Analysis of naturally occurring late flowering in Arabidopsis thaliana

Summary We have examined the late-flowering behavior of two ecotypes of Arabidopsis thaliana, Sf-2 and Le-0. The late-flowering trait segregates as a single dominant gene in crosses with the early-flowering Columbia ecotype. This gene, which we refer to as FLA, is located at one end of chromosome 4 between RFLP markers 506 and 3843 and is thus distinct from previously mapped genes that affect flowering time. The extreme delay in flowering time caused by the FLA gene can be overcome by vernalization in both the ecotypes in which it occurs naturally and in the Columbia ecotype into which this gene has been introgressed.     

Mapping loci controlling vernalization requirement in Brassica rapa

Brassica cultivars are classified as biennial or annual based on their requirement for a period of cold treatment (vernalization) to induce flowering. Genes controlling the vernalization requirement were identified in a Brassica rapa F₂ population derived from a cross between an annual and a biennial oilseed cultivar by using an RFLP linkage map and quantitative trait locus (QTL) analysis of flowering time in F₃ lines. Two genomic regions were strongly associated with variation for flowering time of unvernalized plants and alleles from the biennial parent in these regions delayed flowering. These QTLs had no significant effect on flowering time after plants were vernalized for 6 weeks, suggesting that they control flowering time through the requirement for vernalization. The two B. rapa linkage groups containing these QTLs had RFLP loci in common with two B. napus linkage groups that were shown previously to contain QTLs for flowering time. An RFLP locus detected by the cold-induced gene COR6.6 cloned from Arabidopsis thaliana mapped very near to one of the B. rapa QTLs for flowering time.     

Differential expression of genes important for adaptation in Capsella bursa-pastoris (Brassicaceae)

Understanding the genetic basis of natural variation is of primary interest for evolutionary studies of adaptation. In Capsella bursa-pastoris, a close relative of Arabidopsis (Arabidopsis thaliana), variation in flowering time is correlated with latitude, suggestive of an adaptation to photoperiod. To identify pathways regulating natural flowering time variation in C. bursa-pastoris, we have studied gene expression differences between two pairs of early- and late-flowering C. bursa-pastoris accessions and compared their response to vernalization. Using Arabidopsis microarrays, we found a large number of significant differences in gene expression between flowering ecotypes. The key flowering time gene FLOWERING LOCUS C (FLC) was not differentially expressed prior to vernalization. This result is in contrast to those in Arabidopsis, where most natural flowering time variation acts through FLC. However, the gibberellin and photoperiodic flowering pathways were significantly enriched for gene expression differences between early- and late-flowering C. bursa-pastoris. Gibberellin biosynthesis genes were down-regulated in late-flowering accessions, whereas circadian core genes in the photoperiodic pathway were differentially expressed between early- and late-flowering accessions. Detailed time-series experiments clearly demonstrated that the diurnal rhythm of CIRCADIAN CLOCK-ASSOCIATED1 (CCA1) and TIMING OF CAB EXPRESSION1 (TOC1) expression differed between flowering ecotypes, both under constant light and long-day conditions. Differential expression of flowering time genes was biologically validated in an independent pair of flowering ecotypes, suggesting a shared genetic basis or parallel evolution of similar regulatory differences. We conclude that genes involved in regulation of the circadian clock, such as CCA1 and TOC1, are strong candidates for the evolution of adaptive flowering time variation in C. bursa-pastoris.     

FRIGIDA-independent variation in flowering time of natural Arabidopsis thaliana accessions

FRIGIDA (FRI) and FLOWERING LOCUS C (FLC) are two genes that, unless plants are vernalized, greatly delay flowering time in Arabidopsis thaliana. Natural loss-of-function mutations in FRI cause the early flowering growth habits of many A. thaliana accessions. To quantify the variation among wild accessions due to FRI, and to identify additional genetic loci in wild accessions that influence flowering time, we surveyed the flowering times of 145 accessions in long-day photoperiods, with and without a 30-day vernalization treatment, and genotyped them for two common natural lesions in FRI. FRI is disrupted in at least 84 of the accessions, accounting for only approximately 40% of the flowering-time variation in long days. During efforts to dissect the causes for variation that are independent of known dysfunctional FRI alleles, we found new loss-of-function alleles in FLC, as well as late-flowering alleles that do not map to FRI or FLC. An FLC nonsense mutation was found in the early flowering Van-0 accession, which has otherwise functional FRI. In contrast, Lz-0 flowers late because of high levels of FLC expression, even though it has a deletion in FRI. Finally, eXtreme array mapping identified genomic regions linked to the vernalization-independent, late-flowering habit of Bur-0, which has an alternatively spliced FLC allele that behaves as a null allele.     

Role of FRIGIDA and FLOWERING LOCUS C in determining variation in flowering time of Arabidopsis

Arabidopsis (Arabidopsis thaliana) accessions provide an excellent resource to dissect the molecular basis of adaptation. We have selected 192 Arabidopsis accessions collected to represent worldwide and local variation and analyzed two adaptively important traits, flowering time and vernalization response. There was huge variation in the flowering habit of the different accessions, with no simple relationship to latitude of collection site and considerable diversity occurring within local regions. We explored the contribution to this variation from the two genes FRIGIDA (FRI) and FLOWERING LOCUS C (FLC), previously shown to be important determinants in natural variation of flowering time. A correlation of FLC expression with flowering time and vernalization was observed, but it was not as strong as anticipated due to many late-flowering/vernalization-requiring accessions being associated with low FLC expression and early-flowering accessions with high FLC expression. Sequence analysis of FRI revealed which accessions were likely to carry functional alleles, and, from comparison of flowering time with allelic type, we estimate that approximately 70% of flowering time variation can be accounted for by allelic variation of FRI. The maintenance and propagation of 20 independent nonfunctional FRI haplotypes suggest that the loss-of-function mutations can confer a strong selective advantage. Accessions with a common FRI haplotype were, in some cases, associated with very different FLC levels and wide variation in flowering time, suggesting additional variation at FLC itself or other genes regulating FLC. These data reveal how useful these Arabidopsis accessions will be in dissecting the complex molecular variation that has led to the adaptive phenotypic variation in flowering time.     

Epistatic natural allelic variation reveals a function of AGAMOUS-LIKE6 in axillary bud formation in Arabidopsis

In the Arabidopsis multiparent recombinant inbred line mapping population, a limited number of plants were detected that lacked axillary buds in most of the axils of the cauline (stem) leaves, but formed such buds in almost all rosette axils. Genetic analysis showed that polymorphisms in at least three loci together constitute this phenotype, which only occurs in late-flowering plants. Early flowering is epistatic to two of these loci, called REDUCED SHOOT BRANCHING1 (RSB1) and RSB2, which themselves do not affect flowering time. Map-based cloning and confirmation by transformation with genes from the region where RSB1 was identified by fine-mapping showed that a specific allele of AGAMOUS-Like6 from accession C24 conferred reduced branching in the cauline leaves. Site-directed mutagenesis in the Columbia allele revealed the causal amino acid substitution, which behaved as dominant negative, as was concluded from a loss-of-function mutation that showed the same phenotype in the late-flowering genetic background. This causal allele occurs at a frequency of 15% in the resequenced Arabidopsis thaliana accessions and correlated with reduced stem branching only in late-flowering accessions. The data show the importance of natural variation and epistatic interactions in revealing gene function.     

Genetic base of Arabidopsis thaliana (L.) Heynh.: Fitness of plants for extreme conditions in northern margins of species range

Flowering time and vernalization requirement were studied in eight natural Karelian populations (KPs) of Arabidopsis thaliana. These KPs consisted of late-flowering plants with elevated expression of flowering repressor FLC and a reduced expression level of flowering activator SOC1 compared to the early-flowering ecotypes Dijon-M and Cvi-0. Despite variations in flowering time and the vernalization requirement among the KPs, two-week-old seedlings showed no changes in either the nucleotide sequence of the FRI gene or the relative expression levels of FRI and its target gene FLC that would be responsible for this variation. An analysis of abscisic acid (ABA) biosynthesis and catabolism genes (NCED3 and CYP707A2) did not show significant differences between late-flowering KPs and the early-flowering ecotypes Dijon-M and Cvi-0. Cold treatment (4°C for 24 h) induced the expression of not only NCED3, but also RD29B, a gene involved in the ABA-dependent cold-response pathway. The relative levels of cold activation of these genes were nearly equal in all genotypes under study. Thus, the ABA-dependent cold response pathway does not depend on FLC expression. The lack of significant differences between northern populations, as well as the ecotypes Dijon- M (Europe) and Cvi-0 (Cape Verde Islands), indicates that this pathway is not crucial for fitness to the northern environment.     

Vernalization sensitivity in Arabidopsis thaliana (Brassicaceae): the effects of latitude and FLC variation

Latitudinal variation in climate is predicted to select for latitudinal differentiation in sensitivity to the environmental cues that signal plants to flower at the appropriate time for a given climate. In Arabidopsis thaliana, flowering is promoted by exposure to cold temperatures (vernalization), and several vernalization pathway loci are known. To test whether natural variation in vernalization sensitivity could account for a previously observed latitudinal cline in flowering time in A. thaliana, we exposed 21 European accessions to 0, 10, 20, or 30 d of vernalization and observed leaf number at flowering under short days in a growth chamber. We observed a significant latitudinal cline in vernalization sensitivity: southern accessions were more sensitive to vernalization than northern accessions. In addition, accessions that were late flowering in the absence of vernalization were more sensitive to vernalization cues. Allelic variation at the flowering time regulatory gene FLC was not associated with mean vernalization sensitivity, but one allele class exhibited greater variance in vernalization sensitivity.     

The gentian orthologs of the FT/TFL1 gene family control floral initiation in Gentiana

Gentians are herbaceous perennials blooming in summer through autumn. Although they are popular ornamental flowers in Japan, the regulation of their timing of flowering has not been studied. We identified and characterized gentian orthologs of the Arabidopsis FT/TFL1 gene family to elucidate the mechanisms of flowering initiation. We isolated three gentian orthologs of FT and TFL1, denoted GtFT1, GtFT2 and GtTFL1. Since up-regulation of GtFT1 and GtFT2 as well as down-regulation of GtTFL1 promoted floral initiation in gentian plantlets, these genes affected floral initiation in a similar way to Arabidopsis FT and TFL1. The expression levels of GtFT1 and GtFT2 in leaves of late-flowering gentian increased prior to floral initiation, whereas GtTFL1 was highly expressed in shoot apical meristem at the vegetative stage and decreased drastically just before flowering initiation. Comparison of gene expression patterns showed that GtFT1 expression increased earlier in early-flowering than in late-flowering gentian, whereas the timing of the increase in GtFT2 expression was similar in early- and late-flowering plants. The GtTFL1 expression in early-flowering gentian was extremely low throughout the vegetative and reproductive stages. These results indicated that either the up-regulation of GtFT1 or the down-regulation of GtTFL1 may determine flowering time. Furthermore, we found that early-flowering but not late-flowering gentians have a 320 bp insertion in the promoter region of GtTFL1. Thus, the negligible expression of GtTFL1 in early-flowering lines may be due to this insertion, resulting in a shortened vegetative stage.     

A survey of EMS-induced biennial Beta vulgaris mutants reveals a novel bolting locus which is unlinked to the bolting gene B

Beta vulgaris is a facultative perennial species which exhibits large intraspecific variation in vernalization requirement and includes cultivated biennial forms such as the sugar beet. Vernalization requirement is under the genetic control of the bolting locus B on chromosome II. Previously, ethyl methanesulfonate (EMS) mutagenesis of an annual accession had yielded several mutants which require vernalization to bolt and behave as biennials. Here, five F2 populations derived from crosses between biennial mutants and annual beets were tested for co-segregation of bolting phenotypes with genotypic markers located at the B locus. One mutant appears to be mutated at the B locus, suggesting that an EMS-induced mutation of B can be sufficient to abolish annual bolting. Co-segregation analysis in four populations indicates that the genetic control of bolting also involves previously unknown major loci not linked to B, one of which also affects bolting time and was genetically mapped to chromosome IX.     

Genome-wide identification of flowering time genes associated with vernalization and the regulatory flowering networks in Chinese cabbage

Flowering time (Ft) is the most important characteristic of Chinese cabbage with high leaf yields and late-flowering are favorable traits, while little knowledge on genes involved in Ft and the flowering mechanism in this crop. In this study, we conducted genome-wide RNA-seq analysis using an inbred Chinese cabbage ‘4004’ line in response to vernalization and compared the Ft gene expression with radish crop. A number of Ft genes which play roles in flowering pathways were performed quantitative RT-PCR analysis to verify the regulatory flowering gene network in Chinese cabbage. We found that a total of 223 Ft genes in Chinese cabbage, and 50 of these genes responded to vernalization. The majority of flowering enhancers were upregulated, whereas most flowering repressors were downregulated in response to vernalization as confirmed by RT-qPCR. Among the major Ft genes, the expression of BrCOL1-2, BrFT1/2, BrSOC1/2/3, BrFLC1/2/3/5, and BrMAF was strongly affected by vernalization. In reference to comparative RNA-seq profiling of Ft genes, Chinese cabbage and radish revealed substantially different vernalization response in particular GA flowering pathway. Thus, this study provides new insight into functional divergence in flowering pathways and the regulatory mechanisms in Brassicaceae crops. Further analysis of the major integrator genes between early and late-flowering inbred lines facilitates understanding flowering trait variation and molecular basis of flowering in Chinese cabbage.     

Leaf Growth and Apex Development of Perennial Ryegrass During Winter and Spring

The relationships between rates of leaf extension, leaf appearance,and primordia production on the apex were studied in the fieldduring winter and spring in established swards of four contrastingperennial ryegrass lines (Aurora, Melle, a hybrid selectionfrom a cross between Aurora and Melle and S.24). All four linesshowed an increase in leaf extension rates which commenced whenspikelet primordia were first initiated at the apex. This wassome time after vernalization requirements had been satisfied.In early-flowering lines the stimulus to leaf growth rates occurredearlier than in late-flowering lines. Maximum leaf growth ratesoccurred about the time of double ridge formation, in the middleof the period of spikelet primordia production. The rate andduration of the period of spikelet primordia production variedbetween lines. By the time of flowering, leaf growth rates declinedto values recorded for vegetative plants in the winter. Leafappearance rates followed a similar pattern to leaf growth rates,although the increase in leaf appearance rate was less thanin primordia production or leaf growth rates. Hybrids from across between early- and late-flowering lines showed early enhancementof leaf extension rates due to early initiation of spikeletprimordia production. These high rates of leaf growth were maintainedfor longer, compared with the early-flowering line, as the durationof spikelet production was longer. This illustrates a mechanismfor combining early spring growth with lateness of floweringin ryegrass breeding programmes Leaf growth, apex development, vernalization, initiation, spikelet primordia production, flowering, thermal time, Lolium perenne, perennial ryegrass, spring growth     

Variation in Capsella (shepherd's purse): an example of intraspecific functional diversity

The extent of functional trait diversity is quantified for 157 different Capsella bursa-pastoris (L.) medic (shepherd's purse) accessions. These individuals encompass replicate progeny generated from seed of 53 different Capsella 'maternal lines' that were isolated at random as they emerged from soil cores (used to estimate baseline seed bank numbers and weed diversity) at 34 different arable sites across the United Kingdom. The replicate progeny were subject to ex situ characterisation for traits determining life history and architecture. Seven leaf-type classes were identified and representative parents of each leaf type were distinguishable using four different simple sequence repeat markers. Life-history traits were only loosely associated with leaf shape, and cluster analysis grouped the accessions into three broad types: small plants that flowered early with intermediate reproductive output; large plants, with intermediate time to flowering and a high reproductive output; late-flowering plants, of intermediate size and low reproductive output. The most common leaf-type variants (83% of accessions) demonstrated a short time to flowering (ca. 70 days), while rarer variants included those that flowered after 140 days, accumulated more nitrogen and produced less seed: possibly representing advantageous and disadvantageous traits (respectively), in modern arable rotations. A wide trait variation was therefore found in Capsella bursa-pastoris despite decades of agricultural intensification, the range of time-to-flowering for C. bursa-pastoris being as broad the mean flowering times of the commoner annual and winter annual arable species. We propose the use of traits, rather than species, as the accounting unit to quantify functional biodiversity in arable systems.     

Inheritance of annual habit in celery: cosegregation with isozyme and anthocyanin markers

Summary Vernalization response was determined in an annual and two biennial celery strains, Apium graveolens L. and their F₂ hybrids. Although the annual strain did not require vernalization to bolt, plants exposed to 10°C for 7 days bolted 2 weeks earlier than non-treated plants. Inheritance studies based on F₂ and backcross segregations demonstrate that annual habit in celery is partially dominant over biennial and determined by a single gene designated Hb. Cosegregation studies of this trait with nine isozyme loci and a gene determining petiole anthocyanin pigmentation disclosed the following linkage relationships: Adh-1-Sdh-1-Mdh-1, and Got-1-Mdh-2-Hb-A. The recombination frequency observed for Hb and Mdh-2 was too large to use the latter as a useful marker for annual habit.     

Inheritance of plant height and flowering time in the wild potato species,Solanum verrucosum Schlechtd

The inheritance was studied of plant height and flowering time in a hybrid between the short-stemmed, late-flowering introduction CPC 1339 of Solanum verrucosum and the tall-stemmed, early-flowering introduction PI 195172 of the same species. The range of plant height in CPC 1339 served as a criterion in classifying the populations into tall and short plants from measurements at four growth stages. The averages of these four measurements were used in the genetic analysis. The observed ratios fit a hypothesis of two dominant complementary genes for tall stem. Late flowering of CPC 1339 appears recessive to early flowering. The segregation ratios can be explained on the basis of two complementary dominant genes for early flowering.     

特早花甘蓝型油菜的开花特征及特早花候选基因鉴定

开花是植物从营养生长进入生殖生长的重要阶段.油菜早花早熟,可有效解决油菜与其他夏季作物的茬口矛盾.挖掘不同的早花油菜资源,研究油菜早花性状形成的分子机理,可促进利用分子技术快速选育早熟油菜的育种进程.本研究以1个新发现的稳定遗传的特早花油菜迎春一号为研究对象,在覆盖全年9个月的时间中设计了15个不同的播种期,调查其开花...     

The Role of Leaves in the Perception of Vernalizing Temperatures in Sugar Beet

Annual and biennial sugar beet varieties require long days toinduce flowering but the biennial genotypes additionally requirevernalization. Previous research has suggested that the inabilityof non-vernalized biennial plants to flower can be explainedby a lack of competence of the leaves to respond to long days.In this study defoliation experiments were used to investigatewhich leaves could perceive long daylengths and, in particular,whether leaves initiated from a non-vernalized shoot apicalmeristem could perceive vernalizing temperatures and producea floral stimulus in long days. Annual and vernalized biennialplants flowered if young leaves (i.e. those formed during orafter vernalization) were kept on the plants, but they did notflower if only older expanded leaves (including those expandedprior to vernalization) were present. No evidence was obtainedto indicate that the older leaves contained inhibitors of floweringand it seems most likely that there is a decline in responsivenessto daylength with increasing leaf age. Exposure to vernalizingtemperatures accelerated flowering of the annual and was essentialfor flowering of the biennial. The presence of a single leafinitiated, but not expanded, prior to the transfer of biennialplants to vernalizing temperatures was sufficient to induceflowering. This indicates that expanding leaves do not needto be initiated from a vernalized apical meristem to becomecompetent to produce a floral stimulus in long days. Key words: Beta vulgaris L., sugar beet, vernalization, flowering     

Seasonal change in a pollinator community and the maintenance of style length variation in Mertensia fusiformis (Boraginaceae)

Background and Aims

In sub-alpine habitats, patchiness in snowpack produces marked, small-scale variation in flowering phenology. Plants in early- and late-melting patches are therefore likely to experience very different conditions during their flowering periods. Mertensia fusiformis is an early-flowering perennial that varies conspicuously in style length within and among populations. The hypothesis that style length represents an adaptation to local flowering time was tested. Specifically, it was hypothesized that lower air temperatures and higher frost risk would favour short-styled plants (with stigmas more shielded by corollas) in early-flowering patches, but that the pollen-collecting behaviour of flower visitors in late-flowering patches would favour long-styled plants.

Methods

Floral morphology was measured, temperatures were monitored and pollinators were observed in several matched pairs of early and late populations. To evaluate effects of cold temperatures on plants of different style lengths, experimental pollinations were conducted during mornings (warm) and evenings (cool), and on flowers that either had or had not experienced a prior frost. The effectiveness of different pollinators was quantified as seed set following single visits to plants with relatively short or long styles.

Key Results

Late-flowering populations experienced warmer temperatures than early-flowering populations and a different suite of pollinators. Nectar-foraging bumble-bee queens and male solitary bees predominated in early populations, whereas pollen-collecting female solitary bees were more numerous in later sites. Pollinators differed significantly in their abilities to transfer pollen to stigmas at different heights, in accordance with our prediction. However, temperature and frost sensitivity did not differ between long- and short-styled plants. Although plants in late-flowering patches tended to have longer styles than those in early patches, this difference was not consistent.

Conclusions

Seasonal change in pollinator-mediated selection on style length may help maintain variation in this trait in M. fusiformis, but adaptation to local flowering time is not apparent. The prevalence of short styles in these populations requires further explanation.     

Late-flowering genes interact with early-flowering genes to regulate flowering time in Arabidopsis thaliana.

To investigate the genetic mechanisms regulating the transition from the vegetative to reproductive growth in Arabidopsis, double mutants between three different early-flowering mutants, early flowering 1-1, 2-1, 3-1, (elf 1-1, 2-1, 3-1) and five different late-flowering mutants, gi-1, ft-1, fwa-1, ld-1, and fca-9, were constructed and phenotypes analyzed. Double mutants in all combinations displayed the late-flowering phenotypes which resembled their respective late-flowering parents in both flowering time and the number of vegetative leaves produced. The results indicate that five late-flowering mutants are epistatic to all three early-flowering mutants tested here. This epistatic relationship suggests that ELF1, ELF2, and ELF3 genes function upstream of these five late-flowering genes no matter if they are functioning in autonomous or photoperiod pathways. These three early-flowering genes may negatively modify the activity of most late-flowering genes to influence the time of the vegetative-to-reproductive transition in Arabidopsis.