Time to exploit phenotypic plasticity

[EN] The study of plant phenotypic plasticity complements our knowledge of plant response to stresses obtained from controlled single and multiple stress experiments. Diouf et al. (2020) dissect the genetic control of phenotypic plasticity for several traits in tomato. A few loci control both plasticity and mean phenotypes, while most loci are associated only with plasticity or mean phenotypes. The results can be applied to develop new cultivars for different objectives, from stable behavior to those specifically-adapted to different environments, by combining loci with different contributions to plasticity or mean phenotype.Research in my laboratory is kindly funded by the Spanish Ministry of Science, Innovation and University and FEDER, grant RTI2018-097665-B-C22 and the European Commission 510 H2020 research and innovation programme through the TOMGEM project agreement no. 679796.Monforte Gilabert, AJ. (2020). Time to exploit phenotypic plasticity. Journal of Experimental Botany. 71(18):5295-5297. https://doi.org/10.1093/jxb/eraa268S529552977118Arnold, P. A., Kruuk, L. E. B., & Nicotra, A. B. (2019). How to analyse plant phenotypic plasticity in response to a changing climate. New Phytologist, 222(3), 1235-1241. doi:10.1111/nph.15656Ayenan, M. A. T., Danquah, A., Hanson, P., Ampomah-Dwamena, C., Sodedji, F. A. K., Asante, I. K., & Danquah, E. Y. (2019). Accelerating Breeding for Heat Tolerance in Tomato (Solanum lycopersicum L.): An Integrated Approach. Agronomy, 9(11), 720. doi:10.3390/agronomy9110720Cui, H., Tsuda, K., & Parker, J. E. (2015). Effector-Triggered Immunity: From Pathogen Perception to Robust Defense. Annual Review of Plant Biology, 66(1), 487-511. doi:10.1146/annurev-arplant-050213-040012Diouf, I., Derivot, L., Koussevitzky, S., Carretero, Y., Bitton, F., Moreau, L., & Causse, M. (2020). Genetic basis of phenotypic plasticity and genotype × environment interactions in a multi-parental tomato population. Journal of Experimental Botany, 71(18), 5365-5376. doi:10.1093/jxb/eraa265Gage, J. L., Jarquin, D., Romay, C., Lorenz, A., Buckler, E. S., Kaeppler, S., … de Leon, N. (2017). The effect of artificial selection on phenotypic plasticity in maize. Nature Communications, 8(1). doi:10.1038/s41467-017-01450-2Ganie, S. A., Molla, K. A., Henry, R. J., Bhat, K. V., & Mondal, T. K. (2019). Advances in understanding salt tolerance in rice. Theoretical and Applied Genetics, 132(4), 851-870. doi:10.1007/s00122-019-03301-8Gerszberg, A., & Hnatuszko-Konka, K. (2017). Tomato tolerance to abiotic stress: a review of most often engineered target sequences. Plant Growth Regulation, 83(2), 175-198. doi:10.1007/s10725-017-0251-xHe, M., He, C.-Q., & Ding, N.-Z. (2018). Abiotic Stresses: General Defenses of Land Plants and Chances for Engineering Multistress Tolerance. Frontiers in Plant Science, 9. doi:10.3389/fpls.2018.01771Kusmec, A., de Leon, N., & Schnable, P. S. (2018). Harnessing Phenotypic Plasticity to Improve Maize Yields. Frontiers in Plant Science, 9. doi:10.3389/fpls.2018.01377Mangin, B., Casadebaig, P., Cadic, E., Blanchet, N., Boniface, M.-C., Carrère, S., … Langlade, N. B. (2017). Genetic control of plasticity of oil yield for combined abiotic stresses using a joint approach of crop modelling and genome-wide association. Plant, Cell & Environment, 40(10), 2276-2291. doi:10.1111/pce.12961Morton, M. J. L., Awlia, M., Al‐Tamimi, N., Saade, S., Pailles, Y., Negrão, S., & Tester, M. (2019). Salt stress under the scalpel – dissecting the genetics of salt tolerance. The Plant Journal, 97(1), 148-163. doi:10.1111/tpj.14189Pascual, L., Desplat, N., Huang, B. E., Desgroux, A., Bruguier, L., Bouchet, J.-P., … Causse, M. (2014). Potential of a tomato MAGIC population to decipher the genetic control of quantitative traits and detect causal variants in the resequencing era. Plant Biotechnology Journal, 13(4), 565-577. doi:10.1111/pbi.12282Suzuki, N., Rivero, R. M., Shulaev, V., Blumwald, E., & Mittler, R. (2014). Abiotic and biotic stress combinations. New Phytologist, 203(1), 32-43. doi:10.1111/nph.12797Wu, W., Ma, B., & Whalen, J. K. (2018). Enhancing Rapeseed Tolerance to Heat and Drought Stresses in a Changing Climate: Perspectives for Stress Adaptation from Root System Architecture. Advances in Agronomy, 87-157. doi:10.1016/bs.agron.2018.05.002Zandalinas, S. I., Mittler, R., Balfagón, D., Arbona, V., & Gómez‐Cadenas, A. (2017). Plant adaptations to the combination of drought and high temperatures. Physiologia Plantarum, 162(1), 2-12. doi:10.1111/ppl.12540Zhu, G., Wang, S., Huang, Z., Zhang, S., Liao, Q., Zhang, C., … Huang, S. (2018). Rewiring of the Fruit Metabolome in Tomato Breeding. Cell, 172(1-2), 249-261.e12. doi:10.1016/j.cell.2017.12.01

Using genetic variability available in the breeder's pool to engineer fruit quality

8 páginas, 1 figura, 2 tablas.-- This article is open-access.We substantiate here the opinion that experts in biotechnology and natural biodiversity can work together on the production of successive waves of next-gen GM fruit crops to improve organoleptic and nutritional quality and therefore generate wider public acceptance. In this scenario genetic engineering becomes a faster and more precise way of transferring genes of interest to fruit crop plants from the same or sexually compatible species (intra- or cisgenesis) than more traditional methods, such as MASPB. The availability of complete genome sequences for an increasing number of crop plants, as well as the results from genomics studies, can assist in the identification of gene-to-trait association. The next wave of GM crops will be able to take full advantage of a Synthetic Biology-based strategy in the development of new fruit varieties by using DNA not necessarily present in the breeder's pool for a wide range of applications. There are still a number of challenges which require attention, such as identifying genes and allelic forms associated with traits of interest and improving the precision and stability of the transferred DNA, etc.Peer reviewe

Performance of mixed formulations for the particle finite element method in soil mechanics problems

This paper presents a computational framework for the numerical analysis of fluid-saturated porous media at large strains. The proposal relies, on one hand, on the particle finite element method (PFEM), known for its capability to tackle large deformations and rapid changing boundaries, and, on the other hand, on constitutive descriptions well established in current geotechnical analyses (Darcy’s law; Modified Cam Clay; Houlsby hyperelasticity). An important feature of this kind of problem is that incompressibility may arise either from undrained conditions or as a consequence of material behaviour; incompressibility may lead to volumetric locking of the low-order elements that are typically used in PFEM. In this work, two different three-field mixed formulations for the coupled hydromechanical problem are presented, in which either the effective pressure or the Jacobian are considered as nodal variables, in addition to the solid skeleton displacement and water pressure. Additionally, several mixed formulations are described for the simplified single-phase problem due to its formal similitude to the poromechanical case and its relevance in geotechnics, since it may approximate the saturated soil behaviour under undrained conditions. In order to use equal-order interpolants in displacements and scalar fields, stabilization techniques are used in the mass conservation equation of the biphasic medium and in the rest of scalar equations. Finally, all mixed formulations are assessed in some benchmark problems and their performances are compared. It is found that mixed formulations that have the Jacobian as a nodal variable perform better

Simulation of penetration problems in geomechanics

The simulation of penetration problems in geomaterials is a challenging problem as it involves large deformations and displacements as well as strong non-linearities affecting material behaviour, geometry and contact surfaces. The paper presents examples of modelling of the cone penetration test using two procedures: a discrete approach and a continuum approach. The discrete approach is based on the Discrete Element Method where a granular material is represented by an assembly of separate particles. Cone penetration has been successfully simulated for the case of crushable sands. For the continuum approach, the Particle Finite Element Method has been adopted. The procedure has been effectively applied to the modeling of undrained cone penetration into clays. Although not exempt of problems, both approaches yield realistic results leading to the possibility of a closer examination and an enhanced understanding of the mechanisms underlying penetration problems in geomechanics.Postprint (published version

Undrained strength from CPTu in brittle soils: a numerical perspective

Static liquefaction of soils that have a brittle undrained response (hydraulic fills, mine tailings or sensitive clays) may lead to sudden failures of large consequence. Given the importance of undrained failure, obtaining precise estimates of peak and residual yield strength is important. The CPTu plays a major role in the geotechnical characterization of these geomaterials and so do CPTu-based estimates of undrained strength. Most of the methods available for CPTu-based estimation of undrained strength are empirical, based on correlation with other laboratory or field tests. When such correlations are established difficulties appear due to variable disturbance affecting the reference laboratory samples and parasitic effects, such as unaccounted for partial drainage during penetration or unknown side friction, affecting the cone results. Such difficulties are not present when using numerical simulation. The paper builds upon a series of CPTu simulations using a model able to represent brittle undrained failure. Confounding factors such as partial drainage and cone side friction are systematically varied to examine their effect on the results. The results are then employed to examine the performance of several empirical methods frequently employed to obtain peak and residual strength from CPTu.The authors acknowledge financial support from the Spanish Ministry of Economy and Competitiveness, through the “Severo Ochoa Programme for Centres of Excellence in R&D” (CEX2018-000797-S).Postprint (published version

On the basic phenomenon of soil-structure interaction on the free vibration response of beams : Application to railway brigdes

The dynamic transverse response of beam type bridges under railway traffic is addressed in this contribution. In particular, how soil-structure interaction may affect the critical or resonant velocities and the associated vibratory amplitudes is evaluated in detail. Resonance in beams, due to the circulation of equidistant loads, is highly influenced by the free vibration response that every single load leaves after traversing the structure. On this basis a numerical investigation is carried out analysing the effects of the wave propagation problem on the free vibration response of simply-supported beams in a wide range of travelling velocities. To this end a coupled three-dimensional boundary element-finite element model formulated in the time domain is used to reproduce the soil and structural behaviour, respectively. A catalogue of bridge deck typologies is defined, covering lengths, associated linear masses and fundamental frequencies that may experience high levels of transverse accelerations under resonant conditions, for nowadays existing trains and design velocities. Lengths ranging from 12.5 to 25 m are evaluated, along with fundamental frequencies covering most common typologies. A homogeneous soil is considered with shear wave velocities in the interval 150 to 365 m/s. From the single load free vibration parametric analysis conclusions are derived regarding the conditions of maximum free vibration and cancellation of the deck response. These conclusions are used afterwards to justify how resonant amplitudes of the bridge under the circulation of railway convoys may be affected by the soil properties, leading to substantially amplified responses or to almost imperceptible ones, and a numerical example is included to show the aforementioned situations.The first two authors would like to acknowledge the financial support provided by Universitat Jaume I under the research project P1··1B2015-54. The third and fourth authors would like to acknowledge the financial support provided by the Spanish Ministry of Economy and Competitiveness (Ministerio de Economía y Competitividad) under the research project [BIA2013-43085-P]. The authors also wish to acknowledge the support provided by the Andalusian Scientific Computing Centre (CICA)

A stable mesh-independent approach for numerical modelling of structured soils at large strains

We describe the large strain implementation of an elasto-plastic model for structured soils into G-PFEM, a code developed for geotechnical simulations using the Particle Finite Element Method. The constitutive model is appropriate for naturally structured clays, cement-improved soils and soft rocks. Structure may result in brittle behavior even in contractive paths; as a result, localized failure modes are expected in most applications. To avoid the pathological mesh-dependence that may accompany strain localization, a nonlocal reformulation of the model is employed. The resulting constitutive model is incorporated into a numerical code by means of a local explicit stress integration technique. To ensure computability this is hosted within a more general Implicit-Explicit integration scheme (IMPLEX). The good performance of these techniques is illustrated by means of element tests and boundary value problems.Peer ReviewedPostprint (author's final draft

Performance of mixed formulations for the particle finite element method in soil mechanics problems

This paper presents a computational framework for the numerical analysis of fluid-saturated porous media at large strains. The proposal relies, on one hand, on the particle finite element method (PFEM), known for its capability to tackle large deformations and rapid changing boundaries, and, on the other hand, on constitutive descriptions well established in current geotechnical analyses (Darcy’s law; Modified Cam Clay; Houlsby hyperelasticity). An important feature of this kind of problem is that incompressibility may arise either from undrained conditions or as a consequence of material behaviour; incompressibility may lead to volumetric locking of the low-order elements that are typically used in PFEM. In this work, two different three-field mixed formulations for the coupled hydromechanical problem are presented, in which either the effective pressure or the Jacobian are considered as nodal variables, in addition to the solid skeleton displacement and water pressure. Additionally, several mixed formulations are described for the simplified single-phase problem due to its formal similitude to the poromechanical case and its relevance in geotechnics, since it may approximate the saturated soil behaviour under undrained conditions. In order to use equal-order interpolants in displacements and scalar fields, stabilization techniques are used in the mass conservation equation of the biphasic medium and in the rest of scalar equations. Finally, all mixed formulations are assessed in some benchmark problems and their performances are compared. It is found that mixed formulations that have the Jacobian as a nodal variable perform better.Peer ReviewedPostprint (author's final draft