New Arabidopsis recombinant inbred lines (Landsberg erecta x Nossen) reveal natural variation in phytochrome-mediated responses

Ultra-High-Density QTL Marker Mapping for Seedling Photomorphogenesis Mediating Arabidopsis Establishment in Southern Patagonia

Arabidopsis thaliana shows a wide range of genetic and trait variation among wild accessions. Because of its unparalleled biological and genomic resources, Arabidopsis has a high potential for the identification of genes underlying ecologically important complex traits, thus providing new insights on genome evolution. Previous research suggested that distinct light responses were crucial for Arabidopsis establishment in a peculiar ecological niche of southern Patagonia. The aim of this study was to explore the genetic basis of contrasting light-associated physiological traits that may have mediated the rapid adaptation to this new environment. From a biparental cross between the photomorphogenic contrasting accessions Patagonia (Pat) and Columbia (Col-0), we generated a novel recombinant inbred line (RIL) population, which was entirely next-generation sequenced to achieve ultra-high-density saturating molecular markers resulting in supreme mapping sensitivity. We validated the quality of the RIL population by quantitative trait loci (QTL) mapping for seedling de-etiolation, finding seven QTLs for hypocotyl length in the dark and continuous blue light (Bc), continuous red light (Rc), and continuous far-red light (FRc). The most relevant QTLs, Rc1 and Bc1, were mapped close together to chromosome V; the former for Rc and Rc/dark, and the latter for Bc, FRc, and dark treatments. The additive effects of both QTLs were confirmed by independent heterogeneous inbred families (HIFs), and we explored TZP and ABA1 as potential candidate genes for Rc1 and Bc1QTLs, respectively. We conclude that the Pat × Col-0 RIL population is a valuable novel genetic resource to explore other adaptive traits in Arabidopsis.

Biological activity and dimerization state of modified phytochrome A proteins

To assess potential physical interactions of type I phyA with the type II phyB-phyE phytochromes in vivo, transgenes expressing fusion gene forms of phyA were introduced into the Arabidopsis phyA mutant background. When a single c-Myc (myc) epitope is added to either the N- or C-terminus of phyA, the constructs completely complement phyA mutant phenotypes. However, addition of larger tags, such as six consecutive myc epitopes or the yellow fluorescent protein sequence, result in fusion proteins that show reduced activity. All the tagged phyA proteins migrate as dimers on native gels and co-immunoprecipitation reveals no binding interaction of phyA to any of the type II phys in the dark or under continuous far-red light. Dimers of the phyA 1–615 amino acid N-terminal photosensory domain (NphyA), generated in vivo with a yeast GAL4 dimerization domain and attached to a constitutive nuclear localization sequence, are expressed at a low level and, although they cause a cop phenotype in darkness and mediate a very low fluence response to pulses of FR, have no activity under continuous FR. It is concluded that type I phyA in its Pr form is present in plants predominantly or exclusively as a homodimer and does not stably interact with type II phys in a dimer-to-dimer manner. In addition, its activity in mediating response to continuous FR is sensitive to modification of its N- or C-terminus.

Cell length instead of cell number becomes the predominant factor contributing to hypocotyl length genotypic differences under abiotic stress in Medicago truncatula

Hypocotyl elongation in the dark is a crucial process to ensure seedling emergence. It relies both on the cell number and cell length. The contribution of these two factors to the maximal hypocotyl length and the impact of environmental conditions on this contribution are not known. This is surprising considering the agronomic and economical importance of seedling emergence in crop establishment. Using 14 genotypes from a nested core collection representing Medicago truncatula (barrel medic) natural variation, we investigated how epidermal cell number and cell length contribute to hypocotyl length under optimal, low temperature (8°C) and water deficit (-0.50 MPa) conditions. Both cell number and length vary according to genotypes and contribute to maximal hypocotyl length differences between genotypes. This contribution, however, depends on growth conditions. Cell number is the major contributor under optimal conditions (60%) whereas cell length becomes the major determinant under stress. Maximal hypocotyl length is correlated with hypocotyl elongation rate under both stresses but not under optimal condition, revealing contrasted genotypes for cell elongation capacity under stress. To identify the genetic regulators determining cell number and cell length, quantitative trait loci (QTLs) were detected using a recombinant inbred lines population exhibiting segregation in maximal hypocotyl length. Two QTLs controlling cell number and three QTLs controlling cell length at low temperature were detected. One QTL for cell number and two for cell length were found to be associated with hypocotyl length under low temperature. This study provides new information to improve seedling emergence under abiotic stress.

Light perception and signalling by phytochrome A

In etiolated seedlings, phytochrome A (phyA) mediates very-low-fluence responses (VLFRs), which initiate de-etiolation at the interphase between the soil and above-ground environments, and high-irradiance responses (HIR), which complete de-etiolation under dense canopies and require more sustained activation with far-red light. Light-activated phyA is transported to the nucleus by FAR-RED ELONGATED HYPOCOTYL1 (FHY1). The nuclear pool of active phyA increases under prolonged far-red light of relatively high fluence rates. This condition maximizes the rate of FHY1-phyA complex assembly and disassembly, allowing FHY1 to return to the cytoplasm to translocate further phyA to the nucleus, to replace phyA degraded in the proteasome. The core signalling pathways downstream of nuclear phyA involve the negative regulation of CONSTITUTIVE PHOTOMORPHOGENIC 1, which targets for degradation transcription factors required for photomorphogenesis, and PHYTOCHROME-INTERACTING FACTORs, which are transcription factors that repress photomorphogenesis. Under sustained far-red light activation, released FHY1 can also be recruited with active phyA to target gene promoters as a transcriptional activator, and nuclear phyA signalling activates a positive regulatory loop involving BELL-LIKE HOMEODOMAIN 1 that reinforces the HIR.

The receptor-like kinase ERECTA contributes to the shade-avoidance syndrome in a background-dependent manner

BACKGROUND AND AIMS

Plants growing at high densities perceive a decrease in the red to far-red (R/FR) ratio of incoming light. These changes in light quality trigger a suite of responses collectively known as the shade-avoidance syndrome (SAS) including hypocotyl and stem elongation, inhibition of branching and acceleration of flowering.

METHODS

Quantitative trait loci (QTLs) were mapped for hypocotyl length to end-of-day far-red (EOD), a simulated shade-avoidance response, in recombinant inbred line (RIL) populations of Arabidopsis thaliana seedlings, derived from Landsberg erecta (Ler) and three accessions (Columbia, Col; Nossen, No-0; and Cape Verde Islands, Cvi-0).

KEY RESULTS

Five loci were identified as being responsible for the EOD response, with a positive contribution of Ler alleles on the phenotype independently of the RIL population. Quantitative complementation analysis and transgenic lines showed that PHYB is the candidate gene for EODRATIO5 in the Ler × Cvi-0 RIL population, but not for two co-localized QTLs, EODRATIO1 and EODRATIO2 mapped in the Ler × No-0 and Ler × Col RIL populations, respectively. The ERECTA gene was also implicated in the SAS in a background-dependent manner. For hypocotyl length EOD response, a positive contribution of erecta alleles was found in Col and Van-0, but not in Ler, Cvi-0, Hir-1 or Ws. Furthermore, pleiotropic effects of ERECTA in the EOD response were also detected for petiole and lamina elongation, hyponastic growth, and flowering time.

CONCLUSIONS

The results show that the analysis of multiple mapping populations leads to a better understanding of the SAS genetic architecture. Moreover, the background- and trait-dependent contribution of ERECTA in the SAS suggest that its function in shaded natural environments may be relevant for some populations in different phases of plant development. It is proposed that ERECTA is involved in canalization processes buffering the genetic variation of the SAS against environmental light fluctuations.

Quantitative trait loci involved in regulating seed oil composition in Arabidopsis thaliana and their evolutionary implications

Fatty acid composition is an important determinant of seed oil quality. Overall, 72 QTL for 12 fatty acid traits that control seed oil composition were identified in four recombinant inbred line (RIL) populations (Ler-0 × Sha, Ler-0 × Col-4, Ler-2 × Cvi, Ler-0 × No-0) of Arabidopsis thaliana. The identified QTL explained 3.2-79.8% of the phenotypic variance; 33 of the 59 QTL identified in the Ler-0 × Sha and the Ler-0 × Col RIL populations co-located with several a priori candidate genes for seed oil composition. QTL for fatty acids 18:1, 18:2, 22:1, and fatty acids synthesized in plastids was identified in both Ler-0 × Sha and Ler-0 × Col-4 RIL populations, and QTL for 16:0 was identified in the Ler-0 × Sha and Ler-0 × No-0 RIL populations providing strong support for the importance of these QTL in determining seed oil composition. We identified melting point QTL in three RIL populations, and fatty acid QTL collocated with two of them, suggesting that the loci could be under selection for altering the melting point of seed oils to enhance adaptation and could be useful for breeding purposes. Nuclear-cytoplasmic interactions and epistasis were rare. Analysis of the genetic correlations between these loci and other fatty acids indicated that these correlations would tend to strongly enhance selection for desirable fatty acids.

Quantitative genetic analysis of salicylic acid perception in Arabidopsis

Salicylic acid (SA) is a phytohormone required for a full resistance against some pathogens in Arabidopsis, and NPR1 (Non-Expressor of Pathogenesis Related Genes 1) is the only gene with a strong effect on resistance induced by SA which has been described. There can be additional components of SA perception that escape the traditional approach of mutagenesis. An alternative to that approach is searching in the natural variation of Arabidopsis. Different methods of analyzing the variation between ecotypes have been tried and it has been found that measuring the growth of a virulent isolate of Pseudomonas syringae after the exogenous application of SA is the most effective one. Two ecotypes, Edi-0 and Stw-0, have been crossed, and their F2 has been studied. There are two significant quantitative trait loci (QTLs) in this population, and there is one QTL in each one of the existing mapping populations Col-4 × Laer-0 and Laer-0 × No-0. They have different characteristics: while one QTL is only detectable at low concentrations of SA, the other acts after the point of crosstalk with methyl jasmonate signalling. Three of the QTLs have candidates described in SA perception as NPR1, its interactors, and a calmodulin binding protein.

Resistance and biomass in Arabidopsis: a new model for salicylic acid perception

Salicylic acid (SA) is an essential hormone for plant defence and development. SA perception is usually measured by counting the number of pathogens that grow in planta upon an exogenous application of the hormone. A biological SA perception model based on plant fresh weight reduction caused by disease resistance in Arabidopsis thaliana is proposed. This effect is more noticeable when a chemical analogue of SA is used, like Benzothiadiazole (BTH). By spraying BTH several times, a substantial difference in plant biomass is observed when compared with the mock treatment. Such difference is dose-dependent and does not require pathogen inoculation. The model is robust and allows for the comparison of different Arabidopsis ecotypes, recombinant inbreed lines, and mutants. Our results show that two mutants, non-expresser of pathogenesis-related genes 1 (npr1) and auxin resistant 3 (axr3), fail to lose biomass when BTH is applied to them. Further experiments show that axr3 responds to SA and BTH in terms of defence induction. NPR1-related genotypes also confirm the pivotal role of NPR1 in SA perception, and suggest an active program of depletion of resources in the infected tissues.

A focus on natural variation for abiotic constraints response in the model species Arabidopsis thaliana

Plants are particularly subject to environmental stress, as they cannot move from unfavourable surroundings. As a consequence they have to react in situ. In any case, plants have to sense the stress, then the signal has to be transduced to engage the appropriate response. Stress response is effected by regulating genes, by turning on molecular mechanisms to protect the whole organism and its components and/or to repair damage. Reactions vary depending on the type of stress and its intensity, but some are commonly turned on because some responses to different abiotic stresses are shared. In addition, there are multiple ways for plants to respond to environmental stress, depending on the species and life strategy, but also multiple ways within a species depending on plant variety or ecotype. It is regularly accepted that populations of a single species originating from diverse geographic origins and/or that have been subjected to different selective pressure, have evolved retaining the best alleles for completing their life cycle. Therefore, the study of natural variation in response to abiotic stress, can help unravel key genes and alleles for plants to cope with their unfavourable physical and chemical surroundings. This review is focusing on Arabidopsis thaliana which has been largely adopted by the global scientific community as a model organism. Also, tools and data that facilitate investigation of natural variation and abiotic stress encountered in the wild are set out. Characterization of accessions, QTLs detection and cloning of alleles responsible for variation are presented.

QTL mapping in new Arabidopsis thaliana advanced intercross-recombinant inbred lines

Background

Even when phenotypic differences are large between natural or domesticated strains, the underlying genetic basis is often complex, and causal genomic regions need to be identified by quantitative trait locus (QTL) mapping. Unfortunately, QTL positions typically have large confidence intervals, which can, for example, lead to one QTL being masked by another, when two closely linked loci are detected as a single QTL. One strategy to increase the power of precisely localizing small effect QTL, is the use of an intercross approach before inbreeding to produce Advanced Intercross RILs (AI-RILs).

Methodology/Principal Findings

We present two new AI-RIL populations of Arabidopsis thaliana genotyped with an average intermarker distance of 600 kb. The advanced intercrossing design led to expansion of the genetic map in the two populations, which contain recombination events corresponding to 50 kb/cM in an F₂ population. We used the AI-RILs to map QTL for light response and flowering time, and to identify segregation distortion in one of the AI-RIL populations due to a negative epistatic interaction between two genomic regions.

Conclusions/Significance

The two new AI-RIL populations, EstC and KendC, derived from crosses of Columbia (Col) to Estland (Est-1) and Kendallville (Kend-L) provide an excellent resource for high precision QTL mapping. Moreover, because they have been genotyped with over 100 common markers, they are also excellent material for comparative QTL mapping.

Quantitative trait loci associated with lettuce seed germination under different temperature and light environments

Temperature and light are primary environmental cues affecting seed germination. To elucidate the genetic architecture underlying lettuce (Lactuca sativa L.) seed germination under different environmental conditions, an F8 recombinant inbred line population consisting of 131 families was phenotyped for final germination and germination rate. Seeds were imbibed in water at 20 degrees C under continuous red light (20-Rc), 20 degrees C continuous dark (20-Dc), 31.5 degrees C continuous red light (31.5-Rc), 31.5 degrees C continuous dark (31.5-Dc), or 20 degrees C far-red light for 24 h followed by continuous dark (20-FRc-Dc). Thirty-eight quantitative trait loci (QTL) were identified from two seed maturation environments: 10 for final germination and 28 for germination rate. The amount of variation attributed to an individual QTL ranged from 9.3% to 17.2% and from 5.6% to 26.2% for final germination and germination rate, respectively. Path analysis indicated that factors affecting germination under 31.5-Rc or 31.5-Dc are largely the same, and these appear to differ from those employed under 20-FRc-Dc. QTL and path analysis support the notion of common and unique factors for germination under diverse temperature and light regimes. A highly significant effect of the seed maturation environment on subsequent germination capacity under environmental stress was observed.

Light-related loci controlling seed germination in Ler x Cvi and Bay-0 x Sha recombinant inbred-line populations of Arabidopsis thaliana

BACKGROUND AND AIMS

Dormancy is a complex trait finely regulated by hormones and environmental factors. The phytochromes that sense red:far-red (R:FR) are the sole photoreceptors involved in the termination of dormancy and the induction of germination by light. The aims of this study were to identify and characterize loci controlling this process in seeds of Arabidopsis thaliana.

METHODS

Recombinant inbred lines (RILs) derived from Landsberg erecta and Cape Verde Islands (Ler x Cvi), and Bayreuth and Shahdara (Bay-0 x Sha) were used to map loci related to light effects in seeds previously exposed to chilling and after-ripening periods.

KEY RESULTS

Substantial genetic variation was found between accessions of A. thaliana in the induction of germination by light. Twelve loci were identified under R, FR or darkness, some of which were novel loci: DOG8, DOG9, DOG13, DOG14 and DOG15 detected in the Ler x Cvi RIL population; and DOG10, DOG11 and DOG12 mapped in the Bay-0 x Sha RIL population. Furthermore, independent loci were mapped for the induction of germination by low fluence (DOG-LF1 and DOG-LF2) and very low fluence of light (DOG-VLF1) in the Ler x Cvi RIL population. Several loci were confirmed and characterized after different after-ripening and chilling treatments through near-isogenic lines (NILs) and heterogeneous inbred families (HIFs).

CONCLUSIONS

The results show that one group of loci act in a wide range of environmental scenarios, whereas a smaller group of loci are relevant only under a narrower set of conditions when the influence of the most-prevalent loci is reduced as a consequence of changes in the physiological status of the seeds. In addition, the identification of specific loci controlling the action modes of the phytochromes improves our understanding of the two independent signalling pathways that promote germination in response to light.

PKS1 plays a role in red-light-based positive phototropism in roots

Aerial parts of plants curve towards the light (i.e. positive phototropism), and roots typically grow away from the light (i.e. negative phototropism). In addition, Arabidopsis roots exhibit positive phototropism relative to red light (RL), and this response is mediated by phytochromes A and B (phyA and phyB). Upon light stimulation, phyA and phyB interact with the phytochrome kinase substrate (PKS1) in the cytoplasm. In this study, we investigated the role of PKS1, along with phyA and phyB, in the positive phototropic responses to RL in roots. Using a high-resolution feedback system, we studied the phenotypic responses of roots of phyA, phyB, pks1, phyA pks1 and phyB pks1 null mutants as well as the PKS1-overexpressing line in response to RL. PKS1 emerged as an intermediary in the signalling pathways and appears to promote a negative curvature to RL in roots. In addition, phyA and phyB were both essential for a positive response to RL and act in a complementary fashion. However, either photoreceptor acting without the other results in negative curvature in response to red illumination so that the mode of action differs depending on whether phyA and phyB act independently or together. Our results suggest that PKS1 is part of a signalling pathway independent of phyA and phyB and that PKS1 modulates RL-based root phototropism.

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.

GIGANTEA regulates phytochrome A-mediated photomorphogenesis independently of its role in the circadian clock

GIGANTEA (GI) is a nuclear protein involved in the promotion of flowering by long days, in light input to the circadian clock, and in seedling photomorphogenesis under continuous red light but not far-red light (FR). Here, we report that in Arabidopsis (Arabidopsis thaliana) different alleles of gi have defects in the hypocotyl-growth and cotyledon-unfolding responses to hourly pulses of FR, a treatment perceived by phytochrome A (phyA). This phenotype is rescued by overexpression of GI. The very-low-fluence response of seed germination was also reduced in gi. Since the circadian clock modulates many light responses, we investigated whether these gi phenotypes were due to alterations in the circadian system or light signaling per se. In experiments where FR pulses were given to dark-incubated seeds or seedlings at different times of the day, gi showed reduced seed germination, cotyledon unfolding, and activity of a luciferase reporter fused to the promoter of a chlorophyll a/b-binding protein gene; however, rhythmic sensitivity was normal in these plants. We conclude that while GI does not affect the high-irradiance responses of phyA, it does affect phyA-mediated very-low-fluence responses via mechanisms that do not obviously involve its circadian functions.

Photosensing fungi: phytochrome in the spotlight

Red light triggers asexual development and represses sexual development in the fungus Aspergillus nidulans. This response has been shown to require a phytochrome red/far-red light photoreceptor, FphA, which is cytoplasmic and binds a tetrapyrrole chromophore. FphA exhibits similarities to both plant and bacterial phytochromes.