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At least 55 records · Page 3Linked to original sources

PubMed2005

The Vrn-H2 locus is a major determinant of flowering time in a facultative x winter growth habit barley (Hordeum vulgare L.) mapping population.

With the aim of dissecting the genetic determinants of flowering time, vernalization response, and photoperiod sensitivity, we mapped the candidate genes for Vrn-H2 and Vrn-H1 in a facultative x winter barley mapping population and determined their relationships with flowering time and vernalization via QTL analysis. The Vrn-H2 candidate ZCCT-H genes were completely missing from the facultative parent and present in the winter barley parent. This gene was the major determinant of flowering time under long photoperiods in controlled environment experiments, irrespective of vernalization, and under spring-sown field experiments. It was the sole determinant of vernalization response, but the effect of the deletion was modulated by photoperiods when the vernalization requirement was fulfilled. There was no effect under short photoperiods. The Vrn-H1 candidate gene (HvBM5A) was mapped based on a microsatellite polymorphism we identified in the promoter of this gene. Otherwise, the HvBM5A alleles for the two parents were identical. Therefore, the significant flowering time QTL effect associated with this locus suggests tight linkage rather than pleiotropy. This QTL effect was smaller in magnitude than those associated with the Vrn-H2 locus and was significant in two-way interactions with Vrn-H2. The Vrn-H1 locus had no effect on vernalization response. Our results support the Vrn-H2/Vrn-H1 repressor/structural gene model for vernalization response in barley and suggest that photoperiod may also affect the Vrn genes or tightly linked loci.

Chromosome Mapping↗

PubMed2026

Dissecting genetic architecture and improving machine learning‑based genomic prediction of flowering time in Osmanthus fragrans by integrating structural variants.

Sweet osmanthus (Osmanthus fragrans), a traditional ornamental plant in China, exhibits substantial variation in autumn flowering time, which significantly affects landscape application and cultivation efficiency. Here, we performed a genome-wide association study on 127 resequenced accessions classified into early, intermediate, and late flowering types, using a set of 2,325,410 single-nucleotide polymorphisms (SNPs) and 246,824 structural variants (SVs). By integrating SNP/insertion and deletion (Indel) and SV data with weighted gene co-expression network analysis, machine learning, and genomic prediction, we dissected the genetic architecture of flowering time. We identified 24 associated SNP/Indels and six SVs, mapping to 30 candidate genes, including known flowering regulators FLK, LOS1, Y14, MIF2, and GID1B. These genes showed tissue-specific expression, with some responding to low temperature. The two hub genes, GUX1 and LYG027904, were located within modules of the co-expression network associated with low-temperature treatment. Haplotype analysis revealed a specific three-SNP haplotype associated with late flowering and linked to LOS1, and epistatic interactions among combined genotypes contributed to phenotypic variation. Notably, integrating SVs with SNP/Indels improved genomic prediction accuracy; the gradient boosting decision tree model outperformed other machine learning algorithms, achieving a mean accuracy of 0.859 and an AUC > 0.8 (where AUC is area under receiver operating characteristic curve) for all flowering types. These findings provide insights into the genetic mechanisms underlying flowering time variation in O. fragrans, offer candidate genes and haplotypes for molecular breeding, and highlight the value of integrating SVs with machine learning for genomic prediction in woody ornamentals.

Machine Learning↗

PubMed2003

Using flowering times and leaf numbers to model the phases of photoperiod sensitivity in Antirrhinum majus L.

A model has been developed that can be used to determine the phases of sensitivity to photoperiod for seedlings subjected to reciprocal transfers at regular intervals between long (LD) and short day (SD) conditions. The novel feature of this approach is that it enables the simultaneous analysis of the time to flower and number of leaves below the inflorescence. A range of antirrhinum cultivars were grown, all of which were shown to be quantitative long-day plants. Seedlings were effectively insensitive to photoperiod when very young (juvenile). However, after the end of the juvenile phase, SD delayed flowering and increased the number of leaves below the inflorescence. Plants transferred from LD to SD showed a sudden hastening of flowering and a decrease in leaf number once sufficient LD had been received for flower commitment. Photoperiod had little effect on the rate of flower development. The analysis clearly identified major cultivar differences in the length of the juvenile phase and the photoperiod-sensitive inductive phase in both LD and SD.

Antirrhinum↗

PubMed2001

Multiple flowering time QTLs within several Brassica species could be the result of duplicated copies of one ancestral gene.

Quantitative trait locus (QTL) analysis was used to study the evolution of genes controlling the timing of flowering in four Brassica genomes that are all extensively replicated. Comparative mapping showed that a chromosomal region from the top of Arabidopsis thaliana chromosome 5 corresponded to three homoeologous copies in each of the diploid species Brassica nigra, B. oleracea, and B. rapa and six copies in the amphidiploid B. juncea. QTLs were detected in two of the three replicated segments in each diploid genome and in three of the six replicated segments in B. juncea. These results indicate that, for the studied trait, multiple QTLs resulting from genome duplication is the rule rather than the exception. Brassica homologues to two candidate genes (CO and FLC) identified from the corresponding A. thaliana region were mapped. CO homologues mapped close to the QTL peaks in eight of nine QTLs, while FLC homologues mapped farther away in those cases where the mapping resolution allowed a comparison. Thus, our data are consistent with the hypothesis that all the major QTLs we detected in the different species of Brassica could be the result of duplicated copies of the same ancestral gene, possibly the ancestor of CO.

Arabidopsis Proteins↗

PubMed2005

Fine mapping of the FT1 locus for soybean flowering time using a residual heterozygous line derived from a recombinant inbred line.

Fine-mapping of loci related to complex quantitative traits is essential for map-based cloning. A residual heterozygous line (RHL) of soybean (Glycine max) derived from a recombinant inbred line (RIL) was used for fine-mapping FT1, which is a major quantitative trait locus (QTL) responsible for soybean flowering time. The residual heterozygous line RHL1-156 was selected from the RILs that were derived from two distantly related varieties, Misuzudaizu and Moshidou Gong 503. The genome of RHL1-156 contains a heterozygous segment (approximately 17 cM) surrounding the FT1 locus but is homozygous in other regions, including three other loci affecting flowering time. A large segregating population of 1,006 individuals derived by selfing of RHL1-156 included two homozygous genotypes for the nearest marker of FT1 whose flowering time differed by 26 days. No continuous range of phenotypes was observed, in contrast to the F2 population, suggesting that a single FT1 locus affected the flowering time in the RHL1-156 line. Linkage analysis revealed that the FT1 locus mapped as a single Mendelian factor between two tightly linked DNA markers, Satt365 and GM169, at distances of approximately 0.1 cM and 0.4 cM, respectively. Our results show that a RHL derived from RILs can be used to fine-map a QTL and that RHLs can be an efficient tool for a systematic fine-mapping of QTLs.

Breeding↗

PubMed2005

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.

Arabidopsis↗

PubMed2002

Antagonistic regulation of flowering-time gene SOC1 by CONSTANS and FLC via separate promoter motifs.

Flowering in Arabidopsis is controlled by endogenous and environmental signals relayed by distinct genetic pathways. The MADS-box flowering-time gene SOC1 is regulated by several pathways and is proposed to co-ordinate responses to environmental signals. SOC1 is directly activated by CONSTANS (CO) in long photoperiods and is repressed by FLC, a component of the vernalization (low-temperature) pathway. We show that in transgenic plants overexpressing CO and FLC, these proteins regulate flowering time antagonistically and FLC blocks transcriptional activation of SOC1 by CO. A series of SOC1::GUS reporter genes identified a 351 bp promoter sequence that mediates activation by CO and repression by FLC. A CArG box (MADS-domain protein binding element) within this sequence was recognized specifically by FLC in vitro and mediated repression by FLC in vivo, suggesting that FLC binds directly to the SOC1 promoter. We propose that CO is recruited to a separate promoter element by a DNA-binding factor and that activation by CO is impaired when FLC is bound to an adjacent CArG motif.

Arabidopsis↗

PubMed2004

Genetic architecture of flowering time in maize as inferred from quantitative trait loci meta-analysis and synteny conservation with the rice genome.

Genetic architecture of flowering time in maize was addressed by synthesizing a total of 313 quantitative trait loci (QTL) available for this trait. These were analyzed first with an overview statistic that highlighted regions of key importance and then with a meta-analysis method that yielded a synthetic genetic model with 62 consensus QTL. Six of these displayed a major effect. Meta-analysis led in this case to a twofold increase in the precision in QTL position estimation, when compared to the most precise initial QTL position within the corresponding region. The 62 consensus QTL were compared first to the positions of the few flowering-time candidate genes that have been mapped in maize. We then projected rice candidate genes onto the maize genome using a synteny conservation approach based on comparative mapping between the maize genetic map and japonica rice physical map. This yielded 19 associations between maize QTL and genes involved in flowering time in rice and in Arabidopsis. Results suggest that the combination of meta-analysis within a species of interest and synteny-based projections from a related model plant can be an efficient strategy for identifying new candidate genes for trait variation.

Chromosome Mapping↗

PubMed2003

Analysis of the molecular basis of flowering time variation in Arabidopsis accessions.

Allelic variation at the FRI (FRIGIDA) and FLC (FLOWERING LOCUS C) loci are major determinants of flowering time in Arabidopsis accessions. Dominant alleles of FRI confer a vernalization requirement causing plants to overwinter vegetatively. Many early flowering accessions carry loss-of-function fri alleles containing one of two deletions. However, some accessions categorized as early flowering types do not carry these deletion alleles. We have analyzed the molecular basis of earliness in five of these accessions: Cvi, Shakhdara, Wil-2, Kondara, and Kz-9. The Cvi FRI allele carries a number of nucleotide differences, one of which causes an in-frame stop codon in the first exon. The other four accessions contain nucleotide differences that only result in amino acid substitutions. Preliminary genetic analysis was consistent with Cvi carrying a nonfunctional FRI allele; Wil-2 carrying either a defective FRI or a dominant suppressor of FRI function; and Shakhdara, Kondara, and Kz-9 carrying a functional FRI allele with earliness being caused by allelic variation at other loci including FLC. Allelic variation at FLC was also investigated in a range of accessions. A novel nonautonomous Mutator-like transposon was found in the weak FLC allele in Landsberg erecta, positioned in the first intron, a region required for normal FLC regulation. This transposon was not present in FLC alleles of most other accessions including Shakhdara, Kondara, or Kz-9. Thus, variation in Arabidopsis flowering time has arisen through the generation of nonfunctional or weak FRI and FLC alleles.

5' Untranslated Regions↗

PubMed2002

Control of photoperiod-regulated tuberization in potato by the Arabidopsis flowering-time gene CONSTANS.

Photoperiod controls several responses throughout the plant life cycle, like germination, flowering, tuber formation, onset of bud dormancy, leaf abscission, and cambium activity. From these processes, flowering has been most extensively studied, especially in Arabidopsis thaliana. Photoperiod sensing by the function of photoreceptors and the circadian clock appears to regulate flowering time via Arabidopsis CONSTANS (AtCO), a putative transcription factor that accelerates flowering in response to long days. The genetic factors controlling plant photoperiodic responses other than flowering are little known. However, interspecific grafting experiments demonstrated that the flower-inducing (florigen) and tuber- inducing (tuberigen) signals are functionally exchangeable. Here we show that constitutive overexpression in potato of the Arabidopsis flowering-time gene AtCO impairs tuberization under short-day inductive conditions; AtCO overexpressing lines require prolonged exposure to short days to form tubers. Grafting experiments using these lines indicated that AtCO exerts its inhibitory effect on tuber formation by acting in the leaves. We propose that a conserved photoperiodic functional module may be involved in controlling distinct photoperiod-regulated evocation responses in different species. This module would involve the action of CONSTANS in the production of the elusive and long-distance acting florigen-tuberigen signal(s) in the leaves.

Arabidopsis↗

PubMed2004

Phenology and phenotypic natural selection on the flowering time of a deceit-pollinated tropical orchid, Myrmecophila christinae.

BACKGROUND AND AIMS: Flowering phenology is described and the effect of flowering time on pollination success is evaluated in the deceit-pollinated tropical orchid, Myrmecophila christinae. It was expected that, due to this species' deceit pollination strategy and low observed pollinator visit rate, there would be a higher probability of natural selection events favouring individuals flowering away from the population flowering peak. METHODS: The study covers two consecutive years and four populations of M. christinae located along the north coast of the Yucatán Peninsula. For phenological and pollination success data, a total of 110 individuals were monitored weekly in 1998, and 83 individuals in 1999, during all the flowering and fruiting season. KEY RESULTS: The results showed significant differences in the probability of donating and receiving pollen throughout the flowering season. The probability of receiving or donating pollen increased the further an individual flowering was from the flowering peak. Regression analysis showed directional and disruptive phenotypic natural selection gradients, suggesting the presence of selection events unfavourable to flowering during flowering peak, for both male success (pollen removal) and female success (fruit production). However, the intensity and significance of the natural selection events varied between populations from year to year. The variation between seasons and populations was apparently due to variations in the density of reproductive individuals in each population and each season. CONCLUSIONS: As in other deceit-pollinated orchids, natural selection in M. christinae favours individuals flowering early or late in relation to population peak flowering. However, results also suggested a fluctuating regime of selective events act on flowering time of M. christinae.

Flowers↗

PubMed2000

Forecasting of the flowering time for wild species observed at Guidonia, central Italy.

It is well known that forecasting the flowering time of wild vegetation is useful for various sectors of human activity, particularly for all agricultural practices. Therefore, continuing previous work by Cenci et al., we will present here three new phenoclimatic models of the flowering time for a set of wild species, based on an original data sample of flowering dates for more than 500 species, observed at Guidonia (42 degrees N in central Italy) by Montelucci in the period 1960-1982. However, on applying the bootstrap technique to each species sample to check its basic statistical parameters, we found only about 200 to have data samples with an approximately Gaussian distribution. Eventually only 57 species (subdivided into eight monthly subsets from February to September) were used to formulate the models satisfactorily. The flowering date (represented by the z variable), is expressed in terms of two variables x and y by a nonlinear equation of the form z=axbeta+gammay. The x variable represents either the degree-day sum (in model 1), or the daily-maximum-temperature sum (in model 2), or the daily-global-insolation sum (in model 3), while y for all three models corresponds to the rainy-day sum. Note that all summations involved in the computation of the variables x and y take place over a certain period of time (preceding the flowering phase), which is a parameter to be determined by the fitting procedure. This parameter, together with the threshold temperature (needed to compute the degree-days in model 1), represents the two implicit parameters of the process, thus the total number of parameters (including these last two) becomes respectively, five for model 1, and four for the other two models. The preliminary results of this work were reported at the XVI International Botanical Congress (1-7 August 1999, St. Louis, Missouri USA).

Agriculture↗

PubMed2005

Characterisation of a barley (Hordeum vulgare L.) homologue of the Arabidopsis flowering time regulator GIGANTEA.

Barley cDNA and genomic clones homologous to the Arabidopsis flowering time regulator GIGANTEA were isolated. Genetic mapping showed that GIGANTEA is present as a single copy gene in barley (3HS) and rice (1S), while two copies are present in maize (3S and 8S) at locations consistent with previous comparative mapping studies. Comparison of the barley peptide with rice and Arabidopsis gave 94% and 79% similarity, respectively. Northern and semi-quantitative RT-PCR analysis of the barley gene (HvGI) showed the presence of a single mRNA species, with a peak of expression between 6 h and 9 h after dawn in short days (8 h light) and a peak 15 h after dawn in long days (16 h light). This behaviour is similar to that seen in Arabidopsis and rice, showing that sequence and expression pattern were well conserved. A lack of correspondence with the map positions of QTL affecting flowering time (heading date) suggests that variation at HvGI does not provide a major source of adaptive variation in photoperiod response.

Amino Acid Sequence↗

PubMed2004

The autonomous pathway: epigenetic and post-transcriptional gene regulation in the control of Arabidopsis flowering time.

Mechanisms that mediate the control of flowering time have been accessed through a molecular genetic approach in Arabidopsis. Flowering is regulated by different pathways and, in the past year, all of the known components of the so-called autonomous pathway have been identified. The autonomous pathway comprises a combination of factors involved in RNA processing and epigenetic regulation that downregulate the floral repressor, FLOWERING LOCUS C (FLC). However, components of the autonomous pathway are more widely conserved in plant species other than Arabidopsis than is FLC. Therefore, the broadest lessons we learn from dissecting the function of the autonomous pathway may be in revealing how precision in regulated gene expression is delivered.

AGAMOUS Protein, Arabidopsis↗

PubMed2005

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.

Arabidopsis↗

PubMed2006

Characterization of tomato (Solanum lycopersicum L.) mutants affected in their flowering time and in the morphogenesis of their reproductive structure.

The impact of the season on flowering time and the organization and morphogenesis of the reproductive structures are described in three tomato mutants: compound inflorescence (s), single flower truss (sft), and jointless (j), respectively, compared with their wild-type cultivars Ailsa Craig (AC), Platense (Pl), and Heinz (Hz). In all environmental conditions, the sft mutant flowered significantly later than its corresponding Pl cultivar while flowering time in j was only marginally, but consistently, delayed compared with Hz. The SFT gene and, to a lesser extent, the J gene thus appear to be constitutive flowering promoters. Flowering in s was delayed in winter but not in summer compared with the AC cultivar, suggesting the existence of an environmentally regulated pathway for the control of floral transition. The reproductive structure of tomato is a raceme-like inflorescence and genes regulating its morphogenesis may thus be divided into inflorescence and floral meristem identity genes as in Arabidopsis. The s mutant developed highly branched inflorescences bearing up to 200 flowers due to the conversion of floral meristems into inflorescence meristems. The S gene appears to be a floral meristem identity gene. Both sft and j mutants formed reproductive structures containing flowers and leaves and reverting to a vegetative sympodial growth. The SFT gene appears to regulate the identity of the inflorescence meristem of tomato and is also involved, along with the J gene, in the maintenance of this identity, preventing reversion to a vegetative identity. These results are discussed in relation to knowledge accumulated in Arabidopsis and to domestication processes.

DNA, Complementary↗

PubMed2006

Genetic interactions in the control of flowering time and reproductive structure development in tomato (Solanum lycopersicum).

Different tomato (Solanum lycopersicum) mutants, affected in flowering time, reproductive structure or plant architecture, were crossed to produce double mutants in order to investigate gene interactions in flowering regulation in this autonomous species with a sympodial growth habit. The compound inflorescence: uniflora, uniflora: self pruning, uniflora: blind, and jointless: uniflora double mutants all produced solitary flowers like their uniflora parent, instead of inflorescences. All double mutants were late flowering. uniflora: blind and uniflora: self pruning had flowering times intermediate between those of their two parents. jointless: uniflora and compound inflorescence: uniflora flowered later than uniflora, the mutant with the most delayed flowering. All double mutants developed strong lateral shoots at node levels approximately corresponding to the level at which their parent cultivars initiated their first reproductive structure, which is a typical trait of uniflora. These results suggest that the UNIFLORA gene acts upstream of the other investigated genes in controlling flowering in tomato, and that floral transition of the primary shoot and floral transition of sympodial segments are regulated differently.

Crosses, Genetic↗

PubMed1998

Conserved structure and function of the Arabidopsis flowering time gene CONSTANS in Brassica napus.

The Arabidopsis thaliana CONSTANS (CO) gene which promotes flowering in long days was recently isolated by chromosome walking. The mapping of QTLs controlling flowering time in Brassica species has identified genomic regions that contain homologues of the CO gene. Four genes homologous to the Arabidopsis CO gene were isolated from a pair of homoeologous loci in each of two doubled-haploid Brassica napus lines displaying different flowering times, N-o-1 and N-o-9. The four genes, BnCOa1, BnCOa9, BnCOb1 and BnCOb9, are located on linkage groups N10 and N19, and are highly similar to each other and to the Arabidopsis CO gene. Two regions of the proteins are particularly well conserved, a N-terminal region with two putative zinc fingers and a C-terminal region which may contain a nuclear localization signal. All four genes appear to be expressed in B. napus. The BnCOa1 allele was shown to complement the co-2 mutation in Arabidopsis in a dosage-dependent manner causing earlier flowering than in wild type under both long- and short-day conditions.

Amino Acid Sequence↗