It's time to flower: the genetic control of flowering time

In plants, successful sexual reproduction and the ensuing development of seeds and fruits depend on flowering at the right time. This involves coordinating flowering with the appropriate season and with the developmental history of the plant. Genetic and molecular analysis in the small cruciform weed, Arabidopsis, has revealed distinct but linked pathways that are responsible for detecting the major seasonal cues of day length and cold temperature, as well as other local environmental and internal signals. The balance of signals from these pathways is integrated by a common set of genes to determine when flowering occurs. Excitingly, it has been discovered that many of these same genes regulate flowering in other plants, such as rice. This review focuses on recent advances in how three of the signalling pathways (the day-length, vernalisation and autonomous pathways) function to control flowering.     

Contributions of flowering time genes to sunflower domestication and improvement

Determining the identity and distribution of molecular changes leading to the evolution of modern crop species provides major insights into the timing and nature of historical forces involved in rapid phenotypic evolution. In this study, we employed an integrated candidate gene strategy to identify loci involved in the evolution of flowering time during early domestication and modern improvement of the sunflower (Helianthus annuus). Sunflower homologs of many genes with known functions in flowering time were isolated and cataloged. Then, colocalization with previously mapped quantitative trait loci (QTLs), expression, or protein sequence differences between wild and domesticated sunflower, and molecular evolutionary signatures of selective sweeps were applied as step-wise criteria for narrowing down an original pool of 30 candidates. This process led to the discovery that five paralogs in the flowering locus T/terminal flower 1 gene family experienced selective sweeps during the evolution of cultivated sunflower and may be the causal loci underlying flowering time QTLs. Our findings suggest that gene duplication fosters evolutionary innovation and that natural variation in both coding and regulatory sequences of these paralogs responded to a complex history of artificial selection on flowering time during the evolution of cultivated sunflower.     

The effect of non-additive genetic interactions on selection in multi-locus genetic models

Additive genetic variance might usually be expected to decrease in a finite population because of genetic drift. However, both theoretical and empirical studies have shown that the additive genetic variance of a population could, in some cases, actually increase owing to the action of genetic drift in presence of non-additive effects. We used Monte-Carlo simulations to address a less-well-studied issue: the effects of directional truncation selection on a trait affected by non-additive genetic variation. We investigated the effects on genetic variance and the response to selection. We compared two different genetic models, representing various numbers of loci. We found that the additive genetic variance could also increase in the case of truncation selection, when dominance and epistasis was present. Additive-by-additive epistatic effects generally gave a higher increase in additive variance compared to dominance. However, the magnitude of the increase differed depending on the particular model and on the number of loci.     

Non-linear regression models for time to flowering in wild chickpea combine genetic and climatic factors

Background

Accurate prediction of crop flowering time is required for reaching maximal farm efficiency. Several models developed to accomplish this goal are based on deep knowledge of plant phenology, requiring large investment for every individual crop or new variety. Mathematical modeling can be used to make better use of more shallow data and to extract information from it with higher efficiency. Cultivars of chickpea, Cicer arietanum, are currently being improved by introgressing wild C. reticulatum biodiversity with very different flowering time requirements. More understanding is required for how flowering time will depend on environmental conditions in these cultivars developed by introgression of wild alleles.

Results

We built a novel model for flowering time of wild chickpeas collected at 21 different sites in Turkey and grown in 4 distinct environmental conditions over several different years and seasons. We propose a general approach, in which the analytic forms of dependence of flowering time on climatic parameters, their regression coefficients, and a set of predictors are inferred automatically by stochastic minimization of the deviation of the model output from data. By using a combination of Grammatical Evolution and Differential Evolution Entirely Parallel method, we have identified a model that reflects the influence of effects of day length, temperature, humidity and precipitation and has a coefficient of determination of R²=0.97.

Conclusions

We used our model to test two important hypotheses. We propose that chickpea phenology may be strongly predicted by accession geographic origin, as well as local environmental conditions at the site of growth. Indeed, the site of origin-by-growth environment interaction accounts for about 14.7% of variation in time period from sowing to flowering. Secondly, as the adaptation to specific environments is blueprinted in genomes, the effects of genes on flowering time may be conditioned on environmental factors. Genotype-by-environment interaction accounts for about 17.2% of overall variation in flowering time. We also identified several genomic markers associated with different reactions to climatic factor changes. Our methodology is general and can be further applied to extend existing crop models, especially when phenological information is limited.

     

Modelling the genetic architecture of flowering time control in barley through nested association mapping

Background

Barley, globally the fourth most important cereal, provides food and beverages for humans and feed for animal husbandry. Maximizing grain yield under varying climate conditions largely depends on the optimal timing of flowering. Therefore, regulation of flowering time is of extraordinary importance to meet future food and feed demands. We developed the first barley nested association mapping (NAM) population, HEB-25, by crossing 25 wild barleys with one elite barley cultivar, and used it to dissect the genetic architecture of flowering time.

Results

Upon cultivation of 1,420 lines in multi-field trials and applying a genome-wide association study, eight major quantitative trait loci (QTL) were identified as main determinants to control flowering time in barley. These QTL accounted for 64% of the cross-validated proportion of explained genotypic variance (p_G). The strongest single QTL effect corresponded to the known photoperiod response gene Ppd-H1. After sequencing the causative part of Ppd-H1, we differentiated twelve haplotypes in HEB-25, whereof the strongest exotic haplotype accelerated flowering time by 11 days compared to the elite barley haplotype. Applying a whole genome prediction model including main effects and epistatic interactions allowed predicting flowering time with an unmatched accuracy of 77% of cross-validated p_G.

Conclusions

The elaborated causal models represent a fundamental step to explain flowering time in barley. In addition, our study confirms that the exotic biodiversity present in HEB-25 is a valuable toolbox to dissect the genetic architecture of important agronomic traits and to replenish the elite barley breeding pool with favorable, trait-improving exotic alleles.

     

Connecting the sun to flowering in sunflower adaptation

Species living in seasonal environments often adaptively time their reproduction in response to photoperiod cues. We characterized the expression of genes in the flowering-time regulatory network across wild populations of the common sunflower, Helianthus annuus, that we found to be adaptively differentiated for photoperiod response. The observed clinal variation was associated with changes at multiple hierarchical levels in multiple pathways. Paralogue-specific changes in FT homologue expression and tissue-specific changes in SOC1 homologue expression were associated with loss and reversal of plasticity, respectively, suggesting that redundancy and modularity are gene network characteristics easily exploited by natural selection to produce evolutionary innovation. Distinct genetic mechanisms contribute to convergent evolution of photoperiod responses within sunflower, suggesting regulatory network architecture does not impose strong constraints on the evolution of phenotypic plasticity.     

Quantitative genetic analysis of flowering time in tomato.

Artificial selection of cultivated tomato (Solanum lycopersicum L.) has resulted in the generation of early-flowering, day-length-insensitive cultivars, despite its close relationship to other Solanum species that need more time and specific photoperiods to flower. To investigate the genetic mechanisms controlling flowering time in tomato and related species, we performed a quantitative trait locus (QTL) analysis for flowering time in an F2 mapping population derived from S. lycopersicum and its late-flowering wild relative S. chmielewskii. Flowering time was scored as the number of days from sowing to the opening of the first flower (days to flowering), and as the number of leaves under the first inflorescence (leaf number). QTL analyses detected 2 QTLs affecting days to flowering, which explained 55.3% of the total phenotypic variance, and 6 QTLs for leaf number, accounting for 66.7% of the corresponding phenotypic variance. Four of the leaf number QTLs had not previously been detected for this trait in tomato. Colocation of some QTLs with flowering-time genes included in the genetic map suggests PHYB2, FALSIFLORA, and a tomato FLC-like sequence as candidate genes that might have been targets of selection during the domestication of tomato.     

Environmental control of flowering time in Antirrhinum majus

The effect of different environmental conditions on flowering time and the number of leaves produced before the first flower is formed has been investigated in Antirrhinum majus L. The effect of light quality has been tested by decreasing the red/far‐red ratio, generally resulting in a reduced flowering time and leaf number. Furthermore, it could be shown that photoperiod, temperature and light intensity are inversely correlated with flowering time and leaf number. However, lowering the temperature from 15 to 12°C resulted in a reduction of flowering time. This observation shows that Antirrhinum can be vernalised.
Using defined combinations of the four environmental factors we have been able to reduce flowering time to only 42 days or to delay flowering for at least 2 years. The results obtained allow an optimisation of the screening conditions for identifying flowering time mutants in Antirrhinum .     

植物开花时间的遗传调控通路研究进展

开花时间对植物的繁殖成功至关重要。广泛分布的物种经常发生开花时间的分化, 从而能够更好地适应不同的环境条件。为了探索植物开花行为发生适应性分化的分子机制, 首先要明确调控开花行为的遗传通路。本文梳理了植物各类群调控开花时间的遗传通路, 以期为开花时间适应性分化的分子机制研究提供依据。 植物从营养生长向繁殖转变时, 其开花行为主要受到光照、温度、水分等外界环境因子和赤霉素等内在因素的影响。通过对模式植物拟南芥(Arabidopsis thaliana)和其他类群的研究, 总结出了调控植物开花时间的6条通路, 包括日照长度和光质影响开花的光依赖通路, 长时间冷暴露后促进植物开花的春化通路, 高温或低温环境影响开花的温度通路, 以及赤霉素通路、年龄通路和自主通路3条内部调节过程。植物开花时间调控的6条上游通路信号传递到下游的开花整合基因FT(FLOWERING LOCUS T)和SOC1(SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1), 整合基因将这些复杂的调节因子整合后进一步传递到下游花分生组织, 从而启动开花。此外, 非编码RNA、转座子对开花时间的调控也具有重要作用。部分遗传通路被证实在植物适应环境的过程中起到了重要作用。目前对植物开花调控的研究已经有一百多年历史, 理论相对成熟。然而, 仍然存在许多具有争议和未解决的问题, 如开花基因的表达方式、开花行为的特殊调控机制、开花时间变异的适应性意义等等, 需要更进一步的研究。     

Xiphophorus interspecies hybrids as genetic models of induced neoplasia

Fishes of the genus Xiphophorus (platyfishes and swordtails) are small, internally fertilizing, livebearing, and derived from freshwater habitats in Mexico, Guatemala, Belize, and Honduras. Scientists have used these fishes in cancer research studies for more than 70 yr. The genus is presently composed of 22 species that are quite divergent in their external morphology. Most cancer studies using Xiphophorus use hybrids, which can be easily produced by artificial insemination. Phenotypic traits, such as macromelanophore pigment patterns, are often drastically altered as a result of lack of gene regulation within hybrid fishes. These fish can develop large exophytic melanomas as a result of upregulated expression of these pigment patterns. Because backcross hybrid fish are susceptible to the development of melanoma and other neoplasms, they can be subjected to potentially deleterious chemical and physical agents. It is thus possible to use gene mapping and cloning methodologies to identify and characterize oncogenes and tumor suppressors implicated in spontaneous or induced neoplasia. This article reviews the history of cancer research using Xiphophorus and recent developments regarding DNA repair capabilities, mapping, and cloning of candidate genes involved in neoplastic phenotypes. The particular genetic complexity of melanoma in these fishes is analyzed and reviewed.     

An association mapping approach to identify flowering time genes in natural populations of Lolium perenne (L.)

We describe an association mapping approach using natural populations of perennial ryegrass (Lolium perenne L.) to identify molecular markers associated with heading date, an important trait affecting seasonal production, tillering, digestibility and grassland management regimes. Twenty-three natural populations originating from throughout Europe, with heading date phenotypes ranging from very early to very late, as well as three synthetic populations (varieties) were used for molecular marker genotyping using AFLP. In total, 589 polymorphic markers were identified. Hierarchical clustering, principal coordinate and other statistical analyses identified four outlying populations forming a clearly distinct sub-group. Removal of those four populations from the subsequent analysis reduced population sub-structure twofold. However, this made relatively little difference to the result of the association analysis. Linear regression identified three markers whose frequency of occurrence correlated with the heading date phenotype. Moreover, these markers were shown to be closely linked to each other within a major QTL on Chromosome 7, explaining 70% of the total variation in heading date. Pairwise linkage disequilibrium among them was also significant. These results suggest that association mapping approaches may be feasible in L. perenne, and that the use of natural populations could provide a useful source of genetic variation in traits of importance in crop improvement.     

Comparison of environmental and mutational variation in flowering time in Arabidopsis

Developmental dynamics can be influenced by external and endogenousfactors in a more or less analogous manner. To compare the phenotypiceffects of (i) environmental [i.e. standard (stPhP) and extended(exPhP) photoperiods] changes in Arabidopsis wild types and(ii) endogenous genetic variation in eav1–eav61 earlyflowering mutants, two temporal indicators were analysed, thetime to bolting (DtB) and the number of leaves (TLN). It wasfound that DtB and TLN are differentially affected in differentenvironmental and genetic contexts, and some factors of dynamicconvergence were identified. The quantitative response to photoperiodis markedly contingent on the phototrophic input for DtB, butless so for TLN. To discriminate the light quantity and periodcomponents in DtB, two novel temporal indicators were determined,LtB (photosynthetic time to bolting) and PChron (DtB h^–1of photoperiod), respectively. The use of PChron results ina coincidence of the variation profiles across stPhP and exPhP,interpreted as a buffering of the trophic response. Unlike naturalaccessions and later flowering mutants, the variation profilesacross stPhP and eav mutants are significantly divergent, pointingto differences in environmental and genetic variation in floweringtime. Yet, phenocopy effects and dynamic convergence betweenwild-type and mutant profiles are detected by using exPhP andthe LtB indicator. Additional analyses of the cauline leaf number(CLN) show that the apical and basal boundaries of the primaryinflorescence vary co-ordinately. The finding that the correlativitybetween CLN and TLN changes across photoperiods suggests thatdifferent states of intra-connectedness are involved in ontogeneticspecification of flowering time and embodied in the primaryinflorescence. Key words: Arabidopsis, bolting, correlativity, developmental dynamics, flowering time, early flowering mutant, phase change, phenocopy, phenotypic plasticity, photoperiodic response     

Standing genetic variation in FRIGIDA mediates experimental evolution of flowering time in Arabidopsis

The role of standing genetic variation in adaptive evolution remains unclear. Although there has been much progress in identifying candidate genes that underlie adaptive traits, we still lack direct evidence that natural allelic variation in these genes can actually mediate adaptive evolution. In this study, we investigate the role of natural allelic variation in two candidate flowering time genes, in response to selection for early flowering in Arabidopsis thaliana : FRIGIDA ( FRI ) and FLOWERING LOCUS C ( FLC ). We performed artificial selection for early flowering under 'spring-' and 'winter-annual' growth conditions using an outbred population of A. thaliana produced by intermating 19 natural accessions. FRI and FLC are involved in A. thaliana 's response to winter conditions, and nonfunctional and weak alleles at these loci are know to reduce flowering time, particularly under spring-annual conditions. Our results provide direct evidence that natural allelic variation in FRI can provide rapid and predictable adaptive evolution in flowering time under spring-annual conditions. We observed a strong response to selection, in terms of reducing flowering time, in both growth conditions (~2 standard deviation reduction). Concomitantly, the frequency of functional FRI alleles under spring-annual conditions was reduced by 68%, in agreement with predicted changes. No significant changes in allele frequencies were observed in FRI in the winter-annual growth condition or in FLC for either growth conditions. These results indicate that changes in flowering time are mediated by different genetic factors under spring- and winter-annual growth conditions, and that other loci must also be contributing to the response to selection.     

Genetic control of flowering time in Eucalyptus globulus ssp. globulus

Understanding the factors affecting variation in phenology within a species is important as flowering time constitutes one of the major barriers to gene flow. We studied the genetic and environmental control of flower initiation and anthesis time in E. globulus ssp. globulus. For 5 years, flower initiation and anthesis were monitored in a seed orchard containing clones of 63 genotypes from four different regions of the species’ natural distribution. Anthesis occurred over a long period each year, spanning as much as 9 months in 2008. This variation was under strong genetic control with little genotype by year interaction (broad-sense heritability, Ĥ ² = 0.78 ± 0.04). There were highly significant differences among regions; anthesis occurred earlier for Furneaux and Tasmania than Strzelecki and Otways each year. Surprisingly though, there was little variation in flower initiation time between regions and genotypes, and this was under weak genetic control (Ĥ ² = 0.06 ± 0.05). The average anthesis time in the orchard varied from year to year, and there was evidence that heat sum was a major driver of this environmental variation. Anthesis time is controlled by both genetic and environmental factors, with the responses to each being predictable to some extent, and unrelated to the timing of flower initiation.     

A physiological overview of the genetics of flowering time control

Physiological studies on flowering time control have shown that plants integrate several environmental signals. Predictable factors, such as day length and vernalization, are regarded as 'primary', but clearly interfere with, or can even be substituted by, less predictable factors. All plant parts participate in the sensing of these interacting factors. In the case of floral induction by photoperiod, long-distance signalling is known to occur between the leaves and the shoot apical meristem (SAM) via the phloem. In the long-day plant, Sinapis alba, this long-distance signalling has also been shown to involve the root system and to include sucrose, nitrate, glutamine and cytokinins, but not gibberellins. In Arabidopsis thaliana, a number of genetic pathways controlling flowering time have been identified. Models now extend beyond 'primary' controlling factors and show an ever-increasing number of cross-talks between pathways triggered or influenced by various environmental factors and hormones (mainly gibberellins). Most of the genes involved are preferentially expressed in meristems (the SAM and the root tip), but, surprisingly, only a few are expressed preferentially or exclusively in leaves. However, long-distance signalling from leaves to SAM has been shown to occur in Arabidopsis during the induction of flowering by long days. In this review, we propose a model integrating physiological data and genes activated by the photoperiodic pathway controlling flowering time in early-flowering accessions of Arabidopsis. This model involves metabolites, hormones and gene products interacting as long- or short-distance signalling molecules.