Genetic diversity of Eucalyptus hybrids estimated by genomic and EST microsatellite markers

Cupertino, Fernanda Barbosa; Leal, Jeiza Botelho; Corrêa, Ronan Xavier; Gaiotto, Fernanda Amato

doi:10.1007/s10535-011-0059-x

Cited by 6 publications

(2 citation statements)

References 16 publications

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“…This result demonstrated that the SSR primers had good transferability and that one SSR marker could probably be shared among species with a close genetic relationship. This conclusion is agrees with results reported by Cupertino et al (2011) who found that genomic SSR and EST SSR had no significant differences among 112 hybrid taxa of Eucalyptus. Ellis and Burke (2007) reported that the length of SSRs and their stability varied between different species and between different SSR loci within the one species.…”

Section: The Screening Of Ssr Primerssupporting

confidence: 93%

Analysis of SSR loci and development of SSR primers in Eucalyptus

et al. 2017

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In this study, 28,691 genome sequences and 16,566 expressed sequence tags (ESTs) of Eucalyptus were derived from the GenBank database. A total of 2292 SSR loci were sought out from 1785 effective sequences. Through analyses of SSR loci information, the SSR motif length was negatively correlated with the abundance of the SSRs. In the EST sequences of Eucalyptus, triplet repeat motifs were the most abundant, and dinucleotide repeats motifs had the highest frequencies. Subsequently, 395 pairs of primers were designed based on the SSR loci. Using optimized SSR-PCR conditions, 340 pairs of primers were successfully screened, with a success rate of 86.1%. By construction of a maximum likelihood phylogenetic tree of six eucalypt species, represented by five species of the genus Eucalyptus and one of the genus Corymbia, the genetic relationships of Eucalyptus urophylla and E. camaldulensis suggested by this tree was found to differ from that suggested by traditional morphological taxonomy. The results provide insights for evaluating genetic diversity of Eucalyptus and analysis of Eucalyptus phylogenetics using SSR markers.

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Section: The Screening Of Ssr Primerssupporting

confidence: 93%

Analysis of SSR loci and development of SSR primers in Eucalyptus

et al. 2017

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“…The significance of EST-SSRs as a molecular tool in population genetic studies has been known for long [ 9 ]. In woody trees, EST-SSRs have been applied in population studies and analysis of genetic diversity in Cycas [ 10 ], Picea [ 11 , 12 ], Prunus [ 13 , 14 ], Eucalyptus [ 15 , 16 ] and Populus [ 17 ]; in hybrid selection in e.g., Citrus [ 18 ]; and also in genetic mapping in Citrus [ 19 ], Quercus [ 20 , 21 ] and Pinus [ 22 ]. Furthermore, unlike the genomic SSRs, EST-SSRs are easily transferable across species [ 23 ], therefore allowing studying polymorphism and genetic diversity in related species [ 9 ].…”

Section: Introductionmentioning

confidence: 99%

Comparative in silicoanalysis of EST-SSRs in angiosperm and gymnosperm tree genera

et al. 2014

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BackgroundSimple Sequence Repeats (SSRs) derived from Expressed Sequence Tags (ESTs) belong to the expressed fraction of the genome and are important for gene regulation, recombination, DNA replication, cell cycle and mismatch repair. Here, we present a comparative analysis of the SSR motif distribution in the 5′UTR, ORF and 3′UTR fractions of ESTs across selected genera of woody trees representing gymnosperms (17 species from seven genera) and angiosperms (40 species from eight genera).ResultsOur analysis supports a modest contribution of EST-SSR length to genome size in gymnosperms, while EST-SSR density was not associated with genome size in neither angiosperms nor gymnosperms. Multiple factors seem to have contributed to the lower abundance of EST-SSRs in gymnosperms that has resulted in a non-linear relationship with genome size diversity. The AG/CT motif was found to be the most abundant in SSRs of both angiosperms and gymnosperms, with a relative increase in AT/AT in the latter. Our data also reveals a higher abundance of hexamers across the gymnosperm genera.ConclusionsOur analysis provides the foundation for future comparative studies at the species level to unravel the evolutionary processes that control the SSR genesis and divergence between angiosperm and gymnosperm tree species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0220-8) contains supplementary material, which is available to authorized users.

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Computational prediction and experimental verification of miRNAs in Panicum miliaceum L.

Wang

et al. 2012

Sci. China Life Sci.

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MicroRNAs (miRNAs) are a class of non-coding RNAs that play critical roles in post-transcriptional regulation. Their target genes are involved in a variety of biological processes such as development, metabolism, and stress response. Panicum miliaceum L. (Panicum) is an important grain crop, but, until now, no miRNAs have been identified in this plant. Using a homology search based on expressed sequence tag (EST) analysis and miRNA precursor secondary structure, a total of 43 new miRNAs were identified. The miRNAs were found to be unevenly distributed among 11 miRNA families. Target analysis using the plant small RNA target analysis server psRNATarget showed that the newly identified miRNAs can potentially regulate 68 target genes. Ten of the 11 miRNA families were annotated as involved in RNA regulation, suggesting they may play an essential role in post-transcriptional regulation in Panicum. Selected miRNAs representing eight of the families were verified by northern blotting, indicating that the prediction method that we used to identify the miRNAs was effective.

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Genetic diversity of Eucalyptus hybrids estimated by genomic and EST microsatellite markers

Cited by 6 publications

References 16 publications

Analysis of SSR loci and development of SSR primers in Eucalyptus

Analysis of SSR loci and development of SSR primers in Eucalyptus

Comparative in silicoanalysis of EST-SSRs in angiosperm and gymnosperm tree genera

Computational prediction and experimental verification of miRNAs in Panicum miliaceum L.

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