Sequence variation and haplotype structure surrounding the flowering time locus FRI in Arabidopsis thaliana

Linkage disequilibrium in highly selfing organisms is expected to extend well beyond the scale of individual genes. The pattern of polymorphism in such species must thus be studied over a larger scale. We sequenced 14 short (0.5-1 kb) fragments from a 400-kb region surrounding the flowering time locus FRI in a sample of 20 accessions of Arabidopsis thaliana. The distribution of allele frequencies, as quantified by Tajima's D, varies considerably over the region and is incompatible with a standard neutral model. The region is characterized by extensive haplotype structure, with linkage disequilibrium decaying over 250 kb. In particular, recombination is evident within 35 kb of FRI in a haplotype associated with a functionally important allele. This suggests that A. thaliana may be highly suitable for linkage disequilibrium mapping.     

Correlation between time of flowering and phenotypic plasticity in Arabidopsis thaliana (Brassicaceae)

We observed substantial variation in the time of flowering among 13 populations of Arabidopsis thaliana (Brassicaceae) from an extensive latitudinal range when grown under uniform experimental conditions. The later the onset of flowering, the greater was potential reproduction. Later flowering plants also had greater plasticity in a host of morphological and physiological traits measured in nutrient-rich vs. nutrient-poor test environments. This relationship between flowering time and overall plasticity was only apparent for traits measured at the time of seed production, not at the time of flowering or earlier. At the time of seed production in this short-lived annual, the regression of a multivariate measure of overall plasticity on the time of flowering was linear and highly significant (r² = 0.90, P < 0.0001). These correlations among time of flowering, reproductive fitness, and plasticity support the idea that selection for late-flowering genotypes would select concomitantly for greater plasticity.     

Epistasis and genotype-environment interaction for quantitative trait loci affecting flowering time in Arabidopsis thaliana

A major goal of evolutionary biology is to understand the genetic architecture of the complex quantitative traits that may lead to adaptations in natural populations. Of particular relevance is the evaluation of the frequency and magnitude of epistasis (gene–gene and gene–environment interaction) as it plays a controversial role in models of adaptation within and among populations. Here, we explore the genetic basis of flowering time in Arabidopsis thaliana using a series of quantitative trait loci (QTL) mapping experiments with two recombinant inbred line (RIL) mapping populations [Columbia (Col) x Landsberg erecta (Ler), Ler x Cape Verde Islands (Cvi)]. We focus on the response of RILs to a series of environmental conditions including drought stress, leaf damage, and apical damage. These data were explicitly evaluated for the presence of epistasis using Bayesian based multiple-QTL genome scans. Overall, we mapped fourteen QTL affecting flowering time. We detected two significant QTL–QTL interactions and several QTL–environment interactions for flowering time in the Ler x Cvi population. QTL–environment interactions were due to environmentally induced changes in the magnitude of QTL effects and their interactions across environments – we did not detect antagonistic pleiotropy. We found no evidence for QTL interactions in the Ler x Col population. We evaluate these results in the context of several other studies of flowering time in Arabidopsis thaliana and adaptive evolution in natural populations.     

Differentiation for flowering time and phenotypic integration in Arabidopsis thaliana in response to season length and vernalization

The response of plants or animals to different environmental regimes may take the form of specialization of their life history patterns to match the prevailing conditions in a geographical area. In turn, the evolution of different life histories implies that there are trade-offs between distinct components of the life cycle. We investigate some of the possible explanations for the existence of distinct types of populations in the weed Arabidopsis thaliana (Brassicaceae), differentiated by flowering schedule. The so-called early flowering and late flowering "ecotypes" are hypothesized to result from adaptation to harsh winters or short seasons as opposed to mild winters or long seasons, respectively. We carried out two experiments in which we studied the reaction of natural populations to an increase in season length and to conditions simulating mild winter or spring. Unfortunately, only one of our accessions turned out to be a late flowering population; however, it did have a fitness disadvantage when the season was too short, although it had a higher reproductive output at the end of longer growing seasons. Most populations reacted to the simulation of a mild winter by extending their vegetative phase and increasing their reproductive output; however, this could be offset by increased winter mortality under harsh conditions. Character correlations (phenotypic integration) showed contrasting patterns of change in response to the two environmental factors: at the shortest season's length many correlations were negative, displaying a trade-off between vegetative and reproductive traits; during longer seasons, all correlations were positive and there was no evidence of vegetative-reproductive trade-offs. Exposure to cold did not trigger any major change in the pattern of character correlations.     

Seasonal and plant-density dependency for quantitative trait loci affecting flowering time in multiple populations of Arabidopsis thaliana

Multiple environmental cues regulate the transition to flowering. In natural environments, plants perceive seasonal progression by changes in day length and growth temperature, and plant density is monitored by changes in the light quality reflected from neighbouring vegetation. To understand the seasonal and plant-density dependence associated with natural allelic variation in flowering time, we conducted a quantitative trait loci (QTL) mapping study in Ler x Cvi, Bay x Sha and Ler x No-0 recombinant inbred line (RIL) populations of Arabidopsis thaliana. Days and total leaf number to bolting were examined under low and high plant density (200 or 1600 plants m(-2)) in autumn-winter and spring seasons. We found between 4 and 10 QTLs associated with seasonal and density variations in each RIL population. For Ler x Cvi and Bay x Sha RIL populations, a major proportion of QTLs showed seasonal and density interaction (up to 63%) and four QTLs were common to all environments (21%). Only three QTLs showed seasonal or density dependency. By aligning the linkage maps onto a common physical map, we detected at least one QTL at chromosome 2 and two QTLs at chromosome 5 that overlap between the three RIL populations, suggesting that these QTLs play a crucial role in the adaptive control of flowering time.     

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.     

Genetic basis of adaptation: flowering time in Arabidopsis thaliana

 We have mapped QTLs (quantitative trait loci) for an adaptive trait, flowering time, in a selfing annual, Arabidopsis thaliana. To obtain a mapping population we made a cross between an early-summer, annual strain, Li-5, and an individual from a late over-wintering natural population, Naantali. From the backcross to Li-5 298 progeny were grown, of which 93 of the most extreme individuals were genotyped. The data were analysed with both interval mapping and composite interval mapping methods to reveal one major and six minor QTLs, with at least one QTL on each of the five chromosomes. The QTL on chromosome 4 was a major one with an effect of 17.3 days on flowering time and explaining 53.4% of the total variance. The others had effects of at most 6.5 days, and they accounted for only small portions of the variance. Epistasis was indicated between one pair of the QTLs. The result of finding one major QTL and little epistasis agrees with previous studies on flowering time in Arabidopsis thaliana and other species. That several QTLs were found was expected considering the large number of possible candidate loci. In the light of the suggested genetic models of gene action at the candidate loci, epistasis was to be expected. The data showed that major QTLs for adaptive traits can be detected in non-domesticated species. Received: 15 January 1997/Accepted: 21 February 1997     

Discordant longitudinal clines in flowering time and phytochrome C in Arabidopsis thaliana

Using seasonal cues to time reproduction appropriately is crucial for many organisms. Plants in particular often use photoperiod to signal the time to transition to flowering. Because seasonality varies latitudinally, adaptation to local climate is expected to result in corresponding clines in photoperiod-related traits. By experimentally manipulating photoperiod cues and measuring the flowering responses and photoperiod plasticity of 138 Eurasian accessions of Arabidopsis thaliana, we detected strong longitudinal but not latitudinal clines in flowering responses. The presence of longitudinal clines suggests that critical photoperiod cues vary among populations occurring at similar latitudes. Haplotypes at PHYC, a locus hypothesized to play a role in adaptation to light cues, were also longitudinally differentiated. Controlling for neutral population structure revealed that PHYC haplotype influenced flowering time; however, the distribution of PHYC haplotypes occurred in the opposite direction to the phenotypic cline, suggesting that loci other than PHYC are responsible for the longitudinal pattern in photoperiod response. Our results provide previously missing empirical support for the importance of PHYC in mediating photoperiod sensitivity in natural populations of A. thaliana. However, they also suggest that other loci and epistatic interactions likely play a role in the determination of flowering time and that the environmental factors influencing photoperiod in plants vary longitudinally as well as latitudinally.     

QTL mapping of naturally-occurring variation in flowering time of Arabidopsis thaliana

A segregating F₂ population of Arabidopsis thaliana derived from a cross between the late-flowering ecotype Hannover/Münden (HM) and the early-flowering ecotype Wassilewskija (WS) was analyzed for flowering time and other morphological traits. Two unlinked quantitative trait loci (QTLs) affecting days to first flower (DFF-a and DFF-b) mapped to chromosome 5. QTLs which affect node number (NN), leaf length at flowering (LLF), and leaf length at 35 days (LL35) also mapped to chromosome 5; LLF-a, LL35-a, NN-a map to the same region of chromosome 5 as DFF-a; LLF-b and LL35-bmap to the same region of chromosome 5 as DFF-b. Another QTL affecting leaf length at flowering (LLF-c) maps to chromosome 3. The proximity of DFF-a, LLF-a, LL35-a and NN-a, as well as the similarity in gene action among these QTLs (additivity), suggest that they may be pleiotropic consequences of a single gene at this locus. Similarly, LL35-b and LLF-b map near each other and both display recessive gene action, again suggesting the possibility of pleiotropy. DFF-b, which also maps near LL35-b and LLF-b, displays largely additive gene action (although recessive gene action could not be ruled out). This suggests that DFF-b may represent a different gene from LL35-b and/or LLF-b. DFF-a maps near two previously identified mutants: co (which also affects flowering time and displays gene action consistent with additivity) and flc. Similar map locations and gene actions of QTLs affecting the correlated traits DFF, LLF, LL35 and NN suggest that these genomic regions harbor naturally occurring allelic variants involved in the general transition of the plant from vegetative to reproductive growth.     

模式植物拟南芥开花时间分子调控研究进展

植物从营养生长到生殖生长的转变是开花发育的关键,在合适的时间开花对植物的生长和繁衍极为重要,植物开花时间的调控对农业生产发展意义重大。植物开花是由遗传因子和环境因子协同调节的一个复杂过程。近年来,对不同植物开花调控的研究,特别是对模式植物拟南芥（Arabidopsis thaliana（L.） Heynh.）的开花调控研究取得了显著进展,已探明开花时间分子调控的6条主要途径分别是光周期途径、春化途径、自主途径、温度途径、赤霉素途径和年龄途径。各遗传调控途径既相互独立又相互联系,构成一个复杂的开花调控网络。本文综述了模式植物拟南芥开花时间调控分子机制相关研究的最新进展,并对未来的研究进行了展望。     

Large-scale genomic correlations in Arabidopsis thaliana relate to chromosomal structure

Background

The genome of classical laboratory strains of mice is an artificial mosaic of genomes originated from several mouse subspecies with predominant representation (>90%) of the Mus m. domesticus component. Mice of another subspecies, East European/Asian Mus m. musculus, can interbreed with the classical laboratory strains to generate hybrids with unprecedented phenotypic and genotypic variations. To study these variations in depth we prepared the first genomic large insert BAC library from an inbred strain derived purely from the Mus m. musculus-subspecies. The library will be used to seek and characterize genomic sequences controlling specific monogenic and polygenic complex traits, including modifiers of dominant and recessive mutations.

Results

A representative mouse genomic BAC library was derived from a female mouse of the PWD/Ph inbred strain of Mus m. musculus subspecies. The library consists of 144 768 primary clones from which 97% contain an insert of 120 kb average size. The library represents an equivalent of 6.7 × mouse haploid genome, as estimated from the total number of clones carrying genomic DNA inserts and from the average insert size. The clones were arrayed in duplicates onto eight high-density membranes that were screened with seven single-copy gene probes. The individual probes identified four to eleven positive clones, corresponding to 6.9-fold coverage of the mouse genome. Eighty-seven BAC-ends of PWD/Ph clones were sequenced, edited, and aligned with mouse C57BL/6J (B6) genome. Seventy-three BAC-ends displayed unique hits on B6 genome and their alignment revealed 0.92 single nucleotide polymorphisms (SNPs) per 100 bp. Insertions and deletions represented 0.3% of the BAC end sequences.

Conclusion

Analysis of the novel genomic library for the PWD/Ph inbred strain demonstrated coverage of almost seven mouse genome equivalents and a capability to recover clones for specific regions of PWD/Ph genome. The single nucleotide polymorphism between the strains PWD/Ph and C57BL/6J was 0.92/100 bp, a value significantly higher than between classical laboratory strains. The library will serve as a resource for dissecting the phenotypic and genotypic variations between mice of the Mus m. musculus subspecies and classical laboratory mouse strains.     

Longitudinal trends in climate drive flowering time clines in North American Arabidopsis thaliana

Introduced species frequently show geographic differentiation, and when differentiation mirrors the ancestral range, it is often taken as evidence of adaptive evolution. The mouse-ear cress (Arabidopsis thaliana) was introduced to North America from Eurasia 150-200 years ago, providing an opportunity to study parallel adaptation in a genetic model organism. Here, we test for clinal variation in flowering time using 199 North American (NA) accessions of A. thaliana, and evaluate the contributions of major flowering time genes FRI, FLC, and PHYC as well as potential ecological mechanisms underlying differentiation. We find evidence for substantial within population genetic variation in quantitative traits and flowering time, and putatively adaptive longitudinal differentiation, despite low levels of variation at FRI, FLC, and PHYC and genome-wide reductions in population structure relative to Eurasian (EA) samples. The observed longitudinal cline in flowering time in North America is parallel to an EA cline, robust to the effects of population structure, and associated with geographic variation in winter precipitation and temperature. We detected major effects of FRI on quantitative traits associated with reproductive fitness, although the haplotype associated with higher fitness remains rare in North America. Collectively, our results suggest the evolution of parallel flowering time clines through novel genetic mechanisms.     

An Arabidopsis thaliana RFLP mapping set to localize mutations to chromosomal regions

Mapping of newly identified Arabidopsis thaliana mutants is an important step towards their molecular characterization and the attempt to saturate the genome by known mutations. The classical genetic analysis using phenotypic tester lines is well-established, but laborious, time-consuming and potentially ambiguous. An alternative molecular strategy was developed that is based on RFLPs. Subcloned DNA markers that detect only segregating RFLP bands distinguishing A. thaliana ecotype Landsberg from Columbia or Enkheim after EcoRI restriction digestion compose an Arabidopsis RFLP mapping set (ARMS). Up to 13 markers uniformly cover the five A. thaliana chromosomes and can be scored in only two successive Southern experiments on a single blot without mutual interference of the signals. Thus, this system allows a simple, reliable, rapid and especially inexpensive mapping of any monogenic mutant locus to the A. thaliana chromosomes. Several loci can be analysed in one experiment if the respective blots are hybridized together. This paper demonstrates the mapping of two recessive mutants affecting the development of A. thaliana leaves which had been generated in the Columbia and Enkheim ecotype by analysing less than 20 F₂ individuals. Further markers to refine or verify the result on the same blot can be chosen out of 14 additional probes detecting single segregating EcoRI polymorphic bands as well.     

Variation at two flowering time genes within and among populations of Arabidopsis thaliana: comparison with markers and traits

Flowering Locus C (FLC) and Frigida are two interacting genes controlling flowering time variation in Arabidopsis thaliana. Variation at these genes was surveyed in 12 A. thaliana populations sampled in France. These populations were also screened for variation at molecular markers [12 microsatellites and 19 cleaved amplified polymorphic sequence (CAPS) markers] and at seven quantitative traits measured with and without vernalization. Seven populations were highly polymorphic at markers (H(S) = 0.57 at microsatellites, 0.24 at CAPS) and showed heritable variation for bolting time and some other traits. Five populations were genetically fixed or nearly fixed. Q(ST) for bolting time without vernalization was significantly higher than F(ST), suggesting local divergent selection. One of the two haplotype groups at FLC (FLC(A)) was very predominant (frequency of 99%). The first exon of Frigida showed elevated nonsynonymous variation, and nine loss-of-function mutations were found throughout the gene. The association between loss-of-function and earlier bolting was confirmed. Overall, 18 Frigida haplotypes were detected. The pattern of variation at Frigida was largely similar to that found at markers and traits, with the same populations being fixed or highly diverse. Metapopulation dynamics is thus probably the main factor shaping genetic variation in A. thaliana. However, F(ST) for functional (FRI) vs. nonfunctional (FRI(Delta)) haplotypes was significantly higher than F(ST) at markers. This suggested that loss-of-function at Frigida is under local selection for flowering time.     

Pleiotropic effects of flowering time genes in the annual crucifer Arabidopsis thaliana (Brassicaceae)

Variation in flowering time of Arabidopsis thaliana was studied in an experiment with mutant lines. The pleiotropic effects of flowering time genes on morphology and reproductive yield were assessed under three levels of nutrient supply. At all nutrient levels flowering time and number of rosette leaves at flowering varied among mutant lines. The relationship between these two traits depended strongly on nutrient supply. A lower nutrient supply first led to an extension of the vegetative phase, while the mean number of leaves at flowering was hardly affected. A further reduction resulted in no further extension of the vegetative phase and, on average, plants started flowering with a lower leaf number. At low nutrients, early flowering affected the timing of production of siliques rather than the total output, whereas late flowering was favorable at high nutrients. This may explain the fact that many plant species flower at a relatively small size under poor conditions. Flowering time genes had pleiotropic effects on the leaf length, number of rosette and cauline leaves, and number of axillary flowering shoots of the main inflorescence. Silique production was positively correlated with the number of axillary shoots of the main inflorescence; the number of axillary primordia appeared to have a large impact on reproductive yield.     

Fitness effects associated with the major flowering time gene FRIGIDA in Arabidopsis thaliana in the field

To date, the effect of natural selection on candidate genes underlying complex traits has rarely been studied experimentally, especially under ecologically realistic conditions. Here we report that the effect of selection on the flowering time gene FRIGIDA (FRI) reverses depending on the season of germination and allelic variation at the interacting gene FLOWERING LOCUS C (FLC). In field studies of 136 European accessions of Arabidopsis thaliana, accessions with putatively functional FRI alleles had higher winter survival in one FLC background in a fall-germinating cohort, but accessions with deletion null FRI alleles had greater seed production in the other FLC background in a spring-germinating cohort. Consistent with FRI's role in flowering, selection analyses suggest that the difference in winter survival can be attributed to time to bolting. However, in the spring cohort, the fitness difference was associated with rosette size. Our analyses also reveal that controlling for population structure with estimates of inferred ancestry and a geographical restriction was essential for detecting fitness associations. Overall, our results suggest that the combined effects of seasonally varying selection and epistasis could explain the maintenance of variation at FRI and, more generally, may be important in the evolution of genes underlying complex traits.     

Association of glutathione with flowering in Arabidopsis thaliana

In order to study the relationship between GSH and flowering, wild-type and late-flowering mutant, fca-1, of Arabidopsis thaliana were treated with L-buthionine sulfoximine (BSO), a specific inhibitor of GSH biosynthesis, under long-day conditions. BSO treatment of the fca-1 mutant starting at 17 d after imbibition promoted flowering. However, when the treatment was started at 12 d after imbibition, BSO treatment at 10(-4) M resulted in an inhibition of flowering. This inhibitory effect of BSO on flowering was abolished by GSH treatment at 10(-4) M, although GSH treatment at an increased concentration of 10(-3) M clearly delayed flowering. In contrast, BSO treatment of wild-type plants starting at 12 d after imbibition promoted flowering, whose effect was abolished by GSH application. In the fca-1 mutant, whose endogenous GSH levels were high, chilling treatment lowered the GSH levels and promoted flowering, as was the case in the BSO treatment. An A. thaliana mutant, cad2-1, which has a defect in GSH biosynthesis also exhibited late flowering. The late-flowering phenotype of this mutant tended to be strengthened by BSO and abolished by GSH treatment. These results suggest that flowering is associated with the rate of GSH biosynthesis and/or the levels of GSH in A. thaliana.     

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.     

The association of flowering time quantitative trait loci with duplicated regions and candidate loci in Brassica oleracea.

A population of 150 doubled haploid lines of rapid cycling Brassica oleracea, derived from an F1 from a var. alboglabra x var. italica cross, was scored for flowering time in two trials. Using information on 82 mapped molecular markers, spread evenly across the nine linkage groups, QTL were identified at six locations; one each on linkage groups O2 and O3 and two each on linkage groups O5 and O9. In total, these QTL explained 58 and 93% of the genetical variation in the two trials. Three of these QTL, on linkage groups O2, O3, and O9, were situated in regions showing considerable homology both with each other and with chromosome regions of B. nigra that have been shown to affect flowering time. These same regions are all homologous to a single tract of Arabidopsis chromosome 5, which contains a number of the flowering-related genes, one or more of which may be candidates for the QTL found in Brassica.