The chromosome-scale assembly of endive (Cichorium endivia) genome provides insights into the sesquiterpenoid biosynthesis.

Endive (Cichorium endivia L.) is a leafy vegetable in the Asteraceae family. Sesquiterpene lactones (STLs) in endive leaves bring a bitter taste that varies between varieties. Despite their importance in breeding varieties with unique flavours, sesquiterpenoid biosynthesis pathways in endive are poorly understood. We assembled a chromosome-scale endive genome of 641 Mb with a contig N50 of 5.16 Mb and annotated 46,711 protein-coding genes. Several gene families, especially terpene synthases (TPS) genes, expanded significantly in the C. endivia genome. STLs biosynthesis-related genes and TPS genes in more bitter varieties have shown a higher level of expression, which could be attributed to genomic variations. Our results penetrate the origin and diversity of bitter taste and facilitate the molecular breeding of endive varieties with unique bitter tastes. The high-quality endive assembly would provide a reference genome for studying the evolution and diversity of Asteraceae.

Influence of cultivation sites on sterol, nitrate, total phenolic contents and antioxidant activity in endive and stem chicory edible products.

Chicories produce a wide range of vegetables with important nutritional value. We determined the variation of sterol, total polyphenol, nitrate contents and antioxidant capacity (SC, TPC, NC, AC) in endive leaves and stem-chicory novel vegetables, cultivated in two Italian regions. Within a given area, the SC was similar in smooth- and curly leafed endives (106.3-176.0 mg/kg FW); sitosterol and stigmasterol were major fractions (45-56 versus 38-43%). The stem SC was independent of landrace (101.5-118.6 mg/kg FW); sitosterol prevailed on stigmasterol and fucosterol (73-76 versus 12-14% versus 8-9%); the latter reached 15.7 mg/kg FW, conferring value as potential antidiabetes food. The planting site affected the AC and TPC of endives (893.1-1571.4 µmTE/100 g FW, 30.8-76.1 GAE100/g FW) and chicory stems (729.8-1152.5 µmTE/100 g FW; 56.2-124.4 GAE100/g FW), while the NC was recurrently below dangerous thresholds. PCA showed that environment was the major cause of variation, though it modestly affected these parameters.

Pipeline to Design Inbred Lines and F1 Hybrids of Leaf Chicory (Radicchio) Using Male Sterility and Genotyping-by-Sequencing.

Chicory, a horticultural crop cultivated worldwide, presents many botanical varieties and local biotypes. Among these, cultivars of the Italian radicchio group of the pure species Cichorium intybus L. and its interspecific hybrids with Cichorium endivia L.-as the "Red of Chioggia" biotype-includes several phenotypes. This study uses a pipeline to address the marker-assisted breeding of F1 hybrids: it presents the genotyping-by-sequencing results of four elite inbred lines using a RADseq approach and an original molecular assay based on CAPS markers for screening mutants with nuclear male sterility in the radicchio of Chioggia. A total of 2953 SNP-carrying RADtags were identified and used to compute the actual estimates of homozygosity and overall genetic similarity and uniformity of the populations, as well as to determine their genetic distinctiveness and differentiation. Molecular data were further used to investigate the genomic distribution of the RADtags among the two Cichorium species, allowing their mapping in 1131 and 1071 coding sequences in chicory and endive, respectively. Paralleling this, an assay to screen the genotype at the male sterility locus Cims-1 was developed to discriminate wild-type and mutant alleles of the causative gene myb80-like. Moreover, a RADtag mapped close to this genomic region proved the potential application of this method for future marker-assisted selection tools. Finally, after combining the genotype information of the core collection, the best 10 individuals from each inbred line were selected to compute the observed genetic similarity as a measure of uniformity as well as the expected homozygosity and heterozygosity estimates scorable by the putative progenies derived from selfing (pollen parent) and full-sibling (seed parent) or pair-wise crossing (F1 hybrids). This predictive approach was conducted as a pilot study to understand the potential application of RADseq in the fine tuning of molecular marker-assisted breeding strategies aimed at the development of inbred lines and F1 hybrids in leaf chicory.

The Chloroplast Genome of Endive (Cichorium endivia L.): Cultivar Structural Variants and Transcriptome Responses to Stress Due to Rain Extreme Events.

The chloroplast (cp) genome diversity has been used in phylogeny studies, breeding, and variety protection, and its expression has been shown to play a role in stress response. Smooth- and curly-leafed endives (Cichorium endivia var. latifolium and var. crispum) are of nutritional and economic importance and are the target of ever-changing breeding programmes. A reference cp genome sequence was assembled and annotated (cultivar 'Confiance'), which was 152,809 base pairs long, organized into the angiosperm-typical quadripartite structure, harboring two inverted repeats separated by the large- and short- single copy regions. The annotation included 136 genes, 90 protein-coding genes, 38 transfer, and 8 ribosomal RNAs and the sequence generated a distinct phyletic group within Asteraceae with the well-separated C. endivia and intybus species. SSR variants within the reference genome were mostly of tri-nucleotide type, and the cytosine to uracil (C/U) RNA editing recurred. The cp genome was nearly fully transcribed, hence sequence polymorphism was investigated by RNA-Seq of seven cultivars, and the SNP number was higher in smooth- than curly-leafed ones. All cultivars maintained C/U changes in identical positions, suggesting that RNA editing patterns were conserved; most cultivars shared SNPs of moderate impact on protein changes in the ndhD, ndhA, and psbF genes, suggesting that their variability may have a potential role in adaptive response. The cp transcriptome expression was investigated in leaves of plants affected by pre-harvest rainfall and rainfall excess plus waterlogging events characterized by production loss, compared to those of a cycle not affected by extreme rainfall. Overall, the analyses evidenced stress- and cultivar-specific responses, and further revealed that genes of the Cytochrome b6/f, and PSI-PSII systems were commonly affected and likely to be among major targets of extreme rain-related stress.

MIK2 is a candidate gene of the S-locus for sporophytic self-incompatibility in chicory (Cichorium intybus, Asteraceae).

The Cichorium genus offers a unique opportunity to study the sporophytic self-incompatibility (SSI) system, being composed of species characterized by highly efficient self-incompatibility (e.g., C. intybus) and complete self-compatibility (e.g., C. endivia). To this end, the chicory genome was used to map seven previously identified SSI locus-associated markers. The region containing the S-locus was therefore restricted to an ~4 M bp window on chromosome 5. Among the genes predicted in this region, MDIS1 INTERACTING RECEPTOR LIKE KINASE 2 (ciMIK2) was particularly promising as a candidate for SSI. Its ortholog in Arabidopsis (atMIK2) is involved in pollen-stigma recognition reactions, and its protein structure is similar to that of S-receptor kinase (SRK), a key component of the SSI system in the Brassica genus. The amplification and sequencing of MIK2 in chicory and endive accessions revealed two contrasting scenarios. In C. endivia, MIK2 was fully conserved even when comparing different botanical varieties (i.e., smooth and curly endive). In C. intybus, 387 polymorphic positions and 3 INDELs were identified when comparing accessions of different biotypes all belonging to the same botanical variety (i.e., radicchio). The polymorphism distribution throughout the gene was uneven, with hypervariable domains preferentially localized in the LRR-rich extracellular region, putatively identified as the receptor domain. The gene was hypothesized to be under positive selection, as the nonsynonymous mutations were more than double the synonymous ones (dN/dS = 2.17). An analogous situation was observed when analyzing the first 500 bp of the MIK2 promoter: no SNPs were observed among the endive samples, whereas 44 SNPs and 6 INDELs were detected among the chicory samples. Further analyses are needed to confirm the role of MIK2 in SSI and to demonstrate whether the 23 species-specific nonsynonymous SNPs in the CDS and/or the species-specific 10 bp-INDEL found in a CCAAT box region of the promoter are responsible for the contrasting sexual behaviors of chicory and endive.

AlkB RNA demethylase homologues and N6 -methyladenosine are involved in Potyvirus infection.

Proteins of the alkylation B (AlkB) superfamily show RNA demethylase activity removing methyl adducts from N6 -methyladenosine (m6 A). m6 A is a reversible epigenetic mark of RNA that regulates human virus replication but has unclear roles in plant virus infection. We focused on Potyvirus-the largest genus of plant RNA viruses-and report here the identification of AlkB domains within P1 of endive necrotic mosaic virus (ENMV) and an additional virus of a putative novel species within Potyvirus. We show that Nicotiana benthamiana m6 A levels are reduced by infection of plum pox virus (PPV) and potato virus Y (PVY). The two potyviruses lack AlkB and the results suggest a general involvement of RNA methylation in potyvirus infection and evolution. Methylated RNA immunoprecipitation sequencing of virus-infected samples showed that m6 A peaks are enriched in plant transcript 3' untranslated regions and in discrete internal and 3' terminal regions of PPV and PVY genomes. Down-regulation of N. benthamiana AlkB homologues of the plant-specific ALKBH9 clade caused a significant decrease in PPV and PVY accumulation. In summary, our study provides evolutionary and experimental evidence that supports the m6 A implication and the proviral roles of AlkB homologues in Potyvirus infection.

Comparison of carbohydrate partitioning and expression patterns of some genes involved in carbohydrate biosynthesis pathways in annual and biennial species of Cichorium spp.

Variation in metabolism and partitioning of carbohydrates, particularly fructans, between annual and perennial Cichorium species remains a challenging topic. To address this problem, an annual (endive, Cichorium endive L. var. Crispum; Asteraceae) and a biennial species (chicory, Cichorium intybus L. var. Witloof; Asteraceae) were compared with in terms of variability in carbohydrate accumulation and expression patterns of fructan-active enzyme genes, as well as sucrose metabolism at various growth and developmental stages. In general, constituents such as 1-kestose, nystose, and inulin were detected only in the root of chicory and were not present in any of the endive tissues. For both species, flower tissue contained maximum levels of both fructose and glucose, while for sucrose, more fluctuations were observed. On the other hand, all the genes under study exhibited variation, not only between the two species but also among different tissues at different sampling times. In endive root compared to endive leaf, the expression of cell wall invertase genes and sucrose accumulation decreased simultaneously, indicating the limited capacity of its roots to absorb sucrose, a precursor to inulin production. In addition, low expression of fructan: fructan fructosyltransferase in endive root compared to chicory root confirmed the inability of endive to inulin synthesis. Overall, annual and biennial species were different in the production of inulin, transport, remobilization, and unloading of sucrose.

Reduction of Nitrate Content in Baby-Leaf Lettuce and Cichorium endivia Through the Soilless Cultivation System, Electrical Conductivity and Management of Nutrient Solution.

Soilless cultivation systems are efficient tools to control nitrates by managing nutrient solution (NS) salinity and nitrogen availability, however, these nitrate-lowering strategies require appropriate calibration based on species/genotype-specific responses interacting with climate and growing conditions. Three experiments were carried out on lettuce and Cichorium endivia grown in ebb-and-flow (EF) and floating (FL) systems at two levels of NS salinity (EC = 2.5 and 3.5 dS m-1) (EC2.5, EC3.5, respectively) under autumn and early-spring (lettuce) and winter and late-spring conditions (C. endivia). Nitrogen deprivation (NS withdrawal a few days before the harvest) was tested at EC2.5, in the autumn and winter cycles. The EF-system caused an increase in salinity in the substrate where roots mainly develop so it mimicked the effect of the EC3.5 treatment. In the winter-grown lettuce, the EF-system or EC3.5 treatment was effective in reducing the nitrate level without effects on yield, with the EF baby-leaf showing an improved quality (color, dry matter, chlorophylls, carotenoid, vitamin C, phenol). In both seasons, the EF/EC3.5 treatment resulted in a decline in productivity, despite a further reduction in nitrate content and a rise in product quality occurring. This response was strictly linked to the increasing salt-stress loaded by the EC3.5/EF as highlighted by the concurrent Cl- accumulation. In early-spring, the FL/EC3.5 combination may represent a trade-off between yield, nitrate content and product quality. In contrast, in winter-grown endive/escarole the EC3.5, EF and EC3.5/EF reduced the nitrate level with no effect on yield, product quality or Cl- uptake, thus proving them to be more salt-tolerant than lettuce. High temperatures during the late-spring cycle promoted nitrate and Cl- uptake, overcoming the nitrate-controlling effect of salinity charged by the EF system or EC3.5. The nitrate level decreased after 3 day-long (lettuce) or 6 day-long (C. endivia) NS withdrawal. In C. endivia and EF-grown lettuce, it provoked a decrease in yield, but a concurrent improvement in baby-leaf appearance and nutritional quality. More insights are needed to fine-tune the duration of the NS removal taking into account the soilless system used and species-specific characteristics.

Food intake biomarkers for green leafy vegetables, bulb vegetables, and stem vegetables: a review.

BACKGROUND: Numerous studies acknowledged the importance of an adequate vegetable consumption for human health. However, current methods to estimate vegetable intake are often prone to measurement errors due to self-reporting and/or insufficient detail. More objective intake biomarkers for vegetables, using biological specimens, are preferred. The only concentration biomarkers currently available are blood carotenoids and vitamin C, covering total fruit and vegetable intake. Identification of biomarkers for specific vegetables is needed for a better understanding of their relative importance for human health. Within the FoodBAll Project under the Joint Programming Initiative "A Healthy Diet for a Healthy Life", an ambitious action was undertaken to identify candidate intake biomarkers for all major food groups consumed in Europe by systematically reviewing the existent literature. This study describes the review on candidate biomarkers of food intake (BFIs) for leafy, bulb, and stem vegetables, which was conducted within PubMed, Scopus and Web of Science for studies published through March 2019. RESULTS: In total, 65 full-text articles were assessed for eligibility for leafy vegetables, and 6 full-text articles were screened for bulb and stem vegetables. Putative BFIs were identified for spinach, lettuce, endive, asparagus, artichoke, and celery, but not for rocket salad. However, after critical evaluation through a validation scheme developed by the FoodBAll consortium, none of the putative biomarkers appeared to be a promising BFI. The food chemistry data indicate that some candidate BFIs may be revealed by further studies. CONCLUSION: Future randomized controlled feeding studies combined with observational studies, applying a non-targeted metabolomics approach, are needed in order to identify valuable BFIs for the intake of leafy, bulb, and stem vegetables.

Post-process treatments are effective strategies to reduce Listeria monocytogenes on the surface of leafy greens: A pilot study.

Growth of L. monocytogenes is among the most important factors affecting the risk of human listeriosis. In ready to eat leafy greens, the use of anti-Listeria treatments represents a good alternative to inhibit growth during storage. Several commercially available antimicrobial agents have been suggested as effective intervention strategies. Among them, phage preparations and bacteriocin-producing strains have shown promising results against L. monocytogenes. In this study, we investigate the efficacy of two commercially available surface treatments, the bacteriophage formulation PhageGuard Listex (Micreos Food Safety B.V., NL) and the bacteriocin-producing culture SafePro® (CHR Hansen, DK) to inactivate L. monocytogenes in fresh-cut curly endive after processing and during storage. Fresh-cut endive was inoculated with a cold-adapted L. monocytogenes cocktail of 6 strains (4.4 ±â€¯0.0 log cfu/g) and treated with the anti-Listeria treatments. The treatments were applied using a spray system at two different places within the processing line, on the conveyor belt and in the centrifuge. A total of 5 different treatments were applied: i) Untreated (CT); ii) PhageGuard Listex on the conveyor belt (Listex_Conveyor); iii) PhageGuard Listex during centrifugation (Listex_Centrifuge); iv) SafePro on the conveyor belt (SafePro_Conveyor); and v) SafePro during centrifugation (SafePro_Centrifuge). Samples were stored 3 days at 5 °C plus 5 days at 8 °C. PhageGuard Listex treatment reduced L. monocytogenes in fresh-cut endive by 2.5 logs, regardless of the place of treatment application (conveyor belt or centrifuge). On the other hand, SafePro only reduced L. monocytogenes by 0.2 and 0.4 logs, at the conveyor belt and centrifuge, respectively. Maximum L. monocytogenes reductions of about 3.5 log units were observed in fresh-cut endive treated with PhageGuard Listex after 3 days of storage. At the end of the shelf life (8 days), the initial trends were maintained and the fresh-cut curly endive treated with PhageGuard Listex showed the lowest L. monocytogenes concentration. However, by the end of the shelf-life, L. monocytogenes showed higher levels (1.3-fold) than immediately after the application of the treatment. One hypothesis could be that L. monocytogenes cells, which were able to survive the anti-Listeria treatments, were also able to proliferate under the specific storage conditions. Based on the obtained results, PhageGuard Listex seems to be a promising decontamination agent for leafy greens aiming to reduce growth of the bacteria but further work is needed.

Upcycling of Belgian endive (Cichorium intybus var. foliosum) by-products. Chemical composition and functional properties of dietary fibre root powders.

By-products of Belgian endive represent an interesting yet underutilised source of dietary fibre (DF). Dietary fibre concentrates (DFC) that are low in sugar and neutral in taste are sought by the food industry to increase DF content and improve texture in food products. The aim was to set up a biorefinery process to produce DFC from forced roots of Belgian endive (DFC-BE) and characterise the resulting product. As a control, non-treated forced roots powder (FRP-BE) was tested. Water extraction significantly (p < 0.05) decreased the content of sugars, phenolic acids (PA) and sesquiterpene lactones (SL) in DFC-BE. In contrast, total dietary fibre concentration (TDF) was higher in DFC-BE (81.82 g/100 g DW) in comparison to FRP-BE (49.04 g/100 g DW). DFC-BE offers an excellent water holding capacity (WHC) of 14.71 g water/g DW and a swelling capacity (SWC) of 23.46 mL water/g DW, suggesting possible use as a functional food ingredient.

Genotyping by RAD Sequencing Analysis Assessed the Genetic Distinctiveness of Experimental Lines and Narrowed Down the Genomic Region Responsible for Leaf Shape in Endive (Cichorium endivia L.).

The characterization of genetic diversity in elite breeding stocks is crucial for the registration and protection of new varieties. Moreover, experimental population structure analysis and information about the genetic distinctiveness of commercial materials are essential for crop breeding programs. The purpose of our research was to assess the genetic relationships of 32 endive (Cichorium endivia L.) breeding lines, 18 from var. latifolium (escarole) and 14 from var. crispum (curly), using heterologous Cichorium intybus-derived simple sequence repeats (SSR) markers and single-nucleotide polymorphisms (SNP) markers. We found that 14 out of 29 SSR markers were successfully amplified, but only 8 of them were related to polymorphic loci. To overcome the limitation of the low number of informative SSR marker loci, an alternative SNP-based approach was employed. The 4621 SNPs produced by a restriction site-associated DNA marker sequencing approach were able to fully discriminate the 32 endive accessions; most importantly, as many as 50 marker loci were found to distinguish the curly group from the escarole group. Interestingly, 24 of the marker loci mapped within a peripheral segment of chromosome 8 of lettuce (Lactuca sativa L.), spanning a chromosomal region of 49.6 Mb. Following Sanger sequencing-based validation, three genes were determined to carry nonsynonymous SNPs, and one of them matched a putative ortholog of AtELP1, subunit 1 of the Elongator complex. Considering that several previously characterized Elongator complex subunit mutants exhibited elongated and/or curly leaf phenotypes, this gene should be taken into consideration for a better understanding of the underlying mechanism controlling leaf shape in endive.

Modification of the existing maximum residue levels for mandipropamid in various crops.

In accordance with Article 6 of Regulation (EC) No 396/2005, the applicants Syngenta Crop Protection B.V. and Agriculture and Horticulture Development Board (AHDB) submitted, respectively, a request to the competent national authorities in the Netherlands and United Kingdom to modify the existing maximum residue levels (MRLs) for the active substance mandipropamid in various crops. The data submitted in support of the request were found to be sufficient to derive MRL proposals for beetroots, radishes, cauliflowers, Brussels sprouts, witloofs/Belgian endives, peas (without pods) and globe artichokes. Adequate analytical methods for enforcement are available to control the residues of mandipropamid in plant matrices under consideration at the validated limit of quantification (LOQ) of 0.01 mg/kg. Based on the risk assessment results, EFSA concluded that the intake of residues resulting from the use of mandipropamid according to the reported agricultural practices is unlikely to present a risk to consumer health.

Improving the Microbial Safety of Fresh-Cut Endive with a Combined Treatment of Cinnamon Leaf Oil Emulsion Containing Cationic Surfactants and Ultrasound.

Endive is widely consumed in a fresh-cut form owing to its rich nutritional content. However, fresh-cut vegetables are susceptible to contamination by pathogenic bacteria. This study investigated the antibacterial activities of the combined treatment of cinnamon leaf oil emulsion containing cetylpyridinium chloride or benzalkonium chloride (CLC and CLB, respectively) as a cationic surfactant and ultrasound (US) against Listeria monocytogenes and Escherichia coli O157:H7 on endive. The combined treatment of CLC or CLB with US reduced the population of L. monocytogenes by 1.58 and 1.47 log colony forming units (CFU)/g, respectively, and that of E. coli O157:H7 by 1.60 and 1.46 log CFU/g, respectively, as compared with water washing treatment. The reduction levels of both pathogens were higher than those observed with 0.2 mg/ml sodium hypochlorite. In addition, the combined treatment showed no effect on the quality of the fresh-cut endive (FCE). In particular, the degree of browning in FCE was less for the treatment group than for the control and water washing treatment groups. Thus, cationic surfactant-based cinnamon leaf oil emulsions combined with US may be an effective washing treatment for the microbial safety of FCE.

Modification of the existing maximum residue levels for difenoconazole in various crops.

In accordance with Article 6 of Regulation (EC) No 396/2005, the applicant BASF SE submitted a request to the competent national authority in the United Kingdom to modify the existing maximum residue levels (MRLs) for the active substance difenoconazole in various crops. The data submitted in support of the request were found to be sufficient to derive MRL proposals for all crops under consideration. Adequate analytical methods for enforcement are available to control the residues of difenoconazole in plant matrices under consideration. The estimated long-term and short-term intake to residues of difenoconazole resulting from the existing and the intended uses did not exceed the toxicological reference values established for the active substance difenoconazole. The consumer exposure assessment has to be considered provisional as the impact of a potentially different isomer composition in the residues of difenoconazole on this risk assessment is currently unknown and has to be reconsidered when data on possible preferential metabolism/degradation of the four stereo isomers of difenoconazole in plants is available and guidance on a risk assessment approach for residues containing isomers is implemented.

The impact of sesquiterpene lactones and phenolics on sensory attributes: An investigation of a curly endive and escarole germplasm collection.

In the present study, curly endive (Cichorium endivia L. var. crispum) and escarole (Cichorium endivia L. var. latifolium) accessions were investigated for their sensory characters (bitterness, astringency and herbaceous flavour) and acceptance in relation to sesquiterpene lactone and phenolic content. Different facets of the perception of these sensory traits in relation to lactones and phenolics were brought out. Lactucopicrin and kaempferol malonyl glucoside were consistently related to bitterness, astringency and herbaceous flavour perceptions. Overall acceptance was significantly and inversely related mainly to bitterness. The generic statement that sesquiterpene lactones and phenolic compounds are determinants of bitterness and other related sensory characters does not seem to be fully consistent with our data, that indicated how the balance of different compounds affects these traits individually, in a rather complex manner, with a prevailing negative impact of phenolics. Bitter, astringent, and herbaceous perceptions were significantly affected by variety, with curly endive showing on average higher scores in comparison to escarole, with particular respect to bitterness.