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Arbuscular mycorrhizal (AM) symbiosis alleviates drought stress in plants. However, the intimate mechanisms involved, as well as its effect on the production of signalling molecules associated with the host plant–AM fungus interaction remains largely unknown. In the present work, the effects of drought on lettuce and tomato plant performance and hormone levels were investigated in non-AM and AM plants. Three different water regimes were applied, and their effects were analysed over time. AMplants showed an improved growth rate and efficiency of photosystem II than non-AM plants under drought from very early stages of plant colonization. The levels of the phytohormone abscisic acid, as well as the expression of the correspondingmarker genes, were influenced by drought stress in non-AMandAMplants. The levels of strigolactones and the expression of corresponding marker genes were affected by both AM symbiosis and drought. The results suggest that AM symbiosis alleviates drought stress by altering the hormonal profiles and affecting plant physiology in the host plant. In addition, a correlation between AM root colonization, strigolactone levels and drought severity is shown, suggesting that under these unfavourable conditions, plants might increase strigolactone production in order to promote symbiosis establishment to cope with the stress.

Starch is the most important storage polysaccharide in higher plants. This polysaccharide is used in many industrial applications as it is abundant, renewable and biodegradable and it can be modified into a wide range of products used in food, animal feed, pharmaceuticals and industry. With the understanding of the starch biosynthesis pathway and the isolation of many of the genes involved in this process, the potential for producing novel starches with improved functionality through genetic modification of plants has become more clear. Several different strategies have been used to achieve the rational design of renewable polymers to meet specific requirements. One of these strategies is the regulation of starch biosynthesis and granule assembly in higher plants. A second strategy involves the expression of heterologous genes encoding biosynthetic or modifying enzymes from other organisms to produce novel products with novel functional properties. In this chapter, these recent developments in starch modification in potato plants, such as alteration of starch composition and production of novel storage polysaccharides, are reviewed.

Ricinus communis seeds germinate to a high percentage and faster at 35 °C than at lower temperatures, but with compromised seedling establishment. However, seedlings are able to cope with high temperatures at later stages of seedling establishment if germination occurred at lower temperatures. Our objective was to assess the biochemical and molecular requirements of R. communis germination for successful seedling establishment at varying temperatures. For that, we performed metabolite profiling (GC-TOF-MS) and measured transcript levels of key genes involved in several energy-generating pathways, such as storage oil mobilization, β-oxidation and gluconeogenesis of seeds germinated at three different temperatures. We identified a thermo-sensitive window during seed germination in which high temperatures compromise seedling development, most likely by down-regulating some energy-generating pathways. Overexpression of malate synthase (MLS) and glycerol kinase (GK) genes resulted in higher starch levels in Nicotiana benthamiana leaves, which highlights the importance of these genes in energy-generating pathways for seedling establishment. Additionally, we showed that GABA, which is a stress-responsive metabolite, accumulated in response to the water content of the seeds during the initial phase of imbibition. Herewith, we provide new insights into the molecular requirements for vigorous seedling growth of R. communis under different environmental conditions.

Physiological dormancy has been described as a physiological inhibiting mechanism that prevents radicle emergence. It can be caused by the embryo (embryo dormancy) as well as by the structures that cover the embryo. One of its functions is to time plant growth and reproduction to the most optimal season and therefore, in nature, dormancy is an important adaptive trait that is under selective pressure. Dormancy is a complex trait that is affected by many loci, as well as by an intricate web of plant hormone interactions. Moreover, it is strongly affected by a multitude of environmental factors. Its induction, maintenance, cycling and loss come down to the central paradigm, which is the balance between two key hormonal regulators, i.e. the plant hormone abscisic acid (ABA), which is required for dormancy induction, and gibberellins (GA), which are required for germination. In this review we will summarize recent developments in dormancy research (mainly) in the model plantArabidopsis thaliana, focusing on two key players for dormancy induction, i.e. the plant hormone ABA and theDELAY OF GERMINATION 1 (DOG1)gene. We will address the role of ABA andDOG1in relation to various aspects of seed dormancy, i.e. induction during seed maturation, loss during dry seed afterripening, the rehydrated state (including dormancy cycling) and the switch to germination.

Strigolactones (SLs) are carotenoid-derived plant hormones and signaling molecules. When released into the soil, SLs indicate the presence of a host to symbiotic fungi and root parasitic plants. In planta, they regulate several developmental processes that adapt plant architecture to nutrient availability. Highly branched/tillered mutants in Arabidopsis, pea, and rice have enabled the identification of four SL biosynthetic enzymes: a cis/trans-carotene isomerase, two carotenoid cleavage dioxygenases, and a cytochrome P450 (MAX1). In vitro and in vivo enzyme assays and analysis of mutants have shown that the pathway involves a combination of new reactions leading to carlactone, which is converted by a rice MAX1 homolog into an SL parent molecule with a tricyclic lactone moiety. In this review, we focus on SL biosynthesis, describe the hormonal and environmental factors that determine this process, and discuss SL transport and downstream signaling as well as the role of SLs in regulating plant development.

Seed imbibition is an important process in the plant life cycle and determines whether seed germination and plant growth will be successful or not. Ricinus communis is becoming an important crop for oil production, and therefore, studying the physiological and biochemical aspects of seed imbibition and germination may aid in the improvement of crop quality and yield. Metabolite profiling was performed in order to assess biochemical changes associated with the temperature during early seed imbibition. Changes in the metabolite profile were already detected within 2 h of imbibition, but they were more prominent after 8 h. An increased level of glycerol and fatty acids upon a few hours of imbibition suggests that lipid mobilization occurs shortly after water uptake begins. Fumarate and succinate levels increased after 2 h of imbibition, suggesting that energy metabolism is reactivated relatively early in this species. Seeds imbibed at 20 and 25 °C showed an overall accumulation of carbohydrates, while at 35 °C increased levels of some amino acids were observed. Ascorbate content was 30-fold higher in seeds imbibed for 8 h at 35 °C as compared to seeds imbibed at 20 °C, suggesting that 35 °C is a stress condition for R. communis seeds. In this study, we have demonstrated that temperature plays an important role in water uptake rate, reserve mobilization and reactivation of metabolism during early seed imbibition. Additionally, we demonstrated that this species possess a specific metabolic signature which is not restricted to the imbibition period, but also during seedling establishment and plant growth.

Pectin methylesterase (PME) controls the methylesterification status of pectins and thereby determines the biophysical properties of plant cell walls, which are important for tissue growth and weakening processes. We demonstrate here that tissue-specific and spatiotemporal alterations in cell wall pectin methylesterification occur during the germination of garden cress (Lepidium sativum). These cell wall changes are associated with characteristic expression patterns of PME genes and resultant enzyme activities in the key seed compartments CAP (micropylar endosperm) and RAD (radicle plus lower hypocotyl). Transcriptome and quantitative real-time reverse transcription-polymerase chain reaction analysis as well as PME enzyme activity measurements of separated seed compartments, including CAP and RAD, revealed distinct phases during germination. These were associated with hormonal and compartment-specific regulation of PME group 1, PME group 2, and PME inhibitor transcript expression and total PME activity. The regulatory patterns indicated a role for PME activity in testa rupture (TR). Consistent with a role for cell wall pectin methylesterification in TR, treatment of seeds with PME resulted in enhanced testa permeability and promoted TR. Mathematical modeling of transcript expression changes in germinating garden cress and Arabidopsis (Arabidopsis thaliana) seeds suggested that group 2 PMEs make a major contribution to the overall PME activity rather than acting as PME inhibitors. It is concluded that regulated changes in the degree of pectin methylesterification through CAP- and RAD-specific PME and PME inhibitor expression play a crucial role during Brassicaceae seed germination.

Ascospores of Neosartorya, Byssochlamys and Talaromyces can be regarded as the most stressresistant eukaryotic cells. They can survive exposure at temperatures as high as 85°C for 100 min or more. Neosartorya fischeri ascospores are more viscous and more resistant to the combined stress of heat and desiccation than the ascospores of Talaromyces macrosporus which contain predominantly trehalose. These ascospores contain trehalose-based oligosaccharides (TOS) that are novel compatible solutes, which are accumulated to high levels. These compounds are also found in other members of the genus Neosartorya and in some other genera within the order Eurotiales that also include Byssochlamys and Talaromyces. The presence of oligosaccharides was observed in species that had a relatively high growth temperature. TOS glasses have a higher glass transition temperature (Tg) than trehalose, and they form a stable glass with crystallizing molecules, such as mannitol. Our data indicate that TOS are important for prolonged stabilization of cells against stress. The possible unique role of these solutes in protection against dry heat conditions is discussed.

Phytohormones, auxins in particular, play an important role in plant development and productivity. Earlier data showed positive impact of exogenous auxin on potato (Solanum tuberosum L.) tuberization. The aim of this study was to generate potato plants with increased auxin level predominantly in tubers. To this end, a pBinB33-tms1 vector was constructed harboring the Agrobacterium auxin biosynthesis gene tms1 fused to tuber-specific promoter of the class I patatin gene (B33-promoter) of potato. Among numerous independently generated B33:tms1 lines, those without visible differences from control were selected for detailed studies. In the majority of transgenic lines, tms1 gene transcription was detected, mostly in tubers rather than in shoots. Indoleacetic acid (IAA) content in tubers and the auxin tuber-to-shoot ratio were increased in tms1- expressing transformants. The organ-specific increase in auxin synthesis in B33:tms1-transformants accelerated and intensified the process of tuber formation, reduced the dose of carbohydrate supply required for in vitro tuberization, and decreased the photoperiodic dependence of tuber initiation. Overall, a positive correlation was observed between tms1 expression, IAA content in tubers, and stimulation of tuber formation. The revealed properties of B33:tms1 transformants imply an important role for auxin in potato tuberization and offer prospects tomagnify potato productivity by a moderate organ-specific enhancement of auxin content.

Strigolactones, plant-secreted underground signalling molecules, play an important role in agricultural ecosystems, because they mediate the interaction of crops with symbiotic AM fungi and parasitic weeds like Striga hermonthica. Cereal host plants secret these signalling molecules particularly under nutrient-deficient conditions and especially when phosphate (P) is limiting. The objective of the present study was to see the potential of P seed priming for S. hermonthica management in cereals in relation to strigolactone production. It has been demonstrated that P fertiliser application down-regulates the production of these signalling molecules in the rhizosphere, which results in lower S. hermonthica infection of cereals. The laboratory study showed maximum production of strigolactones from dry and water-soaked seeds, while seed soaking in P solution reduced their production. Similarly, maximum S. hermonthica infection was observed under control treatments with dry sowing or water soaking, while P seed soaking decreased S. hermonthica germination, emergence and dry biomass in all cereal crops. Our study shows that P seed priming resulted in lower exudation of strigolactones, which induced less S. hermonthica seeds germination and hence may lead to lower S. hermonthica infection. P-based seed priming could prove to be an effective and affordable strategy to reduce S. hermonthica infection in cereals. Further research for practical field application is needed

Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is an important technology to analyse gene expression levels during plant development or in response to different treatments. An important requirement to measure gene expression levels accurately is a properly validated set of reference genes. In this context, we analysed the potential use of 17 candidate reference genes across a diverse set of samples, including several tissues, different stages and environmental conditions, encompassing seed germination and seedling growth in Ricinus communis L. These genes were tested by RT-qPCR and ranked according to the stability of their expression using two different approaches: GeNorm and NormFinder. GeNorm and Normfinder indicated that ACT, POB and PP2AA1 comprise the optimal combination for normalization of gene expression data in inter-tissue (heterogeneous sample panel) studies. We also describe the optimal combination of reference genes for a subset of root, endosperm and cotyledon samples. In general, the most stable genes suggested by GeNorm are very consistent with those indicated by NormFinder, which highlights the strength of the selection of reference genes in our study. We also validated the selected reference genes by normalizing the expression levels of three target genes involved in energy metabolism with the reference genes suggested by GeNorm and NormFinder. The approach used in this study to identify stably expressed genes, and thus potential reference genes, was applied successfully for R. communis and it provides important guidelines for RT-qPCR studies in seeds and seedlings for other species (especially in those cases where extensive microarray data are not available).

Parasitism by the root-parasitic plant, Striga (Striga hermonthica L.), is a main threat to pearl millet production in sub-Saharan Africa and nutrient deficiency aggravates this problem, often leading to complete failure of pearl millet crops. Like many other species, pearl millet secretes germination stimulants (strigolactones) into the soil in response to mineral nutrient deficiency, which triggers Striga seed germination resulting in infection. A greenhouse experiment was conducted to evaluate the influence of different doses of di-ammonium phosphate (DAP) fertilizer on strigolactone production and Striga infection in three different African pearl millet cultivars (KBH, Sadore Local and Striga resistance). All the pearl millet genotypes produced varying amounts of different strigolactones like orobanchol, epi-orobanchol, orobanchyl acetate and 5-deoxystrigol, the level of which decreases with increasing doses of DAP. The control treatment (no DAP) showed maximum Striga germination, emergence and dry biomass production in all cultivars of pearl millet. Supply of DAP fertilizer up to 4 g per hill suppressed Striga germination by 69, 64 and 59%; emergence by 87, 85 and 95% and dry biomass by 91, 98 and 83% in cvs KBH, Sadore Local and Striga Resistance, respectively. The present findings reveal that DAP fertilizer minimizes strigolactones production and, as a result, reduces Striga infection in pearl millet. Low doses of DAP fertilizer is a promising strategy to lower the destructive effect of Striga on pearl millet. The use of small doses of DAP fertilizer combined with resistant crop cultivars, intercropping with legumes and hand pulling of Striga at flowering in an integrated Striga control strategy should be developed to help African farmers control this noxious weed.

Feverfew (Tanacetum parthenium) is a medicinal herb which is rich in sesquiterpene lactones. The main sesquiterpene lactone in feverfew is parthenolide. Costunolide has been considered to be the immediate precursor of parthenolide. Parthenolide and costunolide levels in flowers and in leaves collected during the vegetative and generative phase of three feverfew genotypes (diploid, tetraploid and Zardband cv.) and in 2,4-D treated leaves of the diploid genotype were analyzed using UPLC–MS/MS. Parthenolide and costunolide levels showed a similar pattern in all genotypes, and were higher in flowers than in leaves. The developmental pattern of these two compounds was not the same in flowers of the different genotypes and 2,4-D treatment increased both coordinately. In conclusion, we show that genetical, developmental and spatial factors all influence the composition of sesquiterpene lactones in feverfew.

Dormancy is the final stage of tuber life serving to preserve tubers as organs of vegetative reproduction under unfavorable growth conditions. Since the duration of potato tuber dormancy and their sprouting time have significant economic importance, much attention is given to the study of the regulation of these processes. This review considers metabolite, genetic, and hormonal aspects of regulation of potato (Solanum tuberosum L.) tuber dormancy and sprouting. Particular attention is paid to the relationship between processes occurring in different parts of the tuber: its storage tissues and buds. The interaction of hormonal and metabolite (carbohydrate) regulation of dormancy and sprouting is discussed.

A complex phenotype such as seed germination is the result of several genetic and environmental cues and requires the concerted action of many genes. The use of well-structured recombinant inbred lines in combination with “omics” analysis can help to disentangle the genetic basis of such quantitative traits. This so-called genetical genomics approach can effectively capture both genetic and epistatic interactions. However, to understand how the environment interacts with genomic-encoded information, a better understanding of the perception and processing of environmental signals is needed. In a classical genetical genomics setup, this requires replication of the whole experiment in different environmental conditions. A novel generalized setup overcomes this limitation and includes environmental perturbation within a single experimental design. We developed a dedicated quantitative trait loci mapping procedure to implement this approach and used existing phenotypical data to demonstrate its power. In addition, we studied the genetic regulation of primary metabolism in dry and imbibed Arabidopsis (Arabidopsis thaliana) seeds. In the metabolome, many changes were observed that were under both environmental and genetic controls and their interaction. This concept offers unique reduction of experimental load with minimal compromise of statistical power and is of great potential in the field of systems genetics, which requires a broad understanding of both plasticity and dynamic regulation.

BACKGROUND: Most insect-resistant transgenic crops employ toxins to control pests. A novel approach is to enhance the effectiveness of natural enemies by genetic engineering of the biosynthesis of volatile organic compounds (VOCs). Before the commercialisation of such transgenic plants can be pursued, detailed fundamental studies of their effects on herbivores and their natural enemies are necessary. The linalool/nerolidol synthase gene FaNES1 was constitutively expressed from strawberry in three Arabidopsis thaliana accessions, and the behaviour of the aphid Brevicoryne brassicae L., the parasitoid Diaeretiella rapae McIntosh and the predator Episyrphus balteatus de Geer was studied. RESULTS: Transgenic FaNES1-expressing plants emitted (E)-nerolidol and larger amounts of (E)-DMNT and linalool. Brevicoryne brassicae was repelled by the transgenic lines of two of the accessions, whereas its performance was not affected. Diaeretiella rapae preferred aphid-infested transgenic plants over aphid-infested wild-type plants for two of the accessions. In contrast, female E. balteatus predators did not differentiate between aphid-infested transgenic or wild-type plants. CONCLUSION: The results indicate that the genetic engineering of plants to modify their emission of VOCs holds considerable promise for facilitating biological control of herbivores. Validation for crop plants is a necessary next step to assess the usefulness of modified volatile emission in integrated pest management.

The lipid precursor alcohols of pyrethrins—jasmolone, pyrethrolone and cinerolone—have been proposed as sharing parts of the oxylipin pathway with jasmonic acid. This implies that one of the first committed steps of pyrethrin biosynthesis is catalyzed by a lipoxygenase, catalyzing the hydroperoxidation of linolenic acid at position 13. Previously, we showed that the expression and activity of chrysanthemyl diphosphate synthase (TcCDS), the enzyme catalyzing the first committed step in the biosynthesis of the acid moiety of pyrethrins, is trichome-specific and developmentally regulated in flowers. In the present study we characterized the expression pattern of 25 lipoxygenase EST contigs, and subsequently carried out the molecular cloning of two pyrethrum lipoxygenases, TcLOX1 and TcLOX2, that have a similar pattern to TcCDS. Only recombinant TcLOX1 catalyzed the peroxidation of the linolenic acid substrate. Just as TcCDS, TcLOX1, are exclusively expressed in trichomes. Phylogenetic analysis showed that the enzyme shared the highest homology with chloroplast-localized 13-type-lipoxygenases that are involved in maintaining basal levels of jasmonate.

Striga hermonthica infection poses a major constraint to sorghum production in sub-Saharan Africa, and low soil fertility aggravates the S. hermonthica problem. Under mineral nutrient deficiency, the sorghum host secretes large quantities of strigolactones, signalling molecules, into the rhizosphere. These induce S. hermonthica seed germination and subsequent infection of the host roots. In a combination of field and glasshouse experiments, we analysed the effect of microdose applied diammonium hydrogen phosphate (DAP) fertiliser on production of strigolactones, S. hermonthica infection and yield of three different African sorghum genotypes (CGM-19/1-1, Lina-3, DouaG). The sorghum cultivars all produced the strigolactones sorgomol and 5-deoxystrigol, albeit in different quantity and ratio. Without fertiliser, high S. hermonthica infection and emergence occurred under both glasshouse and field conditions. DAP application reduced secretion of sorgomol and 5-deoxystrigol and reduced S. hermonthica germination (66–70%), emergence (49–73%) and dry biomass (90–96%) under glasshouse conditions. Under field conditions, DAP microdosing reduced S. hermonthica emergence by 40–84% and increased sorghum grain yield by 47–142%. Thus DAP application reduced secretion of strigolactones into the rhizosphere and S. hermonthica parasitism both under controlled and field conditions. Microdosing of DAP may prove to be an efficient and cost effective option to reduce S. hermonthica damage in sorghum in sub-Saharan Africa, particularly in combination with other control options, such as intercropping, use of organic fertiliser and hand pulling of S. hermonthica at flowering to achieve integrated S. hermonthica management

Arbuscular mycorrhizal (AM) symbiosis alleviates drought stress in plants. However, the intimate mechanisms involved, as well as its effect on the production of signalling molecules associated with the host plant–AM fungus interaction remains largely unknown. In the present work, the effects of drought on lettuce and tomato plant performance and hormone levels were investigated in non-AM and AM plants. Three different water regimes were applied, and their effects were analysed over time. AMplants showed an improved growth rate and efficiency of photosystem II than non-AM plants under drought from very early stages of plant colonization. The levels of the phytohormone abscisic acid, as well as the expression of the correspondingmarker genes, were influenced by drought stress in non-AMandAMplants. The levels of strigolactones and the expression of corresponding marker genes were affected by both AM symbiosis and drought. The results suggest that AM symbiosis alleviates drought stress by altering the hormonal profiles and affecting plant physiology in the host plant. In addition, a correlation between AM root colonization, strigolactone levels and drought severity is shown, suggesting that under these unfavourable conditions, plants might increase strigolactone production in order to promote symbiosis establishment to cope with the stress.

In response to changes in the reduction state of the plastoquinone pool in its thylakoid membrane, the green alga Chlamydomonas reinhardtti is performing state transitions: remodelling of its thylakoid membrane leads to a redistribution of excitations over photosystems I and II (PSI and PSII). These transitions are accompanied by marked changes in the 77 K fluorescence spectrum, which form the accepted signature of state transitions. The changes are generally thought to reflect a redistribution of light-harvesting complexes (LHCs) over PSII (fluorescing below 700 nm) and PSI (fluorescing above 700 nm). Here we studied the picosecond fluorescence properties of C. reinhardtti over a broad range of wavelengths with very low excitation intensities (0.2 nJ per laser pulse). Cells were directly used for time-resolved fluorescence measurements at 77 K without further treatment, such as medium exchange with glycerol. It is observed that upon going from state 1 (relatively more fluorescence below 700 nm) to state 2 (relatively more fluorescence above 700 nm), a large part of the fluorescence of LHC/PSII becomes substantially quenched in concurrence with LHC detachment from PSII, whereas the absolute amount of PSI fluorescence hardly changes. These results are in agreement with the recent proposal that the amount of LHC moving from PSII to PSI upon going from state 1 to state 2 is rather limited (Unlu et al. Proc Natl Acad Sci USA 111 (9):3460–3465, 2014).

Subcellular monoterpene biosynthesis capacity based on local geranyl diphosphate (GDP) availability or locally boosted GDP production was determined for plastids, cytosol and mitochondria. A geraniol synthase (GES) was targeted to plastids, cytosol, or mitochondria. Transient expression in Nicotiana benthamiana indicated local GDP availability for each compartment but resulted in different product levels. A GDP synthase from Picea abies (PaGDPS1) was shown to boost GDP production. PaGDPS1 was also targeted to plastids, cytosol or mitochondria and PaGDPS1 and GES were coexpressed in all possible combinations. Geraniol and geraniol-derived products were analyzed by GC-MS and LC-MS, respectively. GES product levels were highest for plastid-targeted GES, followed by mitochondrial- and then cytosolic-targeted GES. For each compartment local boosting of GDP biosynthesis increased GES product levels. GDP exchange between compartments is not equal: while no GDP is exchanged from the cytosol to the plastids, 100% of GDP in mitochondria can be exchanged to plastids, while only 7% of GDP from plastids is available for mitochondria. This suggests a direct exchange mechanism for GDP between plastids and mitochondria. Cytosolic PaGDPS1 competes with plastidial GES activity, suggesting an effective drain of isopentenyl diphosphate from the plastids to the cytosol.

The concentration of the lifesaving antimalarial compound artemisinin (AN) in cultivated Artemisia annua (A. annua) plants is relatively low, and thus research in improving the content is important. In the present study, external stress was applied to adult plants of A. annua and the effect was examined on the concentrations of AN and its immediate precursors in leaves, and these concentrations were related to densities and sizes of the glandular trichomes (GT). Plants were stress treated weekly five times by sandblasting or spraying with salicylic acid, chitosan oligosaccharide, H 2O 2, and NaCl solutions. Contents of AN-related compounds (AN-c) were analysed in leaf samples from an upper and a lower position of the plants, and GT were quantified and measured. In lower leaves, several stress treatments had significant negative effects on concentrations of AN-c, whereas the ratios between compounds showed an increased conversion to AN. In the upper leaves, no changes were observed compared to controls. Linear relations were found between the concentrations of metabolites and the density of GT in both upper and lower leaves, and size of GT in lower leaves. Results suggested that older and younger leaves may respond differently to applied stress. A part of the plants were infected by powdery mildew, and this caused significantly different compositions of the AN-c, compared to uninfected plants. In conclusion, changes in concentrations of AN-c seemed largely to be related to changes in GT densities and sizes.

Dormancy is a state of metabolic arrest that facilitates the survival of organisms during environmental conditions incompatible with their regular course of life. Many organisms have deep dormant stages to promote an extended life span (increased longevity). In contrast, plants have seed dormancy and seed longevity described as two traits. Seed dormancy is defined as a temporary failure of a viable seed to germinate in conditions that favor germination, whereas seed longevity is defined as seed viability after dry storage (storability). In plants, the association of seed longevity with seed dormancy has not been studied in detail. This is surprising given the ecological, agronomical, and economic importance of seed longevity. We studied seed longevity to reveal its genetic regulators and its association with seed dormancy in Arabidopsis (Arabidopsis thaliana). Integrated quantitative trait locus analyses for seed longevity, in six recombinant inbred line populations, revealed five loci: Germination Ability After Storage1 (GAAS1) to GAAS5. GAAS loci colocated with seed dormancy loci, Delay Of Germination (DOG), earlier identified in the same six recombinant inbred line populations. Both GAAS loci and their colocation with DOG loci were validated by near isogenic lines. A negative correlation was observed, deep seed dormancy correlating with low seed longevity and vice versa. Detailed analysis on the collocating GAAS5 and DOG1 quantitative trait loci revealed that the DOG1-Cape Verde Islands allele both reduces seed longevity and increases seed dormancy. To our knowledge, this study is the first to report a negative correlation between seed longevity and seed dormancy.

In some species, a crucial role has been demonstrated for the seed endosperm during germination. The endosperm has been shown to integrate environmental cues with hormonal networks that underpin dormancy and seed germination, a process that involves the action of cell wall remodeling enzymes (CWREs). Here, we examine the cell wall architectures of the endosperms of two related Brassicaceae, Arabidopsis (Arabidopsis thaliana) and the close relative Lepidium (Lepidium sativum), and that of the Solanaceous species, tobacco (Nicotiana tabacum). The Brassicaceae species have a similar cell wall architecture that is rich in pectic homogalacturonan, arabinan, and xyloglucan. Distinctive features of the tobacco endosperm that are absent in the Brassicaceae representatives are major tissue asymmetries in cell wall structural components that reflect the future site of radicle emergence and abundant heteromannan. Cell wall architecture of the micropylar endosperm of tobacco seeds has structural components similar to those seen in Arabidopsis and Lepidium endosperms. In situ and biomechanical analyses were used to study changes in endosperms during seed germination and suggest a role for mannan degradation in tobacco. In the case of the Brassicaceae representatives, the structurally homogeneous cell walls of the endosperm can be acted on by spatially regulated CWRE expression. Genetic manipulations of cell wall components present in the Arabidopsis seed endosperm demonstrate the impact of cell wall architectural changes on germination kinetics.

Quantifying gene expression levels is an important research tool to understand biological systems. Reverse transcription-quantitative real-time PCR (RT-qPCR) is the preferred method for targeted gene expression measurements because of its sensitivity and reproducibility. However, normalization, necessary to correct for sample input and reverse transcriptase efficiency, is a crucial step to obtain reliable RT-qPCR results. Stably expressed genes (i.e. genes whose expression is not affected by the treatment or developmental stage under study) are indispensable for accurate normalization of RT-qPCR experiments. Lack of accurate normalization could affect the results and may lead to false conclusions. Since transcriptomes of seeds are different from other plant tissues, we aimed to identify reference genes specifically for RT-qPCR analyses in seeds of two important seed model species, i.e. Arabidopsis and tomato. We mined Arabidopsis seed microarray data to identify stably expressed genes and analyzed these together with putative reference genes from other sources. In total, the expression stability of 24 putative reference genes was validated by RT-qPCR in Arabidopsis seed samples. For tomato, we lacked transcriptome data sets of seeds and therefore we tested the tomato homologs of the reference genes found for Arabidopsis seeds. In conclusion, we identified 14 Arabidopsis and nine tomato reference genes. This provides a valuable resource for accurate normalization of gene expression experiments in seed research for two important seed model species.

Globe artichoke (Cynara cardunculus var. scolymus L., Asteraceae) is a perennial crop traditionally consumed as a vegetable in the Mediterranean countries and rich in nutraceutically and pharmaceutically active compounds, including phenolic and terpenoid compounds. Its bitter taste is caused by its high content of sesquiterpene lactones (STLs), such as cynaropicrin. The biosynthetic pathway responsible for STL biosynthesis in globe artichoke is unknown, but likely proceeds through germacrene A, as has been shown for other Asteraceae species. Here, we investigated the accumulation of cynaropicrin in different tissues of globe artichoke, and compared it to accumulation of phenolic compounds. Cynaropicrin concentration was highest in old leaves. A putative germacrene A synthase (GAS) gene was identified in a set of ~19,000 globe artichoke unigenes. When heterologously expressed in Escherichia coli, the putative globe artichoke GAS converted farnesyl diphosphate (FPP) into (+)-germacrene A. Among various tissues assayed, the level of globe artichoke GAS expression was highest in mature (six week old) leaves. A sequence polymorphism within a mapping population parent allowed the corresponding GAS gene to be positioned on a genetic map. This study reports the isolation, expression and mapping of a key gene involved in STL biosynthesis in C. cardunculus. This is a good basis for further investigation of this pathway.

Summary The rapid increase of ~omics datasets generated by microarray, mass spectrometry and next generation sequencing technologies requires an integrated platform that can combine results from different ~omics datasets to provide novel insights in the understanding of biological systems. MADMAX is designed to provide a solution for storage and analysis of complex ~omics datasets. In addition, analysis results (such as lists of genes) can be merged to reveal candidate genes supported by all datasets. The system constitutes an ISA-Tab compliant LIMS part, which is linked to the different analysis pipelines. A pilot study of different type of ~omics data in Brassica rapa demonstrates the possible use of MADMAX. The web-based user interface provides easy access to data and analysis tools on top of the database.

Phenotypic analyses of two different association panels of tetraploid potato cultivars are presented. Association panels are sets of variously related genotypes assembled for association analysis purposes. The aims of this research were to inspect, analyse and compare two phenotypic data sets, a first step in association mapping analysis. A first panel of 205 contemporary and historical cultivars, selected to represent the commercial potato germplasm pool, was evaluated in two trials in 2006, one on sandy soil and the other on clay soil, both with two replications. It was called the academic panel. Data for the second panel with 299 genotypes were compiled from contributions from five breeding companies and included 66 locations and 18 years. Each of the participating breeding companies contributed data from their clonal selection programmes for 38 advanced breeding clones and a series of standard cultivars. It was called the industrial panel. Variance components for genotypic main effects and genotype-by-environment interactions were calculated, and estimates for the random genotypic main effects were produced. The genotypic main effects for 19 agro-morphological and quality traits were used to study trait by trait correlations within each panel. In addition, for the genotypes shared by both panels, the correlation of genetic main effects between the panels was investigated. The heritability of all traits was high and no large differences were observed between panels. Coefficients of trait variation were highly correlated (r¿=¿0.9) for both panels and trait by trait correlations in both panels showed highly similar patterns. These results demonstrate that a single-year balanced field trial as well as using breeders’ records yields robust phenotypic information that can be used in a genome-wide association study. Issues related to data management and definition of traits are discussed.

In Arabidopsis, a variety of mapping populations have been used for the detection of quantitative trait loci (QTLs) responsible for natural variation. In this study, we present an overview of the advantages and disadvantages of the different types of populations used. To do this, we compare the results of both experimental and natural populations for the commonly analysed trait flowering time. It is expected that genome wide association (GWA) mapping will be an increasingly important tool for QTL mapping because of the high allelic richness and mapping resolution in natural populations. In Arabidopsis, GWA mapping becomes ever more facilitated by the increasing availability of re-sequenced genomes of many accessions. However, specifically designed mapping populations such as recombinant inbred lines and near isogenic lines will remain important. The high QTL detection power of such experimental populations can identify spurious GWA associations, and their unique genomic structure is superior for investigating the role of low-frequency alleles. Future QTL studies will therefore benefit from a combined approach of GWA and classical linkage analysis.

A mutant allele of the transcription factor gene MYB10 from apple induces anthocyanin production throughout the plant. This gene, including its upstream promoter, gene coding region and terminator sequence, was introduced into apple, strawberry and potato plants to determine whether it could be used as a visible selectable marker for plant transformation as an alternative to chemically selectable markers, such as kanamycin resistance. After transformation, red coloured calli, red shoots and red well-growing plants were scored. Red and green shoots were harvested from apple explants and examined for the presence of the MYB10 gene by PCR analysis. Red shoots of apple explants always contained the MYB10 gene but not all MYB10 containing shoots were red. Strawberry plants transformed with the MYB10 gene showed anthocyanin accumulation in leaves and roots. No visible accumulation of anthocyanin could be observed in potato plants grown in vitro, even the ones carrying the MYB10 gene. However, acid methanol extracts of potato shoots or roots carrying the MYB10 gene contained up to four times higher anthocyanin content than control plants. Therefore anthocyanin production as result of the apple MYB10 gene can be used as a selectable marker for apple, strawberry and potato transformation, replacing kanamycin resistance. Electronic supplementary material The online version of this article (doi:10.1007/s11248-011-9490-1) contains supplementary material, which is available to authorized users.

Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop., La lista completa de autores que integran el documento puede consultarse en el archivo., Facultad de Ciencias Exactas

The Brassicaceae family which includes Arabidopsis thaliana, is a natural priority for reaching beyond botanical models to more deeply sample angiosperm genomic and functional diversity. Here we report the draft genome sequence and its annoation of Brassica rapa, one of the two ancestral species of oilseed rape. We modeled 41,174 protein-coding genes in the B. rapa genome. B. rapa has experienced only the second genome triplication reported to date, with its close relationship to A. thaliana providing a useful outgroup for investigating many consequences of triplication for its structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one copy containing a greater proportion of genes expected to have been present in its ancestor (70 percent) than the remaining two (46 percent and 36 percent). Both a generally rapid evolutionary rate, and specific copy number amplifications of particular gene families, may contribute to the remarkable propensity of Brassica species for the development of new morphological variants. The B. rapa genome provides a new resource for comparative and evolutionary analysis of the Brassicaceae genomes and also a platform for genetic improvement of Brassica oil and vegetable crops.

Zinc is an essential micronutrient for all living organisms. When facing a shortage in zinc supply, plants adapt by enhancing the zinc uptake capacity. The molecular regulators controlling this adaptation are not known. We present the identification of two closely related members of the Arabidopsis thaliana basic-region leucine-zipper ( bZIP ) transcription factor gene family, bZIP19 and bZIP23 , that regulate the adaptation to low zinc supply. They were identified, in a yeast-one-hybrid screening, to associate to promoter regions of the zinc deficiency-induced ZIP4 gene of the Zrt- and Irt-related protein (ZIP) family of metal transporters. Although mutation of only one of the bZIP genes hardly affects plants, we show that the bzip19 bzip23 double mutant is hypersensitive to zinc deficiency. Unlike the wild type, the bzip19 bzip23 mutant is unable to induce the expression of a small set of genes that constitutes the primary response to zinc deficiency, comprising additional ZIP metal transporter genes. This set of target genes is characterized by the presence of one or more copies of a 10-bp imperfect palindrome in their promoter region, to which both bZIP proteins can bind. The bZIP19 and bZIP23 transcription factors, their target genes, and the characteristic cis zinc deficiency response elements they can bind to are conserved in higher plants. These findings are a significant step forward to unravel the molecular mechanism of zinc homeostasis in plants, allowing the improvement of zinc bio-fortification to alleviate human nutrition problems and phytoremediation strategies to clean contaminated soils.

Single nucleotide polymorphisms (SNPs) represent the most abundant type of genetic variation that can be used as molecular markers. The SNPs that are hidden in sequence databases can be unlocked using bioinformatic tools. For efficient application of these SNPs, the sequence set should be error-free as much as possible, targeting single loci and suitable for the SNP scoring platform of choice. We have developed a pipeline to effectively mine SNPs from public EST databases with or without quality information using QualitySNP software, select reliable SNP and prepare the loci for analysis on the Illumina GoldenGate genotyping platform. The applicability of the pipeline was demonstrated using publicly available potato EST data, genotyping individuals from two diploid mapping populations and subsequently mapping the SNP markers (putative genes) in both populations. Over 7000 reliable SNPs were identified that met the criteria for genotyping on the GoldenGate platform. Of the 384 SNPs on the SNP array approximately 12% dropped out. For the two potato mapping populations 165 and 185 SNPs segregating SNP loci could be mapped on the respective genetic maps, illustrating the effectiveness of our pipeline for SNP selection and validation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-009-9377-5) contains supplementary material, which is available to authorized users.

Twenty-five years ago, Arabidopsis thaliana emerged as the model organism of choice for research in plant biology. A consensus was reached about the need to focus on a single organism to integrate the classical disciplines of plant science with the expanding fields of genetics and molecular biology. Ten years after publication of its genome sequence, Arabidopsis remains the standard reference plant for all of biology. We reflect here on the major advances and shared resources that led to the extraordinary growth of the Arabidopsis research community. We also underscore the importance of continuing to expand and refine our detailed knowledge of Arabidopsis while seeking to appreciate the remarkable diversity that characterizes the plant kingdom

Plants display enormous diversity in their metabolism. Although the biosynthesis and function of the myriads of plant metabolites has been studied for decades, we have little understanding of the interactions between metabolites, metabolite signaling, interactions with development and the role of metabolism in genotype-to-phenotype relationships. Technologies for the analysis of metabolites have made tremendous progress in recent years, both in terms of the number of metabolites that are identified and of throughput. Recent developments allow the construction of metabolic networks, and study of the role of these networks in plant growth and development. In this review, we discuss what types of information can be obtained from measurements of metabolites and what requirements they have with respect comprehensiveness of coverage and precision of identification and quantification, and outline procedures that can be implemented to validate the measurements. We then discuss what sorts of perturbations can be used to disturb metabolic networks, including environmental and physiological treatments, chemicals, reverse genetics and the use of natural genetic diversity.

Metabolomics is a fast developing field of comprehensive untargeted chemical analyses. It has many applications and can in principle be used on any organism without prior knowledge of the metabolome or genome. The amount of functional information that is acquired with metabolomics largely depends on whether a metabolome database has been developed for the focal species. Metabolomics is a level downstream from transcriptomics and proteomics and has been widely advertised as a functional genomics and systems biology tool. Indeed, it has been successfully applied to link phenotypes to genotypes in the model plant Arabidopsis thaliana. Metabolomics is also increasingly being used in ecology (ecological metabolomics) and environmental sciences (environmental metabolomics). In ecology, the technique has led to novel insights into the mechanisms of plant resistance to herbivores. Some of the most commonly used analytical metabolomic platforms are briefly discussed in this review, as well as their limitations. We will mainly focus on the application of metabolomics in plant ecology and genetics.

Timing of germination is presumably under strong natural selection as it determines the environmental conditions in which a plant germinates and initiates its postembryonic life cycle. To investigate how seed dormancy is controlled, quantitative trait loci (QTL) analyses has been performed in six Arabidopsis thaliana recombinant inbred line populations by analyzing them simultaneously using a mixed model QTL approach. The recombinant inbred line populations were derived from crosses between the reference accession Landsberg erecta (Ler) and accessions fromdifferentworld regions. In total, 11 delay of germination (DOG) QTL have been identified, and nine of them have been confirmed by near isogenic lines (NILs). The absence of strong epistatic interactions between the different DOG loci suggests that they affect dormancy mainly by distinct genetic pathways. This was confirmed by analyzing the transcriptome of freshly harvested dry seeds of five different DOG NILs. All five DOG NILs showed discernible and different expression patterns compared with the expression of their genetic background Ler. The genes identified in the different DOG NILs represent largely different gene ontology profiles. It is proposed that natural variation for seed dormancy in Arabidopsis is mainly controlled by different additive genetic and molecular pathways rather than epistatic interactions, indicating the involvement of several independent pathways., L.B. was supported by grants from The Earth and Life Sciences Foundation subsidized by the Netherlands Organization for Scientific Research. F.v.E. and P.K. were supported by the Generation Challenge Program (Molecular Breeding Platform activity 2.2.1) and the Centre of BioSystems Genomics (Projects BB9 and BB12).

The rise in ultraviolet-B (UV-B) (280-315 nm) radiation levels, that is a consequence of stratospheric ozone layer depletion, has triggered extensive research on the effects of UV-B on plants. Plants raised under natural sunlight conditions are generally well protected from the potentially harmful effects of UV-B radiation. However, it is mostly unknown to which extent UV protection is constitutive and/or induced. In this study, we have analysed the role of constitutive and inducible protection responses in avoiding UV-B damage to photosystem II of photosynthesis. We have assayed the UV susceptibility of photosystem II in 224 Arabidopsis thaliana accessions from across the Northern hemisphere, and found a continuum of constitutive UV-protection levels, with some accessions being UV sensitive and others UV tolerant. Statistical analysis showed only very weak associations between constitutive UV tolerance and the geographic origin of accessions. Instead, most of the variance in constitutive UV-B protection of photosynthesis is present at the level of local Arabidopsis populations originating in the same geographic and climatic area. The variance in constitutive UV protection is, however, small compared to the amplitude of environmentally induced changes in UV protection. Thus, our data emphasise the importance of inducible responses for the protection of photosystem II against UV-B. Remarkably, the conditions that induce UV-protective responses vary; accessions from lower latitudes were found to switch-on UV defences more readily than those of higher latitudes. Such altered regulation of induction may comprise a suitable adaptation response when levels of a stressor are fluctuating in the short term, but predictable over longer periods.

Arabidopsis thaliana natural variation was used to study plant performance viewed as the accumulation of photo-assimilates, their allocation and storage, in relation to other growth-related features and flowering-related traits. Quantitative trait locus (QTL) analysis using recombinant inbred lines derived from the cross between Landsberg erecta (originating from Poland) and Kondara (originating from Tajikistan) grown on hydroponics, revealed QTLs for the different aspects of plant growth-related traits, sugar and starch contents and flowering-related traits. Co-locations of QTLs for these different aspects were detected at different regions, mainly at the ER locus; the top of chromosomes 3, 4 and 5; and the bottom of chromosome 5. Increased plant growth was associated with early flowering and leaf transitory starch, and correlated negatively with the levels of soluble sugar at early phases of development. From the significant correlations and the co-locations of the QTLs for these aspects, we conclude that there is a complex relationship between plant growth-related traits, carbohydrate content and flowering-related traits.

A Brassica rapa collection of 239 accessions, based on two core collections representing different morphotypes from different geographical origins, is presented and its use for association mapping is illustrated for flowering time. We analyzed phenotypic variation of leaf and seed pod traits, plant architecture, and flowering time using data collected from three field experiments and evaluated the genetic diversity with a set of SSR markers. The Wageningen University and Research Centre (WUR) and the Vavilov Research Institute of Plant Industry (VIR) core collections had similar representations of most morphotypes, as illustrated by the phenotypic and genetic variation within these groups. The analysis of population structure revealed five subgroups in the collection, whereas previous studies of the WUR core collection indicated four subgroups; the fifth group identified consisted mainly of oil accessions from the VIR core collection, winter oils from Pakistan, and a number of other types. A very small group of summer oils is described, that is not related to other oil accessions. A candidate gene approach was chosen for association mapping of flowering time with a BrFLC1 biallelic CAPS marker and a BrFLC2 multiallelic SSR marker. The two markers were significantly associated with flowering time, but their effects were confined to certain morphotypes and (or) alleles. Based on these results, we discuss the optimal design for an association mapping population and the need to fix the heterogeneous accessions to facilitate phenotyping and genotyping.

Over the past few decades seed physiology research has contributed to many important scientific discoveries and has provided valuable tools for the production of high quality seeds. An important instrument for this type of research is the accurate quantification of germination; however gathering cumulative germination data is a very laborious task which is often prohibitive to the execution of large experiments. In this paper we present the Germinator package: a simple, highly cost efficient and flexible procedure for high-throughput automatic scoring and evaluation of germination that can be implemented without the use of complex robotics. The Germinator package contains three modules; 1) design of experimental setup with various options to replicate and randomize samples; 2) automatic scoring of germination based on the color contrast between the protruding radicle and seed coat on a single image; 3) curve fitting of cumulative germination data and the extraction, recap and visualization of the various germination parameters. The curve fitting module enables analysis of general cumulative germination data and can be used for all plant species. We show that the automatic scoring system works for Arabidopsis thaliana and Brassica spp. seeds, but is likely to be applicable to other species, as well. In this paper we show the accuracy, reproducibility and flexibility of the Germinator package. We have successfully applied it to evaluate natural variation for salt tolerance in a large population of Recombinant Inbred Lines (RIL) and were able to identify several QTL for salt tolerance. Germinator is a low-cost package that allows the monitoring of several thousands of germination tests, several times a day by a single person.

This work reports for the first time the identification of the major compounds of Pinguicula lusitanica, an endangered carnivorous plant species, using minimal amounts of plant material. A methanol extract was prepared from in vitro cultured plantlets and analyzed by HPLC-SPE-NMR/HPLC-MS. Three iridoid and five caffeoyl phenylethanoid glycosides were identified. These groups of natural compounds were previously reported in the Lentibulariaceae family and have been used as chemotaxonomic markers in related families. (C) 2009 Elsevier Ltd. All rights reserved.

Contains fulltext : 79928scheenen.pdf (Publisher’s version ) (Closed access) Nuclear magnetic resonance imaging (MRI) is a non-destructive and non-invasive technique that can be used to acquire two- or even three-dimensional images of intact plants. The information within the images can be manipulated and used to study the dynamics of plant water relations and water transport in the stem, e.g., as a function of environmental (stress) conditions. Non-spatially resolved portable NMR is becoming available to study leaf water content and distribution of water in different (sub-cellular) compartments. These parameters directly relate to stomatal water conductance, CO(2) uptake, and photosynthesis. MRI applied on plants is not a straight forward extension of the methods discussed for (bio)medical MRI. This educational review explains the basic physical principles of plant MRI, with a focus on the spatial resolution, factors that determine the spatial resolution, and its unique information for applications in plant water relations that directly relate to plant photosynthetic activity.

In order to establish the underlying structure-dependent principles of instant cooking rice, a detailed investigation was carried out on rice kernels that were processed in eight different manners. Milling, parboiling, wet-processing and extrusion were applied, with and without a subsequent puffing treatment. The mesostructure of the rice kernels was examined by DSC and XRD, and the microstructure by μ-CT. Hydration behaviour during cooking was studied by MRI in a real-time manner. Based on simple descriptive models, three different classes of cooking behaviour can be discerned. The water ingress profiles during cooking of these three classes matched well with simulations from a model that was based on water demand of the starch mass and the porous microstructure of the kernels. Thus a clear correlation between meso/microstructure of a rice kernel and the cooking behaviour has been established.

The efficiency of photosynthetic light energy conversion depends largely on the molecular architecture of the photosynthetic membranes. Linear- and circular-dichroism (LD and CD) studies have contributed significantly to our knowledge of the molecular organization of pigment systems at different levels of complexity, in pigment–protein complexes, supercomplexes, and their macroassemblies, as well as in entire membranes and membrane systems. Many examples show that LD and CD data are in good agreement with structural data; hence, these spectroscopic tools serve as the basis for linking the structure of photosynthetic pigment–protein complexes to steady-state and time-resolved spectroscopy. They are also indispensable for identifying conformations and interactions in native environments, and for monitoring reorganizations during photosynthetic functions, and are important in characterizing reconstituted and artificially constructed systems. This educational review explains, in simple terms, the basic physical principles, and theory and practice of LD and CD spectroscopies and of some related quantities in the areas of differential polarization spectroscopy and microscopy. Electronic supplementary material The online version of this article (doi:10.1007/s11120-009-9424-4) contains supplementary material, which is available to authorized users.

The topology of the long N-terminal domain (similar to 100 amino-acid residues) of the photosynthetic Lhc CP29 was studied using electron spin resonance. Wild-type protein containing a single cysteine at position 108 and nine single-cysteine mutants were produced, allowing to label different parts of the domain with a nitroxide spin label. In all cases, the apoproteins were either solubilized in detergent or they were reconstituted with their native pigments (holoproteins) in vitro. The spin-label electron spin resonance spectra were analyzed in terms of a multicomponent spectral simulation approach, based on hybrid evolutionary optimization and solution condensation. These results permit to trace the structural organization of the long N-terminal domain of CP29. Amino-acid residues 97 and 108 are located in the transmembrane pigment-containing protein body of the protein. Positions 65, 81, and 90 are located in a flexible loop that is proposed to extend out of the protein from the stromal surface. This loop also contains a phosphorylation site at Thr81, suggesting that the flexibility of this loop might play a role in the regulatory mechanisms of the light-harvesting process. Positions 4, 33, 40, and 56 are found to be located in a relatively rigid environment, close to the transmembrane protein body. On the other hand, position 15 is located in a flexible region, relatively far away from the transmembrane domain.

The regulation of mineral accumulation in plants is genetically complex, with several genetic loci involved in the control of one mineral and loci affecting the accumulation of different minerals. To investigate the role of growth medium and organ type on the genetics of mineral accumulation, two existing (Ler×Kond, Ler×An-1) and one new (Ler×Eri-1) Arabidopsis thaliana Recombinant Inbred Line populations were raised on soil and hydroponics as substrates. Seeds, roots, and/or rosettes were sampled for the determination of their Ca, Fe, K, Mg, Mn, P or Zn concentrations. For seeds only, the concentration of phytate (IP6), a strong chelator of seed minerals, was determined. Correlations between minerals/IP6, populations, growth conditions, and organs were determined and mineral/IP6 concentration data were used to identify quantitative trait loci (QTLs) for these traits. A striking difference was found between QTLs identified for soil-grown versus hydroponics-grown populations and between QTLs identified for different plant organs. Three common QTLs were identified for several populations, growth conditions, and organs, one of which corresponded to the ERECTA locus, variation of which has a strong effect on plant morphology.