Molecular analysis of FRIGIDA, a major determinant of natural variation in Arabidopsis flowering time

Physical coupling of activation and derepression activities to maintain an active transcriptional state at FLC

Establishment and maintenance of gene expression states is central to development and differentiation. Transcriptional and epigenetic mechanisms interconnect in poorly understood ways to determine these states. We explore these mechanisms through dissection of the regulation of Arabidopsis thaliana FLOWERING LOCUS C (FLC). FLC can be present in a transcriptionally active state marked by H3K36me3 or a silent state marked by H3K27me3. Here, we investigate the trans factors modifying these opposing histone states and find a physical coupling in vivo between the H3K36 methyltransferase, SDG8, and the H3K27me3 demethylase, ELF6. Previous modeling has predicted this coupling would exist as it facilitates bistability of opposing histone states. We also find association of SDG8 with the transcription machinery, namely RNA polymerase II and the PAF1 complex. Delivery of the active histone modifications is therefore likely to be through transcription at the locus. SDG8 and ELF6 were found to influence the localization of each other on FLC chromatin, showing the functional importance of the interaction. In addition, both influenced accumulation of the associated H3K27me3 and H3K36me3 histone modifications at FLC We propose the physical coupling of activation and derepression activities coordinates transcriptional activity and prevents ectopic silencing.

De novo sequencing of Eucommia ulmoides flower bud transcriptomes for identification of genes related to floral development

Eucommia ulmoides Oliver is a woody perennial dioecious species native to China and has great economic value. However, little is known about flower bud development in this species. In this study, the transcriptomes of female and male flower buds were sequenced using the Illumina platform, a next-generation sequencing technology that provides cost-effective, highly efficient transcriptome profiling. In total, 11,558,188,080 clean reads were assembled into 75,065 unigenes with an average length of 1011 bp by de novo assembly using Trinity software. Through similarity comparisons with known protein databases, 47,071 unigenes were annotated, 146 of which were putatively related to the floral development of E. ulmoides. Fifteen of the 146 unigenes had significantly different expression levels between the two samples. Additionally, 24,346 simple sequence repeats were identified in 18,565 unigenes with 12,793 sequences suitable for the designed primers. In total, 67,447 and 58,236 single nucleotide polymorphisms were identified in male and female buds, respectively. This study provides a valuable resource for further conservation genetics and functional genomics research on E. ulmoides.

Quantitative trait loci controlling leaf appearance and curd initiation of cauliflower in relation to temperature

QTL regions on chromosomes C06 and C09 are involved in temperature dependent time to curd induction in cauliflower. Temperature is the main environmental factor influencing curding time of cauliflower (Brassica oleracea var. botrytis). Temperatures above 20-22 °C inhibit development towards curding even in many summer cultivars. To identify quantitative trait loci (QTL) controlling curding time and its related traits in a wide range of different temperature regimes from 12 to 27 °C, a doubled haploid (DH) mapping population segregating for curding time was developed and days to curd initiation (DCI), leaf appearance rate (LAR), and final leaf number (FLN) were measured. The population was genotyped with 176 single nucleotide polymorphism (SNP) markers. Composite interval mapping (CIM) revealed repeatedly detected QTL for DCI on C06 and C09. The estimated additive effect increased at high temperatures. Significant QTL × environment interactions (Q × E) for FLN and DCI on C06 and C09 suggest that these hotspot regions have major influences on temperature mediated curd induction. 25 % of the DH lines did not induce curds at temperatures higher than 22 °C. Applying a binary model revealed a QTL with LOD >15 on C06. Nearly all lines carrying the allele of the reliable early maturing parental line (PL) on that locus induced curds at high temperatures while only half of the DH lines carrying the allele of the unreliable PL reached the generative phase during the experiment. Large variation in LAR was observed. QTL for LAR were detected repeatedly in several environments on C01, C04 and C06. Negative correlations between LAR and DCI and QTL co-localizations on C04 and C06 suggest that LAR has also effects on development towards curd induction.

Root Architecture Diversity and Meristem Dynamics in Different Populations of Arabidopsis thaliana

Arabidopsis thaliana has been an excellent model system for molecular genetic approaches to development and physiology. More recently, the potential of studying various accessions collected from diverse habitats has been started to exploit. Col-0 has been the best-studied accession but we now know that several traits show significant divergences among them. In this work, we focused in the root that has become a key system for development. We studied root architecture and growth dynamics of 12 Arabidopsis accessions. Our data reveal a wide variability in root architecture and root length among accessions. We also found variability in the root apical meristem (RAM), explained mainly by cell size at the RAM transition domain and possibly by peculiar forms of organization at the stem cell niche in some accessions. Contrary to Col-0 reports, in some accessions the RAM size not always explains the variations in the root length; indicating that elongated cell size could be more relevant in the determination of root length than the RAM size itself. This study contributes to investigations dealing with understanding the molecular and cellular basis of phenotypic variation, the role of plasticity on adaptation, and the developmental mechanisms that may restrict phenotypic variation in response to contrasting environmental conditions.

Natural variation involving deletion alleles of FRIGIDA modulate temperature-sensitive flowering responses in Arabidopsis thaliana

Ambient temperature is one of the major environmental factors that modulate plant growth and development. There is extensive natural genetic variation in thermal responses of plants exemplified by the variation exhibited by the accessions of Arabidopsis thaliana. In this work we have studied the enhanced temperature response in hypocotyl elongation and flowering shown by the Tsu-0 accession in long days. Genetic mapping in the Col-0 × Tsu-0 recombinant inbred line (RIL) population identified several QTLs for thermal response including three major effect loci encompassing candidate genes FRIGIDA (FRI), FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT). We confirm and validate these QTLs. We show that the Tsu-0 FRI allele, which is the same as FRI-Ler is associated with late flowering but only at lower temperatures in long days. Using transgenic lines and accessions, we show that the FRI-Ler allele confers temperature-sensitive late flowering confirming a role for FRI in photoperiod-dependent thermal response. Through quantitative complementation with heterogeneous inbred families, we further show that cis-regulatory variation at FT contributes to the observed hypersensitivity of Tsu-0 to ambient temperature. Overall our results suggest that multiple loci that interact epistatically govern photoperiod-dependent thermal responses of A. thaliana.

Phenotypic Evolution With and Beyond Genome Evolution

DNA does not make phenotypes on its own. In this volume entitled "Genes and Phenotypic Evolution," the present review draws the attention on the process of phenotype construction-including development of multicellular organisms-and the multiple interactions and feedbacks between DNA, organism, and environment at various levels and timescales in the evolutionary process. First, during the construction of an individual's phenotype, DNA is recruited as a template for building blocks within the cellular context and may in addition be involved in dynamical feedback loops that depend on the environmental and organismal context. Second, in the production of phenotypic variation among individuals, stochastic, environmental, genetic, and parental sources of variation act jointly. While in controlled laboratory settings, various genetic and environmental factors can be tested one at a time or in various combinations, they cannot be separated in natural populations because the environment is not controlled and the genotype can rarely be replicated. Third, along generations, genotype and environment each have specific properties concerning the origin of their variation, the hereditary transmission of this variation, and the evolutionary feedbacks. Natural selection acts as a feedback from phenotype and environment to genotype. This review integrates recent results and concrete examples that illustrate these three points. Although some themes are shared with recent calls and claims to a new conceptual framework in evolutionary biology, the viewpoint presented here only means to add flesh to the standard evolutionary synthesis.

Florigen distribution determined by a source-sink balance explains the diversity of inflorescence structures in Arabidopsis

The ability to continue flowering after loss of inductive environmental cues that trigger flowering is termed floral commitment. Reversible transition involving a switch from floral development back to vegetative development has been found in Arabidopsis mutants and many plant species. Although the molecular basis for floral commitment remains unclear, recent studies suggest that the persistent activity of FLOWERING LOCUS T (FT) at inflorescences is required for floral commitment in Arabidopsis thaliana. Because FT encodes a mobile signal, florigen, which is generally transported from leaves to meristems through the phloem, understanding the transportation dynamics of FT is required to explore the role of FT on floral commitment. Here we developed a transportation model of leaf- and inflorescence-derived florigen and sucrose based on pressure-flow hypothesis. Depending on the demanded level of florigen supply for floral commitment of each floral meristem, the model predicted the change in inflorescence pattern from stable commitment to flower, transient flowering, and complete reversion. FT activity in inflorescence partly suppressed floral reversion, but complete suppression was achieved only when inflorescence became a source of sucrose. This finding highlights the importance of monitoring the spatio-temporal sucrose distribution and floral stimulus to understand inflorescence development mechanism.

BRR2a Affects Flowering Time via FLC Splicing

Several pathways control time to flowering in Arabidopsis thaliana through transcriptional and posttranscriptional gene regulation. In recent years, mRNA processing has gained interest as a critical regulator of flowering time control in plants. However, the molecular mechanisms linking RNA splicing to flowering time are not well understood. In a screen for Arabidopsis early flowering mutants we identified an allele of BRR2a. BRR2 proteins are components of the spliceosome and highly conserved in eukaryotes. Arabidopsis BRR2a is ubiquitously expressed in all analyzed tissues and involved in the processing of flowering time gene transcripts, most notably FLC. A missense mutation of threonine 895 in BRR2a caused defects in FLC splicing and greatly reduced FLC transcript levels. Reduced FLC expression increased transcription of FT and SOC1 leading to early flowering in both short and long days. Genome-wide experiments established that only a small set of introns was not correctly spliced in the brr2a mutant. Compared to control introns, retained introns were often shorter and GC-poor, had low H3K4me1 and CG methylation levels, and were often derived from genes with a high-H3K27me3-low-H3K36me3 signature. We propose that BRR2a is specifically needed for efficient splicing of a subset of introns characterized by a combination of factors including intron size, sequence and chromatin, and that FLC is most sensitive to splicing defects.

Timing of flowering has a great effect on reproductive success and fitness. It is controlled by many external signals and internal states involving a large set of genes. Here we report that the Arabidopsis thaliana BRR2a gene is needed for normal flowering. BRR2 proteins are components of the spliceosome and highly conserved in eukaryotes. BRR2a is needed for splicing of a subset of introns, most noticeably in the transcript of the flowering repressor FLC. Reduced FLC expression increased transcription of key floral activators, leading to early flowering in both short and long days. Genome-wide experiments established that full BRR2a activity was required only for a small group of introns. We propose that uncompromised BRR2a activity is most important for efficient splicing of a subset of introns of particular size, sequence and chromatin composition, and that FLC is most sensitive to splicing defects.

The mitogen-activated protein kinase phosphatase PHS1 regulates flowering in Arabidopsis thaliana

Arabidopsis PHS1, initially known as an actor of cytoskeleton organization, is a positive regulator of flowering in the photoperiodic and autonomous pathways by modulating both CO and FLC mRNA levels. Protein phosphorylation and dephosphorylation is a major type of post-translational modification, controlling many biological processes. In Arabidopsis thaliana, five genes encoding MAPK phosphatases (MKP)-like proteins have been identified. Among them, PROPYZAMIDE HYPERSENSITIVE 1 (PHS1) encoding a dual-specificity protein tyrosine phosphatase (DsPTP) has been shown to be involved in microtubule organization, germination and ABA-regulated stomatal opening. Here, we demonstrate that PHS1 also regulates flowering under long-day and short-day conditions. Using physiological, genetic and molecular approaches, we have shown that the late flowering phenotype of the knock-out phs1-5 mutant is linked to a higher expression of FLOWERING LOCUS C (FLC). In contrast, a decline of both CONSTANS (CO) and FLOWERING LOCUS T (FT) expression is observed in the knock-out phs1-5 mutant, especially at the end of the light period under long-day conditions when the induction of flowering occurs. We show that this partial loss of sensitivity to photoperiodic induction is independent of FLC. Our results thus indicate that PHS1 plays a dual role in flowering, in the photoperiodic and autonomous pathways, by modulating both CO and FLC mRNA levels. Our work reveals a novel actor in the complex network of the flowering regulation.

Fluctuating, warm temperatures decrease the effect of a key floral repressor on flowering time in Arabidopsis thaliana

The genetic basis of growth and development is often studied in constant laboratory environments; however, the environmental conditions that organisms experience in nature are often much more dynamic. We examined how daily temperature fluctuations, average temperature, day length and vernalization influence the flowering time of 59 genotypes of Arabidopsis thaliana with allelic perturbations known to affect flowering time. For a subset of genotypes, we also assessed treatment effects on morphology and growth. We identified 17 genotypes, many of which have high levels of the floral repressor FLOWERING LOCUS C (FLC), that bolted dramatically earlier in fluctuating - as opposed to constant - warm temperatures (mean = 22°C). This acceleration was not caused by transient VERNALIZATION INSENSITIVE 3-mediated vernalization, differential growth rates or exposure to high temperatures, and was not apparent when the average temperature was cool (mean = 12°C). Further, in constant temperatures, contrary to physiological expectations, these genotypes flowered more rapidly in cool than in warm environments. Fluctuating temperatures often reversed these responses, restoring faster bolting in warm conditions. Independently of bolting time, warm fluctuating temperature profiles also caused morphological changes associated with shade avoidance or 'high-temperature' phenotypes. Our results suggest that previous studies have overestimated the effect of the floral repressor FLC on flowering time by using constant temperature laboratory conditions.

Tuning growth cycles of Brassica crops via natural antisense transcripts of BrFLC

Several oilseed and vegetable crops of Brassica are biennials that require a prolonged winter cold for flowering, a process called vernalization. FLOWERING LOCUS C (FLC) is a central repressor of flowering. Here, we report that the overexpression of natural antisense transcripts (NATs) of Brassica rapa FLC (BrFLC) greatly shortens plant growth cycles. In rapid-, medium- and slow-cycling crop types, there are four copies of the BrFLC genes, which show extensive variation in sequences and expression levels. In Bre, a biennial crop type that requires vernalization, five NATs derived from the BrFLC2 locus are rapidly induced under cold conditions, while all four BrFLC genes are gradually down-regulated. The transgenic Bre lines overexpressing a long NAT of BrFLC2 do not require vernalization, resulting in a gradient of shortened growth cycles. Among them, a subset of lines both flower and set seeds as early as Yellow sarson, an annual crop type in which all four BrFLC genes have non-sense mutations and are nonfunctional in flowering repression. Our results demonstrate that the growth cycles of biennial crops of Brassica can be altered by changing the expression levels of BrFLC2 NATs. Thus, BrFLC2 NATs and their transgenic lines are useful for the genetic manipulation of crop growth cycles.

The genetic architecture of petal number in Cardamine hirsuta

Invariant petal number is a characteristic of most flowers and is generally robust to genetic and environmental variation. We took advantage of the natural variation found in Cardamine hirsuta petal number to investigate the genetic basis of this trait in a case where robustness was lost during evolution. We used quantitative trait locus (QTL) analysis to characterize the genetic architecture of petal number. Αverage petal number showed transgressive variation from zero to four petals in five C. hirsuta mapping populations, and this variation was highly heritable. We detected 15 QTL at which allelic variation affected petal number. The effects of these QTL were relatively small in comparison with alleles induced by mutagenesis, suggesting that natural selection may act to maintain petal number within its variable range below four. Petal number showed a temporal trend during plant ageing, as did sepal trichome number, and multi-trait QTL analysis revealed that these age-dependent traits share a common genetic basis. Our results demonstrate that petal number is determined by many genes of small effect, some of which are age-dependent, and suggests a mechanism of trait evolution via the release of cryptic variation.

Genome-Wide Analysis of Gene Regulatory Networks of the FVE-HDA6-FLD Complex in Arabidopsis

FVE/MSI4 is a homolog of the mammalian RbAp48 protein. We found that FVE regulates flowering time by repressing FLC through decreasing histone H3K4 trimethylation and H3 acetylation. Furthermore, FVE interacts with the histone deacetylase HDA6 and the histone demethylase FLD, suggesting that these proteins may form a protein complex to regulate flowering time. To further investigate the function of the FVE-FLD-HDA6 complex, we compared the gene expression profiles of fve, fld, and hda6 mutant plants by using RNA-seq analysis. Among the mis-regulated genes found in fve plants, 51.8 and 36.5% of them were also mis-regulated in fld and hda6 plants, respectively, suggesting that FVE, HDA6, and FLD may regulate the gene expression in the same developmental processes in Arabidopsis. Gene ontology analysis revealed that among 383 genes co-regulated by FVE, HDA6, and FLD, 15.6% of them are involved in transcription, 8.2% in RNA metabolic process, 7.7% in response to abiotic stress, and 6.3% in hormone stimulus. Taken together, these results indicate that HDA6, FVE, and FLD co-regulate the gene expression in multiple development processes and pathways.

A Polynucleotide Repeat Expansion Causing Temperature-Sensitivity Persists in Wild Irish Accessions of Arabidopsis thaliana

Triplet repeat expansions underlie several human genetic diseases such as Huntington's disease and Friedreich's ataxia. Although such mutations are primarily known from humans, a triplet expansion associated genetic defect has also been reported at the IIL1 locus in the Bur-0 accession of the model plant Arabidopsis thaliana. The IIL1 triplet expansion is an example of cryptic genetic variation as its phenotypic effects are seen only under genetic or environmental perturbation, with high temperatures resulting in a growth defect. Here we demonstrate that the IIL1 triplet expansion associated growth defect is not a general stress response and is specific to particular environmental perturbations. We also confirm and map genetic modifiers that suppress the effect of IIL1 triplet repeat expansion. By collecting and analyzing accessions from the island of Ireland, we recover the repeat expansion in wild populations suggesting that the repeat expansion has persisted at least 60 years in Ireland. Through genome-wide genotyping, we show that the repeat expansion is present in diverse Irish populations. Our findings indicate that even deleterious alleles can persist in populations if their effect is conditional. Our study demonstrates that analysis of groups of wild populations is a powerful tool for understanding the dynamics of cryptic genetic variation.

The Multi-allelic Genetic Architecture of a Variance-Heterogeneity Locus for Molybdenum Concentration in Leaves Acts as a Source of Unexplained Additive Genetic Variance

Genome-wide association (GWA) analyses have generally been used to detect individual loci contributing to the phenotypic diversity in a population by the effects of these loci on the trait mean. More rarely, loci have also been detected based on variance differences between genotypes. Several hypotheses have been proposed to explain the possible genetic mechanisms leading to such variance signals. However, little is known about what causes these signals, or whether this genetic variance-heterogeneity reflects mechanisms of importance in natural populations. Previously, we identified a variance-heterogeneity GWA (vGWA) signal for leaf molybdenum concentrations in Arabidopsis thaliana. Here, fine-mapping of this association reveals that the vGWA emerges from the effects of three independent genetic polymorphisms that all are in strong LD with the markers displaying the genetic variance-heterogeneity. By revealing the genetic architecture underlying this vGWA signal, we uncovered the molecular source of a significant amount of hidden additive genetic variation or “missing heritability”. Two of the three polymorphisms underlying the genetic variance-heterogeneity are promoter variants for Molybdate transporter 1 (MOT1), and the third a variant located ~25 kb downstream of this gene. A fourth independent association was also detected ~600 kb upstream of MOT1. Use of a T-DNA knockout allele highlights Copper Transporter 6; COPT6 (AT2G26975) as a strong candidate gene for this association. Our results show that an extended LD across a complex locus including multiple functional alleles can lead to a variance-heterogeneity between genotypes in natural populations. Further, they provide novel insights into the genetic regulation of ion homeostasis in A. thaliana, and empirically confirm that variance-heterogeneity based GWA methods are a valuable tool to detect novel associations of biological importance in natural populations.

Most biological traits vary in natural populations, and understanding the genetic basis of this variation remains an important challenge. Genome-wide association (GWA) studies have emerged as a powerful tool to address this challenge by dissecting the genetic architecture of trait variation into the contribution of individual genes. This contribution has traditionally been measured as the difference in the phenotypic means between groups of individuals with alternative genotypes at one, or multiple loci. However, instead of altering the trait mean, certain loci alter the variability of the trait. Here, we describe the genetic dissection of one such variance-controlling locus that drives variation in leaf molybdenum concentrations amongst natural accessions of Arabidopsis thaliana. The variance-controlling locus was found to result from the contributions of multiple alleles at multiple loci that are closely linked on the chromosome and is a major contributor to the “missing heritability” for this trait identified in previous studies. This illustrates that multi-allelic genetic architectures can hide large amounts of additive genetic variation, and that it is possible to uncover this hidden variation using the appropriate experimental designs and statistical methods described here.

Genome-Wide Association Analysis of Adaptation Using Environmentally Predicted Traits

Current methods for studying the genetic basis of adaptation evaluate genetic associations with ecologically relevant traits or single environmental variables, under the implicit assumption that natural selection imposes correlations between phenotypes, environments and genotypes. In practice, observed trait and environmental data are manifestations of unknown selective forces and are only indirectly associated with adaptive genetic variation. In theory, improved estimation of these forces could enable more powerful detection of loci under selection. Here we present an approach in which we approximate adaptive variation by modeling phenotypes as a function of the environment and using the predicted trait in multivariate and univariate genome-wide association analysis (GWAS). Based on computer simulations and published flowering time data from the model plant Arabidopsis thaliana, we find that environmentally predicted traits lead to higher recovery of functional loci in multivariate GWAS and are more strongly correlated to allele frequencies at adaptive loci than individual environmental variables. Our results provide an example of the use of environmental data to obtain independent and meaningful information on adaptive genetic variation.

Finding genes involved in adaptation to the environment has long been of interest to evolutionary biologists and ecologists. Most commonly, researchers look for loci whose differences in allelic state correlate with differences in a particular trait or environmental variable such as temperature. The implicit assumption behind such methods is that natural selection by the environment will shape variation in adaptive traits through associated changes in allele frequencies. This means that both environmental and phenotypic variation are relevant for detecting adaptive genes, although we have incomplete knowledge of how the two types of variation relate to adaptation. Here we present a method that aims to identify adaptive genes by combining phenotypic and environmental data. We first predict trait variation from a set of environmental variables as a way to extract the most biologically relevant information from the environment and then look for genes associated with both the predicted and observed trait. Using simulations and published data from the model plant Arabidopsis thaliana, we show that this approach may find adaptive genes more effectively compared to existing methods. We also demonstrate that predicted traits can be used to identify relevant loci in individuals for which no phenotypic data is available.

Modulation of Ambient Temperature-Dependent Flowering in Arabidopsis thaliana by Natural Variation of FLOWERING LOCUS M

Plants integrate seasonal cues such as temperature and day length to optimally adjust their flowering time to the environment. Compared to the control of flowering before and after winter by the vernalization and day length pathways, mechanisms that delay or promote flowering during a transient cool or warm period, especially during spring, are less well understood. Due to global warming, understanding this ambient temperature pathway has gained increasing importance. In Arabidopsis thaliana, FLOWERING LOCUS M (FLM) is a critical flowering regulator of the ambient temperature pathway. FLM is alternatively spliced in a temperature-dependent manner and the two predominant splice variants, FLM-ß and FLM-δ, can repress and activate flowering in the genetic background of the A. thaliana reference accession Columbia-0. The relevance of this regulatory mechanism for the environmental adaptation across the entire range of the species is, however, unknown. Here, we identify insertion polymorphisms in the first intron of FLM as causative for accelerated flowering in many natural A. thaliana accessions, especially in cool (15°C) temperatures. We present evidence for a potential adaptive role of this structural variation and link it specifically to changes in the abundance of FLM-ß. Our results may allow predicting flowering in response to ambient temperatures in the Brassicaceae.

Modeling development and quantitative trait mapping reveal independent genetic modules for leaf size and shape

Improved predictions of fitness and yield may be obtained by characterizing the genetic controls and environmental dependencies of organismal ontogeny. Elucidating the shape of growth curves may reveal novel genetic controls that single-time-point (STP) analyses do not because, in theory, infinite numbers of growth curves can result in the same final measurement. We measured leaf lengths and widths in Brassica rapa recombinant inbred lines (RILs) throughout ontogeny. We modeled leaf growth and allometry as function valued traits (FVT), and examined genetic correlations between these traits and aspects of phenology, physiology, circadian rhythms and fitness. We used RNA-seq to construct a SNP linkage map and mapped trait quantitative trait loci (QTL). We found genetic trade-offs between leaf size and growth rate FVT and uncovered differences in genotypic and QTL correlations involving FVT vs STPs. We identified leaf shape (allometry) as a genetic module independent of length and width and identified selection on FVT parameters of development. Leaf shape is associated with venation features that affect desiccation resistance. The genetic independence of leaf shape from other leaf traits may therefore enable crop optimization in leaf shape without negative effects on traits such as size, growth rate, duration or gas exchange.

"Missing" G x E Variation Controls Flowering Time in Arabidopsis thaliana

Understanding how genetic variation interacts with the environment is essential for understanding adaptation. In particular, the life cycle of plants is tightly coordinated with local environmental signals through complex interactions with the genetic variation (G x E). The mechanistic basis for G x E is almost completely unknown. We collected flowering time data for 173 natural inbred lines of Arabidopsis thaliana from Sweden under two growth temperatures (10°C and 16°C), and observed massive G x E variation. To identify the genetic polymorphisms underlying this variation, we conducted genome-wide scans using both SNPs and local variance components. The SNP-based scan identified several variants that had common effects in both environments, but found no trace of G x E effects, whereas the scan using local variance components found both. Furthermore, the G x E effects appears to be concentrated in a small fraction of the genome (0.5%). Our conclusion is that G x E effects in this study are mostly due to large numbers of allele or haplotypes at a small number of loci, many of which correspond to previously identified flowering time genes.

When natural selection gives gene function the cold shoulder

It is tempting to invoke organismal selection as perpetually optimizing the function of any given gene. However, natural selection can drive genic functional change without improvement of biochemical activity, even to the extinction of gene activity. Detrimental mutations can creep in owing to linkage with other selectively favored loci. Selection can promote functional degradation, irrespective of genetic drift, when adaptation occurs by loss of gene function. Even stabilizing selection on a trait can lead to divergence of the underlying molecular constituents. Selfish genetic elements can also proliferate independent of any functional benefits to the host genome. Here we review the logic and evidence for these diverse processes acting in genome evolution. This collection of distinct evolutionary phenomena - while operating through easily understandable mechanisms - all contribute to the seemingly counterintuitive notion that maintenance or improvement of a gene's biochemical function sometimes do not determine its evolutionary fate.

The Arabidopsis TAC Position Viewer: a high-resolution map of transformation-competent artificial chromosome (TAC) clones aligned with the Arabidopsis thaliana Columbia-0 genome

We present a high-resolution map of genomic transformation-competent artificial chromosome (TAC) clones extending over all Arabidopsis thaliana (Arabidopsis) chromosomes. The Arabidopsis genomic TAC clones have been valuable genetic tools. Previously, we constructed an Arabidopsis genomic TAC library consisting of more than 10,000 TAC clones harboring large genomic DNA fragments extending over the whole Arabidopsis genome. Here, we determined 13,577 end sequences from 6987 Arabidopsis TAC clones and mapped 5937 TAC clones to precise locations, covering approximately 90% of the Arabidopsis chromosomes. We present the large-scale data set of TAC clones with high-resolution mapping information as a Java application tool, the Arabidopsis TAC Position Viewer, which provides ready-to-go transformable genomic DNA clones corresponding to certain loci on Arabidopsis chromosomes. The TAC clone resources will accelerate genomic DNA cloning, positional walking, complementation of mutants and DNA transformation for heterologous gene expression.

Allelic variants in the PRR37 gene and the human-mediated dispersal and diversification of sorghum

Allele phylogenetic analysis of the sorghum flowering-time gene PRR37 provided new insight into the human-mediated selection of a key adaptive gene that occurred during sorghum's diversification and worldwide dispersal. The domestication and spread of the tropical cereal sorghum is associated with the historic movement of humans. We show that an allelic series at PRR37 (pseudo-response regulator 37), a circadian clock-associated transcription factor, was selected in long-day ecosystems worldwide to permit floral initiation and grain production. We identified a series of loss-of-function (photoperiod-insensitive) alleles encoding truncated PRR37 proteins, alleles with key amino acid substitutions in the pseudo-receiver domain, and a novel splice variant in which the pseudo-receiver domain is truncated. Each PRR37 allelic variant was traced to a specific geographic location or specialized agronomic type. We present a graphical model that shows evidence of human selection and gene flow of the PRR37 allelic variants during the global dispersal and agronomic diversification of sorghum. With the recent identification of the Ghd7 gene as an important regulator of flowering date in sorghum, we briefly examine whether loss-of-function Ghd7 allelic variants were selected prior to the human-mediated movement of sorghum from its equatorial center of origin to temperate climates worldwide.

Flowering Locus C's Lessons: Conserved Chromatin Switches Underpinning Developmental Timing and Adaptation

Analysis of how seasonal cues influence the timing of the floral transition has revealed many important principles for how epigenetic regulation can integrate a variety of environmental cues with developmental signals. The study of the pathways that necessitate overwintering in plants and their ability to respond to prolonged cold (the vernalization requirement and response pathways) has elaborated different chromatin regulatory pathways and the involvement of noncoding RNAs. The major target of these vernalization pathways in Arabidopsis (Arabidopsis thaliana) is Flowering Locus C (FLC). A relatively simple picture of FLC regulation is emerging of a few core complexes and mechanisms that antagonize each other's actions. This balance provides a fine degree of control that has nevertheless permitted evolution of a wide range of natural variation in vernalization in Arabidopsis. Similar simple routes of adaptation may underlie life history variation between species.

Genetic variation in the flowering and yield formation of timothy (Phleum pratense L.) accessions after different photoperiod and vernalization treatments

Timothy is a perennial forage grass grown commonly in Boreal regions. This study explored the effect of vernalization and photoperiod (PP) on flowering and growth characteristics and how this related to changes in expression of three flowering related genes in accessions from different geographic origin. Large variation was found in accessions in their vernalization and PP responses. In southern accessions vernalization response or requirement was not observed, the heading date remained unchanged, and plants flowered without vernalization. On the contrary, northern types had obligatory requirement for vernalization and long PP, but the tiller elongation did not require vernalization at 16-h PP. Longer vernalization or PP treatments reduced the genotypical differences in flowering. Moreover, the vernalization saturation progressed stepwise from main tiller to lateral tillers, and this process was more synchronized in southern accessions. The expression of PpVRN1 was associated with vernalization while PpVRN3 accumulated at long PP. A crucial role for PpVRN3 in the transition to flowering was supported as in southern accession the transcript accumulated in non-vernalized plants after transfer to 16-h PP, and the apices transformed to generative stage. Differences in vernalization requirements were associated with variation in expression levels of PpVRN1 and PpVRN3, with higher expression levels in southern type. Most divergent transcript accumulation of PpMADS10 was found under different vernalization conditions. These differences between accessions can be translated into agronomic traits, such as the tiller composition of canopy, which affects the forage yield. The southern types, with minimal vernalization response, have fast re-growth ability and rapidly decreasing nutritive value, whereas northern types grow slowly and have better quality. This information can be utilized in breeding for new cultivars for longer growing seasons at high latitudes.

Plant development regulation: Overview and perspectives

Plant development, as occur in other eukaryotes, is conducted through a complex network of hormones, transcription factors, enzymes and micro RNAs, among other cellular components. They control developmental processes such as embryo, apical root and shoot meristem, leaf, flower, or seed formation, among others. The research in these topics has been very active in last decades. Recently, an explosion of new data concerning regulation mechanisms as well as the response of these processes to environmental changes has emerged. Initially, most of investigations were carried out in the model eudicot Arabidopsis but currently data from other plant species are available in the literature, although they are still limited. The aim of this review is focused on summarize the main molecular actors involved in plant development regulation in diverse plant species. A special attention will be given to the major families of genes and proteins participating in these regulatory mechanisms. The information on the regulatory pathways where they participate will be briefly cited. Additionally, the importance of certain structural features of such proteins that confer ductility and flexibility to these mechanisms will also be reported and discussed.

Evolution of CONSTANS Regulation and Function after Gene Duplication Produced a Photoperiodic Flowering Switch in the Brassicaceae

Environmental control of flowering allows plant reproduction to occur under optimal conditions and facilitates adaptation to different locations. At high latitude, flowering of many plants is controlled by seasonal changes in day length. The photoperiodic flowering pathway confers this response in the Brassicaceae, which colonized temperate latitudes after divergence from the Cleomaceae, their subtropical sister family. The CONSTANS (CO) transcription factor of Arabidopsis thaliana, a member of the Brassicaceae, is central to the photoperiodic flowering response and shows characteristic patterns of transcription required for day-length sensing. CO is believed to be widely conserved among flowering plants; however, we show that it arose after gene duplication at the root of the Brassicaceae followed by divergence of transcriptional regulation and protein function. CO has two close homologs, CONSTANS-LIKE1 (COL1) and COL2, which are related to CO by tandem duplication and whole-genome duplication, respectively. The single CO homolog present in the Cleomaceae shows transcriptional and functional features similar to those of COL1 and COL2, suggesting that these were ancestral. We detect cis-regulatory and codon changes characteristic of CO and use transgenic assays to demonstrate their significance in the day-length-dependent activation of the CO target gene FLOWERING LOCUS T. Thus, the function of CO as a potent photoperiodic flowering switch evolved in the Brassicaceae after gene duplication. The origin of CO may have contributed to the range expansion of the Brassicaceae and suggests that in other families CO genes involved in photoperiodic flowering arose by convergent evolution.

Natural genetic variation in Arabidopsis thaliana defense metabolism genes modulates field fitness

Natural populations persist in complex environments, where biotic stressors, such as pathogen and insect communities, fluctuate temporally and spatially. These shifting biotic pressures generate heterogeneous selective forces that can maintain standing natural variation within a species. To directly test if genes containing causal variation for the Arabidopsis thaliana defensive compounds, glucosinolates (GSL) control field fitness and are therefore subject to natural selection, we conducted a multi-year field trial using lines that vary in only specific causal genes. Interestingly, we found that variation in these naturally polymorphic GSL genes affected fitness in each of our environments but the pattern fluctuated such that highly fit genotypes in one trial displayed lower fitness in another and that no GSL genotype or genotypes consistently out-performed the others. This was true both across locations and within the same location across years. These results indicate that environmental heterogeneity may contribute to the maintenance of GSL variation observed within Arabidopsis thaliana.

DOI:http://dx.doi.org/10.7554/eLife.05604.001

‘Genetic variation’ describes the naturally occurring differences in DNA sequences that are found among individuals of the same species. These genetic differences arise from random mutations and may be passed on to their offspring. Some of these mutations may improve the ability of an individual to survive and reproduce—known as fitness—and are likely to become more common in the population. Other mutations may reduce an individual's fitness and are likely to be lost. However, it is believed that most of the mutations will have no effect on the fitness of individuals.

It is not known why many of these ‘neutral’ genetic differences are maintained in populations. Some researchers have proposed that they are kept by chance and that there is no direct advantage to the population of keeping them unless these neutral mutations later become beneficial. However, other researchers think that the genetic variation itself may improve the fitness of the population by allowing it to quickly adapt to changes in the environment.

Arabidopsis thaliana is a small plant that lives in many different environments and has high levels of genetic variation in many of its physical traits. One of these traits is the production of molecules called glucosinolates, which help the plants to defend against herbivores and infection by microbes. Previous studies have suggested that variation in the genes that make glucosinolates may improve the fitness of A. thaliana populations.

To test this idea, Kerwin et al. carried out a field trial using A. thaliana plants that were genetically identical except for some of the genes involved in the production of glucosinolates. Kerwin et al. grew the plants in several different environments over several years. The field trial shows that variation in these genes affected the fitness of the plants in each of the different environments. However, the fitness benefit depended on the environment, and no single gene variant provided the best fitness across all environments, or over all the years of the trial.

Kerwin et al.'s findings suggest that changes in the environment may contribute to the maintenance of genetic variation in the genes that make glucosinolates. This raises the questions of how many other genes in plants (or other species such as humans) have genetic variation that contributes to fitness across varied environments; and how can this link be tested in natural settings.

DOI:http://dx.doi.org/10.7554/eLife.05604.002

Natural variation for anthocyanin accumulation under high-light and low-temperature stress is attributable to the ENHANCER OF AG-4 2 (HUA2) locus in combination with PRODUCTION OF ANTHOCYANIN PIGMENT1 (PAP1) and PAP2

Growing conditions combining high light intensities and low temperatures lead to anthocyanin accumulation in plants. This response was contrasted between two Arabidopsis thaliana accessions, which were used to decipher the genetic and molecular bases underlying the variation of this response. Quantitative trait loci (QTLs) for flowering time (FT) and anthocyanin accumulation under a high-light and low-temperature scenario versus a control environment were mapped. Major QTLs were confirmed using near-isogenic lines. Candidate genes were examined using mutants and gene expression studies as well as transgenic complementation. Several QTLs were found for FT and for anthocyanin content, of which one QTL co-located at the ENHANCER OF AG-4 2 (HUA2) locus. That HUA2 is a regulator of both pathways was confirmed by the analysis of loss-of-function mutants. For a strong expression of anthocyanin, additional allelic variation was detected for the PRODUCTION OF ANTHOCYANIN PIGMENT1 (PAP1) and PAP2 genes which control the anthocyanin pathway. The genetic control of variation for anthocyanin content was dissected in A. thaliana and shown to be affected by a common regulator of flowering and anthocyanin biosynthesis together with anthocyanin-specific regulators.

A flowering integrator, SOC1, affects stomatal opening in Arabidopsis thaliana

Stomatal movements are regulated by multiple environmental signals. Recent investigations indicate that photoperiodic flowering components, such as CRY, GI, CO, FT and TSF, are expressed in guard cells and positively affect stomatal opening in Arabidopsis thaliana. Here we show that SOC1, which encodes a MADS box transcription factor and integrates multiple flowering signals, also exerts a positive effect on stomatal opening. FLC encodes a potent repressor of FT and SOC1, and FRI acts as an activator of FLC. Thus, we examined stomatal phenotypes in FRI-Col, which contains an active FRI allele of accession Sf-2 by introgression. We found higher expression of FLC and lower expression of FT, SOC1 and TSF in guard cells from FRI-Col than in those from Col. Light-induced stomatal opening was significantly suppressed in FRI-Col. Interestingly, vernalization of FRI-Col partially restored light-induced stomatal opening, concomitant with a decrease of FLC and increase of FT, SOC1 and TSF. Furthermore, we observed the constitutive open-stomata phenotype in transgenic plants overexpressing SOC1-GFP (green fluorescent protein) in guard cells (SOC1-GFP overexpressor), and found that light-induced stomatal opening was significantly suppressed in a soc1 knockout mutant. RNA sequencing using epidermis from the SOC1-GFP overexpressor revealed that the expression levels of several genes involved in stomatal opening, such as BLUS1 and the plasma membrane H(+)-ATPases, were higher than those in background plants. From these results, we conclude that SOC1 is involved in the regulation of stomatal opening via transcriptional regulation in guard cells.

Phenotypic evolution through variation in splicing of the noncoding RNA COOLAIR

The extent to which natural polymorphisms in noncoding sequences have functional consequences is still unknown. A large proportion of the natural variation in flowering in Arabidopsis thaliana accessions is due to noncoding cis polymorphisms that define distinct haplotypes of FLOWERING LOCUS C (FLC). Here, we show that a single natural intronic polymorphism in one haplotype affects FLC expression and thus flowering by specifically changing splicing of the FLC antisense transcript COOLAIR. Altered antisense splicing increases FLC expression via a cotranscriptional mechanism involving capping of the FLC nascent transcript. Single noncoding polymorphisms can therefore be a major contributor to phenotypic evolution through modulation of noncoding transcripts.

To bloom or not to bloom: role of microRNAs in plant flowering

During the course of their life cycles, plants undergo various morphological and physiological changes underlying juvenile-to-adult and adult-to-flowering phase transitions. To flower or not to flower is a key step of plasticity of a plant toward the start of its new life cycle. In addition to the previously revealed intrinsic genetic programs, exogenous cues, and endogenous cues, a class of small non-coding RNAs, microRNAs (miRNAs), plays a key role in plants making the decision to flower by integrating into the known flowering pathways. This review highlights the age-dependent flowering pathway with a focus on a number of timing miRNAs in determining such a key process. The contributions of other miRNAs which exist mainly outside the age pathway are also discussed. Approaches to study the flowering-determining miRNAs, their interactions, and applications are presented.

Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight in chickpea

Phylogenetic footprinting identified 666 genome-wide paralogous and orthologous CNMS (conserved non-coding microsatellite) markers from 5'-untranslated and regulatory regions (URRs) of 603 protein-coding chickpea genes. The (CT)n and (GA)n CNMS carrying CTRMCAMV35S and GAGA8BKN3 regulatory elements, respectively, are abundant in the chickpea genome. The mapped genic CNMS markers with robust amplification efficiencies (94.7%) detected higher intraspecific polymorphic potential (37.6%) among genotypes, implying their immense utility in chickpea breeding and genetic analyses. Seventeen differentially expressed CNMS marker-associated genes showing strong preferential and seed tissue/developmental stage-specific expression in contrasting genotypes were selected to narrow down the gene targets underlying seed weight quantitative trait loci (QTLs)/eQTLs (expression QTLs) through integrative genetical genomics. The integration of transcript profiling with seed weight QTL/eQTL mapping, molecular haplotyping, and association analyses identified potential molecular tags (GAGA8BKN3 and RAV1AAT regulatory elements and alleles/haplotypes) in the LOB-domain-containing protein- and KANADI protein-encoding transcription factor genes controlling the cis-regulated expression for seed weight in the chickpea. This emphasizes the potential of CNMS marker-based integrative genetical genomics for the quantitative genetic dissection of complex seed weight in chickpea.

Combinatorial activities of SHORT VEGETATIVE PHASE and FLOWERING LOCUS C define distinct modes of flowering regulation in Arabidopsis

Background

The initiation of flowering is an important developmental transition as it marks the beginning of the reproductive phase in plants. The MADS-box transcription factors (TFs) FLOWERING LOCUS C (FLC) and SHORT VEGETATIVE PHASE (SVP) form a complex to repress the expression of genes that initiate flowering in Arabidopsis. Both TFs play a central role in the regulatory network by conferring seasonal patterns of flowering. However, their interdependence and biological relevance when acting as a complex have not been extensively studied.

Results

We characterized the effects of both TFs individually and as a complex on flowering initiation using transcriptome profiling and DNA-binding occupancy. We find four major clusters regulating transcriptional responses, and that DNA binding scenarios are highly affected by the presence of the cognate partner. Remarkably, we identify genes whose regulation depends exclusively on simultaneous action of both proteins, thus distinguishing between the specificity of the SVP:FLC complex and that of each TF acting individually. The downstream targets of the SVP:FLC complex include a higher proportion of genes regulating floral induction, whereas those bound by either TF independently are biased towards floral development. Many genes involved in gibberellin-related processes are bound by the SVP:FLC complex, suggesting that direct regulation of gibberellin metabolism by FLC and SVP contributes to their effects on flowering.

Conclusions

The regulatory codes controlled by SVP and FLC were deciphered at the genome-wide level revealing substantial flexibility based on dependent and independent DNA binding that may contribute to variation and robustness in the regulation of flowering.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0597-1) contains supplementary material, which is available to authorized users.

A methyltransferase required for proper timing of the vernalization response in Arabidopsis

Prolonged exposure to winter cold enables flowering in many plant species through a process called vernalization. In Arabidopsis, vernalization results from the epigenetic silencing of the floral repressor flowering locus C (FLC) via a Polycomb Repressive Complex 2 (PRC2)-mediated increase in the density of the epigenetic silencing mark H3K27me3 at FLC chromatin. During cold exposure, a gene encoding a unique, cold-specific PRC2 component, vernalization insensitive 3 (VIN3), which is necessary for PRC2-mediated silencing of FLC, is induced. Here we show that set domain group 7 (SDG7) is required for proper timing of VIN3 induction and of the vernalization process. Loss of SDG7 results in a vernalization-hypersensitive phenotype, as well as more rapid cold-mediated up-regulation of VIN3. In the absence of cold, loss of SDG7 results in elevated levels of long noncoding RNAs, which are thought to participate in epigenetic repression of FLC. Furthermore, loss of SDG7 results in increased H3K27me3 deposition on FLC chromatin in the absence of cold exposure and enhanced H3K27me3 spreading during cold treatment. Thus, SDG7 is a negative regulator of vernalization, and loss of SDG7 creates a partially vernalized state without cold exposure.

Natural variation in cross-talk between glucosinolates and onset of flowering in Arabidopsis

Naturally variable regulatory networks control different biological processes including reproduction and defense. This variation within regulatory networks enables plants to optimize defense and reproduction in different environments. In this study we investigate the ability of two enzyme-encoding genes in the glucosinolate pathway, AOP2 and AOP3, to affect glucosinolate accumulation and flowering time. We have introduced the two highly similar enzymes into two different AOP (null) accessions, Col-0 and Cph-0, and found that the genes differ in their ability to affect glucosinolate levels and flowering time across the accessions. This indicated that the different glucosinolates produced by AOP2 and AOP3 serve specific regulatory roles in controlling these phenotypes. While the changes in glucosinolate levels were similar in both accessions, the effect on flowering time was dependent on the genetic background pointing to natural variation in cross-talk between defense chemistry and onset of flowering. This variation likely reflects an adaptation to survival in different environments.

Genome-wide gene expression perturbation induced by loss of C2 chromosome in allotetraploid Brassica napus L

Aneuploidy with loss of entire chromosomes from normal complement disrupts the balanced genome and is tolerable only by polyploidy plants. In this study, the monosomic and nullisomic plants losing one or two copies of C2 chromosome from allotetraploid Brassica napus L. (2n = 38, AACC) were produced and compared for their phenotype and transcriptome. The monosomics gave a plant phenotype very similar to the original donor, but the nullisomics had much smaller stature and also shorter growth period. By the comparative analyses on the global transcript profiles with the euploid donor, genome-wide alterations in gene expression were revealed in two aneuploids, and their majority of differentially expressed genes (DEGs) resulted from the trans-acting effects of the zero and one copy of C2 chromosome. The higher number of up-regulated genes than down-regulated genes on other chromosomes suggested that the genome responded to the C2 loss via enhancing the expression of certain genes. Particularly, more DEGs were detected in the monosomics than nullisomics, contrasting with their phenotypes. The gene expression of the other chromosomes was differently affected, and several dysregulated domains in which up- or downregulated genes obviously clustered were identifiable. But the mean gene expression (MGE) for homoeologous chromosome A2 reduced with the C2 loss. Some genes and their expressions on C2 were correlated with the phenotype deviations in the aneuploids. These results provided new insights into the transcriptomic perturbation of the allopolyploid genome elicited by the loss of individual chromosome.

Heat can erase epigenetic marks of vernalization in Arabidopsis

Vernalization establishes a memory of winter that must be maintained for weeks or months in order to promote flowering the following spring. The stability of the vernalized state varies among plant species and depends on the duration of cold exposure. In Arabidopsis thaliana, winter leads to epigenetic silencing of the floral repressor gene FLOWERING LOCUS C (FLC) and the duration of cold is measured through the dynamics of chromatin modifications during and after cold. The growing conditions encountered post-vernalization are thus critical for the maintenance of the vernalized state. We reported that high temperature leads to devernalization and, consistently, to FLC reactivation in Arabidopsis seedlings. Here we show that the repressive epigenetic mark H3K27me3 decreases at the FLC locus when vernalized seedlings are grown at 30°C, unless they were first exposed to a stabilizing period at 20°C. Ambient temperature thus controls the epigenetic memory of winter.

Photoperiodic Regulation of Florigen Function in Arabidopsis thaliana

One mechanism through which flowering in response to seasonal change is brought about is by sensing the fluctuation in day-length; the photoperiod. Flowering induction occurs through the production of the florigenic protein FLOWERING LOCUS T (FT) and its movement from the phloem companion cells in the leaf vasculature into the shoot apex, where meristematic reprogramming occurs. FT activation in response to photoperiod condition is accomplished largely through the activity of the transcription factor CONSTANS (CO). Regulation of CO expression and protein stability, as well as the timing of other components via the circadian clock, is a critical mechanism by which plants are able to respond to photoperiod to initiate the floral transition. Modulation of FT expression in response to external and internal stimuli via components of the flowering network is crucial to mediate a fluid flowering response to a variety of environmental parameters. In addition, the regulated movement of FT protein from the phloem to the shoot apex, and interactions that determine floral meristem cell fate, constitute novel mechanisms through which photoperiodic information is translated into flowering time.

Epigenetic reprogramming that prevents transgenerational inheritance of the vernalized state

The reprogramming of epigenetic states in gametes and embryos is essential for correct development in plants and mammals. In plants, the germ line arises from somatic tissues of the flower, necessitating the erasure of chromatin modifications that have accumulated at specific loci during development or in response to external stimuli. If this process occurs inefficiently, it can lead to epigenetic states being inherited from one generation to the next. However, in most cases, accumulated epigenetic modifications are efficiently erased before the next generation. An important example of epigenetic reprogramming in plants is the resetting of the expression of the floral repressor locus FLC in Arabidopsis thaliana. FLC is epigenetically silenced by prolonged cold in a process called vernalization. However, the locus is reactivated before the completion of seed development, ensuring the requirement for vernalization in every generation. In contrast to our detailed understanding of the polycomb-mediated epigenetic silencing induced by vernalization, little is known about the mechanism involved in the reactivation of FLC. Here we show that a hypomorphic mutation in the jumonji-domain-containing protein ELF6 impaired the reactivation of FLC in reproductive tissues, leading to the inheritance of a partially vernalized state. ELF6 has H3K27me3 demethylase activity, and the mutation reduced this enzymatic activity in planta. Consistent with this, in the next generation of mutant plants, H3K27me3 levels at the FLC locus stayed higher, and FLC expression remained lower, than in the wild type. Our data reveal an ancient role for H3K27 demethylation in the reprogramming of epigenetic states in plant and mammalian embryos.

The relationship between flowering time and growth responses to drought in the Arabidopsis Landsberg erecta x Antwerp-1 population

Limited water availability is one of the most prominent abiotic constraints to plant survival and reproduction. Thus, plants have evolved different strategies to cope with water deficit, including modification of their growth and timing of developmental events such as flowering. In this work, we explore the link between flowering time and growth responses to moderate drought stress in Arabidopsis thaliana using natural variation for these traits found in the Landsberg erecta x Antwerp-1 recombinant inbred line population. We developed and phenotyped near isogenic lines containing different allelic combinations at three interacting quantitative trait loci (QTL) affecting both flowering time and growth in response to water deficit. We used these lines to confirm additive and epistatic effects of the three QTL and observed a strong association between late flowering and reduced sensitivity to drought. Analyses of growth responses to drought over time revealed that late flowering plants were able to recover their growth in the second half of their vegetative development. In contrast, early flowering, a common drought escape strategy that ensures plant survival under severe water deficit, was associated with strongly impaired plant fitness. The results presented here indicate that late flowering may be advantageous under continuous mild water deficit as it allows stress acclimatization over time.

GmFLD, a soybean homolog of the autonomous pathway gene FLOWERING LOCUS D, promotes flowering in Arabidopsis thaliana

BACKGROUND

Flowering at an appropriate time is crucial for seed maturity and reproductive success in all flowering plants. Soybean (Glycine max) is a typical short day plant, and both photoperiod and autonomous pathway genes exist in soybean genome. However, little is known about the functions of soybean autonomous pathway genes. In this article, we examined the functions of a soybean homolog of the autonomous pathway gene FLOWERING LOCUS D (FLD), GmFLD in the flowering transition of A. thaliana.

RESULTS

In soybean, GmFLD is highly expressed in expanded cotyledons of seedlings, roots, and young pods. However, the expression levels are low in leaves and shoot apexes. Expression of GmFLD in A. thaliana (Col) resulted in early flowering of the transgenic plants, and rescued the late flowering phenotype of the A. thaliana fld mutant. In GmFLD transgenic plants (Col or fld background), the FLC (FLOWERING LOCUS C) transcript levels decreased whereas the floral integrators, FT and SOC1, were up-regulated when compared with the corresponding non-transgenic genotypes. Furthermore, chromatin immuno-precipitation analysis showed that in the transgenic rescued lines (fld background), the levels of both tri-methylation of histone H3 Lys-4 and acetylation of H4 decreased significantly around the transcriptional start site of FLC. This is consistent with the function of GmFLD as a histone demethylase.

CONCLUSIONS

Our results suggest that GmFLD is a functional ortholog of the Arabidopsis FLD and may play an important role in the regulation of chromatin state in soybean. The present data provides the first evidence for the evolutionary conservation of the components in the autonomous pathway in soybean.

A plant-specific HUA2-LIKE (HULK) gene family in Arabidopsis thaliana is essential for development

In Arabidopsis thaliana, the HUA2 gene is required for proper expression of FLOWERING LOCUS C (FLC) and AGAMOUS, key regulators of flowering time and reproductive development, respectively. Although HUA2 is broadly expressed, plants lacking HUA2 function have only moderately reduced plant stature, leaf initiation rate and flowering time. To better understand HUA2 activity, and to test whether redundancy with similar genes underlies the absence of strong phenotypes in HUA2 mutant plants, we identified and subsequently characterized three additional HUA2-LIKE (HULK) genes in Arabidopsis. These genes form two clades (HUA2/HULK1 and HULK2/HULK3), with members broadly conserved in both vascular and non-vascular plants, but not present outside the plant kingdom. Plants with progressively reduced HULK activity had increasingly severe developmental defects, and plants homozygous for loss-of-function mutations in all four HULK genes were not recovered. Multiple mutants displayed reproductive, embryonic and post-embryonic abnormalities, and provide detailed insights into the overlapping and unique functions of individual HULK genes. With regard to flowering time, opposing influences were apparent: hua2 hulk1 plants were early-flowering, while hulk2 hulk3 mutants were late-flowering, and hua2 acted epistatically to cause early flowering in all combinations. Genome-wide expression profiling of mutant combinations using RNA-Seq revealed complex transcriptional changes in seedlings, with FLC, a known target of HUA2, among the most affected. Our studies, which include characterization of HULK expression patterns and subcellular localization, suggest that the HULK genes encode conserved nuclear factors with partially redundant but essential functions associated with diverse genetic pathways in plants.

Epigenetic regulation in plant responses to the environment

In this article, we review environmentally mediated epigenetic regulation in plants using two case histories. One of these, vernalization, mediates adaptation of plants to different environments and it exemplifies processes that are reset in each generation. The other, virus-induced silencing, involves transgenerationally inherited epigenetic modifications. Heritable epigenetic marks may result in heritable phenotypic variation, influencing fitness, and so be subject to natural selection. However, unlike genetic inheritance, the epigenetic modifications show instability and are influenced by the environment. These two case histories are then compared with other phenomena in plant biology that are likely to represent epigenetic regulation in response to the environment.

Regulation of flowering time by the miR156-mediated age pathway

Precise flowering time is critical to reproductive success. In response to diverse exogenous and endogenous cues including age, hormones, photoperiod, and temperature, the floral transition is controlled by a complex regulatory network, which involves extensive crosstalks, feedback, or feedforward loops between the components within flowering time pathways. The newly identified age pathway, which is controlled by microRNA156 (miR156) and its target SQUAMOSA PROMOTER BINDING-LIKE (SPL) transcription factors, ensures plants flower under non-inductive conditions. In this review, I summarize the recent advance in understanding of the age pathway, focusing on the regulatory basis of the developmental decline in miR156 level by age and the molecular mechanism by which the age pathway is integrated into other flowering time pathways.

Nuclear organization changes and the epigenetic silencing of FLC during vernalization

Changes in nuclear organization are considered an important complement to trans-acting factors, histone modifications and non-coding RNAs in robust and stable epigenetic silencing. However, how these multiple layers interconnect mechanistically to reinforce each other's activity is still unclear. A system providing long timescales facilitating analysis of these interconnections is vernalization. This involves the Polycomb-mediated epigenetic silencing of flowering locus C (FLC) that occurs as Arabidopsis plants are exposed to prolonged cold. Analysis of changes in nuclear organization during vernalization has revealed that disruption of a gene loop and physical clustering of FLC loci are part of the vernalization mechanism. These events occur at different times and thus contribute to distinct aspects of the silencing mechanism. The physical clustering of FLC loci is tightly correlated with the accumulation of specific Polycomb complexes/H3K27me3 at a localized intragenic site during the cold. Since the quantitative nature of vernalization is a reflection of a bistable cell autonomous switch in an increasing number of cells, this correlation suggests a tight connection between the switching mechanism and changes in nuclear organization. This integrated picture is likely to be informative for many epigenetic mechanisms.

Functional analysis of the Landsberg erecta allele of FRIGIDA

BACKGROUND

Most of the natural variation in flowering time in Arabidopsis thaliana can be attributed to allelic variation at the gene FRIGIDA (FRI, AT4G00650), which activates expression of the floral repressor FLOWERING LOCUS C (FLC, AT5G10140). Usually, late-flowering accessions carry functional FRI alleles (FRI-wt), whereas early flowering accessions contain non-functional alleles. The two most frequent alleles found in early flowering accessions are the ones present in the commonly used lab strains Columbia (FRI-Col) and Landsberg erecta (FRI-Ler), which contain a premature stop codon and a deletion of the start codon respectively.

RESULTS

Analysis of flowering time data from various Arabidopsis natural accessions indicated that the FRI-Ler allele retains some functionality. We generated transgenic lines carrying the FRI-Col or FRI-Ler allele in order to compare their effect on flowering time, vernalization response and FLC expression in the same genetic background. We characterize their modes of regulation through allele-specific expression and their relevance in nature through re-analysis of published datasets. We demonstrate that the FRI-Ler allele induces FLC expression, delays flowering time and confers sensitivity to vernalization in contrast to the true null FRI-Col allele. Nevertheless, the FRI-Ler allele revealed a weaker effect when compared to the fully functional FRI-wt allele, mainly due to reduced expression.

CONCLUSIONS

The present study defines for the first time the existence of a new class of Arabidopsis accessions with an intermediate phenotype between slow and rapid cycling types. Although using available data from a common garden experiment we cannot observe fitness differences between accessions carrying the FRI-Ler or the FRI-Col allele, the phenotypic changes observed in the lab suggest that variation in these alleles could play a role in adaptation to specific natural environments.