ABSTRACT
In order to enrich the library of SSR and provide more powerful tools for molecular marker-assisted breeding in Astragalus membranaceus var. mongholicus, simple sequence repeats (SSR) loci in its transcriptome were searched in 18 040 unigenes (>=1 kb) by using MISA. SSR loci information was analyzed and SSR primers were designed by Primer 3. Furthermore, 110 pairs of primers were randomly selected for the polymorphic analysis on 20 plants collected from different habitats. A total of 5 640 SSRs were found in the transcriptome of A. membranaceus var. mongholicus, distributed in 4 462 unigenes with the distribution frequency of 31.26%. SSR loci occurred every 6 514 bp. Mono-nucleotide repeat was the main type, accounted for as much as 36.72% of all SSRs, followed by tri-nucleotide(32.57%) and di-nucleotide(27.73%) repeat motif. Among all 75 repeat types, A/T(2 026) was the predominant one followed by AG/CT(1 179), AAG/CTT(477). For validating the availability of the SSR primers designed using Primer 3, 110 pairs of primers were randomly selected for PCR amplification. Among them, 97 pairs of primers (88.18%) produced clear and reproductive bands. Using 19 pairs of primers showed polymorphism, 20 plants were divded into two groups by UPGMA. There are numerous SSRs in A. membranaceus var. mongholicus transcriptome with high frequency and various types, this will provide the abundant candidate molecular markers for genetic diversity, molecular identification, and marker-assisted breeding study for this plant.
ABSTRACT
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.