Mutational and evolutionary dynamics of Brassicaceae plant organs

Modern wheat varieties that were selected since the Green Revolution are generally grown with synthetic chemical inputs, and ancient varieties released before1960 without. Thus, when changes occur in rhizosphere microbiota structure, it is not possible to distinguish if they are due to (i) changes in wheat genotypes by breeding, (ii) modifications of the environment via synthetic chemical inputs, or (iii) phenotypic plasticity, the interaction between wheat genotype and the environment. Using a crossed factorial design in the field, we evaluated the effects of either modern or ancient wheat varieties grown with or without chemical inputs (a N fertilizer, a fungicide, and an herbicide) on “microbiome as a phenotype.” We analyzed the rhizosphere microbiota by bacterial and fungal amplicon sequencing, coupled with microscope observations of mycorrhizal associations. We found that plant genotype and phenotypic plasticity had the most influence on rhizosphere microbiota, whereas inputs had only marginal effects. Phenotypic plasticity was particularly important in explaining diversity variations in bacteria and fungi but had no impact on the mycorrhizal association. Our results show an interest in considering the interaction between wheat genotype and the environment in breeding programs, by focusing on genes involved in the phenotypic plasticity of plant-microbe interactions.

Control of Phenotypic Plasticity Via Regulatory Genes

Collections‐based systematics and biogeography in the 21st century: A tribute to Dr. Vicki Funk

Plants show phenotypic plasticity in response to changing or extreme abiotic environments; but over millions of years they also have co-evolved to respond to the presence of soil microbes. Studies on phenotypic plasticity in plants have focused mainly on the effects of the changing environments on plants’ growth and survival. Evidence is now accumulating that the presence of microbes can alter plant phenotypic plasticity in a broad range of traits in response to a changing environment. In this review, we discuss the effects of microbes on plant phenotypic plasticity in response to changing environmental conditions, and how this may affect plant fitness. By using a range of specific plant-microbe interactions as examples, we demonstrate that one way that microbes can alleviate the effect of environmental stress on plants and thus increase plant fitness is to remove the stress, e.g., nutrient limitation, directly. Furthermore, microbes indirectly affect plant phenotypic plasticity and fitness through modulation of plant development and defense responses. In doing so, microbes affect fitness by both increasing or decreasing the degree of phenotypic plasticity, depending on the phenotype and the environmental stress studied, with no clear difference between the effect of prokaryotic and eukaryotic microbes in general. Additionally, plants have the ability to modulate microbial behaviors, suggesting that they manipulate bacteria, enhancing interactions that help them cope with stressful environments. Future challenges remain in the identification of the many microbial signals that modulate phenotypic plasticity, the characterization of plant genes, e.g. receptors, that mediate the microbial effects on plasticity, and the elucidation of the molecular mechanisms that link phenotypic plasticity with fitness. The characterization of plant and microbial mutants defective in signal synthesis or perception, together with carefully designed glasshouse or field experiments that test various environmental stresses will be necessary to understand the link between molecular mechanisms controlling plastic phenotypes with the resulting effects on plant fitness.

Phenotypic plasticity, a key mechanism by which plants respond to environmental change, tends to be lower under stressful conditions. Phenotypic integration refers to the degree of trait correlation and is thought to limit phenotypic plasticity and to be higher under stressful conditions, thus potentially explaining the limits to plasticity. Yet, the evidence of whether integrated traits are less plastic is largely mixed. Alternative evidence suggests that phenotypic integration might limit the variation rather than the strength in plastic responses, resulting in correlated plastic responses. We performed a phylogenetically controlled meta‐analysis to evaluate whether phenotypic integration limits the magnitude or the variation in plastic responses under stressful conditions. The meta‐analysis included data from 156 study cases obtained from 41 experimental studies, encompassing 83 different plant species. We also tested whether the association between phenotypic integration and plasticity depended on the level of phenotypic integration in the population, experimental treatment, functional group, or ontogeny. Lastly, to understand the conditions under which limits to plasticity may occur, we evaluated whether phenotypic integration increased in response to biotic or abiotic stress. Overall, more strongly integrated traits were not found to be less plastic. Instead, we found greater phenotypic integration to be associated with lower variation in plastic responses, that is resulting in a greater correlation among plastic responses across traits. The association between plastic responses and phenotypic integration was independent of experimental treatment, plant functional group and ontogeny. Phenotypic integration did not consistently increase with biotic or abiotic stress. Our study reveals a different type of limit imposed on plastic responses by phenotypic integration, reducing the variation rather than the magnitude of plastic responses, which is consistent with previous evidence indicating correlated plasticity among correlated traits. The ecological implications of these limits must be addressed: whether they constrain plant functional responses to the environment or are rather adaptive. Our results could help reconcile the seemingly contradictory evidence in the literature, showing both positive and negative associations between trait‐level phenotypic integration and trait‐level phenotypic plasticity; we suggest that it depends on whether correlated traits are all highly or barely plastic, respectively. Read the free Plain Language Summary for this article on the Journal blog.

Functional ecology is the study of the interactions of individuals, populations, and species with their environments. This broad definition embraces fields ranging from physiological ecology to evolutionary ecology. These fields are unified in their study of the process of adaptation to different environments and how different properties of the organism confer adaptation to the environment. The observation that an organism’s traits depend on its environment easily leads to the hypothesis that phenotypic plasticity functions as a way of adapting to a variable environment. The different fields comprising functional ecology have all addressed this hypothesis but have followed very different lines of evidence. In evolutionary biology, phenotypic plasticity is assessed in terms of genetic variation and fitness consequences; in physiological ecology, in terms of the functional consequences to stress tolerance and carbon acquisition; and in developmental biology, in terms of the mechanisms by which the environment can affect development of a trait. In this chapter, I describe some of the areas of concordance from these different fields of plant functional ecology, and how they can inform each other to suggest new areas of research on phenotypic plasticity in plants. Bradshaw (1965) and many others have suggested that the sessile nature of plants particularly favors phenotypic plasticity as a mechanism for adaptation to a variable environment. There is considerable evidence that plants defend against predators, cope with stress, and compete and forage for resources through cued patterns of growth and environmentally determined development. Acclimation responses demonstrate that a plant’s ability to tolerate a particular environmental stress is increased by prior exposure to that stress. Transplant and common garden experiments have demonstrated that the environment rather than the genotype causes much of the character variation within a species.

Due to a specific structure of its main organs (root, stem, leaves, and head), sunflower can be successfully grown on marginal soils and in semiarid conditions, and it is more resist‐ ant to abiotic stresses, than other field crops. Unfortunately, it is very sensitive to biotic stresses. In sunflower breeding for resistance to abiotic stresses, the greatest progress has been made in selection for drought resistance. Breeders use over 30 different parameters in sunflower screening for drought resistance, with physiological ones being the predomi‐ nant type. The best breeding results have been achieved using the phenomenon of staygreen, with the added bonus that this method incorporates into the cultivated sunflower not only drought resistance but resistance to Macrophomina and Phomopsis as well. The di‐ versity of the wild Helianthus species offers great possibilities for increasing the genetic resistance of the cultivated sunflower toward abiotic stresses. In using wild sunflower species in sunflower breeding for drought resistance and resistance to salinity, best re‐ sults have so far been achieved with H. argophyllus and H. paradoxus, respectively. In ad‐ dition to the use of wild Helianthus species, sunflower breeding for abiotic stress resistance should also make more use of molecular breeding techniques. More progress has been made in sunflower breeding for heat resistance than in that for cold resistance. Specific breeding programs dealing with sunflower resistance to mineral deficiency and mineral toxicity have yet to be established. Concerning biotic stresses, the main problem in sunflower cultivation is caused by fungal diseases. Genetic variability of cultivated sunflower is very low and deficient in diseaseresistance genes. Due to wild sunflower species of the Helianthus genus, genes that con‐ fer resistance to certain diseases were discovered and incorporated into the genotypes of the cultivated sunflower. Based on the wild species, genes were found that confer resist‐ ance to Plasmopara halstedii, Puccinia helianthi, Verticillium dahliae, V. albo-atrum, and Erysi‐ phe cichoracearum. Furthermore, wild sunflower species provide a high level of tolerance (field resistance) to Phomopsis/Diaporthe helianthi, Macrophomina phaseolina, Albugo erago‐ pognis, and Alternaria ssp. Sources of resistance to other harmful diseases are sought after within wild sunflower species. © 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. With the use of one wild species of H. annuus from Kansas (USA.), genes conferring re‐ sistance to a group of imidazolinone (IMI) or sulfonylurea herbicides were discovered. Moreover, similar genes were found through induced mutations. These sources of resist‐ ance provide successful control over a broad spectrum of weeds, which infest sunflower crops, including broomrape. The growth of the parasitic weed sunflower broomrape (Orobanche cumana Wallr) is a ma‐ jor issue in sunflower production, especially in Central and Eastern Europe, as well as in Spain. Six races of broomrape have been detected (A, B, C, D, E, and F) and dominant resistance genes (Or1, Or2, Or3, Or4, Or4, and Or6) were found in wild sunflower species. During the last 4–10 years, new virulent races of broomrape emerged in several European countries. Geneticists and breeders work on finding the sources of resistance to the new broomrape races in wild sunflower species. Numerous insect species cause economic damages during sunflower production, espe‐ cially in North America (the homeland of sunflower). Homoeosoma species are the most widespread insects that infest sunflower. Homoeosoma nebulella infests sunflower in Eu‐ rope and Asia, while infestation with H. electellum poses a major problem in USA, Cana‐ da, and Mexico. Based on the use of wild sunflower species H. tuberosus, genes conferring resistance to Homoeosoma species were incorporated. Sunflower has an armored layer in the hull, which provides resistance to this insect. Sources of resistance to other economi‐ cally harmful insects are sought after. New methods in biotechnology, particularly marker genes, have been frequently used in breeding for abiotic and biotic stresses.

Plants are exposed to heterogeneity in the environment where new stress factors (i.e., climate change, land use change, and invasiveness) are introduced, and where inter- and intraspecies differences may reflect resource limitation and/or environmental stress factors. Phenotypic plasticity is considered one of the major means by which plants can cope with environmental factor variability. Nevertheless, the extent to which phenotypic plasticity may facilitate survival under environmental condition changes still remains largely unknown because results are sometimes controversial. Thus, it is important to identify plant functional traits in which plasticity may play a determinant role in plant response to global change as well as on the ecological consequences at an ecosystem level for the competition between wild and invasive species, considering that species with a greater adaptive plasticity may be more likely to survive in novel environmental conditions. In the near future, it will be important to increase long-term studies on natural populations in order to understand plant response to environmental factor fluctuations including climate change. There is the necessity to analyze variations at phenotypic and genetic levels for the same species and, in particular, for endemic and rare species because these could have drastic effects at an ecosystem level.

Predicting plastic responses is crucial to assess plant species potential to adapt to climate change, but little is known about which factors drive the biogeographical patterns of phenotypic plasticity in plants. Theory predicts that climatic variability would select for increased phenotypic plasticity, whereas evidence indicates that stressful conditions can limit phenotypic plasticity. Using a meta-analytic, phylogeny-corrected approach to global data on plant phenotypic plasticity, we tested whether latitude, climate, climatic variability and/or stressful conditions are predictors of plastic responses at a biogeographical scale. We found support for a positive association between phenotypic plasticity and climatic variability only for plasticity in allocation. Plasticity in leaf morphology, size and physiology were positively associated with mean annual temperature. We also found evidence that phenotypic plasticity in physiology is limited by cold stress. Overall, plant plastic responses to non-climatic factors were stronger than responses to climatic factors. However, while climatic conditions were associated with plant plastic responses to climatic factors, they generally did not relate to plastic responses to other abiotic or biotic factors. Our study highlights the need to consider those factors that favour and limit phenotypic plasticity in order to improve predictive frameworks addressing plant species' potential to adapt to climate change.

Based on empirical evidence from the literature we propose that, in nature, phenotypic plasticity in plants is usually expressed at a subindividual level. While reaction norms (i.e. the type and the degree of plant responses to environmental variation) are a property of genotypes, they are expressed at the level of modular subunits in most plants. We thus contend that phenotypic plasticity is not a whole-plant response, but a property of individual meristems, leaves, branches and roots, triggered by local environmental conditions. Communication and behavioural integration of interconnected modules can change the local responses in different ways: it may enhance or diminish local plastic effects, thereby increasing or decreasing the differences between integrated modules exposed to different conditions. Modular integration can also induce qualitatively different responses, which are not expressed if all modules experience the same conditions. We propose that the response of a plant to its environment is the sum of all modular responses to their local conditions plus all interaction effects that are due to integration. The local response rules to environmental variation, and the modular interaction rules may be seen as evolving traits targeted by natural selection. Following this notion, whole-plant reaction norms are an integrative by-product of modular plasticity, which has far-reaching methodological, ecological and evolutionary implications.

Changes in resource-use strategy and phenotypic plasticity associated with selection for yield in wild species native to arid environments

The phenotypic plasticity of plants in response to change in their light environment, and in particularly, to shade is a schoolbook example of ecologically relevant phenotypic plasticity with evolutionary adaptive implications. Epigenetic variation is known to potentially underlie plant phenotypic plasticity. Yet, little is known about its role in ecologically and evolutionary relevant mechanisms shaping the diversity of plant populations in nature. Here we used a reference-free reduced representation bisulfite sequencing method for non-model organisms (epiGBS) to investigate changes in DNA methylation patterns across the genome in snapdragon plants (Antirrhinum majus L.). We exposed plants to sunlight versus artificially induced shade in four highly inbred lines to exclude genetic confounding effects. Our results showed that phenotypic plasticity in response to light versus shade shaped vegetative traits. They also showed that DNA methylation patterns were modified under light versus shade, with a trend towards global effects over the genome but with large effects found on a restricted portion. We also detected the existence of a correlation between phenotypic and epigenetic variation that neither supported nor rejected its potential role in plasticity. While our findings imply epigenetic changes in response to light versus shade environments in snapdragon plants, whether these changes are directly involved in the phenotypic plastic response of plants remains to be investigated. Our approach contributed to this new finding but illustrates the limits in terms of sample size and statistical power of population epigenetic approaches in non-model organisms. Pushing this boundary will be necessary before the relationship between environmentally induced epigenetic changes and phenotypic plasticity is clarified for ecologically relevant mechanisms with evolutionary implications.

竹类植物对异质生境的适应：表型可塑性

Most modern carnation (Dianthus caryophyllus L.) cultivars have weak fragrances dominated by the scent of methyl benzoate. Wild Dianthus species with strong or unique scents may be useful gene resources for the improvement of carnation fragrances. We investigated the scents of interspecific hybrids between carnations and fragrant wild species by gas chromatography-mass spectrometry (GC-MS), and evaluated the usefulness of wild species for fragrant breeding in carnations. Dianthus hungaricus, which produced large amounts of various benzenoids, was crossed with a carnation with a floral scent dominated by methyl benzoate, but benzenoid diversity was not increased in the interspecific hybrid. We also analyzed some existing interspecific hybrids. Dianthus superbus var. longicalycinus had high amounts of β-ocimene and β-caryophyllene. These terpenoids were acquired as principal scent compounds by some interspecific hybrids between this species and a carnation lacking terpenoids. Three unidentified wild species (Dianthus sp. 4, 5, and 6) emitted high amounts of benzenoids, including eugenol, benzyl alcohol, methyl o-anisate, and methyl salicylate. These benzenoids were also detected in interspecific hybrids between carnations and the wild species, and the amounts were increased compared to the parental carnation. The emission of these scent compounds of wild Dianthus species was inherited by most hybrids lines; the variety and amounts of scent compounds tended to increase compared to parental carnations, although there was no general hereditary pattern. As we actually sensed the fragrances of the principal compounds from some hybrid flowers, the usefulness of interspecific hybridizations for the improvement of flower fragrances was confirmed. Dianthus superbus var. longicalycinus and Dianthus sp. 4, 5, and 6 seemed promising resources regarding the addition of terpenoids and the increase in benzenoid variation in the floral volatiles of carnations.

SUMMARY Due to a specific structure of its main organs (root, stem, leaves, head), sunflower can be successfully grown on marginal soils and in semi-arid conditions and it is more resistant to abiotic stresses than other field crops. In sunflower breeding for resistance to abiotic stresses, the greatest progress has been made in selection for drought resistance. Breeders use over 30 different parameters in sunflower screening for drought resistance, with physiological ones being the predominant type. Best breeding results have been achieved using the phenomenon of stay-green, with the added bonus that this method incorporates into the cultivated sunflower not only drought resistance but resistance to Macrophomina and Phomopsis as well. The diversity of the wild Helianthus species offers great possibilities for increasing the genetic resistance of the cultivated sunflower towards abiotic stresses. In using wild sunflower species in sunflower breeding for drought resistance and resistance to salinity, best results have so far been achieved with H. argophyllus and H. paradoxus , respectively. In addition to the use of wild Helianthus species, sunflower breeding for abiotic stress resistance should also make more use of molecular breeding techniques. More progress has been made in sunflower breeding for heat resistance than in that for cold resistance. Specific breeding programs dealing with sunflower resistance to mineral deficiency and mineral toxicity have yet to be established. Sunflower breeders worldwide should commit to a greater use of wild Helianthus species in breeding for resistance to abiotic stresses. RESUMEN Debido a la estructura de sus órganos principales (raíz, hojas, tallo, capítulo), el girasol puede cultivarse exitosamente en suelos marginales y condiciones semiáridas y es más resistente a estreses abióticos que otros cultivos. En lo referido a mejoramiento de girasol por resistencia a estreses abióticos, el mayor progreso logrado ha sido en mejoramiento por resistencia a sequía. Los mejoradores utilizan más de 30 parámetros diferentes en la evaluación de girasol por resistencia a sequía, siendo los atributos fisiológicos los caracteres predominantes. Los mejores resultados del mejoramiento se han alcanzado a través de la utilización del fenómeno stay-green, con el bonus agregado de que este método no sólo incorpora resistencia a sequía en el girasol cultivado, sino también resistencia a Macrophomina y Phomopsis . La riqueza encontrada entre las especies silvestres del género Helianthus ofrece grandes posibilidades de incrementar la resistencia genética del girasol cultivado a los estreses abióticos. Los mejores resultados en la utilización de especies silvestres en mejoramiento de girasol por resistencia a sequía y salinidad se han alcanzado mediante la utilización de H. argophyllus y H. paradoxus , respectivamente. El mejoramiento de girasol por resistencia a estreses abióticos debería hacer un mayor uso de las herramientas moleculares disponibles, además del uso de especies silvestres del género Helianthus . Ha habido un mayor progreso en la obtención de resistencia a estrés por alta temperatura en girasol que por resistencia a frío. Todavía falta establecer programas específicos por resistencia a deficiencias minerales y toxicidad por minerales. Los mejoradores de girasol a lo largo del mundo deberían comprometerse a hacer un mayor uso de las especies silvestres del género Helianthus en mejoramiento por resistencia a estreses abióticos. RÉSUMÉ Du fait de la structure spécifique de ses principaux organes (racine, tige, feuilles, capitule), le tournesol peut être cultivé avec succès sur des sols marginaux et dans des conditions semi-arides, et est plus résistant aux stress abiotiques que les autres plantes de grande culture. Dans l’amélioration génétique du tournesol pour sa résistance aux stress abiotiques, les plus grands progrès ont été réalisés pour sa résistance à la sécheresse. Les sélectionneurs ont utilisé plus de 30 paramètres différents dans le screening du tournesol pour sa résistance à la sécheresse, et parmi ceux-là, les critères physiologiques ont été prédominants. Les meilleurs résultats ont été obtenus par l’utilisation du phénomène de “stay green”, par le bonus que cette méthode apporte non seulement pour la résistance à la sécheresse mais encore pour la résistance à Macrophomina et à Phomopsis . La richesse des espèces sauvages du genre Helianthus offre de grandes possibilités pour augmenter la résistance du tournesol cultivé aux stress abiotiques. Par l’utilisation des formes sauvages dans l’amélioration du tournesol pour la résistance à la sécheresse et à la salinité , les meilleurs résultats ont été obtenus avec H. argophyllus et H. paradoxus , respectivement. En addition à l’utilisation de ces formes sauvages, l’amélioration génétique devrait faire un usage plus important des techniques de sélection moléculaire. Des progrès plus importants ont été réalisés pour la résistance aux fortes températures que pour la résistance au froid. Des programmes spécifiques pour la résistance à des déficits et toxicités minérales doivent maintenant être mis en place. Les sélectionneurs de tournesol de part le monde devraient consacrer des efforts plus importants à l’utilisation des formes sauvages pour l’amélioration génétique de la résistance aux stress abiotiques.