Special issue of Organic Agriculture — Organic 3.0

It is an honor to be able to present this special issue of Organic Agriculture: Organic 3.0 for the Organic World Congress in India 2017. In this issue, we have collected a number of papers relevant for the theme Organic 3.0. This special issue of Organic Agriculture about Organic 3.0 is published in connection to the science track “Innovative research for Organic 3.0” at the Organic World Congress in Delhi, India, November 2017. In the foreword to the proceedings (Rahmann et al. 2017), the challenges listed correspond well to those described and discussed in these five papers. The fact that the paper by Rahmann et al. (2016) that has been online in Organic Agriculture since December 2016, already after 6 months has been downloaded more than 3,000 times shows the great interest in this subject. Together, these papers give a valuable basis for the further discussion of Organic 3.0 and the future development for the organic sector and beyond. Organic agriculture—whether 2.0 or 3.0—can be one option to solve future problems, and the ideas behind organic agriculture should be integrated as much as possible in many types of agriculture: agroecological, small-holder, conventional, conservation tillage, etc. But organic agriculture should also learn from conventional and other types of agriculture and if necessary take a critical view on, e.g., minimum requirements that result in negative effects on public goods. Governments, NGO’s, farmers, researchers, and other stakeholders should all contribute to developing organic as well as other forms of agriculture. It is our hope that this special issue will be one step in bringing organic and truly sustainable agriculture forward

Variation in flavonoids in a collection of peppers (Capsicum sp.) under organic and conventional cultivation: effect of the genotype, ripening stage, and growing system

This is the peer reviewed version of the following article: Ribes-Moya, A.M., Adalid, A.M., Raigón, M.D., Hellín, P., Fita, A. and Rodríguez-Burruezo, A. (2020), Variation in flavonoids in a collection of peppers (Capsicum sp.) under organic and conventional cultivation: effect of the genotype, ripening stage, and growing system. J Sci Food Agric, 100: 2208-2223, which has been published in final form at https://doi.org/10.1002/jsfa.10245. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.[EN] BACKGROUND In recent years, the acreage used for organic agriculture and the demand for organic fruit and vegetables have increased considerably. Given this scenario, landraces, such as Capsicum landraces, can provide valuable germplasm. Capsicum peppers are very interesting because of their high phenolic content, and particularly their flavonoid content, which provides a high added value. Moreover, the broad genetic diversity in local varieties expands the opportunities for adaptation to organic production and for exploiting genotype x environment interactions to select peppers with the highest phenolic content. RESULTS In this work, the main flavonoids of peppers were exhaustively evaluated over 2 years in a wide collection of heirlooms, both unripe and fully ripe, under organic and conventional cultivation. The genotype and ripening stage contributed to a high degree to the variation in flavonoids. The growing system influenced this variation to a lesser extent. Luteolin and quercetin showed the highest contributions to total phenolic content (70% and > 20%, respectively) at both ripening stages, while myricetin, apigenin, and kaempferol showed lower contributrions. The average flavonoid content was higher in ripe fruits, and organic management significantly increased the accumulation of total flavonoids and luteolin. Positive correlations between flavonoids were found at both ripening stages, especially between main flavonoids luteolin and quercetin and between kaempferol and quercetin (rho > 0.7). CONCLUSION Genotype x environment interaction enabled the identification of accessions with high flavonoid content grown under organic conditions at both ripening stages, particularly total flavonoids and luteolin at the fully ripe stage. Our results reinforce the importance of a wide genetic variation and of considering different ripening stages and growing conditions for breeding high-quality peppers.This work has been funded by the Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA) project RTA2014-00041-C02-02, Fondo Europeo de Desarrollo Regional (FEDER) funds. A.M. Ribes-Moya expresses her gratitude to the Universitat Politecnica de Valencia (UPV) for her scholarship FPI-UPV-2017 (PAID-01-17). The authors also thank the farmers' association Unio de Llauradors i Ramaders (LA UNI) for the arrangement and management of fields - specifically Manuel Figueroa, Rafael Hurtado, Ricard Ballester, and Antonio Munoz, and seed providers P.W. Bosland, S. Lanteri, Francois Jourdan, Santiago Larregla, and the Regulatory Boards of the PDOs and PGIs included in this work. The authors are also grateful for the support of Professor Jaime Prohens with statistical methods.Ribes Moya, AM.; Adalid-Martinez, AM.; Raigón Jiménez, MD.; Hellín, P.; Fita, A.; Rodríguez Burruezo, A. (2020). Variation in flavonoids in a collection of peppers (Capsicum sp.) under organic and conventional cultivation: effect of the genotype, ripening stage, and growing system. Journal of the Science of Food and Agriculture. 100(5):2208-2223. https://doi.org/10.1002/jsfa.10245S220822231005WillerH European organic market grew by double digits and organic area reached 13.5 million hectares in2016 [Online]. FiBL‐Media release (2018). Available:https://www.fibl.org/en/media/media-archive/media-archive18/media-release18/article/bio-in-europa-legt-weiter-zu-biomarkt-waechst-zweistellig-bioflaeche-steigt-auf-fast-14-millionen-h.html[8 August 2019]BENGTSSON, J., AHNSTRÖM, J., & WEIBULL, A.-C. (2005). The effects of organic agriculture on biodiversity and abundance: a meta-analysis. Journal of Applied Ecology, 42(2), 261-269. doi:10.1111/j.1365-2664.2005.01005.xHunter, D., Foster, M., McArthur, J. O., Ojha, R., Petocz, P., & Samman, S. (2011). Evaluation of the Micronutrient Composition of Plant Foods Produced by Organic and Conventional Agricultural Methods. Critical Reviews in Food Science and Nutrition, 51(6), 571-582. doi:10.1080/10408391003721701Fita, A., Rodríguez-Burruezo, A., Boscaiu, M., Prohens, J., & Vicente, O. (2015). Breeding and Domesticating Crops Adapted to Drought and Salinity: A New Paradigm for Increasing Food Production. Frontiers in Plant Science, 6. doi:10.3389/fpls.2015.00978FAOSTAT Data[Online]. FAOSTAT (2019). Available:http://www.fao.org/faostat/en/#data/QC[17 January 2019]Denominaciones de Origen e Indicaciones Geográficas Protegidas. [Online]. MAPAMA. (2019). Available:https://www.mapa.gob.es/es/alimentacion/temas/calidad-agroalimentaria/calidad-diferenciada/dop/default.aspx[6 February 2019]Hill, T. A., Ashrafi, H., Reyes-Chin-Wo, S., Yao, J., Stoffel, K., Truco, M.-J., … Van Deynze, A. (2013). Characterization of Capsicum annuum Genetic Diversity and Population Structure Based on Parallel Polymorphism Discovery with a 30K Unigene Pepper GeneChip. PLoS ONE, 8(2), e56200. doi:10.1371/journal.pone.0056200Kumar, S., Kumar, R., & Singh, J. (2006). Cayenne/American pepper. Handbook of Herbs and Spices, 299-312. doi:10.1533/9781845691717.3.299Bosland, P. W., & Votava, E. J. (Eds.). (2012). Peppers: vegetable and spice capsicums. doi:10.1079/9781845938253.0000Pellegrini, N., Serafini, M., Colombi, B., Del Rio, D., Salvatore, S., Bianchi, M., & Brighenti, F. (2003). Total Antioxidant Capacity of Plant Foods, Beverages and Oils Consumed in Italy Assessed by Three Different In Vitro Assays. The Journal of Nutrition, 133(9), 2812-2819. doi:10.1093/jn/133.9.2812Zimmer, A. R., Leonardi, B., Miron, D., Schapoval, E., Oliveira, J. R. de, & Gosmann, G. (2012). Antioxidant and anti-inflammatory properties of Capsicum baccatum: From traditional use to scientific approach. Journal of Ethnopharmacology, 139(1), 228-233. doi:10.1016/j.jep.2011.11.005Morales-Soto, A., García-Salas, P., Rodríguez-Pérez, C., Jiménez-Sánchez, C., Cádiz-Gurrea, M. de la L., Segura-Carretero, A., & Fernández-Gutiérrez, A. (2014). Antioxidant capacity of 44 cultivars of fruits and vegetables grown in Andalusia (Spain). Food Research International, 58, 35-46. doi:10.1016/j.foodres.2014.01.050BHATTACHARYA, A., SOOD, P., & CITOVSKY, V. (2010). The roles of plant phenolics in defence and communication during Agrobacterium and Rhizobium infection. Molecular Plant Pathology, no-no. doi:10.1111/j.1364-3703.2010.00625.xBlum, U., Shafer, S. R., & Lehman, M. E. (1999). Evidence for Inhibitory Allelopathic Interactions Involving Phenolic Acids in Field Soils: Concepts vs. an Experimental Model. Critical Reviews in Plant Sciences, 18(5), 673-693. doi:10.1080/07352689991309441Alasalvar, C., Grigor, J. M., Zhang, D., Quantick, P. C., & Shahidi, F. (2001). Comparison of Volatiles, Phenolics, Sugars, Antioxidant Vitamins, and Sensory Quality of Different Colored Carrot Varieties. Journal of Agricultural and Food Chemistry, 49(3), 1410-1416. doi:10.1021/jf000595hRomero, N., Saavedra, J., Tapia, F., Sepúlveda, B., & Aparicio, R. (2015). Influence of agroclimatic parameters on phenolic and volatile compounds of Chilean virgin olive oils and characterization based on geographical origin, cultivar and ripening stage. Journal of the Science of Food and Agriculture, 96(2), 583-592. doi:10.1002/jsfa.7127Ferrer-Gallego, R., Hernández-Hierro, J. M., Rivas-Gonzalo, J. C., & Escribano-Bailón, M. T. (2012). Influence of climatic conditions on the phenolic composition of Vitis vinifera L. cv. Graciano. Analytica Chimica Acta, 732, 73-77. doi:10.1016/j.aca.2011.12.072Tomás-Barberán, F. A., & Espín, J. C. (2001). Phenolic compounds and related enzymes as determinants of quality in fruits and vegetables. Journal of the Science of Food and Agriculture, 81(9), 853-876. doi:10.1002/jsfa.885Sun, J., Chu, Y.-F., Wu, X., & Liu, R. H. (2002). Antioxidant and Antiproliferative Activities of Common Fruits. Journal of Agricultural and Food Chemistry, 50(25), 7449-7454. doi:10.1021/jf0207530Sala, A., Recio, M. del C., Giner, R. M., Máñez, S., Tournier, H., Schinella, G., & Ríos, J.-L. (2002). Anti-inflammatory and antioxidant properties of Helichrysum italicum. Journal of Pharmacy and Pharmacology, 54(3), 365-371. doi:10.1211/0022357021778600Cai, Y., Luo, Q., Sun, M., & Corke, H. (2004). Antioxidant activity and phenolic compounds of 112 traditional Chinese medicinal plants associated with anticancer. Life Sciences, 74(17), 2157-2184. doi:10.1016/j.lfs.2003.09.047WOJDYLO, A., OSZMIANSKI, J., & CZEMERYS, R. (2007). Antioxidant activity and phenolic compounds in 32 selected herbs. Food Chemistry, 105(3), 940-949. doi:10.1016/j.foodchem.2007.04.038Bae, H., Jayaprakasha, G. K., Jifon, J., & Patil, B. S. (2012). Extraction efficiency and validation of an HPLC method for flavonoid analysis in peppers. Food Chemistry, 130(3), 751-758. doi:10.1016/j.foodchem.2011.07.041Jeong, W. Y., Jin, J. S., Cho, Y. A., Lee, J. H., Park, S., Jeong, S. W., … Shin, S. C. (2011). Determination of polyphenols in three Capsicum annuum L. (bell pepper) varieties using high-performance liquid chromatography-tandem mass spectrometry: Their contribution to overall antioxidant and anticancer activity. Journal of Separation Science, 34(21), 2967-2974. doi:10.1002/jssc.201100524Materska, M. (2014). Bioactive phenolics of fresh and freeze-dried sweet and semi-spicy pepper fruits (Capsicum annuum L.). Journal of Functional Foods, 7, 269-277. doi:10.1016/j.jff.2014.02.002Plazas, M., Prohens, J., Cuñat, A., Vilanova, S., Gramazio, P., Herraiz, F., & Andújar, I. (2014). Reducing Capacity, Chlorogenic Acid Content and Biological Activity in a Collection of Scarlet (Solanum aethiopicum) and Gboma (S. macrocarpon) Eggplants. International Journal of Molecular Sciences, 15(10), 17221-17241. doi:10.3390/ijms151017221Wickham, H. (2011). ggplot2. Wiley Interdisciplinary Reviews: Computational Statistics, 3(2), 180-185. doi:10.1002/wics.147Ribes-Moya, A. M., Raigón, M. D., Moreno-Peris, E., Fita, A., & Rodríguez-Burruezo, A. (2018). Response to organic cultivation of heirloom Capsicum peppers: Variation in the level of bioactive compounds and effect of ripening. PLOS ONE, 13(11), e0207888. doi:10.1371/journal.pone.0207888Rodríguez-Burruezo, A., Prohens, J., & Nuez, F. (2002). Genetic Analysis of Quantitative Traits in Pepino (Solanum muricatum) in Two Growing Seasons. Journal of the American Society for Horticultural Science, 127(2), 271-278. doi:10.21273/jashs.127.2.271Metsalu, T., & Vilo, J. (2015). ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap. Nucleic Acids Research, 43(W1), W566-W570. doi:10.1093/nar/gkv468Bhandari, S. R., Jung, B.-D., Baek, H.-Y., & Lee, Y.-S. (2013). Ripening-dependent Changes in Phytonutrients and Antioxidant Activity of Red Pepper (Capsicum annuum L.) Fruits Cultivated under Open-field Conditions. HortScience, 48(10), 1275-1282. doi:10.21273/hortsci.48.10.1275Howard, L. R., Talcott, S. T., Brenes, C. H., & Villalon, B. (2000). Changes in Phytochemical and Antioxidant Activity of Selected Pepper Cultivars (Capsicum Species) As Influenced by Maturity. Journal of Agricultural and Food Chemistry, 48(5), 1713-1720. doi:10.1021/jf990916tBae, H., Jayaprakasha, G. K., Crosby, K., Yoo, K. S., Leskovar, D. I., Jifon, J., & Patil, B. S. (2014). Ascorbic acid, capsaicinoid, and flavonoid aglycone concentrations as a function of fruit maturity stage in greenhouse-grown peppers. Journal of Food Composition and Analysis, 33(2), 195-202. doi:10.1016/j.jfca.2013.11.009Ghasemnezhad, M., Sherafati, M., & Payvast, G. A. (2011). Variation in phenolic compounds, ascorbic acid and antioxidant activity of five coloured bell pepper (Capsicum annum) fruits at two different harvest times. Journal of Functional Foods, 3(1), 44-49. doi:10.1016/j.jff.2011.02.002Hallmann, E., & Rembiałkowska, E. (2012). Characterisation of antioxidant compounds in sweet bell pepper (Capsicum annuum L.) under organic and conventional growing systems. Journal of the Science of Food and Agriculture, 92(12), 2409-2415. doi:10.1002/jsfa.5624Slimestad, R., & Verheul, M. (2009). Review of flavonoids and other phenolics from fruits of different tomato (Lycopersicon esculentum Mill.) cultivars. Journal of the Science of Food and Agriculture, 89(8), 1255-1270. doi:10.1002/jsfa.3605NAVARRO, J., FLORES, P., GARRIDO, C., & MARTINEZ, V. (2006). Changes in the contents of antioxidant compounds in pepper fruits at different ripening stages, as affected by salinity. Food Chemistry, 96(1), 66-73. doi:10.1016/j.foodchem.2005.01.057Martí, M. C., Camejo, D., Vallejo, F., Romojaro, F., Bacarizo, S., Palma, J. M., … Jiménez, A. (2011). Influence of Fruit Ripening Stage and Harvest Period on the Antioxidant Content of Sweet Pepper Cultivars. Plant Foods for Human Nutrition, 66(4), 416-423. doi:10.1007/s11130-011-0249-xLEE, Y., HOWARD, L. ., & VILLALÓN, B. (1995). Flavonoids and Antioxidant Activity of Fresh Pepper (Capsicum annuum) Cultivars. Journal of Food Science, 60(3), 473-476. doi:10.1111/j.1365-2621.1995.tb09806.xSerrano, M., Zapata, P. J., Castillo, S., Guillén, F., Martínez-Romero, D., & Valero, D. (2010). Antioxidant and nutritive constituents during sweet pepper development and ripening are enhanced by nitrophenolate treatments. Food Chemistry, 118(3), 497-503. doi:10.1016/j.foodchem.2009.05.006Pérez-López, A. J., del Amor, F. M., Serrano-Martínez, A., Fortea, M. I., & Núñez-Delicado, E. (2007). Influence of agricultural practices on the quality of sweet pepper fruits as affected by the maturity stage. Journal of the Science of Food and Agriculture, 87(11), 2075-2080. doi:10.1002/jsfa.2966Kim, J. K., Lee, S. Y., Chu, S. M., Lim, S. H., Suh, S.-C., Lee, Y.-T., … Ha, S.-H. (2010). Variation and Correlation Analysis of Flavonoids and Carotenoids in Korean Pigmented Rice (Oryza sativa L.) Cultivars. Journal of Agricultural and Food Chemistry, 58(24), 12804-12809. doi:10.1021/jf103277gMoriguchi, T., Kita, M., Tomono, Y., Endo-Inagaki, T., & Omura, M. (2001). Gene expression in flavonoid biosynthesis: Correlation with flavonoid accumulation in developing citrus fruit. Physiologia Plantarum, 111(1), 66-74. doi:10.1034/j.1399-3054.2001.1110109.

Finding Nested Common Intervals Efficiently

International audienceIn this paper, we study the problem of effi ciently fi nding gene clusters formalized by nested common intervals between two genomes represented either as permutations or as sequences. Considering permutations, we give several algorithms whose running time depends on the size of the actual output rather than the output in the worst case. Indeed, we first provide a straightforward O(n^3) time algorithm for finding all nested common intervals. We reduce this complexity by providing an O(n^2) time algorithm computing an irredundant output. Finally, we show, by providing a third algorithm, that fi nding only the maximal nested common intervals can be done in linear time. Considering sequences, we provide solutions (modi cations of previously de ned algorithms and a new algorithm) for di fferent variants of the problem, depending on the treatment one wants to apply to duplicated genes

Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms

Baumbach J, Rahmann S, Tauch A. Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms. BMC Systems Biology. 2009;3(1):8.Background: Transcriptional regulation of gene activity is essential for any living organism. Transcription factors therefore recognize specific binding sites within the DNA to regulate the expression of particular target genes. The genome-scale reconstruction of the emerging regulatory networks is important for biotechnology and human medicine but cost-intensive, time-consuming, and impossible to perform for any species separately. By using bioinformatics methods one can partially transfer networks from well-studied model organisms to closely related species. However, the prediction quality is limited by the low level of evolutionary conservation of the transcription factor binding sites, even within organisms of the same genus. Results: Here we present an integrated bioinformatics workflow that assures the reliability of transferred gene regulatory networks. Our approach combines three methods that can be applied on a large-scale: re-assessment of annotated binding sites, subsequent binding site prediction, and homology detection. A gene regulatory interaction is considered to be conserved if (1) the transcription factor, (2) the adjusted binding site, and (3) the target gene are conserved. The power of the approach is demonstrated by transferring gene regulations from the model organism Corynebacterium glutamicum to the human pathogens C. diphtheriae, C. jeikeium, and the biotechnologically relevant C. efficiens. For these three organisms we identified reliable transcriptional regulations for similar to 40% of the common transcription factors, compared to similar to 5% for which knowledge was available before. Conclusion: Our results suggest that trustworthy genome-scale transfer of gene regulatory networks between organisms is feasible in general but still limited by the level of evolutionary conservation

Ganzheitliche Untersuchungsmethoden zur Erfassung und Prüfung der Qualität ökologischer Lebensmittel: Stand der Entwicklung und Validierung

In dem wachsenden Markt ökologischer Lebensmittel werden Methoden zur produktorientierten Qualitätserfassung gefordert. Dabei geht es u.a. um die Unterscheidung von Produkten aus unterschiedlichen Anbauverfahren. Die Ziele des Projektes waren daher: 1. ausgewählte ganzheitliche Methoden gemäß ISO 17025 zu validieren, d.h. Laborprozesse festzulegen, sowie Einflussgrößen und Verfahrensmerkmale zu bestimmen, 2. zu testen, ob diese Verfahren eine Differenzierung von definierten Proben statistisch abgesichert zeigen können. . Diese Ziele konnten erreicht werden. Es wurde bestätigt, dass einige der Methoden auf Grundlage dokumentierter Prozeduren Lebensmittel aus definierten Anbauversuchen (u.a. aus dem DOK-Versuch am FIBL/CH) reproduzierbar unterscheiden können. Die Koordination und die Validierung der Kupferchlorid-Kristallisation sowie die Messung der Polyphenole lag bei der Universität Kassel, FG Ökologische Lebensmittelqualität und Ernährungskultur. Die KWALIS GmbH, Dipperz, validierte die Fluoreszenz-Anregungsspektroskopie und die Bestimmung des Physiologischen Aminosäurestatus, die EQC GmbH, Weidenbach die elektrochemischen Messungen. Dr. Kromidas, Saarbrücken übernahm die Beratung der Validierungsprozeduren. . An Blindproben wurde untersucht, ob die Verfahren für Weizen- und Möhrenproben aus definierten Anbau- und Sortenversuchen geeignet sind (Fragestellung der Validierung). Die Proben wurden von unabhängiger Stelle (OEL-FAL, Trenthorst) codiert. Die Proben wurden gleichzeitig an alle Partner versandt; dadurch konnten die Methoden auch untereinander verglichen werden. Die Methoden Kupferchlorid-Kristallisation, Fluoreszenz-Anregungsspektroskopie und Physiologischer Aminosäurestatus sind für die Fragestellung geeignet. Mit allen drei Methoden konnten die Proben differenziert und gruppiert werden. Darüber hinaus konnten mit der Fluoreszenz-Anregungsspektroskopie und über den physiologischen Aminosäurestatus die Proben auch den Anbauweisen richtig zugeordnet werden. Allerdings ist damit noch keine Aussage über die Fähigkeit dieser Verfahren möglich, generell Proben aus ökologischer und konventioneller Herkunft zu unterscheiden. Dafür sind weitere Untersuchungen sowohl an Proben definierter Herkunft als auch an Marktproben notwendig

Nanoscale transient magnetization gratings excited and probed by femtosecond extreme ultraviolet pulses

We utilize coherent femtosecond extreme ultraviolet (EUV) pulses derived from a free electron laser (FEL) to generate transient periodic magnetization patterns with periods as short as 44 nm. Combining spatially periodic excitation with resonant probing at the dichroic M-edge of cobalt allows us to create and probe transient gratings of electronic and magnetic excitations in a CoGd alloy. In a demagnetized sample, we observe an electronic excitation with 50 fs rise time close to the FEL pulse duration and ~0.5 ps decay time within the range for the electron-phonon relaxation in metals. When the experiment is performed on a sample magnetized to saturation in an external field, we observe a magnetization grating, which appears on a sub-picosecond time scale as the sample is demagnetized at the maxima of the EUV intensity and then decays on the time scale of tens of picoseconds via thermal diffusion. The described approach opens prospects for studying dynamics of ultrafast magnetic phenomena on nanometer length scales