Detection of honey adulteration by conventional and real-time PCR

[EN] This work applies both conventional and real-time PCR DNA amplification techniques for detecting and quantifying rice molasses in honey. Different levels of adulteration were simulated (1, 2, 5, 10, 20, 50%) using commercial rice molasses. Among the different specific genes of rice tested by PCR, the PLD1 primer was the most effective. This allowed the visualization in agarose gel of this type of adulterant up to 5-20%. Moreover, by means of real-time PCR it was possible to distinguish the different levels of rice DNA, and therefore the percentage of adulteration (1-50%). A standard curve built with the DNA serial dilutions of rice genomic DNA concentrations showed that the quantification level was between 2-5%. These results offer compelling evidence that DNA techniques could be useful not only for the detection of adulterations of honey with rice molasses but also for the quantification of levels lower than those of conventional techniques.This study is part of part of the projects funded by the "Agencia Estatal de Investigacion" (AGL2016-77702-R) and by the "Generalitat Valenciana" (AICO/2015/104) of Spain, for which the authors are grateful.Sobrino-Gregorio, L.; Vilanova Navarro, S.; Prohens Tomás, J.; Escriche Roberto, MI. (2019). Detection of honey adulteration by conventional and real-time PCR. Food Control. 95:57-62. https://doi.org/10.1016/j.foodcont.2018.07.037S57629

HS-SPME analysis of the volatiles profile of water celery (Apium nodiflorum), a wild vegetable with increasing culinary interest

[EN] Water celery (Apium nodiflorum) is a wild plant traditionally harvested in some Mediterranean areas for being consumed raw. Despite its appreciated organoleptic properties, the aromatic profile of the fresh vegetable remains to be studied. In the present study, volatile compounds from five wild populations were extracted by the headspace-solid phase microextraction technique, analysed by gas cromatography-mass spectrometry, and compared to related crops. The wild species had a high number of aromatic compounds. It was rich in monoterpenes (49.2%), sesquiterpenes (39.4%) and phenylpropanoids (9.6%), with quantitative differences among populations, in absolute terms and relative abundance. On average, germacrene D was the main compound (16.6%), followed by allo-ocimene (11.9%) and limonene (11.1%). Only in one population, the levels of limonene were greater than those of germacrene D. Among phenylpropanoids, dillapiol displayed the highest levels, and co-occurred with myristicin in all populations except one. These differences may have a genetic component, which would indicate the possibility of establishing selection programmes for the development of water celery as a crop adapted to different market preferences. On the other hand, comparison with related crops revealed some similarities among individual volatiles present in the different crops, which would be responsible of the common aroma notes. However, water celery displayed a unique profile, which was in addition quantitatively richer than others. Thus, this differentiation may promote the use of water celery as a new crop.C. Guijarro-Real thanks the Ministerio de Educacion, Cultura y Deporte of Spain (MECD) for the financial support with a predoctoral FPU grant (FPU14-06798). Authors also thank Manuel Figueroa for his unvaluable ethnobotanical knowledge and advice, as well as his support in the survey of water celery in the Horta Nord shireGuijarro-Real, C.; Rodríguez Burruezo, A.; Prohens Tomás, J.; Raigón Jiménez, MD.; Fita, A. (2019). HS-SPME analysis of the volatiles profile of water celery (Apium nodiflorum), a wild vegetable with increasing culinary interest. Food Research International. 121:765-775. https://doi.org/10.1016/j.foodres.2018.12.05476577512

The Use of Proline in Screening for Tolerance to Drought and Salinity in Common Bean (Phaseolus vulgaris L.) Genotypes

[EN] The selection of stress-resistant cultivars, to be used in breeding programmes aimed at enhancing the drought and salt tolerance of our major crops, is an urgent need for agriculture in a climate change scenario. In the present study, the responses to water deficit and salt stress treatments, regarding growth inhibition and leaf proline (Pro) contents, were analysed in 47 Phaseolus vulgaris genotypes of di erent origins. A two-way analysis of variance (ANOVA), Pearson moment correlations and principal component analyses (PCAs) were performed on all measured traits, to assess the general responses to stress of the investigated genotypes. For most analysed growth variables and Pro, the e ects of cultivar, treatment and their interactions were highly significant (p Phaseolus (Leguminosae): A Recent Diversification in an Ancient Landscape. Systematic Botany, 31(4), 779-791. doi:10.1600/036364406779695960Broughton, W. J., Hernández, G., Blair, M., Beebe, S., Gepts, P., & Vanderleyden, J. (2003). Beans (Phaseolus spp.) – model food legumes. Plant and Soil, 252(1), 55-128. doi:10.1023/a:1024146710611Rendón-Anaya, M., Montero-Vargas, J. M., Saburido-Álvarez, S., Vlasova, A., Capella-Gutierrez, S., Ordaz-Ortiz, J. J., … Herrera-Estrella, A. (2017). Genomic history of the origin and domestication of common bean unveils its closest sister species. Genome Biology, 18(1). doi:10.1186/s13059-017-1190-6Berglund-Brücher, O., & Brücher, H. (1976). The south American wild bean (Phaseolus aborigineus Burk.) as ancestor of the common bean. Economic Botany, 30(3), 257-272. doi:10.1007/bf02909734Arteaga, S., Yabor, L., Torres, J., Solbes, E., Muñoz, E., Díez, M. J., … Boscaiu, M. (2019). Morphological and Agronomic Characterization of Spanish Landraces of Phaseolus vulgaris L. Agriculture, 9(7), 149. doi:10.3390/agriculture9070149Molina, J. C., Moda-Cirino, V., Fonseca Júnior, N. S., Faria, R. T., & Destro, D. (2001). Response of Common Bean Cultivars and Lines to Water Stress. Cropp Breeding and Applied Biotechnology, 1(4), 363-372. doi:10.13082/1984-7033.v01n04a05Graham, P. H., & Ranalli, P. (1997). Common bean (Phaseolus vulgaris L.). Field Crops Research, 53(1-3), 131-146. doi:10.1016/s0378-4290(97)00112-3Singh, S. P. (2007). Drought Resistance in the Race Durango Dry Bean Landraces and Cultivars. Agronomy Journal, 99(5), 1219-1225. doi:10.2134/agronj2006.0301CUELLAR-ORTIZ, S. M., DE LA PAZ ARRIETA-MONTIEL, M., ACOSTA-GALLEGOS, J., & COVARRUBIAS, A. A. (2008). Relationship between carbohydrate partitioning and drought resistance in common bean. Plant, Cell & Environment, 31(10), 1399-1409. doi:10.1111/j.1365-3040.2008.01853.xMaas, E. V., & Hoffman, G. J. (1977). Crop Salt Tolerance—Current Assessment. Journal of the Irrigation and Drainage Division, 103(2), 115-134. doi:10.1061/jrcea4.0001137Zhumabayeva, B. A., Aytasheva, Z. G., Dzhangalina, E. D., Esen, A., … Lebedeva, L. P. (2019). Screening of domestic common bean cultivar for salt tolerance during in vitro cell cultivation. International Journal of Biology and Chemistry, 12(1), 94-102. doi:10.26577/ijbch-2019-1-i12Fess, T. L., Kotcon, J. B., & Benedito, V. A. (2011). Crop Breeding for Low Input Agriculture: A Sustainable Response to Feed a Growing World Population. Sustainability, 3(10), 1742-1772. doi:10.3390/su3101742Hurtado, M., Vilanova, S., Plazas, M., Gramazio, P., Andújar, I., Herraiz, F. J., … Prohens, J. (2014). Enhancing conservation and use of local vegetable landraces: the Almagro eggplant (Solanum melongena L.) case study. Genetic Resources and Crop Evolution, 61(4), 787-795. doi:10.1007/s10722-013-0073-2Szabados, L., & Savouré, A. (2010). Proline: a multifunctional amino acid. Trends in Plant Science, 15(2), 89-97. doi:10.1016/j.tplants.2009.11.009Verslues, P. E., & Sharma, S. (2010). Proline Metabolism and Its Implications for Plant-Environment Interaction. The Arabidopsis Book, 8, e0140. doi:10.1199/tab.0140Kapuya, J. A., Barendse, G. W. M., & Linskens, H. F. (1985). WATER STRESS TOLERANCE AND PROLINE ACCUMULATION IN PHASEOLUS VULGARIS L. Acta Botanica Neerlandica, 34(3), 293-300. doi:10.1111/j.1438-8677.1985.tb01921.xMisra, N., & Gupta, A. K. (2005). Effect of salt stress on proline metabolism in two high yielding genotypes of green gram. Plant Science, 169(2), 331-339. doi:10.1016/j.plantsci.2005.02.013C醨denas-Avila, ML, Verde-Star, J., Maiti, R., Foroughbakhch-P, R., G醡ez-Gonz醠ez, H., … Morales-Vallarta, M. (2006). Variability in accumulation of free proline on in vitro calli of four bean (Phaseolus vulgaris L.) varieties exposed to salinity and induced moisture stress. Phyton, 75(1), 103-108. doi:10.32604/phyton.2006.75.103WANG, Q. (2019). EFFECTS OF DROUGHT STRESS ON ENDOGENOUS HORMONES AND OSMOTIC REGULATORY SUBSTANCES OF COMMON BEAN (PHASEOLUS VULGARIS L.) AT SEEDLING STAGE. Applied Ecology and Environmental Research, 17(2), 4447-4457. doi:10.15666/aeer1702_44474457Jiménez-Bremont, J. F., Becerra-Flora, A., Hernández-Lucero, E., Rodríguez-Kessler, M., Acosta-Gallegos, J. A., & Ramírez-Pimentel, J. G. (2006). Proline accumulation in two bean cultivars under salt stress and the effect of polyamines and ornithine. Biologia plantarum, 50(4), 763-766. doi:10.1007/s10535-006-0126-xAl Hassan, M., Morosan, M., López-Gresa, M., Prohens, J., Vicente, O., & Boscaiu, M. (2016). Salinity-Induced Variation in Biochemical Markers Provides Insight into the Mechanisms of Salt Tolerance in Common (Phaseolus vulgaris) and Runner (P. coccineus) Beans. International Journal of Molecular Sciences, 17(9), 1582. doi:10.3390/ijms17091582Morosan, M., Hassan, M. A., Naranjo, M. A., López-Gresa, M. P., Boscaiu, M., & Vicente, O. (2017). Comparative analysis of drought responses in Phaseolus vulgaris (common bean) and P. coccineus (runner bean) cultivars. The EuroBiotech Journal, 1(3), 247-252. doi:10.24190/issn2564-615x/2017/03.09Bates, L. S., Waldren, R. P., & Teare, I. D. (1973). Rapid determination of free proline for water-stress studies. Plant and Soil, 39(1), 205-207. doi:10.1007/bf00018060Arteaga, S., Al Hassan, M., Chaminda Bandara, W., Yabor, L., Llinares, J., Boscaiu, M., & Vicente, O. (2018). Screening for Salt Tolerance in Four Local Varieties of Phaseolus lunatus from Spain. Agriculture, 8(12), 201. doi:10.3390/agriculture8120201Andrade, E. R., Ribeiro, V. N., Azevedo, C. V. G., Chiorato, A. F., Williams, T. C. R., & Carbonell, S. A. M. (2016). Biochemical indicators of drought tolerance in the common bean (Phaseolus vulgaris L.). Euphytica, 210(2), 277-289. doi:10.1007/s10681-016-1720-4Bacha, H., Tekaya, M., Drine, S., Guasmi, F., Touil, L., Enneb, H., … Ferchichi, A. (2017). Impact of salt stress on morpho-physiological and biochemical parameters of Solanum lycopersicum cv. Microtom leaves. South African Journal of Botany, 108, 364-369. doi:10.1016/j.sajb.2016.08.018Sen, A., Ozturk, I., Yaycili, O., & Alikamanoglu, S. (2017). Drought Tolerance in Irradiated Wheat Mutants Studied by Genetic and Biochemical Markers. Journal of Plant Growth Regulation, 36(3), 669-679. doi:10.1007/s00344-017-9668-8Koźmińska, A., Wiszniewska, A., Hanus-Fajerska, E., Boscaiu, M., Al Hassan, M., Halecki, W., & Vicente, O. (2019). Identification of Salt and Drought Biochemical Stress Markers in Several Silene vulgaris Populations. Sustainability, 11(3), 800. doi:10.3390/su11030800Verbruggen, N., & Hermans, C. (2008). Proline accumulation in plants: a review. Amino Acids, 35(4), 753-759. doi:10.1007/s00726-008-0061-6Parvaiz, A., & Satyawati, S. (2008). Salt stress and phyto-biochemical responses of plants – a review. Plant, Soil and Environment, 54(No. 3), 89-99. doi:10.17221/2774-pseHayat, S., Hayat, Q., Alyemeni, M. N., Wani, A. S., Pichtel, J., & Ahmad, A. (2012). Role of proline under changing environments. Plant Signaling & Behavior, 7(11), 1456-1466. doi:10.4161/psb.21949KAVI KISHOR, P. B., & SREENIVASULU, N. (2013). Is proline accumulationper secorrelated with stress tolerance or is proline homeostasis a more critical issue? Plant, Cell & Environment, 37(2), 300-311. doi:10.1111/pce.12157Al Hassan, M., López-Gresa, M. del P., Boscaiu, M., & Vicente, O. (2016). Stress tolerance mechanisms in Juncus: responses to salinity and drought in three Juncus species adapted to different natural environments. Functional Plant Biology, 43(10), 949. doi:10.1071/fp16007Al Hassan, M., Pacurar, A., López-Gresa, M. P., Donat-Torres, M. P., Llinares, J. V., Boscaiu, M., & Vicente, O. (2016). Effects of Salt Stress on Three Ecologically Distinct Plantago Species. PLOS ONE, 11(8), e0160236. doi:10.1371/journal.pone.0160236Plazas, M., Nguyen, H. T., González-Orenga, S., Fita, A., Vicente, O., Prohens, J., & Boscaiu, M. (2019). Comparative analysis of the responses to water stress in eggplant (Solanum melongena) cultivars. Plant Physiology and Biochemistry, 143, 72-82. doi:10.1016/j.plaphy.2019.08.031Chen, Z., Cuin, T. A., Zhou, M., Twomey, A., Naidu, B. P., & Shabala, S. (2007). Compatible solute accumulation and stress-mitigating effects in barley genotypes contrasting in their salt tolerance. Journal of Experimental Botany, 58(15-16), 4245-4255. doi:10.1093/jxb/erm284Kozminska, A., Al Hassan, M., Hanus-Fajerska, E., Naranjo, M. A., Boscaiu, M., & Vicente, O. (2018). Comparative analysis of water deficit and salt tolerance mechanisms in Silene. South African Journal of Botany, 117, 193-206. doi:10.1016/j.sajb.2018.05.022Rosales, M. A., Ocampo, E., Rodríguez-Valentín, R., Olvera-Carrillo, Y., Acosta-Gallegos, J., & Covarrubias, A. A. (2012). Physiological analysis of common bean (Phaseolus vulgaris L.) cultivars uncovers characteristics related to terminal drought resistance. Plant Physiology and Biochemistry, 56, 24-34. doi:10.1016/j.plaphy.2012.04.007Sánchez, E., López-Lefebre, L. R., García, P. C., Rivero, R. M., Ruiz, J. M., & Romero, L. (2001). Proline metabolism in response to highest nitrogen dosages in green bean plants (Phaseolus vulgaris L. cv. Strike). Journal of Plant Physiology, 158(5), 593-598. doi:10.1078/0176-1617-00268Mackay, C. E., Christopher Hall, J., Hofstra, G., & Fletcher, R. A. (1990). Uniconazole-induced changes in abscisic acid, total amino acids, and proline in Phaseolus vulgaris. Pesticide Biochemistry and Physiology, 37(1), 74-82. doi:10.1016/0048-3575(90)90110-nAbdelhamid, M. T., Rady, M. M., Osman, A. S., & Abdalla, M. A. (2013). Exogenous application of proline alleviates salt-induced oxidative stress inPhaseolus vulgarisL. plants. The Journal of Horticultural Science and Biotechnology, 88(4), 439-446. doi:10.1080/14620316.2013.11512989Gürel, F., Öztürk, Z. N., Uçarlı, C., & Rosellini, D. (2016). Barley Genes as Tools to Confer Abiotic Stress Tolerance in Crops. Frontiers in Plant Science, 7. doi:10.3389/fpls.2016.01137Yoshida, J., Tomooka, N., Yee Khaing, T., Shantha, P. G. S., Naito, H., Matsuda, Y., & Ehara, H. (2019). Unique responses of three highly salt-tolerant wild Vigna species against salt stress. Plant Production Science, 23(1), 114-128. doi:10.1080/1343943x.2019.169896

Les varietats tradicionals de tomàquet de la conca mediterrània: origen i diversitat cultivada

Aquest treball ha estat finançat pel programa d’investigació i innovació Horitzó 2020 de la Unió Europea a través del contracte número 634561 (TRADITOM: Traditional tomato varieties and cultural practices: a case for agricultucultural diversification with impacto n food security and health of European population). Els autors també agraeixen al mateix programa d’investigació el finançament a través dels contractes número 677379 (G2P-SOL: Linking genetic resources, genomes and phenotypes of Solanaceous crops), número 679796 (TomGEM: A holistic multi-actor approach towards the design of new tomato varieties and management practices to improve yield and quality in the fase of climate change) i número 774244 (BRESOV: Breeding for resilient sustainable organic vegetable production).Díez Niclós, MJTDJ.; Prohens Tomás, J.; Granell Richart, A. (2018). Les varietats tradicionals de tomàquet de la conca mediterrània: origen i diversitat cultivada. Dossier Tècnic. 94:3-8. http://hdl.handle.net/10251/136158S389

ddRAD sequencing-based genotyping for population structure analysis in cultivated tomato provides new insights into the genomic diversity of Mediterranean 'da serbo' type long shelf-life germplasm

[EN] Double digest restriction-site associated sequencing (ddRAD-seq) is a flexible and cost-effective strategy for providing in-depth insights into the genetic architecture of germplasm collections. Using this methodology, we investigated the genomic diversity of a panel of 288 diverse tomato (Solanum lycopersicum L.) accessions enriched in 'da serbo' (called 'de penjar' in Spain) long shelf life (LSL) materials (152 accessions) mostly originating from Italy and Spain. The rest of the materials originate from different countries and include landraces for fresh consumption, elite cultivars, heirlooms, and breeding lines. Apart from their LSL trait, 'da serbo' landraces are of remarkable interest for their resilience. We identified 32,799 high-quality SNPs, which were used for model ancestry population structure and non-parametric hierarchical clustering. Six genetic subgroups were revealed, clearly separating most 'da serbo' landraces, but also the Spanish germplasm, suggesting a subdivision of the population based on type and geographical provenance. Linkage disequilibrium (LD) in the collection decayed very rapidly within <5kb. We then investigated SNPs showing contrasted minor frequency allele (MAF) in 'da serbo' materials, resulting in the identification of high frequencies in this germplasm of several mutations in genes related to stress tolerance and fruit maturation such as CTR1 and JAR1. Finally, a mini-core collection of 58 accessions encompassing most of the diversity was selected for further exploitation of key traits. Our findings suggest the presence of a genetic footprint of the 'da serbo' germplasm selected in the Mediterranean basin. Moreover, we provide novel insights on LSL 'da serbo' germplasm as a promising source of alleles for tolerance to stresses.The authors thank the European Union Horizon 2020 Research and Innovation program for funding this research under grant agreement No 774244 (Breeding for Resilient, Efficient and Sustainable Organic Vegetable Production; BRESOV).Esposito, S.; Cardi, T.; Campanelli, G.; Sestili, S.; Díez Niclós, MJTDJ.; Soler Aleixandre, S.; Prohens Tomás, J.... (2020). ddRAD sequencing-based genotyping for population structure analysis in cultivated tomato provides new insights into the genomic diversity of Mediterranean 'da serbo' type long shelf-life germplasm. Horticulture Research. 7(1):1-14. https://doi.org/10.1038/s41438-020-00353-611471Faostat 2018 http://www.fao.org/Jenkins, J. A. The origin of the cultivated tomato. Econ. Bot. 2, 379–392 (1948).Blanca, J. et al. Variation revealed by SNP genotyping and morphology provides insight into the origin of the tomato. PLoS ONE 7, e48198 (2012).Razifard, H. et al. Genomic evidence for complex domestication history of the cultivated tomato in Latin America. Mol. Biol. Evol. 37, 1118–1132 (2020).Bauchet, G. & Causse, M., Genetic diversity in tomato (Solanum lycopersicum) and its wild relatives. In Genetic Diversity in Plants (INTECH Open Access Publisher, 2012).Bai, Y. & Lindhout, P. Domestication and breeding of tomatoes: what have we gained and what can we gain in the future? Ann. Bot. 100, 1085–1094 (2007).Dwivedi, S., Goldman, I. & Ortiz, R. Pursuing the potential of heirloom cultivars to improve adaptation, nutritional, and culinary features of food crops. Agronomy 9, 441 (2019).Casañas, F., Simó, J., Casals, J. & Prohens, J. Toward an evolved concept of landrace. Front. Plant Sci. 8, 145 (2017).Klee, H. J. & Tieman, D. M. The genetics of fruit flavour preferences. Nat. Rev. Genet. 19, 347–356 (2018).Conesa, M. À., Fullana-Pericàs, M., Granell, A. & Galmés, J. Mediterranean long shelf-life landraces: an untapped genetic resource for tomato improvement. Front. Plant Sci. 10, 1651 (2020).Casals, J., Martí, R., Casañas, F. & Cebolla, J. Sugar-and-acid profile of Penjar tomatoes and its evolution during storage. Sci. Agric. 72, 314–321 (2015).Casals, J. et al. Genetic basis of long shelf life and variability into Penjar tomato. Genet. Resour. Crop Evol. 59, 219–229 (2012).van Berloo, R. et al. Diversity and linkage disequilibrium analysis within a selected set of cultivated tomatoes. Theor. Appl. Genet. 117, 89–101(2008).Robbins, M. D. et al. Mapping and linkage disequilibrium analysis with a genome-wide collection of SNPs that detect polymorphism in cultivated tomato. J. Exp. Bot. 62, 1831–1845 (2011).Sim, S. C., Robbins, M. D., Deynze, A. V., Michel, A. P. & Francis, D. M. Population structure and genetic differentiation associated with breeding history and selection in tomato (Solanum lycopersicum L.). Heredity 106, 927–935 (2011).Corrado, G., Piffanelli, P., Caramante, M., Coppola, M. & Rao, R. SNP genotyping reveals genetic diversity between cultivated landraces and contemporary varieties of tomato. BMC Genomics 14, 835 (2013).Corrado, G., Caramante, M., Piffanelli, P. & Rao, R. Genetic diversity in Italian tomato landraces: implications for the development of a core collection. Sci. Hortic. 168, 138–144 (2014).Sim, S. C. et al. High-density SNP genotyping of tomato (Solanum lycopersicum L.) reveals patterns of genetic variation due to breeding. PloS ONE 7, e45520 (2012).Sacco, A. et al. Exploring a tomato landraces collection for fruit-related traits by the aid of a high-throughput genomic platform. PLoS ONE 10, e0137139 (2015).Tranchida-Lombardo, V. et al. Genetic diversity in a collection of Italian long storage tomato landraces as revealed by SNP markers array. Plant Biosyst. 153, 288–297 (2019).Pérez de, Castro et al. Application of genomic tools in plant breeding. Curr. Genomics 13, 179–195 (2012).Peterson, B. K. et al. Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE 7, e37135 (2012).Shirasawa, K., Hirakawa, H. & Isobe, S. Analytical workflow of double-digest restriction site-associated DNA sequencing based on empirical and in silico optimization in tomato. DNA Res. 23, 145–153 (2016).Yang, G. et al. Development of a universal and simplified ddRAD library preparation approach for SNP discovery and genotyping in angiosperm plants. Plant Met. 12, 39 (2016).Okada, Y. et al. Genome-wide association studies (GWAS) for yield and weevil resistance in sweet potato (Ipomoea batatas (L.) Lam. Plant Cell Rep. 38, 1383–1392 (2019).The Tomato Genome Consortium. The tomato gene sequence provides insights into fleshy fruit evolution. Nature 485, 635–641 (2012).Hosmani, P. S. et al. An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation and optical maps. Preprint at https://www.biorxiv.org/content/10.1101/767764v1 (2020).Aguirre, N. et al. Optimizing ddRADseq in non-model species: a case study in Eucalyptus dunnii maiden. Agronomy 9, 484 (2019).Catchen, J., Hohenlohe, P., Bassham, S., Amores, A. & Cresko, W. Stacks: an analysis tool set for population genomics. Mol. Ecol. 22, 3124–3140 (2013).Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).Weir, B. S. Genetic Data Analysis II (Sinauer Associates Inc., Sunderland, MA, 1996).Botstein, D., White, R. L., Skolnick, M. & Davis, R. W. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32, 314–331 (1980).Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009).Gao, X. & Starmer, J. D. AWclust: point‐and‐click software for non‐parametric population structure analysis. BMC Bioinformatics 9, 77 (2008).Liu, K. & Muse, S. V. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21, 2128–2129 (2005).RStudio Team RStudio: Integrated Development for R (RStudio, Inc., Boston, MA, 2016).De Beukelaer, H., Smýkal, P., Davenport, G. F., Fack, V. & Core Hunter, I. I. fast core subset selection based on multiple genetic diversity measures using Mixed Replica search. BMC Bioinforma. 13, 312 (2012).Schwacke, R. et al. MapMan4: a refined protein classification and annotation framework applicable to multi-omics data analysis. Mol. Plant 12, 879–892 (2019).Kong, Z. et al. Kinesin-4 functions in vesicular transport on cortical microtubules and regulates cell wall mechanics during cell elongation in plants. Mol. Plant 8, 1011–1023 (2015).Wang, X., Cai, X., Xu, C., Wang, Q. & Dai, S. Drought-responsive mechanisms in plant leaves revealed by proteomics. Int. J. Mol. Sci. 17, 1706 (2016).Xu, X., Walter, W. J., Liu, Q., Machens, I. & Nick, P. A rice class-XIV kinesin enters the nucleus in response to cold. Sci. Rep. 8, 3588 (2018).Opiyo, S. O. & Moriyama, E. N. Mining Cytochrome b561 proteins from plant genomes. Int. J. Bioinform. Res. Appl. 6, 209–221 (2010).Lee, S. et al. The small GTPase, nucleolar GTP-binding protein 1 (NOG1), has a novel role in plant innate immunity. Sci. Rep. 7, 9260 (2017).Usadel, B. et al. Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses. Plant Physiol. 138, 1195–1204 (2005).Sáez-Vásquez, J. & Delseny, M. Ribosome biogenesis in plants: from functional 45S ribosomal DNA organization to ribosome assembly factors. Plant Cell 31, 1945–1967 (2019).Mareri, L., Romi, M. & Cai, G. Arabinogalactan proteins: actors or spectators during abiotic and biotic stress in plants? Plant Biosyst. 153, 173–185 (2018).Zhong, S., Chang, C. in Ethylene signalling: the CTR1 protein kinase, Vol. 44 (eds Oxford, UK: Wiley-Blackwell) ch. 6 (Annual Plant Reviews, 2012).Suza, W. P. & Staswick, P. E. The role of JAR1 in jasmonoyl-L-isoleucine production in Arabidopsis wound response. Planta 227, 1221–1232 (2008).Barry, C. S. & Giovannoni, J. J. Ethylene and fruit ripening. J. Plant Growth Regul. 26, 143–159 (2007).Giovannoni, J. J. Fruit ripening mutants yield insights into ripening control. Curr. Opin. Plant Biol. 10, 283–289 (2007).Wang, R. et al. The rin, nor and Cnr spontaneous mutations inhibit tomato fruit ripening in additive and epistatic manners. Plant Sci. 294, 110436 (2020).Albrecht, E., Escobar, M. & Chetelat, R. Genetic diversity and population structure in the tomato-like nightshades Solanum lycopersicoides and S. sitiens. Ann. Bot. 105, 535–554 (2010).Xu, J. et al. Phenotypic diversity and association mapping for fruit quality traits in cultivated tomato and related species. Theor. Appl. Genet. 126, 567–581 (2013).Bauchet, G. et al. Use of modern tomato breeding germplasm for deciphering the genetic control of agronomical traits by Genome Wide Association study. Theor. Appl. Genet. 130, 875–889 (2017).Rothan, C., Diouf, I. & Causse, M. Trait discovery and editing in tomato. Plant J. 97, 73–90 (2018).Wang, T. et al. Analysis of genetic diversity and population structure in a tomato (Solanum lycopersicum L.) germplasm collection based on single nucleotide polymorphism. Genet. Mol. Res. 15, 1–12 (2016).Massaretto, I. L. et al. Recovering tomato landraces to simultaneously improve fruit yield and nutritional quality against salt stress. Front. Plant Sci. 9, 1778 (2018).Aflitos, S. et al. Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. Plant J. 80, 136–148 (2014).Leimu, R., Mutikainen, P. I. A., Koricheva, J. & Fischer, M. How general are positive relationships between plant population size, fitness and genetic variation? J. Ecol. 94, 942–952 (2006).Mackay, I. & Powell, W. Methods for linkage disequilibrium mapping in crops. Trends Plant Sci. 12, 57–63 (2007).Ersoz, E. S., Yu, J., Buckler, E. S. Applications of linkage disequilibrium and association mapping in Genomics-assisted crop improvement, Vol. 1 (eds. Varshney R. K., Tuberosa R.) (Dordrecht, Springer, 2008).D’Agostino, N. & Tripodi, P. NGS-based genotyping, high-throughput phenotyping and genome-wide association studies laid the foundations for next-generation breeding in horticultural crops. Diversity 9, 38 (2017).Kopeliovitch, E., Rabinowitch, H. D., Mizrahi, Y. & Kedar, N. Mode of inheritance of Alcobaca, a tomato fruit-ripening mutant. Euphytica 30, 223–225 (1981).Lobo, M., Bassett, M. J. & Hannah, L. C. Inheritance and characterization of the fruit ripening mutation in ‘alcobaca’ tomato. J. Am. Soc. Hortic. Sci. 109, 741–745 (1984).Mutschler, M., Guttieri, M., Kinzer, S., Grierson, D. & Tucker, G. Changes in ripening-related processes in tomato conditioned by the alc mutant. Theor. Appl. Genet. 76, 285–292 (1988).Conesa, M. A. et al. The postharvest tomato fruit quality of long shelf-life Mediterranean landraces is substantially influenced by irrigation regimes. Postharvest Biol. Technol. 93, 114–121 (2014).Bota, J. et al. Characterization of a landrace collection for Tomàtiga de Ramellet (Solanum lycopersicum L.) from the Balearic Islands. Genet. Resour. Crop Evol. 61, 1131–1146 (2014).Kumar, R., Tamboli, V., Sharma, R. & Sreelakshmi, Y. NAC-NOR mutations in tomato Penjar accessions attenuate multiple metabolic processes and prolong the fruit shelf life. Food Chem. 259, 234–244 (2018).Cho, Y. H. & Yoo, S. D. Novel connections and gaps in ethylene signaling from the ER membrane to the nucleus. Front. Plant Sci. 5, 733 (2015).Ju, C. et al. CTR1 phosphorylates the central regulator EIN2 to control ethylene hormone signaling from the ER membrane to the nucleus in Arabidopsis. Proc. Natl. Acad. Sci. USA 109, 19486–19491 (2012).Achard, P. et al. Integration of plant responses to environmentally activated phytohormonal signals. Science 311, 91–94 (2006).Morello, L., Giani, S., Troina, F. & Breviario, D. Testing the IMEter on rice introns and other aspects of intron-mediated enhancement of gene expression. J. Exp. Bot. 62, 533–544 (2011).Rose, A. B., Carter, A., Korf, I. & Kojima, N. Intron sequences that stimulate gene expression in Arabidopsis. Plant Mol. Biol. 92, 337–346 (2016).Moore, S., Vrebalov, J., Payton, P. & Giovannoni, J. J. Use of genomics tools to isolate key ripening genes and analyse fruit maturation in tomato. J. Exp. Bot. 53, 2023–2030 (2002).Vrebalov, J. et al. A MADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor (rin) locus. Science 296, 343–346 (2002).Zhou, J. L., Qiu, J. & Ye, Z. H. Alteration in secondary wall deposition by overexpression of the Fragile Fiber1 kinesin-like protein in Arabidopsis. J. Integr. Plant Biol. 49, 1235–1243 (2007).Vallés, D. et al. A cysteine protease isolated from ripe fruits of Solanum granulosoleprosum (Solanaceae). Protein J. 27, 267 (2008).Guerrero, F. D., Jones, J. T. & Mullet, J. E. Turgor-responsive gene transcription and RNA levels increase rapidly when pea shoots are wilted. Sequence and expression of three inducible genes. Plant Mol. Biol. 15, 11–26 (1990).Yamaguchi-Shinozaki, K., Koizumi, M., Urao, S. & Shinozaki, K. Molecular cloning and characterization of 9 cDNAs for genes that are responsive to desiccation in Arabidopsis thaliana: sequence analysis of one cDNA clone that encodes a putative transmembrane channel protein. Plant Cell Physiol. 33, 217–224 (1992).Koizumi, M., Yamaguchi-Shinozaki, K., Tsuji, H. & Shinozaki, K. Structure and expression of two genes that encode distinct drought-inducible cysteine proteinases in Arabidopsis thaliana. Gene 129, 175–182 (1993).Krüger, J. et al. A tomato cysteine protease required for Cf-2-dependent disease resistance and suppression of autonecrosis. Science 296, 744–747 (2002).Fan, Y., Yang, W., Yan, Q., Chen, C. & Li, J. Genome-wide identification and expression analysis of the protease inhibitor gene families in tomato. Genes 11, 1 (2020).Noctor, G. & Foyer, C. H. Ascorbate and glutathione: keeping active oxygen under control. Annu. Rev. Plant Physiol. 49, 249–279 (1998).Mittler, R. Oxidative stress, antioxidants and stress tolerance. Trends Plant Sci. 7, 405–410 (2002).Nanasato, Y., Akashi, K. & Yokota, A. Co-expression of cytochrome b561 and ascorbate oxidase in leaves of wild watermelon under drought and high light conditions. Plant Cell Physiol. 46, 1515–1524 (2005).Feeley, E. M. et al. Galectin-3 directs antimicrobial guanylate binding proteins to vacuoles furnished with bacterial secretion systems. Proc. Natl. Acad. Sci. USA 114, E1698–E1706 (2017)

Distribution of the volatiles fraction in different tissues of Capsicum fruits

This work has been partially financed by INIA through Project RTA2010-00038-C03-03Moreno Peris, E.; Gonzalez Más, MC.; Fita, A.; Prohens Tomás, J.; Rodríguez Burruezo, A. (2011). Distribution of the volatiles fraction in different tissues of Capsicum fruits. Bulletin of University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca : Horticulture. 68(1):532-533. http://hdl.handle.net/10251/62874S53253368

Fine tuning European geographic quality labels, an opportunity for the horticulture diversification: A tentative proposal for the Spanish case

[EN] European horticulture, especially in the southern states, must exploit new qualities to increase the added value of its vegetables. This article aims to analyze the situation of the European geographical quality labels Protected Designation of Origin (PDO) and Protected Geographical Indication (PGI) to ascertain whether they are useful for this purpose. To this end, we studied the registers of the current horticultural products awarded PDO or PGI status, and we surveyed the authorities responsible for managing the labels for these products. We found that protected labels have grown steadily since their inception about thirty years ago, becoming a powerful mechanism for landrace conservation and a source of added benefits. The strongest points in the management of these labels include anchoring the products in the local history and culture roots and defining the prominent characteristics of their external appearance, and the weakest points are the lack of information about chemical traits and especially about sensory traits (texture, odor, taste). To strengthen PDO and PGI labels, we propose increasing the requirements for sensory descriptions, homogenizing protocols for analyzing sensory traits, incorporating methods combining trained sensory panels and instrumental methods such as spectroscopy, and involving public administrations in both obtaining and managing the labels. As an example of the potential impact of European geographical labels on territorial rebalancing and the organization of European horticulture, we propose a panoply of products in Spain that are good candidates for protected status.This work was supported by the ¿Departament d¿Agricultura de la Generalitat de Catalunya¿.Romero Del Castillo-Shelly, R.; Sans, S.; Casañas Artigas, F.; Soler Aleixandre, S.; Prohens Tomás, J.; Díez Niclós, MJTDJ.; Casals Missio, J. (2021). Fine tuning European geographic quality labels, an opportunity for the horticulture diversification: A tentative proposal for the Spanish case. Food Control. 129:1-14. https://doi.org/10.1016/j.foodcont.2021.10819611412

Genotypic and environmental effects on morpho-physiological and agronomic performances of a tomato diversity panel in relation to nitrogen and water stress under organic farming

[EN] The agricultural scenario of the upcoming decades will face major challenges for the increased and sustainable agricultural production and the optimization of the efficiency of water and fertilizer inputs. Considering the current and foreseen water scarcity in several marginal and arid areas and the need for a more sustainable farming production, the selection and development of cultivars suitable to grow under low-input conditions is an urgent need. In this study, we assayed 42 tomato genotypes for thirty-two morphophysiological and agronomic traits related to plant, fruit, and root characteristics under standard (control) and no-nitrogen fertilization or water deficit (30% of the amount given to non-stressed trials) treatments in two sites (environments), which corresponded to organic farms located in Italy and Spain. A broad range of variation was found for all traits, with significant differences between the applied treatments and the cultivation sites. Dissection of genotypic (0), environmental (E), and treatment (T) factors revealed that the three main factors were highly significant for many traits, although G was the main source of variation in most cases. G x E interactions were also important, while G x T and E x T were less relevant. Only fruit weight and blossom end rot were highly significant for the triple interaction (G x E x T). Reduction of water supply significantly increased the soluble solid content in both locations, whereas both nitrogen and water stress led to a general decrease in fruit weight and total yield. Despite so, several accessions exhibited better performances than the control when cultivated under stress. Among the accessions evaluated, hybrids were promising in terms of yield performance, while overall landraces and heirlooms exhibited a better quality. This suggests the possibility of exploiting both the variation within ancient varieties and the heterosis for yield of hybrids to select and breed new varieties with better adaptation to organic farming conditions, both under optimal and suboptimal conditions. The results shed light on the strategies to develop novel varieties for organic farming, giving hints into the management of inputs to adopt for a more sustainable tomato cultivation.This work has been funded by the European Union's Horizon 2020 Research and Innovation Programme under grant agreement no. 774244 (Breeding for resilient, efficient and sustainable organic vegetable production; BRESOV).Tripodi, P.; Figás-Moreno, MDR.; Leteo, F.; Soler Aleixandre, S.; Díez Niclós, MJTDJ.; Campanelli, G.; Cardi, T.... (2022). Genotypic and environmental effects on morpho-physiological and agronomic performances of a tomato diversity panel in relation to nitrogen and water stress under organic farming. Frontiers in Plant Science. 13:1-19. https://doi.org/10.3389/fpls.2022.9365961191

Fruit composition diversity in land races and modern pepino (Solanum muricatum) varieties and wild related species

[EN] Pepino (Solanum muricatum) fruits from 15 accessions of cultivated pepino as well as six accessions from wild relatives were evaluated for contents in dry matter, protein, b-carotene, chlorophylls and seven minerals. Several-fold differences among accessions were found for most traits. Average values obtained were similar to those of melon and cucumber, but the phenolic contents were much higher. Wild species had significantly higher average contents for all traits vs. the cultivated pepino accessions. And, the comparisons among the cultivated pepino varieties showed that the modern varieties were more uniform in composition, and they possessed significantly lower concentrations of protein, P, K, and Zn than local land races. Most of the significant correlations among composition traits were positive. Our studies show that regular consumption of pepino fruits could make a significant contribution to the recommended daily intake of P, K, Fe and Cu as well as to the average daily intake of phenolics. Furthermore, the higher values for most nutrients measured in the wild species and in the local land races indicate that new pepino varieties with improved fruit contents in nutrient and bioactive compounds can be developed.Pietro Gramazio is grateful to Universitat Politecnica de Valencia for a pre-doctoral (Programa FPI de la UPV-Subprograma 1/2013 call) contract.Herraiz García, FJ.; Raigón Jiménez, MD.; Vilanova Navarro, S.; García-Martínez, MD.; Gramazio, P.; Plazas Ávila, MDLO.; Rodríguez Burruezo, A.... (2016). Fruit composition diversity in land races and modern pepino (Solanum muricatum) varieties and wild related species. Food Chemistry. 203:49-58. https://doi.org/10.1016/j.foodchem.2016.02.035S495820