Differential detection of transposable elements between Saccharum species

Souza, Marislane Carvalho Paz de; Silva, Jéssica Naiana

doi:10.1590/s1415-47572013005000030

Cited by 6 publications

(3 citation statements)

References 27 publications

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“…The occurrence of somatic recombination in addition to somatic mutations in grapes that were vegetatively propagated was reported as an event that may promote gene homozygosis in the heterozygous condition (Oliveira-Collet et al, 2005). It is possible that transposable genetic elements described in the genomes of S. officinarum and S. spontaneum (de Souza et al, 2013), can mediate the chromosomal rearrangements in the varieties of Saccharum spp. Epigenetic variability due to differential methylation levels in a complex genome as the sugarcane may also lead to genotypic and phenotypic instability (Marfil et al, 2009).…”

Section: Discussionmentioning

confidence: 99%

Changes on microsatellites of expressed sequence tag of sugarcane (Saccharum spp) during vegetative propagation

Augusto¹,

Maranho²,

Mangolin³

et al. 2017

Genet. Mol. Res.

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ABSTRACT. The reduction in sugarcane productivity in subsequent cutting stages may be related to a gradual decrease of the allele number and mean observed heterozygosity (H O ) in the sugarcane ratoon. This hypothesis was tested assessing the number of alleles and H O values in 10 expressed sequence tag microsatellites (Est-SSR loci) of the sugarcane varieties RB72454 and RB867515 in different cutting stages. Changes of allele numbers in samples of different cutting stages were observed in seven and six EstSSR loci of the RB72454 and RB867515 varieties, respectively. Reduction of allele numbers was observed in the samples collected in the fourth and sixth cutting stages of the RB72454 variety. In contrast, an increase of the allele numbers was detected in the samples collected on fourth, sixth, and seventh cutting stages of the RB867515 variety. Unchanged allele numbers were observed only in EstB41, EstC84, and EstB130 loci of the RB72454 variety, and EstB41, EstC67, EstA68, and EstB130 loci of the RB867515 variety. The variety RB867515 has lower polymorphism and values of H O than the RB72454 variety in different stages of cutting. At molecular level, in Est-SSR loci, the RB72454 variety showed higher changes in subsequent stages of cutting than RB867515. The similarities and divergences at molecular level between varieties RB72454 and RB867515 observed in the 10 Est-SSR loci during subsequent cutting stages can not explain the reduced productivity frequently observed after subsequent cutting stages but showed that phenotypic and physiological changes after each cutting stage are also accompanied by changes at genomic level.

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Section: Discussionmentioning

confidence: 99%

Changes on microsatellites of expressed sequence tag of sugarcane (Saccharum spp) during vegetative propagation

Augusto¹,

Maranho²,

Mangolin³

et al. 2017

Genet. Mol. Res.

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“…The genus Saccharum is an important member of the Poaceae family. The most widely considered concept by sugarcane breeder is that it consists of six species, including Saccharum officinarum , Saccharum robustum , Saccharum spontaneum , Saccharum sinense , Saccharum barberi , and Saccharum edule [ 8 ]. S. spontaneum is widely recognized as the most primitive species within the genus Saccharum , whereas S. robustum has been postulated to be the progenitor of the high sugar content species, S. officinarum [ 9 ].…”

Section: Introductionmentioning

confidence: 99%

An improved suppression subtractive hybridization technique to develop species-specific repetitive sequences from Erianthus arundinaceus (Saccharum complex)

et al. 2018

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BackgroundSugarcane has recently attracted increased attention for its potential as a source of bioethanol and methane. However, a narrow genetic base has limited germplasm enhancement of sugarcane. Erianthus arundinaceus is an important wild genetic resource that has many excellent traits for improving cultivated sugarcane via wide hybridization. Species-specific repetitive sequences are useful for identifying genome components and investigating chromosome inheritance in noblization between sugarcane and E. arundinaceus. Here, suppression subtractive hybridization (SSH) targeting E. arundinaceus-specific repetitive sequences was performed. The five critical components of the SSH reaction system, including enzyme digestion of genomic DNA (gDNA), adapters, digested gDNA concentrations, primer concentrations, and LA Taq polymerase concentrations, were improved using a stepwise optimization method to establish a SSH system suitable for obtaining E. arundinaceus-specific gDNA fragments.ResultsSpecificity of up to 85.42% was confirmed for the SSH method as measured by reverse dot blot (RDB) of an E. arundinaceus subtractive library. Furthermore, various repetitive sequences were obtained from the E. arundinaceus subtractive library via fluorescence in situ hybridization (FISH), including subtelomeric and centromeric regions. EaCEN2-166F/R and EaSUB1-127F/R primers were then designed as species-specific markers to accurately validate E. arundinaceus authenticity.ConclusionsThis is the first report that E. arundinaceus-specific repetitive sequences were obtained via an improved SSH method. These results suggested that this novel SSH system could facilitate screening of species-specific repetitive sequences for species identification and provide a basis for development of similar applications for other plant species.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1471-6) contains supplementary material, which is available to authorized users.

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“…Over the past two decades, molecular cytogenetics and markers have contributed to inference of the phylogenetic relationship of the species within the genus Saccharum [ 3 – 7 ], and therefore the classification of the species within this genus has gradually been elucidated. The currently accepted taxonomy for the genus Saccharum comprises six species, including Saccharum officinarum , Saccharum robustum , Saccharum spontaneum , Saccharum sinense , Saccharum barberi , and Saccharum edule [ 8 ]. Of these, S .…”

Section: Introductionmentioning

confidence: 99%

Comparative genetic analysis of the 45S rDNA intergenic spacers from three Saccharum species

Huang

Fan

et al. 2017

PLoS ONE

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The 45S ribosomal DNA (rDNA) units are separated by an intergenic spacer (IGS) containing the signals for transcription and processing of rRNAs. For the first time, we sequenced and analyzed the entire IGS region from three original species within the genus Saccharum, including S. spontaneum, S. robustum, and S. officinarum in this study. We have compared the IGS organization within three original species of the genus Saccharum. The IGS of these three original species showed similar overall organizations comprised of putative functional elements needed for rRNA gene activity as well as a non-transcribed spacer (NTS), a promoter region, and an external transcribed spacer (ETS). The variability in length of the IGS sequences was assessed at the individual, intraspecies, and interspecies levels of the genus Saccharum, including S. spontaneum, S. robustum, and S. officinarum. The ETS had greater similarity than the NTS across species, but nevertheless exhibited variation in length. Within the IGS of the Saccharum species, base substitutions and copy number variation of sub-repeat were causes of the divergence in IGS sequences. We also identified a significant number of methylation sites. Furthermore, fluorescent in situ hybridization (FISH) co-localization of IGS and pTa71 probes was detected on all representative species of the genus Saccharum tested. Taken together, the results of this study provide a better insight into the structure and organization of the IGS in the genus Saccharum.

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Differential detection of transposable elements between Saccharum species

Cited by 6 publications

References 27 publications

Changes on microsatellites of expressed sequence tag of sugarcane (Saccharum spp) during vegetative propagation

Changes on microsatellites of expressed sequence tag of sugarcane (Saccharum spp) during vegetative propagation

An improved suppression subtractive hybridization technique to develop species-specific repetitive sequences from Erianthus arundinaceus (Saccharum complex)

Comparative genetic analysis of the 45S rDNA intergenic spacers from three Saccharum species

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