The PLUMED consortium (2019). Promoting transparency and reproducibility in enhanced molecular simulations. Nature Methods, 16(8), 670-673. https://doi.

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The multitude of forms observed in flowering plants is largely because of their ability to establish new axes of growth during postembryonic development. This process is initiated by the formation of secondary meristems that develop into vegetative or reproductive branches. In the blind and torosa mutants of tomato, initiation of lateral meristems is blocked during shoot and inflorescence development, leading to a strong reduction in the number of lateral axes. In this study, it is shown that blind and torosa are allelic. The Blind gene has been isolated by positional cloning, and it was found that the mutant phenotype is caused by a loss of function of an R2R3 class Myb gene. RNA interference-induced blind phenocopies confirmed the identity of the isolated gene. Double mutant analysis shows that Blind acts in a novel pathway different from the one to which the previously identified Lateral suppressor gene belongs. The findings reported add a new class of transcription factors to the group of genes controlling lateral meristem initiation and reveal a previously uncharacterized function of R2R3 Myb genes.I n flowering plants, postembryonic shoot development is controlled by the activity of the shoot apical meristem (SAM). The SAM established during embryogenesis produces in a regular fashion leaf, node, and internode primordia, which generate the primary shoot of a plant. Secondary meristems arise in the axils of leaves as well as on the flanks of the inflorescence meristems. Lateral meristems produced during the vegetative phase develop into shoots repeating, at least in part, the growth pattern of the primary shoot, whereas after floral transition lateral meristems develop into flowers or new inflorescence axes.In Arabidopsis thaliana, Zea mays, and several other plant species, genes have been isolated that are required for SAM initiation, maintenance, and function, and interactions between these genes are being studied (1). However, much less is known about the genetic control of lateral meristem initiation and function during shoot and inflorescence development. In tomato, lateral meristems are formed in all leaf axils and are first detectable in the axil of the fifth youngest primordium (2). They develop into fast-growing side shoots that give the plant a bushy appearance. Whereas in many higher plants the primary SAM remains active throughout the entire lifespan, in tomato, it is transformed into a terminal inflorescence, and the uppermost axillary meristem takes over its function to continue the main stem. After formation of three leaves, this sympodial shoot terminates itself in an inflorescence, and sympodial shoots of progressively higher order elongate the main axis (3, 4). The tomato inf lorescence has been described as a cyme, i.e., flowers arise as terminal structures, and the inflorescence axis grows because of a lateral meristem, which will again be transformed into a floral meristem and so on (3). Recent analysis has in part modified this view by demonstrating that the inflorescence meristem is s...

A small insert genomic library of Olea europaea L., highly enriched in (GA/CT) n repeats, was obtained using the procedure of Kandpal et al. (1994). The sequencing of 103 clones randomly extracted from this library allowed the identification of 56 unique genomic inserts containing simple sequence repeat regions made by at least three single repeats. A sample of 20 primer pairs out of the 42 available were tested for functionality using the six olive varieties whose DNA served for library construction. All primer pairs succeeded in amplifying at least one product from the six DNA samples, and ten pairs detecting more than one allele were used for the genetic characterisation of a panel of 20 olive accessions belonging to 16 distinct varieties. A total of 57 alleles were detected among the 20 genotypes at the ten polymorphic SSR loci. The remaining primer pair allowed the amplification of a single SSR allele for all accessions plus a longer fragment for some genotypes. Considering the simple sequence repeat polymorphism, 5.7 alleles were scored on average for each of the ten SSR loci. A genetic dissimilarity matrix, based on the proportion of shared alleles among all the pair-wise combinations of genotypes, was constructed and used to disentangle the genetic relationships among varieties by means of the UPGMA clustering algorithm. Graphical representation of the results showed the presence of two distinct clusters of varieties. The first cluster grouped the varieties cultivated on the Ionian Sea coasts. The second cluster showed two subdivisions: the first sub-cluster agglomerated the varieties from some inland areas of Calabria; the second grouped the remaining varieties from Basilicata and Apulia cultivated in nearby areas. Results of cluster analysis showed a significant relationship between the multilocus genetic similarities and the geographic origin of the cultivars.

BackgroundIn the last decade, the availability of gene sequences of many plant species, including tomato, has encouraged the development of strategies that do not rely on genetic transformation techniques (GMOs) for imparting desired traits in crops. One of these new emerging technology is TILLING (Targeting Induced Local Lesions In Genomes), a reverse genetics tool, which is proving to be very valuable in creating new traits in different crop species.ResultsTo apply TILLING to tomato, a new mutant collection was generated in the genetic background of the processing tomato cultivar Red Setter by treating seeds with two different ethylemethane sulfonate doses (0.7% and 1%). An associated phenotype database, LycoTILL, was developed and a TILLING platform was also established. The interactive and evolving database is available online to the community for phenotypic alteration inquiries. To validate the Red Setter TILLING platform, induced point mutations were searched in 7 tomato genes with the mismatch-specific ENDO1 nuclease. In total 9.5 kb of tomato genome were screened and 66 nucleotide substitutions were identified. The overall mutation density was estimated and it resulted to be 1/322 kb and 1/574 kb for the 1% EMS and 0.7% EMS treatment respectively.ConclusionsThe mutation density estimated in our collection and its comparison with other TILLING populations demonstrate that the Red Setter genetic resource is suitable for use in high-throughput mutation discovery. The Red Setter TILLING platform is open to the research community and is publicly available via web for requesting mutation screening services.

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25Progress in remote sensing and robotic technologies decreases the hardware costs of 26 phenotyping. Here, we first review cost-effective imaging devices and environmental sensors, 27 and present a trade-off between investment and manpower costs. We then discuss the structure 28 of costs in various real-world scenarios. Hand-held low-cost sensors are suitable for quick and 29 infrequent plant diagnostic measurements. In experiments for genetic or agronomic analyses, (i) 30 major costs arise from plant handling and manpower; (ii) the total costs per pot/microplot are 31 similar in robotized platform or field experiments with drones, hand-held or robotized ground 32 vehicles; (iii) the cost of vehicles carrying sensors represents only 5-26% of the total costs. These 33 conclusions depend on the context, in particular for labor cost, the quantitative demand of 34 phenotyping and the number of days available for phenotypic measurements due to climatic 35 constraints. Data analysis represents 10-20% of total cost if pipelines have already been 36 developed. A trade-off exists between the initial high cost of pipeline development and labor cost 37 of manual operations. Overall, depending on the context and objectives, "cost-effective" 38 phenotyping may involve either low investment ("affordable phenotyping"), or initial high 39 investments in sensors, vehicles and pipelines that result in higher quality and lower operational 40 costs. 41 Highlights 42 -New technologies considerably reduce the costs of sensors and automated vehicles 43 -Low investment in sensors, vehicles or pipelines present trade-offs with labor costs 44 -Plant/plot handling and labor costs represent the major proportion of costs in phenotyping 45 experiments 46 -The costs of high-throughput experiments in the field and in automated platforms is similar 47 regardless of vehicles 48 -The development of software applications (e.g. imaging, phenotypic analyses, models, 49 information system) is a major part of costs 50 51 52 54 I Imaging techniques with a range of hardware costs 55 1.1 Handheld phenotyping technologies 56 1.2 Aerial imaging for large-scale phenotyping 57 1.3 Imaging with ground vehicles 58 1.4 Environmental measurements 59 II Costs associated with image capture represent a fraction of the overall cost of phenotyping 60 2.1 A method for calculating costs in field and greenhouse platforms 61 2.2 A high cost for plant management 62 2.3 Investing in appropriate environmental characterization results in comparatively low cost 63 for a high return 64 2.4 Imaging costs: a trade-off between investment and labor costs 65 2.4.1 The choice of vehicle mostly depends on the demand for microplots per year 66 2.4.2 The cost of imaging devices is similar to that of vehicles that carry sensors 67 2.5 Costs of typical experiments 68 2.5.1 Image analysis: a tradeoff between investment in automated workflows and day-to-day 69 labor costs 70 2.5.2 High costs for data analysis for the identification of traits 71 2.5.3 Costs associated with data storag...