The VERNALIZATION INDEPENDENCE 4 gene encodes a novel regulator of FLOWERING LOCUS C

The late-flowering, vernalization-responsive habit of many Arabidopsis ecotypes is mediated predominantly through repression of the floral programme by the FLOWERING LOCUS C (FLC) gene. To better understand this repressive mechanism, we have taken a genetic approach to identify novel genes that positively regulate FLC expression. We identified recessive mutations in a gene designated VERNALIZATION INDEPENDENCE 4 (VIP4), that confer early flowering and loss of FLC expression in the absence of cold. We cloned the VIP4 gene and found that it encodes a highly hydrophilic protein with similarity to proteins from yeasts, Drosophila, and Caenorhabditis elegans. Consistent with a proposed role as a direct activator of FLC, VIP4 is expressed throughout the plant in a pattern similar to that of FLC. However, unlike FLC, VIP4 RNA expression is not down-regulated in vernalized plants, suggesting that VIP4 is probably not sufficient to activate FLC, and that VIP4 is probably not directly involved in a vernalization mechanism. Epistasis analysis suggests that VIP4 could act in a separate pathway from previously identified FLC regulators, including FRIGIDA and the autonomous flowering promotion pathway gene LUMINIDEPENDENS. Mutants lacking detectable VIP4 expression flower earlier than FLC null mutants, suggesting that VIP4 regulates flowering-time genes in addition to FLC. Floral morphology is also disrupted in vip4 mutants; thus, VIP4 has multiple roles in development.     

Genome‐wide signatures of flowering adaptation to climate temperature: Regional analyses in a highly diverse native range of Arabidopsis thaliana

Current global change is fueling an interest to understand the genetic and molecular mechanisms of plant adaptation to climate. In particular, altered flowering time is a common strategy for escape from unfavourable climate temperature. In order to determine the genomic bases underlying flowering time adaptation to this climatic factor, we have systematically analysed a collection of 174 highly diverse Arabidopsis thaliana accessions from the Iberian Peninsula. Analyses of 1.88 million single nucleotide polymorphisms provide evidence for a spatially heterogeneous contribution of demographic and adaptive processes to geographic patterns of genetic variation. Mountains appear to be allele dispersal barriers, whereas the relationship between flowering time and temperature depended on the precise temperature range. Environmental genome‐wide associations supported an overall genome adaptation to temperature, with 9.4% of the genes showing significant associations. Furthermore, phenotypic genome‐wide associations provided a catalogue of candidate genes underlying flowering time variation. Finally, comparison of environmental and phenotypic genome‐wide associations identified known (Twin Sister of FT, FRIGIDA‐like 1, and Casein Kinase II Beta chain 1) and new (Epithiospecifer Modifier 1 and Voltage‐Dependent Anion Channel 5) genes as candidates for adaptation to climate temperature by altered flowering time. Thus, this regional collection provides an excellent resource to address the spatial complexity of climate adaptation in annual plants.     

Natural variation in Arabidopsis lyrata vernalization requirement conferred by a FRIGIDA indel polymorphism

Species share homologous genes to a large extent, but it isnot yet known to what degree the same loci have been targetsfor natural selection in different species. Natural variationin flowering time is determined to a large degree by 2 genes,FLOWERING LOCUS C and FRIGIDA, in Arabidopsis thaliana. Here,we examine whether FRIGIDA has a role in differences in floweringtime between and within natural populations of Arabidopsis lyrata,a close outcrossing perennial relative of A. thaliana. We found2 FRIGIDA sequence variants producing potentially functionalproteins but with a length difference of 14 amino acids. Thesevariants conferred a 15-day difference in flowering time inan association experiment in 2 Scandinavian populations. Thedifference in flowering time between alleles was confirmed withtransformation to A. thaliana. Because the north European late-floweringpopulations harbor both late- and early sequence variants atintermediate frequencies and the late-flowering variant is mostfrequent in the southern early flowering European population,other genetic factors must be responsible for the floweringtime differences between the populations. The length polymorphismoccurs at high frequencies also in several North American populations.The occurrence of functional variants at intermediate frequenciesin several populations suggests that the variation may be maintainedby balancing selection. This is in contrast to A. thaliana,where independent loss-of-function mutations at the FRIGIDAgene are responsible for differences between populations andlocal adaptation.     

Plasticity genes and plasticity costs: a new approach using an Arabidopsis recombinant inbred population

Earlier flowering is triggered by vernalization in some but not all Arabidopsis ecotypes, often reflecting allelic variation at the FRIGIDA (FRI) locus. Using a recombinant inbred (RI) population polymorphic at FRI, we examined fitness consequences of variation for plasticity. Flowering and fitness were scored for 68 RI genotypes following full and partial vernalization treatments. Within-environment and mixed-model anovas estimated variance components for a genotype effect and a G x E term, respectively. Selection analyses examined whether delayed bolting increases fitness; a plasticity costs analysis asked whether increased plasticity lowers fitness. We also explored whether trait QTL had environment-specific effects, colocated in the immediate vicinity of FRI, or overlapped with fitness QTL. Selection may favor fri alleles and constitutive early flowering, especially in conditions that only partially vernalize plants. Plasticity costs, detected only after partial vernalization and only marginally significant, were nonetheless consistent with FRI-FLC function. We discuss how information about QTL with environment-specific effects, fitness QTL, and knowledge about plasticity genes can improve interpretation of selection or plasticity cost analyses.     

The Arabidopsis TALE homeobox gene ATH1 controls floral competency through positive regulation of FLC

Floral induction is controlled by a plethora of genes acting in different pathways that either repress or promote floral transition at the shoot apical meristem (SAM). During vegetative development high levels of floral repressors maintain the Arabidopsis SAM as incompetent to respond to promoting factors. Among these repressors, FLOWERING LOCUS C (FLC) is the most prominent. The processes underlying downregulation of FLC in response to environmental and developmental signals have been elucidated in considerable detail. However, the basal induction of FLC and its upregulation by FRIGIDA (FRI) are still poorly understood. Here we report the functional characterization of the ARABIDOPSIS THALIANA HOMEOBOX 1 (ATH1) gene. A function of ATH1 in floral repression is suggested by a gradual downregulation of ATH1 in the SAM prior to floral transition. Further evidence for such a function of ATH1 is provided by the vernalization-sensitive late flowering of plants that constitutively express ATH1. Analysis of lines that differ in FRI and/or FLC allele strength show that this late flowering is caused by upregulation of FLC as a result of synergism between ATH1 overexpression and FRI. Lack of ATH1, however, results in attenuated FLC levels independently of FRI, suggesting that ATH1 acts as a general activator of FLC expression. This is further corroborated by a reduction of FLC-mediated late flowering in fca-1 and fve-1 autonomous pathway backgrounds when combined with ath1. Since other floral repressors of the FLC clade are not significantly affected by ATH1, we conclude that ATH1 controls floral competency as a specific activator of FLC expression.     

Cloning and characterization of a flowering time gene from Thellungiella halophila

Thellungiella halophila (T. halophila) (salt cress) is a close relative of Arabidopsis and a model plant for salt tolerance research. However, the nature of its later flowering causes some difficulties in genetic analysis. The FRIGIDA (FRT) gene plays a key role in the Arabidopsis vernalization flowering pathway, whose homolog in T. halophila may also be a key factor in controlling flowering time. In order to study the molecular mechanism of vernalization responses in T. halophila , a full length cDNA named ThFRI (Thellungiella halophila FRIGIDA) was isolated from the young seedlings of T. halophila by RT-PCR and RACE. The ThFRI cDNA was 2017 bp in length and contained an open reading frame encoding a putative protein of 605 ami no acids. The ThFRI showed significant homology to AtFRI (74.5% at the nucleotide level and 63.9% at the ami no acid level). To study its function, ThFRI cDNA was transformed into Arabidopsis thaliana , driven by CaMV 35S promoter. Transgenic plants expressing ThFRI exhibited late-flowering phenotype, which suggests that ThFRI is the funtional FRI homolog in T. halophila . The cloning and funtional characterization of the FRI homolog of T. halophila will faciliate further study of flowering time control in T. halophila .     

Genetic variation in Arabidopsis thaliana for night-time leaf conductance

Night-time leaf conductance ( g _night) and transpiration may have several adaptive benefits related to plant water, nutrient and carbon relations. Little is known, however, about genetic variation in g _night and whether this variation correlates with other gas exchange traits related to water use and/or native habitat climate. We investigated g _night in 12 natural accessions and three near isogenic lines (NILs) of Arabidopsis thaliana . Genetic variation in g _night was found for the natural accessions, and g _night was negatively correlated with native habitat atmospheric vapour pressure deficit (VPD_air), suggesting lower g _night may be favoured by natural selection in drier habitats. However, there were also significant genetic correlations of g _night with daytime gas exchange traits expected to affect plant fitness [i.e. daytime leaf conductance, photosynthesis and intrinsic water-use efficiency (WUE_i)], indicating that selection on daytime gas exchange traits may result in indirect selection on g _night. The comparison of three NILs to their parental genotypes identified one quantitative trait locus (QTL) contributing to variation in g _night. Further characterization of genetic variation in g _night within and among populations and species, and of associations with other traits and native habitats will be needed to understand g _night as a putatively adaptive trait.