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Heritability and Reversibility of DNA Methylation Induced by in vitro Grafting between Brassica juncea and B. oleracea

ABSTRACT: We found that compared with the expression of siRNAs in leaves of TTT, 3284, 4789, and 6208 unique siRNAs were significantly up-regulated, and 3420, 3850, and 4245 unique siRNAs were significantly down-regulated in GS1, GS3, and GS5, respectively through the high-throughput sequencing of small RNAs

OTHER RELATED OMICS DATASETS IN: PRJNA319668

ORGANISM(S): Brassica juncea Brassica juncea x Brassica oleracea

PROVIDER: GSE80684 | GEO | 2016/09/01

SECONDARY ACCESSION(S): PRJNA319668

REPOSITORIES: GEO

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Heritability and Reversibility of DNA Methylation Induced by in vitro Grafting between Brassica juncea and B. oleracea.

Project description:Grafting between tuber mustard and red cabbage produced a chimeric shoot apical meristem (SAM) of TTC, consisting of Layers I and II from Tuber mustard and Layer III from red Cabbage. Phenotypic variations, which mainly showed in leaf shape and SAM, were observed in selfed progenies GSn (GS = grafting-selfing, n = generations) of TTC. Here the heritability of phenotypic variation and its association with DNA methylation changes in GSn were investigated. Variation in leaf shape was found to be stably inherited to GS5, but SAM variation reverted over generations. Subsequent measurement of DNA methylation in GS1 revealed 5.29-6.59% methylation changes compared with tuber mustard (TTT), and 31.58% of these changes were stably transmitted to GS5, but the remainder reverted to the original status over generations, suggesting grafting-induced DNA methylation changes could be both heritable and reversible. Sequence analysis of differentially methylated fragments (DMFs) revealed methylation mainly changed within transposons and exon regions, which further affected the expression of genes, including flowering time- and gibberellin response-related genes. Interestingly, DMFs could match differentially expressed siRNA of GS1, GS3 and GS5, indicating that grafting-induced DNA methylation could be directed by siRNA changes. These results suggest grafting-induced DNA methylation may contribute to phenotypic variations induced by grafting.

| S-EPMC4891673 | biostudies-literature

Heritability and Reversibility of DNA Methylation Induced by in vitro Grafting between Brassica juncea and B. oleracea

Project description:Heritability and Reversibility of DNA Methylation Induced by in vitro Grafting between Brassica juncea and B. oleracea

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Brassica juncea, Brassica oleracea

Project description:Brassica juncea and B. oleracea Hybridization and Polyploidization Transcriptome

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Heritable variation and small RNAs in the progeny of chimeras of Brassica juncea and Brassica oleracea.

Project description:Chimeras have been used to study the transmission of genetic material and the resulting genetic variation. In this study, two chimeras, TCC and TTC (where the origin of the outer, middle, and inner cell layers, respectively, of the shoot apical meristem is designated by a 'T' for tuber mustard and 'C' for red cabbage), as well as their asexual and sexual progeny, were used to analyse the mechanism and the inheritance of the variation induced by grafting. Asexual TCC progeny were obtained by adventitious shoot regeneration, while TTC sexual progeny were produced by self-crossing. This study observed similar morphological variations in both the asexual and sexual progeny, including changes in leaf shape and the pattern of shoot apical meristem termination. The leaf shape variation was stable, while the rate of shoot apical meristem termination in the TTC progenies decreased from 74.52% to 3.01% after three successive rounds of self-crossing. Specific red cabbage small RNAs were found in the asexually regenerated plants (rTTT) that were not present in TTT, indicating that small RNAs might be transmitted from red cabbage to tuber mustard during grafting. Moreover, in parallel with the variations in phenotype observed in the progeny, some conserved miRNAs were differentially expressed in rTTT and TTT, which correlated with changes in expression of their target genes. These results suggest that the change in small RNA expression induced by grafting may be an important factor for introducing graft-induced genetic variations, providing a basis for further investigating the mechanism of graft-induced genetic variation through epigenetics.

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Transcriptome Analysis Between Green Cabbage (Brassica oleracea var. capitata) and Savoy Cabbage (Brassica oleracea var. sabauda)

Project description:We found several candidate genes might be involved in the crinkled leaf phenotype of savoy cabbage.

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Transcriptome sequencing of Brassica oleracea tissues

Project description:Deep sequencing of mRNA from seven different tissues of Brassica oleracea

2014-05-27 | GSE42891 | GEO

Transcriptome of Brassica juncea nectaries and leaves

Project description:Comparative RNA-Seq study of expression in B.juncea nectaries from different lines.

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Transcriptome sequencing of Brassica oleracea tissues

Project description:Deep sequencing of mRNA from seven different tissues of Brassica oleracea Analysis of ploy(A)+ RNA of multiple different tissues of Brassica oleracea containing Bud, Callus, Root, Stem, Leaf, Flower and Silique.

2014-05-27 | E-GEOD-42891 | biostudies-arrayexpress

Spontaneous gene flow from rapeseed (Brassica napus) to wild Brassica oleracea.

Project description:Research on the environmental risks of gene flow from genetically modified (GM) crops to wild relatives has traditionally emphasized recipients yielding most hybrids. For GM rapeseed (Brassica napus), interest has centred on the 'frequently hybridizing' Brassica rapa over relatives such as Brassica oleracea, where spontaneous hybrids are unreported in the wild. In two sites, where rapeseed and wild B. oleracea grow together, we used flow cytometry and crop-specific microsatellite markers to identify one triploid F1 hybrid, together with nine diploid and two near triploid introgressants. Given the newly discovered capacity for spontaneous introgression into B. oleracea, we then surveyed associated flora and fauna to evaluate the capacity of both recipients to harm cohabitant species with acknowledged conservational importance. Only B. oleracea occupies rich communities containing species afforded legislative protection; these include one rare micromoth species that feeds on B. oleracea and warrants further assessment. We conclude that increased attention should now focus on B. oleracea and similar species that yield few crop-hybrids, but possess scope to affect rare or endangered associates.

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The broccoli (Brassica oleracea) phloem tissue proteome.

Project description:BackgroundThe transport of sugars, hormones, amino acids, proteins, sugar alcohols, and other organic compounds from the sites of synthesis to the sites of use or storage occurs through the conducting cells of the phloem. To better understand these processes a comprehensive understanding of the proteins involved is required. While a considerable amount of data has been obtained from proteomic analyses of phloem sap, this has mainly served to identify the soluble proteins that are translocated through the phloem network.ResultsIn order to obtain more comprehensive proteomic data from phloem tissue we developed a simple dissection procedure to isolate phloem tissue from Brassica oleracea. The presence of a high density of phloem sieve elements was confirmed using light microscopy and fluorescently labeled sieve element-specific antibodies. To increase the depth of the proteomic analysis for membrane bound and associated proteins, soluble proteins were extracted first and subsequent extractions were carried out using two different detergents (SDS and CHAPSO). Across all three extractions almost four hundred proteins were identified and each extraction method added to the analysis demonstrating the utility of an approach combining several extraction protocols.ConclusionsThe phloem was found to be enriched in proteins associated with biotic and abiotic stress responses and structural proteins. Subsequent expression analysis identified a number of genes that appear to be expressed exclusively or at very high levels in phloem tissue, including genes that are known to express specifically in the phloem as well as novel phloem genes.

| S-EPMC3833381 | biostudies-literature

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