Integrative transcriptomics reveals genotypic impact on sugar beet storability
Open Access
- 4 August 2020
- journal article
- research article
- Published by Springer Science and Business Media LLC in Plant Molecular Biology
- Vol. 104 (4-5), 359-378
- https://doi.org/10.1007/s11103-020-01041-8
Abstract
Key message An integrative comparative transcriptomic approach on six sugar beet varieties showing different amount of sucrose loss during storage revealed genotype-specific main driver genes and pathways characterizing storability. Abstract Sugar beet is next to sugar cane one of the most important sugar crops accounting for about 15% of the sucrose produced worldwide. Since its processing is increasingly centralized, storage of beet roots over an extended time has become necessary. Sucrose loss during storage is a major concern for the sugar industry because the accumulation of invert sugar and byproducts severely affect sucrose manufacturing. This loss is mainly due to ongoing respiration, but changes in cell wall composition and pathogen infestation also contribute. While some varieties can cope better during storage, the underlying molecular mechanisms are currently undiscovered. We applied integrative transcriptomics on six varieties exhibiting different levels of sucrose loss during storage. Already prior to storage, well storable varieties were characterized by a higher number of parenchyma cells, a smaller cell area, and a thinner periderm. Supporting these findings, transcriptomics identified changes in genes involved in cell wall modifications. After 13 weeks of storage, over 900 differentially expressed genes were detected between well and badly storable varieties, mainly in the category of defense response but also in carbohydrate metabolism and the phenylpropanoid pathway. These findings were confirmed by gene co-expression network analysis where hub genes were identified as main drivers of invert sugar accumulation and sucrose loss. Our data provide insight into transcriptional changes in sugar beet roots during storage resulting in the characterization of key pathways and hub genes that might be further used as markers to improve pathogen resistance and storage properties.Keywords
Funding Information
- Österreichische Forschungsförderungsgesellschaft (855706)
This publication has 118 references indexed in Scilit:
- Pathview: an R/Bioconductor package for pathway-based data integration and visualizationBioinformatics, 2013
- Functional Characterization of CEBiP and CERK1 Homologs in Arabidopsis and Rice Reveals the Presence of Different Chitin Receptor Systems in PlantsPlant and Cell Physiology, 2012
- Full-length transcriptome assembly from RNA-Seq data without a reference genomeNature Biotechnology, 2011
- Chalcone synthase and its functions in plant resistancePhytochemistry Reviews, 2011
- Uncoupling of sustained MAMP receptor signaling from early outputs in an Arabidopsis endoplasmic reticulum glucosidase II alleleProceedings of the National Academy of Sciences of the United States of America, 2009
- Establishment of the Winter-Annual Growth Habit viaFRIGIDA-Mediated Histone Methylation atFLOWERING LOCUS CinArabidopsisTHE PLANT CELL ONLINE, 2009
- A homolog of human ski-interacting protein in rice positively regulates cell viability and stress toleranceProceedings of the National Academy of Sciences of the United States of America, 2009
- Xyloglucan Endotransglucosylase Activity Loosens a Plant Cell WallAnnals of Botany, 2007
- Arabidopsis RIN4 Is a Target of the Type III Virulence Effector AvrRpt2 and Modulates RPS2-Mediated ResistanceCell, 2003
- How to measure and predict the molar absorption coefficient of a proteinProtein Science, 1995