The late-flowering phenotype of FRIGIDA and mutations in LUMINIDEPENDENS is suppressed in the Landsberg erecta strain of Arabidopsis

The late-flowering phenotype of mutations in the LUMINIDEPENDENS (LD) gene and the late flowering caused by the naturally occurring dominant gene FRIGIDA (FRI) are suppressed in the Landsberg erecta (Ler) strain of Arabidopsis thaliana. This suppression is dependent on a locus on chromosome 5 designated FLC. Of the ecotypes tested, only the Ler strain contains the suppressor allele of FLC; ld mutations and FRI cause late flowering in the other genetic backgrounds. The allele at FLC also has a moderate effect on flowering time in the absence of FRI or ld mutations. The flowering time effects of FLC are gene dosage dependent.     

Interaction ofFLC and late-flowering mutations inArabidopsis thaliana

The phenotype caused by mutations that affect the timing of flowering inArabidopsis thaliana has been most extensively analyzed in the Landsbergerecta (Ler) genetic background. In Ler, the late-flowering phenotype ofFRIGIDA and mutations inLUMINIDEPENDENS is suppressed by the Ler allele ofFLC. In this study, the interactions of nine mutations conferring late flowering with theFLC allele of the Columbia ecotype (FLC-Col), which does not suppress late flowering, were examined. The effect on flowering time of combining six of the mutations withFLC-Col was additive; plants containingFLC-Col withfd, gi, fwa, fha, ft, andfe flowered slightly later than plants containing these mutations with theLer allele ofFLC. In contrast, a synergistic effect was observed betweenFLC-Col and three mutations;fca, fpa, andfve plants became extremely late flowering when combined withFLC-Col. Maximum delay in flowering for the majority of the mutant strains requiredFLC-Col in a homozygous state, although forfpa andfe a single copy ofFLC-Col allowed maximum lateness. In addition, thefd andfe mutations became more dominant in the presence ofFLC-Col.     

Interaction ofFLC and late-flowering mutations inArabidopsis thaliana

The phenotype caused by mutations that affect the timing of flowering inArabidopsis thaliana has been most extensively analyzed in the Landsbergerecta (Ler) genetic background. In Ler, the late-flowering phenotype ofFRIGIDA and mutations inLUMINIDEPENDENS is suppressed by the Ler allele ofFLC. In this study, the interactions of nine mutations conferring late flowering with theFLC allele of the Columbia ecotype (FLC-Col), which does not suppress late flowering, were examined. The effect on flowering time of combining six of the mutations withFLC-Col was additive; plants containingFLC-Col withfd, gi, fwa, fha, ft, andfe flowered slightly later than plants containing these mutations with theLer allele ofFLC. In contrast, a synergistic effect was observed betweenFLC-Col and three mutations;fca, fpa, andfve plants became extremely late flowering when combined withFLC-Col. Maximum delay in flowering for the majority of the mutant strains requiredFLC-Col in a homozygous state, although forfpa andfe a single copy ofFLC-Col allowed maximum lateness. In addition, thefd andfe mutations became more dominant in the presence ofFLC-Col.     

Development of an AFLP based linkage map of Ler, Col and Cvi Arabidopsis thaliana ecotypes and construction of a Ler/Cvi recombinant inbred line population

An amplified fragment polymorphism (AFLP) based linkage map has been generated for a new Landsberg erecta/Cape Verde Islands (Ler/Cvi) recombinant inbred line (RIL) population. A total of 321 molecular PCR based markers and the erecta mutation were mapped. AFLP markers were also analysed in the Landsberg erecta/Columbia (Ler/Col) RIL population ( Lister & Dean 1993) and 395 AFLP markers have been integrated into the previous Arabidopsis molecular map of 122 RFLPs, CAPSs and SSLPs. This enabled the evaluation of the efficiency and robustness of AFLP technology for linkage analyses in Arabidopsis. AFLP markers were found throughout the linkage map. The two RIL maps could be integrated through 49 common markers which all mapped at similar positions. Comparison of both maps led to the conclusion that segregating bands from a common parent can be compared between different populations, and that AFLP bands of similar molecular size, amplified with the same primer combination in two different ecotypes, are likely to correspond to the same locus. AFLPs were found clustering around the centromeric regions, and the authors have established the map position of the centromere of chromosome 3 by a quantitative analysis of AFLP bands using trisomic plants. AFLP markers were also used to estimate the polymorphism rate among the three ecotypes. The larger polymorphism rate found between Ler and Cvi compared to Ler and Col will mean that the new RIL population will provide a useful material to map DNA polymorphisms and quantitative trait loci.     

A role of flowering genes in the tolerance of Arabidopsis thaliana to cucumber mosaic virus

The genetic basis of plant tolerance to parasites is poorly understood. We have previously shown that tolerance of Arabidopsis thaliana to its pathogen cucumber mosaic virus is achieved through changes in host life-history traits on infection that result in delaying flowering and reallocating resources from vegetative growth to reproduction. In this system we analyse here genetic determinants of tolerance using a recombinant inbred line family derived from a cross of two accessions with extreme phenotypes. Three major quantitative trait loci for tolerance were identified, which co-located with three flowering repressor genes, FLC, FRI, and HUA2. The role of these genes in tolerance was further examined in genotypes carrying functional or nonfunctional alleles. Functional alleles of FLC together with FRI and/or HUA2 were required for both tolerance and resource reallocation from growth to reproduction. Analyses of FLC alleles from wild accessions that differentially modulate flowering time showed that they ranked differently for their effects on tolerance and flowering. These results pinpoint a role of FLC in A. thaliana tolerance to cucmber mosaic virus, which is a novel major finding, as FLC has not been recognized previously to be involved in plant defence. Although tolerance is associated with a delay in flowering that allows resource reallocation, our results indicate that FLC regulates tolerance and flowering initiation by different mechanisms. Thus, we open a new avenue of research on the interplay between defence and development in plants.     

Butyrate sensitive suppressor of position-effect variegation mutations in drosophila melanogaster

Summary Mutations at a locus on chromosome II of D. melanogaster suppressing position-effect variegation mutations have been identified which display recessive butyrate sensitivity. Survival of homozygous mutant flies is significantly reduced on medium containing sodium n-butyrate. The butyrate sensitive suppressor mutations are further characterized by recessive female sterility and reduced survival of homozygotes. Complementation analysis showed their allelism. The locus of these mutations, Su-var (2) 1, has been localized to 40.5±0.2 and, by using interstitial duplications, to region 31CD on the cytogenetic map. Moreover, the mutant alleles of the Su-var (2) 1 locus display a lethal interaction with the heterochromatic Y chromosome. The presence or absence of a Y chromosome in males or females has a strong influence on the viability of homozygous or transheterozygous suppressor flies. All the genetic properties of Su-var (2) 1 mutants suggest strongly that this locus affects chromosome condensation.     

Environmental and genetic interactions reveal FLOWERING LOCUS C as a modulator of the natural variation for the plasticity of flowering in Arabidopsis

The timing of flowering initiation depends strongly on the environment, a property termed as the plasticity of flowering. Such plasticity determines the adaptive potential of plants because it provides phenotypic buffer against environmental changes, and its natural variation contributes to evolutionary adaptation. We addressed the genetic mechanisms of the natural variation for this plasticity in Arabidopsis thaliana by analysing a population of recombinant inbred lines derived from Don‐0 and Ler accessions collected from distinct climates. Quantitative trait locus (QTL) mapping in four environmental conditions differing in photoperiod, vernalization treatment and ambient temperature detected the folllowing: (i) FLOWERING LOCUS C (FLC) as a large effect QTL affecting flowering time differentially in all environments; (ii) numerous QTL displaying smaller effects specifically in some conditions; and (iii) significant genetic interactions between FLC and other loci. Hence, the variation for the plasticity of flowering is determined by a combination of environmentally sensitive and specific QTL, and epistasis. Analysis of FLC from Don identified a new and more active allele likely caused by a cis‐regulatory deletion covering the non‐coding RNA COLDAIR. Further characterization of four FLC natural alleles showed different environmental and genetic interactions. Thus, FLC appears as a major modulator of the natural variation for the plasticity of flowering to multiple environmental factors.     

The vernalization gene FRIGIDA in cultivated Brassica species

The repressor FLOWERING LOCUS C (FLC) holds a key position among the genes, which drive Arabidopsis floral transition along the vernalization pathway. The FRIGIDA (FRI) gene activates FLC expression, and the interplay of strong and weak alleles of FLC and FRI in many cases explains the variations in Arabidopsis requirement for cold induction. In annual and biennial life forms of Brassica, the variations in time to flower have been also related to FLC; whereas the place of FRI in the vernalization process has not been sufficiently elucidated. In contrast to Arabidopsis, FRI in Brassica genomes A and C and presumably B is represented by two expressible loci, FRI.a and FRI.b, each of them manifesting genome-specific polymorphisms. FRI.a and FRI.b sequences from diploid species B. rapa (genome A) and B. oleracea (genome C) are conserved (96–99% similarity) in subgenomes A and C of tetraploid species B. carinata (genome BC), B. juncea (genome AB), and B. napus (genome AC). Phylogenetic analysis of FRI sequences in the genus Brassica clearly discerns the lineages A/C and B, while in the family Brassicaceae, two FRI clusters discriminated by such analysis correspond to the lineages I (including the genus Arabidopsis) and II (including the genus Brassica). The origin of two FRI loci is discussed in the context of the Brassicaceae evolution via paleopolyploidy and subsequent genome reorganization.     

Accelerated flowering time reduces lifetime water use without penalizing reproductive performance in Arabidopsis

Natural selection driven by water availability has resulted in considerable variation for traits associated with drought tolerance and leaf‐level water‐use efficiency (WUE). In Arabidopsis, little is known about the variation of whole‐plant water use (PWU) and whole‐plant WUE (transpiration efficiency). To investigate the genetic basis of PWU, we developed a novel proxy trait by combining flowering time and rosette water use to estimate lifetime PWU. We validated its usefulness for large‐scale screening of mapping populations in a subset of ecotypes. This parameter subsequently facilitated the screening of water use and drought tolerance traits in a recombinant inbred line population derived from two Arabidopsis accessions with distinct water‐use strategies, namely, C24 (low PWU) and Col‐0 (high PWU). Subsequent quantitative trait loci mapping and validation through near‐isogenic lines identified two causal quantitative trait loci, which showed that a combination of weak and nonfunctional alleles of the FRIGIDA (FRI) and FLOWERING LOCUS C (FLC) genes substantially reduced plant water use due to their control of flowering time. Crucially, we observed that reducing flowering time and consequently water use did not penalize reproductive performance, as such water productivity (seed produced per unit of water transpired) improved. Natural polymorphisms of FRI and FLC have previously been elucidated as key determinants of natural variation in intrinsic WUE (δ¹³C). However, in the genetic backgrounds tested here, drought tolerance traits, stomatal conductance, δ¹³C. and rosette water use were independent of allelic variation at FRI and FLC, suggesting that flowering is critical in determining lifetime PWU but not always leaf‐level traits.     

Establishment of the Winter-Annual Growth Habit via FRIGIDA-Mediated Histone Methylation at FLOWERING LOCUS C in Arabidopsis

In Arabidopsis thaliana, flowering-time variation exists among accessions, and the winter-annual (late-flowering without vernalization) versus rapid-cycling (early flowering) growth habit is typically determined by allelic variation at FRIGIDA (FRI) and FLOWERING LOCUS C (FLC). FRI upregulates the expression of FLC, a central floral repressor, to levels that inhibit flowering, resulting in the winter-annual habit. Here, we show that FRI promotes histone H3 lysine-4 trimethylation (H3K4me3) in FLC to upregulate its expression. We identified an Arabidopsis homolog of the human WDR5, namely, WDR5a, which is a conserved core component of the human H3K4 methyltransferase complexes called COMPASS-like. We found that recombinant WDR5a binds H3K4-methylated peptides and that WDR5a also directly interacts with an H3K4 methyltransferase, ARABIDOPSIS TRITHORAX1. FRI mediates WDR5a enrichment at the FLC locus, leading to increased H3K4me3 and FLC upregulation. WDR5a enrichment is not required for elevated H3K4me3 in FLC upon loss of function of an FLC repressor, suggesting that two distinct mechanisms underlie elevated H3K4me3 in FLC. Our findings suggest that FRI is involved in the enrichment of a WDR5a-containing COMPASS-like complex at FLC chromatin that methylates H3K4, leading to FLC upregulation and thus the establishment of the winter-annual growth habit.     

Genetic interactions between FLM and other flowering-time genes in Arabidopsis thaliana

FLOWERING LOCUS M (FLM) is a MADS-domain gene that acts as an inhibitor of flowering in Arabidopsis. Here we describe the genetic interaction of FLM with genes in the photoperiod and autonomous flowering pathways. Although the sequence of FLM is most similar to that of FLC, FLM and FLC interact with different flowering pathways. It has been previously shown that flc lesions suppress the late-flowering phenotype of FRI-containing lines and autonomous-pathway mutants. However, flm lesions suppress the late-flowering phenotype of photoperiod-pathway mutants but not that of FRI-containing lines or autonomous-pathway mutants. Another MADS-domain flowering repressor with a mutant phenotype similar to FLM is SVP. The late-flowering phenotype of FLM over-expression is suppressed by the svp mutation, and an svp flm double mutant behaves like the single mutants. Thus FLM and SVP are in the same flowering pathway which interacts with the photoperiod pathway. Abbreviations: CO, CONSTANS; FLC, FLOWERING LOCUS C; FLM, FLOWERING LOCUS M; FRI, FRIGIDA; GI, GIGANTEA; LD, LUMINIDEPENDENS; SVP, SHORT VEGETATIVE PHASE; FCA is not an abbreviation     

QTL analysis of flowering time inArabidopsis thaliana

Quantitative trait loci (QTL) analyses based on restriction fragment length polymorphism maps have been used to resolve the genetic control of flowering time in a cross between twoArabidopsis thaliana ecotypes H51 and Landsbergerecta, differing widely in flowering time. Five quantitative trait loci affecting flowering time were identified in this cross (RLN1-5), four of which are located in regions containing mutations or loci previously identified as conferring a late-flowering phenotype. One of these loci is coincident with theFRI locus identified as the major determinant for late flowering and vernalization responsiveness in theArabidopsis ecotype Stockholm.RLN5, which maps to the lower half of chromosome five (between markers mi69 and m233), only affected flowering time significantly under short day conditions following a vernalization period. The late-flowering phenotype of H51 compared to Landsbergerecta was due to alleles conferring late flowering at only two of the five loci. At the three other loci, H51 possessed alleles conferring early flowering in comparison to those of Landsbergerecta. Combinations of alleles conferring early and late flowering from both parents accounted for the transgressive segregation of flowering time observed within the F₂ population. Three QTL,RLN1,RLN2 andRLN3 displayed significant genotype-by-environment interactions for flowering time. A significant interaction between alleles atRLN3 andRLN4 was detected.     

Analysis of a Plant Complex Resistance Gene Locus Underlying Immune-Related Hybrid Incompatibility and Its Occurrence in Nature

Mechanisms underlying speciation in plants include detrimental (incompatible) genetic interactions between parental alleles that incur a fitness cost in hybrids. We reported on recessive hybrid incompatibility between an Arabidopsis thaliana strain from Poland, Landsberg erecta (Ler), and many Central Asian A. thaliana strains. The incompatible interaction is determined by a polymorphic cluster of Toll/interleukin-1 receptor-nucleotide binding-leucine rich repeat (TNL) RPP1 (Recognition of Peronospora parasitica1)-like genes in Ler and alleles of the receptor-like kinase Strubbelig Receptor Family 3 (SRF3) in Central Asian strains Kas-2 or Kond, causing temperature-dependent autoimmunity and loss of growth and reproductive fitness. Here, we genetically dissected the RPP1-like Ler locus to determine contributions of individual RPP1-like Ler (R1–R8) genes to the incompatibility. In a neutral background, expression of most RPP1-like Ler genes, except R3, has no effect on growth or pathogen resistance. Incompatibility involves increased R3 expression and engineered R3 overexpression in a neutral background induces dwarfism and sterility. However, no individual RPP1-like Ler gene is sufficient for incompatibility between Ler and Kas-2 or Kond, suggesting that co-action of at least two RPP1-like members underlies this epistatic interaction. We find that the RPP1-like Ler haplotype is frequent and occurs with other Ler RPP1-like alleles in a local population in Gorzów Wielkopolski (Poland). Only Gorzów individuals carrying the RPP1-like Ler haplotype are incompatible with Kas-2 and Kond, whereas other RPP1-like alleles in the population are compatible. Therefore, the RPP1-like Ler haplotype has been maintained in genetically different individuals at a single site, allowing exploration of forces shaping the evolution of RPP1-like genes at local and regional population scales.     

Genes conferring late flowering inArabidopsis thaliana

Three naturally occurring late flowering, vernalization responsive ecotypes ofArabidopsis thaliana, Pitztal, Innsbruck and Kiruna-2, were each crossed with the early flowering ecotypes of Landsbergerecta, Columbia and Niederzenz. Analysis of the subsequent generations suggested that late flowering in Kiruna-2 is recessive and mainly determined by a single, late flowering gene. This late flowering gene is not, however, the same as that in any of the late flowering mutants generated in the Landsbergerecta background. Both Pitztal and Innsbruck appear to contain the same dominant gene which confers late flowering to these ecotypes. The early flowering parents Niederzenz and Landsberg both contain genes which modify the phenotype of this dominant late flowering locus, causing F₁ plants to flower either earlier (Landsberg) or later (Niederzenz) than the late parent. Mapping of the dominant late flowering locus from Pitztal demonstrated that late flowering co-segregated with an RFLP marker from one end of chromosome 4. This is a similar position to that ofFLA, the gene responsible for late flowering of theArabidopsis ecotypes Sf-2 and Le-O.     

The NADH dehydrogenase subunit 7 gene is interrupted by four group II introns in the wheat mitochondrial genome

Two loci FRI (FRIGIDA) and KRY (KRYOPHILA) have previously been identified as having major influences on the flowering time of the late-flowering, vernalization-responsive Arabidopsis ecotype, Stockholm. We report here on the mapping and subsequent analysis of these two loci. FRI was mapped to the top of chromosome 4 between markers w122 and m506, using restriction fragment length polymorphism (RFLP) analysis. Due to lack of segregation in of the late-flowering phenotype under the environmental conditions used, KRY could only be localized, by subtractive genotyping, to chromosome 5 or part of chromosome 3. The map position of FRI indicates that it is not allelic to any of the late-flowering loci identified by mutagenesis of the early-flowering ecotype Landsberg erecta. The late-flowering phenotype conferred by the Stockholm allele of FRI is modified (towards earlier flowering) by Landsberg erecta alleles at an unknown number of loci, perhaps accounting for the absence of fri mutations among mutant lines recovered in Landsberg erecta.     

RFLP mapping of the genes controlling hybrid breakdown in rice (Oryza sativa L.)

 Complementary recessive genes hwd1 and hwd2 controlling hybrid breakdown (weakness of F₂ and later generations) were mapped in rice using RFLP markers. These genes produce a plant that is shorter and has fewer tillers than normal plants when the two loci have only one or no dominant allele at both loci. A cultivar with two dominant alleles at the hwd1 locus and a cultivar with two dominant alleles at the hwd2 locus were crossed with a double recessive tester line. Linkage analysis was carried out for each gene independently in two F₂ populations derived from these crosses. hwd1 was mapped on the distal region of rice genetic linkage map for chromosome 10, flanked by RFLP markers C701 and R2309 at a distance of 0.9 centiMorgans (cM) and 0.6 cM, respectively. hwd2 was mapped in the central region of rice genetic linkage map for chromosome 7, tightly linked with 4 RFLP markers without detectable recombination. The usefulness of RFLP mapping and map information for the genes controlling reproductive barriers are discussed in the context of breeding using diverse rice germplasm, especially gene introduction by marker-aided selection.     

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

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

Two Recessive Suppressors of SACCHAROMYCES CEREVISIAE CHO1 That Are Unlinked but Fall in the Same Complementation Group

Phenotypic reversion of ethanolamine-requiring Saccharomyces cerevisiae cho1 mutants is predominantly due to recessive mutations at genes unlinked to the chromosome V cho1 locus. The recessive suppressors do not correct the primary cho1 defect in phosphatidylserine synthesis but circumvent it with a novel endogenous supply of ethanolamine. One suppressor (eam1) was previously mapped to chromosome X, and 135 suppressor isolates were identified as eam1 alleles by complementation analysis. Additional meiotic recombination studies have identified a second genetic locus, eam2, that falls in the eam1 complementation group but maps close to the centromere of chromosome IV. Although the normal EAM1 and EAM2 alleles are fully dominant over recessive mutant alleles, their dominance fails in diploids heterozygous for defects in both genes simultaneously. The unusual complementation pattern could be explained by interaction of the gene products in formation of the same enzyme.     

Growth habit determination by the balance of histone methylation activities in Arabidopsis

In Arabidopsis, the rapid‐flowering summer‐annual versus the vernalization‐requiring winter‐annual growth habit is determined by natural variation in FRIGIDA (FRI) and FLOWERING LOCUS C (FLC). However, the biochemical basis of how FRI confers a winter‐annual habit remains elusive. Here, we show that FRI elevates FLC expression by enhancement of histone methyltransferase (HMT) activity. EARLY FLOWERING IN SHORT DAYS (EFS), which is essential for FRI function, is demonstrated to be a novel dual substrate (histone H3 lysine 4 (H3K4) and H3K36)‐specific HMT. FRI is recruited into FLC chromatin through EFS and in turn enhances EFS activity and engages additional HMTs. At FLC, the HMT activity of EFS is balanced by the H3K4/H3K36‐ and H3K4‐specific histone demethylase (HDM) activities of autonomous‐pathway components, RELATIVE OF EARLY FLOWERING 6 and FLOWERING LOCUS D, respectively. Loss of HDM activity in summer annuals results in dominant HMT activity, leading to conversion to a winter‐annual habit in the absence of FRI. Thus, our study provides a model of how growth habit is determined through the balance of the H3K4/H3K36‐specific HMT and HDM activities.