abundant candidate molecular markers for genetic diversity study and genetic map for this plant.
ABSTRACT
<p><b>OBJECTIVE</b>Erigeron breviscapus is a medicinal plant with the most developmental potential in Yunnan province, which is belongs to Erigeron genus of Compositae family. Scutellarin, the main active component of Erigeron breviscapus is one of flavone 7-O-glucuronide derivatives, its biosynthesis pathway is still not clear.</p><p><b>METHOD</b>Full length cDNA encoding flavone syhthase II gene in E. breviscapus was cloned in this study using R-PCR, 3'-RACE and 5'-RACE.</p><p><b>RESULT</b>The opening reading frame of FS II cDNA of E. breviscapus is 1 557 bp long and encoding 518 amino acids, designed as EbFS II, which is highly homologous with FS II of Compositae species, like Callistephus chinensis, Cynara cardunculus var. scolymus, Gerbera hybrida, Dahlia pinnata and Lobelia erinus.</p><p><b>CONCLUSION</b>Phylogenetic analysis showed that EbFS II might has the function of directly converting flavanone to flavone.</p>