A Single Nucleotide Deletion in Gibberellin20-oxidase1 Causes Alpine Dwarfism in Arabidopsis

Gravitropic Gene Expression Divergence Associated With Adaptation to Contrasting Environments in an Australian Wildflower

Plants adapt to their local environment through complex interactions between genes, gene networks and hormones. Although the impact of gene expression on trait regulation and evolution has been recognised for many decades, its role in the evolution of adaptation is still a subject of intense exploration. We used a Multi-parent Advanced Generation Inter-Cross (MAGIC) population, which we derived from crossing multiple parents from two distinct coastal ecotypes of an Australia wildflower, Senecio lautus. We focused on studying the contrasting gravitropic behaviours of these ecotypes, which have evolved independently multiple times and show strong responses to natural selection in field experiments, emphasising the role of natural selection in their evolution. Here, we investigated how gene expression differences have contributed to the adaptive evolution of gravitropism. We studied gene expression in 60 pools at five time points (30, 60, 120, 240 and 480 min) after rotating half of the pools 90°. We found 428 genes with differential expression in response to the 90° rotation treatment. Of these, 81 genes (~19%) have predicted functions related to the plant hormones auxin and ethylene, which are crucial for the gravitropic response. By combining insights from Arabidopsis mutant studies and analysing our gene networks, we propose a preliminary model to explain the differences in gravitropism between ecotypes. This model suggests that the differences arise from changes in the transport and availability of the two hormones auxin and ethylene. Our findings indicate that the genetic basis of adaptation involves interconnected signalling pathways that work together to give rise to new ecotypes.

Characterization of the gibberellic oxidase gene SdGA20ox1 in Sophora davidii (Franch.) skeels and interaction protein screening

Gibberellin 20-oxidases (GA20oxs) are multifunctional enzymes involved in regulating gibberellin (GA) biosynthesis and controlling plant growth. We identified and characterized the GA20ox1 gene in a plant height mutant of Sophora davidii, referred to as SdGA20ox1. This gene was expressed in root, stem, and leaf tissues of the adult S. davidii plant height mutant, with the highest expression observed in the stem. The expression of SdGA20ox1 was regulated by various exogenous hormones. Overexpression of SdGA20ox1 in Arabidopsis resulted in significant elongation of hypocotyl and root length in seedlings, earlier flowering, smaller leaves, reduced leaf chlorophyll content, lighter leaf color, a significant increase in adult plant height, and other phenotypes. Additionally, transgenic plants exhibited a substantial increase in biologically active endogenous GAs (GA1, GA3, and GA4) content, indicating that overexpression of SdGA20ox1 accelerates plant growth and development. Using a yeast two-hybrid (Y2H) screen, we identified two SdGA20ox1-interacting proteins: the ethylene receptor EIN4 (11430582) and the rbcS (11416005) protein. These interactions suggest a potential regulatory mechanism for S. davidii growth. Our findings provide new insights into the role of SdGA20ox1 and its interacting proteins in regulating the growth and development of S. davidii.

Allelic variants confer Arabidopsis adaptation to small regional environmental differences

Natural populations of Arabidopsis thaliana provide powerful systems to study the adaptation of wild plant species. Previous research has predominantly focused on global populations or accessions collected from regions with diverse climates. However, little is known about the genetics underlying adaptation in regions with mild environmental clines. We have examined a diversity panel consisting of 192 A. thaliana accessions collected from the Netherlands, a region with limited climatic variation. Despite the relatively uniform climate, we identified evidence of local adaptation within this population. Notably, semidwarf accessions, due to mutation of the GIBBERELLIC ACID REQUIRING 5 (GA5) gene, occur at a relatively high frequency near the coast and these displayed enhanced tolerance to high wind velocities. Additionally, we evaluated the performance of the population under iron deficiency conditions and found that allelic variation in the FE SUPEROXIDE DISMUTASE 3 (FSD3) gene affects tolerance to low iron levels. Moreover, we explored patterns of local adaptation to environmental clines in temperature and precipitation, observing that allelic variation at LA RELATED PROTEIN 1C (LARP1c) likely affects drought tolerance. Not only is the genetic variation observed in a diversity panel of A. thaliana collected in a region with mild environmental clines comparable to that in collections sampled over larger geographic ranges but it is also sufficiently rich to elucidate the genetic and environmental factors underlying natural plant adaptation.

Candidate Genes for the High-Altitude Adaptations of Two Mountain Pine Taxa

Mountain plants, challenged by vegetation time contractions and dynamic changes in environmental conditions, developed adaptations that help them to balance their growth, reproduction, survival, and regeneration. However, knowledge regarding the genetic basis of species adaptation to higher altitudes remain scarce for most plant species. Here, we attempted to identify such corresponding genomic regions of high evolutionary importance in two closely related European pines, Pinus mugo and P. uncinata, contrasting them with a reference lowland relative—P. sylvestris. We genotyped 438 samples at thousands of single nucleotide polymorphism (SNP) markers, tested their genetic differentiation and population structure followed by outlier detection and gene ontology annotations. Markers clearly differentiated the species and uncovered patterns of population structure in two of them. In P. uncinata three Pyrenean sites were grouped together, while two outlying populations constituted a separate cluster. In P. sylvestris, Spanish population appeared distinct from the remaining four European sites. Between mountain pines and the reference species, 35 candidate genes for altitude-dependent selection were identified, including such encoding proteins responsible for photosynthesis, photorespiration and cell redox homeostasis, regulation of transcription, and mRNA processing. In comparison between two mountain pines, 75 outlier SNPs were found in proteins involved mainly in the gene expression and metabolism.

Genome-Wide Characterization of Cucumber (Cucumis sativus L.) GRAS Genes and Their Response to Various Abiotic Stresses

The GRAS (gibberellic acid insensitive, repressor of GAI, and scarecrow) proteins are a family of plant-specific transcription factors that regulate plant growth, development, and stress response. Currently, the role of GRAS transcription factors in various abiotic stress responses has not been systematically studied in cucumber (Cucumis sativus L.), a popular vegetable crop. Here, we provide a comprehensive bioinformatics analysis of the 35 GRAS genes identified in the cucumber genome. In this study, cucumber genotypes, i.e., “CG104”, which is stress-tolerant, and genotype “CG37”, which is stress-sensitive, were examined to provide insight on potential differences in the GRAS-regulated abiotic stress pathways. Transcriptional analysis by RNA-seq or qRT-PCR of these two genotypes revealed common and divergent functions of CsGRAS genes regulated by low and high temperatures, salinity, and by exposure to the phytohormones gibberellin (GA) and abscisic acid (ABA). Notably, CsGRAS2 (DELLA) and CsGRAS26 (LISCL) were regulated by all abiotic stresses and hormone treatments, suggesting that they may function in the biological cross-talk between multiple signaling pathways. This study provides candidate genes for improving cucumber tolerance to various environmental stresses.

A mutation in the intron splice acceptor site of a GA3ox gene confers dwarf architecture in watermelon (Citrullus lanatus L.)

Dwarf architecture is an important trait associated with plant yield, lodging resistance and labor cost. Here, we aimed to identify a gene causing dwarfism in watermelon. The ‘w106’ (dwarf) and ‘Charleston Gray’ (vine) were used as parents to construct F₁ and F₂ progeny. Dwarf architecture of ‘w106’ was mainly caused by longitudinal cell length reduction and was controlled by a single recessive gene. Whole-genome sequencing of two parents and two bulk DNAs of F₂ population localized this gene to a 2.63-Mb region on chromosome 9; this was further narrowed to a 541-kb region. Within this region, Cla015407, encoding a gibberellin 3β-hydroxylase (GA3ox), was the candidate gene. Cla015407 had a SNP mutation (G → A) in the splice acceptor site of the intron, leading to altered splicing event and generating two splicing isoforms in dwarf plants. One splicing isoform retained the intron sequences, while the other had a 13-bp deletion in the second exon of GA3ox transcript, both resulting in truncated proteins and loss of the functional Fe2OG dioxygenase domain in dwarf plants. RNA-Seq analysis indicated that expression of Cla015407 and other GA biosynthetic and metabolic genes were mostly up-regulated in the shoots of dwarf plants compared with vine plants in F₂ population. Measurement of endogenous GA levels indicated that bioactive GA₄ was significantly decreased in the shoots of dwarf plants. Moreover, the dwarf phenotype can be rescued by exogenous applications of GA₃ or GA₄₊₇, with the latter having a more distinct effect than the former. Subcellular localization analyses of GA3ox proteins from two parents revealed their subcellular targeting in nucleus and cytosol. Here, a GA3ox gene controlling dwarf architecture was identified, and loss function of GA3ox leads to GA₄ reduction and dwarfism phenotype in watermelon.

Plant's-eye view of temperature governs elevational distributions

Explaining species geographic distributions by macroclimate variables is the most common approach for getting mechanistic insights into large-scale diversity patterns and range shifts. However, species' traits influencing biophysical processes can produce a large decoupling from ambient air temperature, which can seriously undermine biogeographical inference. We combined stable oxygen isotope theory with a trait-based approach to assess leaf temperature during carbon assimilation (T_L ) and its departure (ΔT) from daytime free air temperature during the growing season (T_gs ) for 158 plant species occurring from 3,400 to 6,150 m a.s.l. in Western Himalayas. We uncovered a general extent of temperature decoupling in the region. The interspecific variation in ΔT was best explained by the combination of plant height and δ¹³ C, and leaf dry matter content partly captured the variation in T_L . The combination of T_L and ΔT, with ΔT contributing most, explained the interspecific difference in elevational distributions. Stable oxygen isotope theory appears promising for investigating how plants perceive temperatures, a pivotal information to species biogeographic distributions.

Microclimate predicts frost hardiness of alpine Arabidopsis thaliana populations better than elevation

In mountain regions, topological differences on the microscale can strongly affect microclimate and may counteract the average effects of elevation, such as decreasing temperatures. While these interactions are well understood, their effect on plant adaptation is understudied. We investigated winter frost hardiness of Arabidopsis thaliana accessions originating from 13 sites along altitudinal gradients in the Southern Alps during three winters on an experimental field station on the Swabian Jura and compared levels of frost damage with the observed number of frost days and the lowest temperature in eight collection sites. We found that frost hardiness increased with elevation in a log-linear fashion. This is consistent with adaptation to a higher frequency of frost conditions, but also indicates a decreasing rate of change in frost hardiness with increasing elevation. Moreover, the number of frost days measured with temperature loggers at the collection sites correlated much better with frost hardiness than the elevation of collection sites, suggesting that populations were adapted to their local microclimate. Notably, the variance in frost days across sites increased exponentially with elevation. Together, our results suggest that strong microclimate heterogeneity of high alpine environments can preserve functional genetic diversity among small populations. Synthesis: Here, we tested how plant populations differed in their adaptation to frost exposure along an elevation gradient and whether microsite temperatures improve the prediction of frost hardiness. We found that local temperatures, particularly the number of frost days, are a better predictor of the frost hardiness of plants than elevation. This reflects a substantial variance in frost frequency between sites at similar high elevations. We conclude that high mountain regions harbor microsites that differ in their local microclimate and thereby can preserve a high functional genetic diversity among them. Therefore, high mountain regions have the potential to function as a refugium in times of global change.

CRISPR-Based Assessment of Gene Specialization in the Gibberellin Metabolic Pathway in Rice

Gibberellin (GA) functions as an essential natural regulator of growth and development in plants. For each step of the GA metabolic pathway, different copy numbers can be found in different species, as is the case with the 13 genes across four enzymatic steps in rice (Oryza sativa). A common view is that such gene duplication creates homologs that buffer organisms against loss-of-function (LOF) mutations. Therefore, knockouts of any single homolog might be expected to have little effect. To test this question, we generated clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) knockouts for these homologs and measured effects on growth and reproduction. Surprisingly, we report here that there is consistently one or more essential gene at each enzymatic step, for which LOF mutation induces death or sterility-suggesting that the GA pathway does not have a redundancy route and that each gene family is essential for GA metabolism. In most of these genes from the same gene family, we observed defects in plant height and infertility, suggesting that the duplicated members retain functions related to GA synthesis or degradation. We identified both subfunctionalization of the three recently diversified homologs OsKO1, OsKO2, and OsKO5 and neofunctionalization in OsKO3 and OsKO4 Thus, although the function of each step is conserved, the evolution of duplicates in that step is diversified. Interestingly, the CRISPR/Cas9 lines at the SD1 locus were typically sterile, whereas the natural sd1 mutants, related to the "Green Revolution" in rice, show normal setting rates. Collectively, our results identify candidates for control of GA production and provide insight into the evolution of four critical gene families in plants.

A Molecular View of Plant Local Adaptation: Incorporating Stress-Response Networks

Ecological specialization in plants occurs primarily through local adaptation to different environments. Local adaptation is widely thought to result in costly fitness trade-offs that result in maladaptation to alternative environments. However, recent studies suggest that such trade-offs are not universal. Further, there is currently a limited understanding of the molecular mechanisms responsible for fitness trade-offs associated with adaptation. Here, we review the literature on stress responses in plants to identify potential mechanisms underlying local adaptation and ecological specialization. We focus on drought, high and low temperature, flooding, herbivore, and pathogen stresses. We then synthesize our findings with recent advances in the local adaptation and plant molecular biology literature. In the process, we identify mechanisms that could cause fitness trade-offs and outline scenarios where trade-offs are not a necessary consequence of adaptation. Future studies should aim to explicitly integrate molecular mechanisms into studies of local adaptation.

Trait differentiation and adaptation of plants along elevation gradients

Studies of genetic adaptation in plant populations along elevation gradients in mountains have a long history, but there has until now been neither a synthesis of how frequently plant populations exhibit adaptation to elevation nor an evaluation of how consistent underlying trait differences across species are. We reviewed studies of adaptation along elevation gradients (i) from a meta-analysis of phenotypic differentiation of three traits (height, biomass and phenology) from plants growing in 70 common garden experiments; (ii) by testing elevation adaptation using three fitness proxies (survival, reproductive output and biomass) from 14 reciprocal transplant experiments; (iii) by qualitatively assessing information at the molecular level, from 10 genomewide surveys and candidate gene approaches. We found that plants originating from high elevations were generally shorter and produced less biomass, but phenology did not vary consistently. We found significant evidence for elevation adaptation in terms of survival and biomass, but not for reproductive output. Variation in phenotypic and fitness responses to elevation across species was not related to life history traits or to environmental conditions. Molecular studies, which have focussed mainly on loci related to plant physiology and phenology, also provide evidence for adaptation along elevation gradients. Together, these studies indicate that genetically based trait differentiation and adaptation to elevation are widespread in plants. We conclude that a better understanding of the mechanisms underlying adaptation, not only to elevation but also to environmental change, will require more studies combining the ecological and molecular approaches.

Temperature fine-tunes Mediterranean Arabidopsis thaliana life-cycle phenology geographically

To understand how adaptive evolution in life-cycle phenology operates in plants, we need to unravel the effects of geographic variation in putative agents of natural selection on life-cycle phenology by considering all key developmental transitions and their co-variation patterns. We address this goal by quantifying the temperature-driven and geographically varying relationship between seed dormancy and flowering time in the annual Arabidopsis thaliana across the Iberian Peninsula. We used data on genetic variation in two major life-cycle traits, seed dormancy (DSDS50) and flowering time (FT), in a collection of 300 A. thaliana accessions from the Iberian Peninsula. The geographically varying relationship between life-cycle traits and minimum temperature, a major driver of variation in DSDS50 and FT, was explored with geographically weighted regressions (GWR). The environmentally varying correlation between DSDS50 and FT was analysed by means of sliding window analysis across a minimum temperature gradient. Maximum local adjustments between minimum temperature and life-cycle traits were obtained in the southwest Iberian Peninsula, an area with the highest minimum temperatures. In contrast, in off-southwest locations, the effects of minimum temperature on DSDS50 were rather constant across the region, whereas those of minimum temperature on FT were more variable, with peaks of strong local adjustments of GWR models in central and northwest Spain. Sliding window analysis identified a minimum temperature turning point in the relationship between DSDS50 and FT around a minimum temperature of 7.2 °C. Above this minimum temperature turning point, the variation in the FT/DSDS50 ratio became rapidly constrained and the negative correlation between FT and DSDS50 did not increase any further with increasing minimum temperatures. The southwest Iberian Peninsula emerges as an area where variation in life-cycle phenology appears to be restricted by the duration and severity of the hot summer drought. The temperature-driven varying relationship between DSDS50 and FT detected environmental boundaries for the co-evolution between FT and DSDS50 in A. thaliana. In the context of global warming, we conclude that A. thaliana phenology from the southwest Iberian Peninsula, determined by early flowering and deep seed dormancy, might become the most common life-cycle phenotype for this annual plant in the region.

Hormone Distribution and Transcriptome Profiles in Bamboo Shoots Provide Insights on Bamboo Stem Emergence and Growth

Growth and development are tightly co-ordinated events in the lifetime of living organisms. In temperate bamboo plants, spring is the season when environmental conditions are suitable for the emergence of new shoots. Previous studies demonstrated that bamboo plants undergo an energy-consuming 'fast stem growth' phase. However, the events during the initiation of stem elongation in bamboo are poorly understood. To understand the onset of bamboo stem growth, we performed hormone and transcriptome profiling of tissue regions in newly elongating shoots of the Moso bamboo Phyllostachys edulis. The growth hormones auxins, cytokinins and gibberellins accumulated in the shoot apex, while the stress hormones ABA, salicylic acid (SA) and jasmonic acid (JA) are predominantly found in the lower part of the stem. The mature basal part of the stem showed enrichment of transcripts associated with cell wall metabolism and biosynthesis of phenylpropanoid metabolites, such as lignin. In the young upper stem region, expression of cell formation- and DNA synthesis-related genes was enriched. Moreover, the apical region showed enhanced expression of genes involved in meristem maintenance, leaf differentiation and development, abaxial/adaxial polarity and flowering. Our findings integrate the spatial regulation of hormones and transcriptome programs during the initiation of bamboo stem growth.

Genomic and phenotypic differentiation of Arabidopsis thaliana along altitudinal gradients in the North Italian Alps

Altitudinal gradients in mountain regions are short-range clines of different environmental parameters such as temperature or radiation. We investigated genomic and phenotypic signatures of adaptation to such gradients in five Arabidopsis thaliana populations from the North Italian Alps that originated from 580 to 2350 m altitude by resequencing pools of 19-29 individuals from each population. The sample includes two pairs of low- and high-altitude populations from two different valleys. High-altitude populations showed a lower nucleotide diversity and negative Tajima's D values and were more closely related to each other than to low-altitude populations from the same valley. Despite their close geographic proximity, demographic analysis revealed that low- and high-altitude populations split between 260 000 and 15 000 years before present. Single nucleotide polymorphisms whose allele frequencies were highly differentiated between low- and high-altitude populations identified genomic regions of up to 50 kb length where patterns of genetic diversity are consistent with signatures of local selective sweeps. These regions harbour multiple genes involved in stress response. Variation among populations in two putative adaptive phenotypic traits, frost tolerance and response to light/UV stress was not correlated with altitude. Taken together, the spatial distribution of genetic diversity reflects a potentially adaptive differentiation between low- and high-altitude populations, whereas the phenotypic differentiation in the two traits investigated does not. It may resemble an interaction between adaptation to the local microhabitat and demographic history influenced by historical glaciation cycles, recent seed dispersal and genetic drift in local populations.

Phenotype of Arabidopsis thaliana semi-dwarfs with deep roots and high growth rates under water-limiting conditions is independent of the GA5 loss-of-function alleles

BACKGROUND AND AIMS

The occurrence of Arabidopsis thaliana semi-dwarf accessions carrying inactive alleles at the gibberellin (GA) biosynthesis GA5 locus has raised the question whether there are pleiotropic effects on other traits at the root level, such as rooting depth. In addition, it is unknown whether semi-dwarfism in arabidopsis confers a growth advantage under water-limiting conditions compared with wild-type plants. The aim of this research was therefore to investigate whether semi-dwarfism has a pleiotropic effect in the root system and also whether semi-dwarfs might be more tolerant of water-limiting conditions.

METHODS

The root systems of different arabidopsis semi-dwarfs and GA biosynthesis mutants were phenotyped in vitro using the GROWSCREEN-ROOT image-based software. Semi-dwarfs were phenotyped together with tall, near-related accessions. In addition, root phenotypes were investigated in soil-filled rhizotrons. Rosette growth trajectories were analysed with the GROWSCREEN-FLUORO setup based on non-invasive imaging.

KEY RESULTS

Mutations in the early steps of the GA biosynthesis pathway led to a reduction in shoot as well as root size. Depending on the genetic background, mutations at the GA5 locus yielded phenotypes characterized by decreased root length in comparison with related wild-type ones. The semi-dwarf accession Pak-3 showed the deepest root system both in vitro and in soil cultivation experiments; this comparatively deep root system, however, was independent of the ga5 loss-of-function allele, as shown by co-segregation analysis. When the accessions were grown under water-limiting conditions, semi-dwarf accessions with high growth rates were identified.

CONCLUSIONS

The observed diversity in root system growth and architecture occurs independently of semi-dwarf phenotypes, and is probably linked to a genetic background effect. The results show that there are no clear advantages of semi-dwarfism at low water availability in arabidopsis.