Development of EST-SSR markers of Ipomoea nil.
Ontology highlight
ABSTRACT:
SUBMITTER: Ly T
PROVIDER: S-EPMC3405949 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:BACKGROUND: Currently there exists a limited availability of genetic marker resources in sweetpotato (Ipomoea batatas), which is hindering genetic research in this species. It is necessary to develop more molecular markers for potential use in sweetpotato genetic research. With the newly developed next generation sequencing technology, large amount of transcribed sequences of sweetpotato have been generated and are available for identifying SSR markers by data mining. RESULTS: In this study, we investigated 181,615 ESTs for the identification and development of SSR markers. In total, 8,294 SSRs were identified from 7,163 SSR-containing unique ESTs. On an average, one SSR was found per 7.1 kb of EST sequence with tri-nucleotide motifs (42.9%) being the most abundant followed by di- (41.2%), tetra- (9.2%), penta- (3.7%) and hexa-nucleotide (3.1%) repeat types. The top five motifs included AG/CT (26.9%), AAG/CTT (13.5%), AT/TA (10.6%), CCG/CGG (5.8%) and AAT/ATT (4.5%). After removing possible duplicate of published EST-SSRs of sweetpotato, a total of non-repeat 7,958 SSR motifs were identified. Based on these SSR-containing sequences, 1,060 pairs of high-quality SSR primers were designed and used for validation of the amplification and assessment of the polymorphism between two parents of one mapping population (E Shu 3 Hao and Guang 2k-30) and eight accessions of cultivated sweetpotatoes. The results showed that 816 primer pairs could yield reproducible and strong amplification products, of which 195 (23.9%) and 342 (41.9%) primer pairs exhibited polymorphism between E Shu 3 Hao and Guang 2k-30 and among the 8 cultivated sweetpotatoes, respectively. CONCLUSION: This study gives an insight into the frequency, type and distribution of sweetpotato EST-SSRs and demonstrates successful development of EST-SSR markers in cultivated sweetpotato. These EST-SSR markers could enrich the current resource of molecular markers for the sweetpotato community and would be useful for qualitative and quantitative trait mapping, marker-assisted selection, evolution and genetic diversity studies in cultivated sweetpotato and related Ipomoea species.
| S-EPMC3206431 | biostudies-literature
Project description:A set of expressed sequence tag (EST) microsatellite markers were developed and characterized using next-generation sequencing technology for the Chinese genus Ostryopsis (Betulaceae). • A total of 38 high-quality simple sequence repeat (SSR) primers were identified, of which 15 could be successfully amplified. Subsequently, we selected 80 individuals to represent the three species of the genus to evaluate the efficacy of these markers for examining genetic diversity of each species in the future. We found that the number of alleles per locus ranged from one to nine, with an average of 3.8. The expected heterozygosity and observed heterozygosity per locus varied from 0 to 0.829 and from 0 to 1, respectively, with their respective mean values as 0.483 and 0.416. • These EST-SSR markers will be useful for evaluating the range-wide genetic diversity of each species and examining genetic divergence and gene flow between the three species.
| S-EPMC4103604 | biostudies-literature
Project description:PREMISE OF THE STUDY:Bombax ceiba (Malvaceae), commonly known as silk cotton tree, is a multipurpose tree species of tropical forests. Novel expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed and characterized for the species using transcriptome analysis. METHODS AND RESULTS:A total of 33 new EST-SSR markers were developed for B. ceiba, of which 13 showed polymorphisms across the 24 individuals from four distant populations tested in the study. The results showed that the number of alleles per polymorphic locus ranged from two to four, and the expected heterozygosity and observed heterozygosity per locus varied from 0.043 to 0.654 and from 0 to 0.609, respectively. CONCLUSIONS:These newly developed EST-SSR markers can be used in phylogeographic and population genetic studies to investigate the origin of B. ceiba populations. Furthermore, these EST-SSR markers could also greatly promote the development of molecular breeding studies pertaining to silk cotton tree.
| S-EPMC4406838 | biostudies-literature
Project description:Microsatellite primers were developed for Begonia luzhaiensis (Begoniaceae) to assess genetic diversity and population genetic structure. Based on the transcriptome data of B. luzhaiensis, 60 primer pairs were selected for initial validation, of which 16 yielded polymorphic microsatellite loci in 57 individuals. The number of alleles observed for these 16 loci ranged from one to nine. The observed and expected heterozygosity ranged from 0.000 to 1.000 and from 0.000 to 0.804 with averages of 0.370 and 0.404, respectively. Five loci could be successfully amplified in B. leprosa. The expressed sequence tag-simple sequence repeat markers are the first specifically developed for B. luzhaiensis and the first developed in Begonia sect. Coelocentrum. These markers will be useful for future studies of the genetic structure and phylogeography of B. luzhaiensis.
| S-EPMC5435407 | biostudies-literature
Project description:Premise of the studyCatalpa bungei (Bignoniaceae) is a deciduous tree native to China. We developed microsatellite markers for C. bungei to investigate its population genetics.Methods and resultsOne hundred seventy-seven expressed sequence tag (EST)-simple sequence repeat (SSR) primer pairs were isolated and characterized using next-generation sequencing. Thirty of these primer pairs were polymorphic loci in 52 individuals of C. bungei. The number of alleles ranged from two to 18 with observed and expected heterozygosity values of 0.05-1.00 and 0.18-0.95, respectively. The fixation index ranged from -1.00 to 1.00 with an average of 0.32. No linkage disequilibrium was detected in any pair of loci. All markers showed good amplification results in four species (C. bungei, C. fargesii, C. duclouxii, and C. ovata) except three loci.ConclusionsThese polymorphic markers are expected to be helpful in further studies on the systematics and phylogeography of C. bungei and related species.
| S-EPMC4850053 | biostudies-literature
Project description:Stipa breviflora (Poaceae) is one of the dominant species of the desert steppe in the eastern Eurasian grasslands. Simple sequence repeat (SSR) markers were developed for use in genetic diversity studies of this species. A total of 1954 potentially polymorphic loci were obtained by comparing transcriptome data of eight different S. breviflora individuals. We selected 81 loci to verify polymorphism and 63 loci amplified, of which 21 loci exhibited polymorphism. The number of alleles per locus varied from two to 24, the observed heterozygosity ranged from 0.083 to 0.958, and the expected heterozygosity ranged from 0.396 to 0.738. These newly identified SSR loci can be used for population genetic and landscape genetic studies of S. breviflora. In addition, 14 loci also amplified in six related Stipa species (S. grandis, S. krylovii, S. bungeana, S. aliena, S. gobica, and S. purpurea).
| S-EPMC5400433 | biostudies-literature
Project description:Polymorphic microsatellite markers were developed for Artocarpus hypargyreus (Moraceae), a threatened species endemic to China, to investigate the genetic diversity and structure of the species. Based on the transcriptome data of A. hypargyreus, 63 primer pairs were preliminarily designed and tested, of which 34 were successfully amplified and 10 displayed clear polymorphisms across the 67 individuals from four populations of A. hypargyreus. The results showed the number of alleles per locus ranged from three to 10, and the observed heterozygosity and expected heterozygosity per locus varied from 0.000 to 0.706 and from 0.328 to 0.807, respectively. These microsatellite markers will be useful in exploring genetic diversity and structure of A. hypargyreus. Furthermore, most loci were successfully cross-amplified in A. nitidus and A. heterophyllus, indicating that they will be of great value for genetic study across this genus.
| S-EPMC5238703 | biostudies-literature
Project description:Tibetan annual wild barley is rich in genetic variation. This study was aimed at the exploitation of new SSRs for the genetic diversity and phylogenetic analysis of wild barley by data mining. We developed 49 novel EST-SSRs and confirmed 20 genomic SSRs for 80 Tibetan annual wild barley and 16 cultivated barley accessions. A total of 213 alleles were generated from 69 loci with an average of 3.14 alleles per locus. The trimeric repeats were the most abundant motifs (40.82%) among the EST-SSRs, while the majority of the genomic SSRs were di-nuleotide repeats. The polymorphic information content (PIC) ranged from 0.08 to 0.75 with a mean of 0.46. Besides this, the expected heterozygosity (He) ranged from 0.0854 to 0.7842 with an average of 0.5279. Overall, the polymorphism of genomic SSRs was higher than that of EST-SSRs. Furthermore, the number of alleles and the PIC of wild barley were both higher than that of cultivated barley, being 3.12 vs 2.59 and 0.44 vs 0.37. Indicating more polymorphism existed in the Tibetan wild barley than in cultivated barley. The 96 accessions were divided into eight subpopulations based on 69 SSR markers, and the cultivated genotypes can be clearly separated from wild barleys. A total of 47 SSR-containing EST unigenes showed significant similarities to the known genes. These EST-SSR markers have potential for application in germplasm appraisal, genetic diversity and population structure analysis, facilitating marker-assisted breeding and crop improvement in barley.
| S-EPMC3988095 | biostudies-literature
Project description:Premise of the study:Microsatellite primers were developed for Primula ovalifolia, a member of Primula section Petiolares (Primulaceae), to study the population genetics and species delimitation in this section. Methods and Results:A total of 4753 markers were successfully designated from 5139 putative simple sequence repeat loci. We isolated 38 expressed sequence tag-simple sequence repeat markers from 220 selected marker sites and tested polymorphism in three populations of P. ovalifolia, one of P. tardiflora, and one of P. epilosa. The number of alleles per locus ranged from one to 19, and the observed and expected levels of heterozygosity varied from 0 to 0.938 and 0 to 0.915, respectively. Most of the loci could be successfully cross-amplified in the two congeneric species. Conclusions:These markers will be useful for further population genetic analysis and gene flow estimation of P. ovalifolia and its relatives.
| S-EPMC5749821 | biostudies-literature
Project description:PremiseCamellia reticulata, which is native to southwestern China, is an economically important plant belonging to the family Theaceae. We developed expressed sequence tag-simple sequence repeat (EST-SSR) markers for C. reticulata, which can be used to investigate its genetic diversity, population structure, and evolutionary history.Methods and resultsWe detected 4780 SSRs in C. reticulata from Camellia RNA-Seq data deposited in the National Center for Biotechnology Information's expressed sequence tags database (dbEST). Primer pairs for 70 SSR loci were designed and used for PCR amplification using 90 individuals from four populations of C. reticulata. Of these loci, 50 microsatellite markers were successfully identified, including 11 polymorphic markers. The allele number per locus ranged from two to seven (mean = 4.182), and the levels of observed and expected heterozygosity ranged from 0.044 to 0.567 and from 0.166 to 0.642, respectively. Eleven primer pairs amplified PCR products in three other species of Camellia (C. saluenensis, C. pitardii, and C. yunnanensis).ConclusionsThe set of microsatellite markers developed here can be used to study the genetic variation and population structure of C. reticulata and related species and thereby help to develop conservation strategies for this species.
| S-EPMC7249272 | biostudies-literature