Phenotypic Variation In Plants Research Articles

Evolutionary and ecological functional genomics, from lab to the wild.

Plant phenotypes are the result of both genetic and environmental forces that act to modulate trait expression. Over the last few years, numerous approaches in functional genomics and systems biology have led to a greater understanding of plant phenotypic variation and plant responses to the environment. These approaches, and the questions that they can address, have been loosely termed evolutionary and ecological functional genomics (EEFG), and have been providing key insights on how plants adapt and evolve. In particular, by bringing these studies from the laboratory to the field, EEFG studies allow us to gain greater knowledge of how plants function in their natural contexts.

Partial maintenance of organ-specific epigenetic marks during plant asexual reproduction leads to heritable phenotypic variation

Plants differ from animals in their capability to easily regenerate fertile adult individuals from terminally differentiated cells. This unique developmental plasticity is commonly observed in nature, where many species can reproduce asexually through the ectopic initiation of organogenic or embryogenic developmental programs. While organ-specific epigenetic marks are not passed on during sexual reproduction, the fate of epigenetic marks during asexual reproduction and the implications for clonal progeny remain unclear. Here we report that organ-specific epigenetic imprints in Arabidopsis thaliana can be partially maintained during asexual propagation from somatic cells in which a zygotic program is artificially induced. The altered marks are inherited even over multiple rounds of sexual reproduction, becoming fixed in hybrids and resulting in heritable molecular and physiological phenotypes that depend on the identity of the founder tissue. Consequently, clonal plants display distinct interactions with beneficial and pathogenic microorganisms. Our results demonstrate how novel phenotypic variation in plants can be unlocked through altered inheritance of epigenetic marks upon asexual propagation.

Uncovering the contribution of epigenetics to plant phenotypic variation in Mediterranean ecosystems.

Epigenetic signals can affect plant phenotype and fitness and be stably inherited across multiple generations. Epigenetic regulation plays a key role in the mechanisms of plant response to the environment, without altering DNA sequence. As plants cannot adapt behaviourally or migrate instantly, such dynamic epigenetic responses may be particularly crucial for survival of plants within changing and challenging environments, such as the Mediterranean-Type Ecosystems (MTEs). These ecosystems suffer recurrent stressful events (warm and dry summers with associated fire regimes) that have selected for plants with similar phenotypic complex traits, resulting in similar vegetation growth forms. However, the potential role of epigenetics in plant adaptation to recurrent stressful environments such as the MTEs has generally been ignored. To understand the full spectrum of adaptive processes in such contexts, it is imperative to prompt study of the causes and consequences of epigenetic variation in natural populations. With this purpose, we review here current knowledge on epigenetic variation in natural populations and the genetic and epigenetic basis of some key traits for plants in the MTEs, namely those traits involved in adaptation to drought, fire and oligotrophic soils. We conclude there is still much to be learned about 'plant epigenetics in the wild' and, thus, we propose future research steps in the study of natural epigenetic variation of key traits in the MTEs at different scales.

Response-based selection of barley cultivars and legume species for complementarity: Root morphology and exudation in relation to nutrient source

Phosphorus (P) and nitrogen (N) use efficiency may be improved through increased biodiversity in agroecosystems. Phenotypic variation in plants’ response to nutrient deficiency may influence positive complementarity in intercropping systems. A multicomponent screening approach was used to assess the influence of P supply and N source on the phenotypic plasticity of nutrient foraging traits in barley (H. vulgare L.) and legume species. Root morphology and exudation were determined in six plant nutrient treatments. A clear divergence in the response of barley and legumes to the nutrient treatments was observed. Root morphology varied most among legumes, whereas exudate citrate and phytase activity were most variable in barley. Changes in root morphology were minimized in plants provided with ammonium in comparison to nitrate but increased under P deficiency. Exudate phytase activity and pH varied with legume species, whereas citrate efflux, specific root length, and root diameter lengths were more variable among barley cultivars. Three legume species and four barley cultivars were identified as the most responsive to P deficiency and the most contrasting of the cultivars and species tested. Phenotypic response to nutrient availability may be a promising approach for the selection of plant combinations for minimal input cropping systems.

Non-targeted Metabolomics in Diverse Sorghum Breeding Lines Indicates Primary and Secondary Metabolite Profiles Are Associated with Plant Biomass Accumulation and Photosynthesis.

Metabolomics is an emerging method to improve our understanding of how genetic diversity affects phenotypic variation in plants. Recent studies have demonstrated that genotype has a major influence on biochemical variation in several types of plant tissues, however, the association between metabolic variation and variation in morphological and physiological traits is largely unknown. Sorghum bicolor (L.) is an important food and fuel crop with extensive genetic and phenotypic variation. Sorghum lines have been bred for differing phenotypes beneficial for production of grain (food), stem sugar (food, fuel), and cellulosic biomass (forage, fuel), and these varying phenotypes are the end products of innate metabolic programming which determines how carbon is allocated during plant growth and development. Further, sorghum has been adapted among highly diverse environments. Because of this geographic and phenotypic variation, the sorghum metabolome is expected to be highly divergent; however, metabolite variation in sorghum has not been characterized. Here, we utilize a phenotypically diverse panel of sorghum breeding lines to identify associations between leaf metabolites and morpho-physiological traits. The panel (11 lines) exhibited significant variation for 21 morpho-physiological traits, as well as broader trends in variation by sorghum type (grain vs. biomass types). Variation was also observed for cell wall constituents (glucan, xylan, lignin, ash). Non-targeted metabolomics analysis of leaf tissue showed that 956 of 1181 metabolites varied among the lines (81%, ANOVA, FDR adjusted p < 0.05). Both univariate and multivariate analyses determined relationships between metabolites and morpho-physiological traits, and 384 metabolites correlated with at least one trait (32%, p < 0.05), including many secondary metabolites such as glycosylated flavonoids and chlorogenic acids. The use of metabolomics to explain relationships between two or more morpho-physiological traits was explored and showed chlorogenic and shikimic acid to be associated with photosynthesis, early plant growth and final biomass measures in sorghum. Taken together, this study demonstrates the integration of metabolomics with morpho-physiological datasets to elucidate links between plant metabolism, growth, and architecture.

Morphological diversity of mango germplasm from the upper Athi River region of Eastern Kenya: An analysis based on non- fruit descriptors

Phenotypic variation in plants can be evaluated by morphological characterization using visual attributes. Fruits have been the major descriptors for identification of different varieties of fruit crops. However, even in their absence, farmers, breeders and interested stakeholders require to distinguish between different mango varieties. This study aimed at determining diversity in mango germplasm from the Upper Athi River (UAR) and providing useful alternative descriptors for the identification of different mango varieties in the absence of fruits. A total of 20 International Plant Genetic Resources Institute (IPGRI) descriptors for mango were selected for use in the visual assessment of 98 mango accessions from 15 sites of the UAR region of eastern Kenya. Purposive sampling was used to identify farmers growing diverse varieties of mangoes. Evaluation of the descriptors was performed on-site and the data collected were then subjected to multivariate analysis including Principal Component Analysis (PCA) and Cluster analysis, one- way analysis of variance (ANOVA) and Chi square tests. Results classified the accessions into two major groups corresponding to indigenous and exotic varieties. The PCA showed the first six principal components accounting for 75.12% of the total variance. A strong and highly significant correlation was observed between the color of fully grown leaves, leaf blade width, leaf blade length and petiole length and also between the leaf attitude, color of young leaf, stem circumference, tree height, leaf margin, growth habit and fragrance. Useful descriptors for morphological evaluation were 14 out of the selected 20; however, ANOVA and Chi square test revealed that diversity in the accessions was majorly as a result of variations in color of young leaves, leaf attitude, leaf texture, growth habit, leaf blade length, leaf blade width and petiole length traits. These results reveal that mango germplasm in the UAR has significant diversity and that other morphological traits apart from fruits can be useful in morphological characterization of mango. Keywords: Mango, morphological characterization, Principal Component Analysis, IPGRI, eastern Kenya

Drift effects on the multivariate floral phenotype of Calceolaria polyrhiza during a post-glacial expansion in Patagonia.

Quaternary environmental changes substantially impacted the landscape and promoted rapid evolutionary changes in many species; however, analyses of adaptive phenotypic variation in plants have usually neglected the underlying historical context. Here, we associate phylogeography and phenotypic evolution by analysing the divergence of Calceolaria polyrhiza multivariate floral phenotype after a Pleistocene post-glacial expansion in Patagonia. Phenotypic matrix (P) properties (size, shape, orientation and phenotypic integration) of six refugium and six recent populations from two different phylogroups were compared following different approaches. We found that P-matrix shape and orientation remained stable despite the strong phylogeographic footprint of post-glacial expansion. However, average proportional reductions in matrix size supported the expectation that drift had a significant effect on the floral phenotype in the northern phylogroup. When phylogeographic history was not included in the analyses, the results overestimated phenotypic differences, whereas under explicit phylogeographic control, drift appeared as the best explanation for matrix differences. In general, recent populations showed a larger phenotypic divergence among them, but a lower overall phenotypic variation than refugium populations. Random Skewers analyses indicated a lower potential response to selection in recently colonized populations than in refugium populations. We discuss that the combination of phylogeographic analyses with geographical distribution of functional phenotypic (genotypic) variation is critical not only to understand how historical effects influence adaptive evolution, but also to improve field comparisons in evolutionary ecology studies.

Transcriptomes of Plant Gametophytes Have a Higher Proportion of Rapidly Evolving and Young Genes than Sporophytes.

Reproductive traits in plants tend to evolve rapidly due to various causes that include plant-pollinator coevolution and pollen competition, but the genomic basis of reproductive trait evolution is still largely unknown. To characterize evolutionary patterns of genome wide gene expression in reproductive tissues in the gametophyte and to compare them to developmental stages of the sporophyte, we analyzed evolutionary conservation and genetic diversity of protein-coding genes using microarray-based transcriptome data from three plant species, Arabidopsis thaliana, rice (Oryza sativa), and soybean (Glycine max). In all three species a significant shift in gene expression occurs during gametogenesis in which genes of younger evolutionary age and higher genetic diversity contribute significantly more to the transcriptome than in other stages. We refer to this phenomenon as “evolutionary bulge” during plant reproductive development because it differentiates the gametophyte from the sporophyte. We show that multiple, not mutually exclusive, causes may explain the bulge pattern, most prominently reduced tissue complexity of the gametophyte, a varying extent of selection on reproductive traits during gametogenesis as well as differences between male and female tissues. This highlights the importance of plant reproduction for understanding evolutionary forces determining the relationship of genomic and phenotypic variation in plants.

Genetic characterization of fig tree mutants with molecular markers

The fig (Ficus carica L.) is a fruit tree of great world importance and, therefore, the genetic improvement becomes an important field of research for better crops, being necessary to gather information on this species, mainly regarding its genetic variability so that appropriate propagation projects and management are made. The improvement programs of fig trees using conventional procedures in order to obtain new cultivars are rare in many countries, such as Brazil, especially due to the little genetic variability and to the difficulties in obtaining plants from gamete fusion once the wasp Blastophaga psenes, responsible for the natural pollinating, is not found in Brazil. In this way, the mutagenic genetic improvement becomes a solution of it. For this reason, in an experiment conducted earlier, fig plants formed by cuttings treated with gamma ray were selected based on their agronomic characteristics of interest. We determined the genetic variability in these fig tree selections, using RAPD and AFLP molecular markers, comparing them to each other and to the Roxo-de-Valinhos, used as the standard. For the reactions of DNA amplification, 140 RAPD primers and 12 primer combinations for AFLP analysis were used. The selections did not differ genetically between themselves and between them and the Roxo-de-Valinhos cultivar. Techniques that can detect polymorphism between treatments, such as DNA sequencing, must be tested. The phenotypic variation of plants may be due to epigenetic variation, necessitating the use of techniques with methylation-sensitive restriction enzymes.

Natural Variation in Biogenesis Efficiency of Individual Arabidopsis thaliana MicroRNAs

Like protein-coding genes, loci that produce microRNAs (miRNAs) are generally considered to be under purifying selection, consistent with miRNA polymorphisms being able to cause disease. Nevertheless, it has been hypothesized that variation in miRNA genes may contribute to phenotypic diversity. Here we demonstrate that a naturally occurring polymorphism in the MIR164A gene affects leaf shape and shoot architecture in Arabidopsis thaliana, with the effects being modified by additional loci in the genome. A single base pair substitution in the miRNA complementary sequence alters the predicted stability of the miRNA:miRNA(∗) duplex. It thereby greatly reduces miRNA accumulation, probably because it interferes with precursor processing. We demonstrate that this is not a rare exception and that natural strains of Arabidopsis thaliana harbor dozens of similar polymorphisms that affect processing of a wide range of miRNA precursors. Our results suggest that natural variation in miRNA biogenesis resulting from cis mutations is a common contributor to phenotypic variation in plants.

Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana

A major challenge in evolutionary biology and plant breeding is to identify the genetic basis of complex quantitative traits, including those that contribute to adaptive variation. Here we review the development of new methods and resources to fine-map intraspecific genetic variation that underlies natural phenotypic variation in plants. In particular, the analysis of 107 quantitative traits reported in the first genome-wide association mapping study in Arabidopsis thaliana sets the stage for an exciting time in our understanding of plant adaptation. We also argue for the need to place phenotype-genotype association studies in an ecological context if one is to predict the evolutionary trajectories of plant species.

Genome‐wide DNA methylation alterations of Alternanthera philoxeroides in natural and manipulated habitats: implications for epigenetic regulation of rapid responses to environmental fluctuation and phenotypic variation

Alternanthera philoxeroides (alligator weed) is an invasive weed that can colonize both aquatic and terrestrial habitats. Individuals growing in different habitats exhibit extensive phenotypic variation but little genetic differentiation in its introduced range. The mechanisms underpinning the wide range of phenotypic variation and rapid adaptation to novel and changing environments remain uncharacterized. In this study, we examined the epigenetic variation and its correlation with phenotypic variation in plants exposed to natural and manipulated environmental variability. Genome-wide methylation profiling using methylation-sensitive amplified fragment length polymorphism (MSAP) revealed considerable DNA methylation polymorphisms within and between natural populations. Plants of different source populations not only underwent significant morphological changes in common garden environments, but also underwent a genome-wide epigenetic reprogramming in response to different treatments. Methylation alterations associated with response to different water availability were detected in 78.2% (169/216) of common garden induced polymorphic sites, demonstrating the environmental sensitivity and flexibility of the epigenetic regulatory system. These data provide evidence of the correlation between epigenetic reprogramming and the reversible phenotypic response of alligator weed to particular environmental factors.

Experimental alteration of DNA methylation affects the phenotypic plasticity of ecologically relevant traits in Arabidopsis thaliana

Heritable phenotypic variation in plants can be caused not only by underlying genetic differences, but also by variation in epigenetic modifications such as DNA methylation. However, we still know very little about how relevant such epigenetic variation is to the ecology and evolution of natural populations. We conducted a greenhouse experiment in which we treated a set of natural genotypes of Arabidopsis thaliana with the demethylating agent 5-azacytidine and examined the consequences of this treatment for plant traits and their phenotypic plasticity. Experimental demethylation strongly reduced the growth and fitness of plants and delayed their flowering, but the degree of this response varied significantly among genotypes. Differences in genotypes’ responses to demethylation were only weakly related to their genetic relatedness, which is consistent with the idea that natural epigenetic variation is independent of genetic variation. Demethylation also altered patterns of phenotypic plasticity, as well as the amount of phenotypic variation observed among plant individuals and genotype means. We have demonstrated that epigenetic variation can have a dramatic impact on ecologically important plant traits and their variability, as well as on the fitness of plants and their ecological interactions. Epigenetic variation may thus be an overlooked factor in the evolutionary ecology of plant populations.

Review Article In vitro propagation of kiwifruit

SummaryKiwifriut has gained enormous popularity in the past two decades in many countries of the world and is in great demand due to its nutritional and medicinal value. For commercialization of this crop and to meet the growing demand for planting material, tissue and organ culture techniques are being used as alternative methods for propagation in many countries. Until now, most of the work has been on plant regeneration by adventitious organogenesis from callus which may result in phenotypic variation in plants. Only a few reports are available using explants from mature vines, which is desirable to maintain uniformity and genetic purity. Hardening and acclimatization of this fruit requires more attention as hairless thin roots produced in vitro die shortly after transplanting to soil. This makes the establishment of small plants a difficult proposition. From the literature cited, it is evident that kiwifruit is highly amenable for in vitro studies as various explants have been favourably found to respond to different culture media with different types and concentrations of growth regulators.

Testing for prerequisites of local adaptation in an insect herbivore, Epirrita autumnata

There are three necessary requirements for local adaptation of insect herbivores to individual plants, namely the existence of i) plant phenotypic variation for traits affecting herbivore performance, ii) genotypic variation in the responses of herbivores to these traits, and iii) a genotypic trade-off to deal with different plant individuals (i.e., G ¥ E interaction). In this paper we checked prerequisites 2 and 3 for Epirrita autumnata (Borkhausen) and its main host plant in northeastern Europe, birch trees (Betula spp.). Phenotypic variation in plant features affecting performance of this herbivore species (point 1) had been thoroughly verified earlier on. We studied additive genetic variation and maternal effects on larval feeding parameters (consumption, digestibility, growth) and pupal masses of the insect with a paternal half-sib design. The experiment was replicated on four trees with different chemical profiles to check for the existence of G ¥ E interaction. Additive genetic variance was not significant for pupal mass nor for the feeding parameters studied at 3rd and 5th instar. However, we detected a significant maternal effect on both pupal masses, and rates of consumption and growth of 5th instar larvae. Absence of G ¥ E interactions for all the study traits suggests that local adaptation of E. autumnata to individual trees within populations is not likely.

Synergy of Empirical Breeding, Marker‐Assisted Selection, and Genomics to Increase Crop Yield Potential

ABSTRACTThis paper was presented as part of the symposium entitled “Post‐Green Revolution Trends in Crop Yield Potential: Increasing, Stagnant or Greater Resistance to Stress.” In this presentation, we have focused on (i) uses of marker technology in determining the genetic basis of phenotypic expression and the manipulation of phenotypic variation in plants. This included the use of markers in understanding heterosis, in attempts to improve hybrid predictions, in quantitative trait locus (QTL) identification and mapping, in marker‐assisted selection (MAS), and in enhancing breeding success in the development of improved lines and hybrids; (ii) the role of genomics in developing a precise understanding of the genetic basis of phenotypic expression which will then provide more precision in the manipulation of phenotypic variation; and (iii) some attempts to integrate marker technology and genomics into empirical breeding strategies. In addition, we have focused on what has been successful as well as what has fallen short of expectations, and have suggested some of the possible reasons for the lack of success. Because of page limitations, we could not include an exhaustive review of the plant literature and have limited many of our examples to investigations in maize (Zea mays L).

Interpreting phenotypic variation in plants

Plant ecologists and evolutionary biologists frequently examine patterns of phenotypic variation across variable environments or genetic identities. Too often, we ignore the fact that most phenotypic traits change throughout growth and development of individual plants, and that rates of growth and development are highly variable. Plants growing in different environments are likely to grow at different rates, and will be of different sizes and stages of development at a particular age. When we compare plants as a function of plant size or developmental stage, as well as a function of age, we broaden our understanding of phenotypic variation between plants.

Variation in performance of Phragmites australis in experimental culture

Phragmites australis (Cav.) Trin. ex Steud. (common reed) is a widespread clonal species which shows variation in growth characteristics in the field, although the extent to which this variation is attributable to inherent differences between genetically distinct ecotypes has not been fully separated from differences due to variation in edaphic and hydrological conditions. By a combination of a trial using seed from different parents in four different populations and a replicated experiment at two different locations, this study distinguished some effects of genetic and phenotypic variation in plants grown from seed and rhizome segments. In both experiments, differences were found between plants taken from different populations, but grown under the same conditions. Although the site at which plants were grown had a strong influence on growth and productivity, plants from different populations did not necessarily react in the same way at the two experimental sites.

The frequency of marker changes in sugarcane plants regenerated from callus culture

This study investigates the frequency of apparent and permanent expression of marker change following two types of tissue culture, conventional callus and direct regeneration cultures, and for two markers it relates this frequency to that following breeding. Each clone was used for only one marker. After conventional callus culture, plants of the sugarcane clone Arundoid B, a clone having a growth habit with shortened internodes and leaves, were freed of this marker at a rate of 1 in 172 plants. Marker remission in a second clone with a leaf blotch was enhanced in the presence of a mutagen. Callus culture alone gave a remission rate of 1/280 plants, while treatment of callus with ethyl methanesulfonate gave a remission rate of 1/42 plants. Of two markers subjected to vegetative and sexual transmission, the first, a leaf marker, was stable in callus culture with no remissions; crossing with non-marker parents produced progeny with 54% lacking the marker. The second, a stalk marker (multibud), showed epigenetic effects during two generations of vegetative propagation; plants lacking the multibud marker produced vegetative progeny in which the marker reappeared. Nine crosses to nonmarker parents produced progeny of which an average of 29% had the marker. The use of stalk chimeras as markers demonstrated that passage through conventional callus or direct regeneration culture resulted in the loss of the donor phenotype in all plants regenerated. Phenotypic variation in plants derived from callus culture appears to arise from several sources; chimeral segregants, epigenetic transients, and mutational variants.

Taxonomy and the conservation of the critically endangered Bakersfield saltbush, Atriplex tularensis

The Bakersfield saltbush Atriplex tularensis is a salt-tolerant, monoecious annual member of the alkali sink scrub plant community which was once widely distributed in southern San Joaquin Valley, California. The plant has been reduced, by conversion of habitat to agriculture, to a single population at Kern Lake Preserve, about 25 km south of Bakersfield. Seed bank status, soil moisture, germination requirements, and artificial propagation were investigated to determine the most effective strategy for conservation of that remnant population and the associated eccological community. Five seedlings were successfully transferred from the preserve site to greenhouse facilities where they have produced numerous fruits. Phenotypic variation of plants in the field and greenhouse, however, indicates incomplete reproductive isolation between A. tularensis and A. serenana, a widespread, closely related species. The possibility that introgressive hybridization is occurring and its impact on potential conservation strategies are discussed.