Background Root restriction is a physical and ecological cultivation mode which restricts plant roots into a limited container to regulate vegetative and reproduction growth by reshaping root architecture. However, little is known about related molecular mechanisms. To uncover the root-related regulatory network of endogenous RNAs under root restriction, transcriptome-wide analyses of mRNAs, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) involved in root development was performed. Results In this study, a total of 26588 mRNAs, 1971 lncRNAs and 2615 circRNAs were identified in root of annual ‘Muscat Hamburg’ grapevine by the next generation sequencing, respectively. The expression profile of mRNAs, lncRNAs and circRNA were further confirmed by the quantitative real-time PCR (qRT-PCR). Gene ontology enrichment analysis showed that a majority of the differentially expressed mRNAs, lncRNAs and circRNAs were annotated to the categories of cellular process, metabolic process, cell part, binding and catalytic activity. In addition, the regulatory network of endogenous RNAs was then constructed by the prediction of lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA, implying that these RNAs play significant regulatory roles for root architecture shaping in response to root restriction. Conclusion Our results, for the first time, integrated the regulatory network of competitive endogenous RNAs (ceRNAs) functions of lncRNA and circRNA, and provided a basis for studying the potential functions of non-coding RNAs during root development of grapevine.

Aneuploid ermpglasm is an important resource for genetic studies and identification of individual chromosomes in the cells of the aneuploid is an important step. The karyotype has already been established for purple coneflower (Echinacea purpurea L.), but due to the high similarity in the morphology of several pairs of chromosomes in this species, it cannot be used to identify individual chromosomes in its own complement. The objectives of this study are to develop and evaluate the Giemsa C-banding technique for the purpose of identifying the individual chromosomes in Echinacea purpurea. The established karyotype with C-bands showed that all the 11 pairs of chromosomes possessed centromeric bands. Telomeric bands appeared most frequently in almost all the chromosomes with only two exceptions, the short arm of the chromosome 9 and the long arm of the chromosome 10. Intercalary bands were found mainly in the long arm of some chromosomes with only two exceptions, the chromosomes 1 and 2 that had intercalary bands on both arms. The chromosome 4 was the only chromosome where intercalary bands were absent. Chromosomes in E. purpurea could be stained with Giemsa to bear C-bands. By classifying the chromosomes into groups and judging the C-bands, each chromosome could be identified. The methods established in this study might be used for the identification of chromosome constitution in aneuploid E. purpurea created in a breeding program.