Modelling risk-based inspections in EU organic certification: data requirements and analysis tools

Abstrac

D6.7 Report on the experience of conducting the case studies

One of the main aims of the case studies was to publish improved market reports. The data collected as part of the six case studies have been, or will shortly be, published in the five improved national organic market reports and one first regional market report (MOAN case study). This will make a contribution towards filling the many gaps that continue to exist in organic market data collection in Europe

Increasing the source/sink ratio in Vitis vinifera (cv Sangiovese) induces extensive transcriptome reprogramming and modifies berry ripening

<p>Abstract</p> <p>Background</p> <p>Cluster thinning is an agronomic practice in which a proportion of berry clusters are removed from the vine to increase the source/sink ratio and improve the quality of the remaining berries. Until now no transcriptomic data have been reported describing the mechanisms that underlie the agronomic and biochemical effects of thinning.</p> <p>Results</p> <p>We profiled the transcriptome of <it>Vitis vinifera </it>cv. Sangiovese berries before and after thinning at veraison using a genome-wide microarray representing all grapevine genes listed in the latest V1 gene prediction. Thinning increased the source/sink ratio from 0.6 to 1.2 m²leaf area per kg of berries and boosted the sugar and anthocyanin content at harvest. Extensive transcriptome remodeling was observed in thinned vines 2 weeks after thinning and at ripening. This included the enhanced modulation of genes that are normally regulated during berry development and the induction of a large set of genes that are not usually expressed.</p> <p>Conclusion</p> <p>Cluster thinning has a profound effect on several important cellular processes and metabolic pathways including carbohydrate metabolism and the synthesis and transport of secondary products. The integrated agronomic, biochemical and transcriptomic data revealed that the positive impact of cluster thinning on final berry composition reflects a much more complex outcome than simply enhancing the normal ripening process.</p

Sugar and abscisic acid signaling orthologs are activated at the onset of ripening in grape

The onset of ripening involves changes in sugar metabolism, softening, and color development. Most understanding of this process arises from work in climacteric fruits where the control of ripening is predominately by ethylene. However, many fruits such as grape are nonclimacteric, where the onset of ripening results from the integration of multiple hormone signals including sugars and abscisic acid (ABA). In this study, we identified ten orthologous gene families in Vitis vinifera containing components of sugar and ABA-signaling pathways elucidated in model systems, including PP2C protein phosphatases, and WRKY and homeobox transcription factors. Gene expression was characterized in control- and deficit-irrigated, field-grown Cabernet Sauvignon. Sixty-seven orthologous genes were identified, and 38 of these were expressed in berries. Of the genes expressed in berries, 68% were differentially expressed across development and/or in response to water deficit. Orthologs of several families were induced at the onset of ripening, and induced earlier and to higher levels in response to water deficit; patterns of expression that correlate with sugar and ABA accumulation during ripening. Similar to field-grown berries, ripening phenomena were induced in immature berries when cultured with sucrose and ABA, as evidenced by changes in color, softening, and gene expression. Finally, exogenous sucrose and ABA regulated key orthologs in culture, similar to their regulation in the field. This study identifies novel candidates in the control of nonclimacteric fruit ripening and demonstrates that grape orthologs of key sugar and ABA-signaling components are regulated by sugar and ABA in fleshy fruit

Chemical PARP Inhibition Enhances Growth of Arabidopsis and Reduces Anthocyanin Accumulation and the Activation of Stress Protective Mechanisms

Poly-ADP-ribose polymerase (PARP) post-translationally modifies proteins through the addition of ADP-ribose polymers, yet its role in modulating plant development and stress responses is only poorly understood. The experiments presented here address some of the gaps in our understanding of its role in stress tolerance and thereby provide new insights into tolerance mechanisms and growth. Using a combination of chemical and genetic approaches, this study characterized phenotypes associated with PARP inhibition at the physiological level. Molecular analyses including gene expression analysis, measurement of primary metabolites and redox metabolites were used to understand the underlying processes. The analysis revealed that PARP inhibition represses anthocyanin and ascorbate accumulation under stress conditions. The reduction in defense is correlated with enhanced biomass production. Even in unstressed conditions protective genes and molecules are repressed by PARP inhibition. The reduced anthocyanin production was shown to be based on the repression of transcription of key regulatory and biosynthesis genes. PARP is a key factor for understanding growth and stress responses of plants. PARP inhibition allows plants to reduce protection such as anthocyanin, ascorbate or Non-Photochemical-Quenching whilst maintaining high energy levels likely enabling the observed enhancement of biomass production under stress, opening interesting perspectives for increasing crop productivity

Nitric Oxide Controls Constitutive Freezing Tolerance in Arabidopsis by Attenuating the Levels of Osmoprotectants, Stress-Related Hormones and Anthocyanins

[EN] Plant tolerance to freezing temperatures is governed by endogenous constitutive components and environmental inducing factors. Nitric oxide (NO) is one of the endogenous components that participate in freezing tolerance regulation. A combined metabolomic and transcriptomic characterization of NO-deficient nia1,2noa1¿2 mutant plants suggests that NO acts attenuating the production and accumulation of osmoprotective and regulatory metabolites, such as sugars and polyamines, stress-related hormones, such as ABA and jasmonates, and antioxidants, such as anthocyanins and flavonoids. Accordingly, NO-deficient plants are constitutively more freezing tolerant than wild type plants.This work was supported by grants BIO2011-27526 and BIO2014-56067-P from the Spanish Ministry of Economy and Competitiveness and FEDER funds. We thank support and comments from Janice Jones and Danny Alexander (Metabolon Inc., USA) on metabolomic analyses.Costa-Broseta, Á.; Perea-Resa, C.; Castillo López Del Toro, MC.; Ruíz, MF.; Salinas, J.; Leon Ramos, J. (2018). Nitric Oxide Controls Constitutive Freezing Tolerance in Arabidopsis by Attenuating the Levels of Osmoprotectants, Stress-Related Hormones and Anthocyanins. Scientific Reports. 8. https://doi.org/10.1038/s41598-018-27668-8S8Janská, A., Marsík, P., Zelenková, S. & Ovesná, J. Cold stress and acclimation - what is important for metabolic adjustment? Plant Biol (Stuttg) 12, 395–405 (2010).Eremina, M., Rozhon, W. & Poppenberger, B. Hormonal control of cold stress responses in plants. Cell Mol Life Sci 73, 797–810 (2016).Winkel-Shirley, B. Biosynthesis of flavonoids and effects of stress. Curr Opin Plant Biol 5, 218–223 (2002).Cuevas, J. C. et al. 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Alternative processing of its precursor is related to miR319 decreasing in melon plants exposed to cold

[EN] miRNAs are fundamental endogenous regulators of gene expression in higher organisms. miRNAs modulate multiple biological processes in plants. Consequently, miRNA accumulation is strictly controlled through miRNA precursor accumulation and processing. Members of the miRNA319 family are ancient ribo-regulators that are essential for plant development and stress responses and exhibit an unusual biogenesis that is characterized by multiple processing of their precursors. The significance of the high conservation of these non-canonical biogenesis pathways remains unknown. Here, we analyze data obtained by massive sRNA sequencing and 5 ' - RACE to explore the accumulation and infer the processing of members of the miR319 family in melon plants exposed to adverse environmental conditions. Sequence data showed that miR319c was down regulated in response to low temperature. However, the level of its precursor was increased by cold, indicating that miR319c accumulation is not related to the stem loop levels. Furthermore, we found that a decrease in miR319c was inversely correlated with the stable accumulation of an alternative miRNA (#miR319c) derived from multiple processing of the miR319c precursor. Interestingly, the alternative accumulation of miR319c and #miR319c was associated with an additional and non-canonical partial cleavage of the miR319c precursor during its loop-to-base-processing. Analysis of the transcriptional activity showed that miR319c negatively regulated the accumulation of HY5 via TCP2 in melon plants exposed to cold, supporting its involvement in the low temperature signaling pathway associated with anthocyanin biosynthesis. 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