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1.  Population genetic structure of two Medicago species shaped by distinct life form, mating system and seed dispersal 
Annals of Botany  2009;103(6):825-834.
Background and Aims
Life form, mating system and seed dispersal are important adaptive traits of plants. In the first effort to characterize in detail the population genetic structure and dynamics of wild Medicago species in China, a population genetic study of two closely related Medicago species, M. lupulina and M. ruthenica, that are distinct in these traits, are reported. These species are valuable germplasm resources for the improvement of Medicago forage crops but are under threat of habitat destruction.
Three hundred and twenty-eight individuals from 16 populations of the annual species, M. lupulina, and 447 individuals from 15 populations of the perennial species, M. ruthenica, were studied using 15 and 17 microsatellite loci, respectively. Conventional and Bayesian-clustering analyses were utilized to estimate population genetic structure, mating system and gene flow.
Key Results
Genetic diversity of M. lupulina (mean HE = 0·246) was lower than that of M. ruthenica (mean HE = 0·677). Populations of M. lupulina were more highly differentiated (FST = 0·535) than those of M. ruthenica (FST = 0·130). For M. lupulina, 55·5 % of the genetic variation was partitioned among populations, whereas 76·6 % of the variation existed within populations of M. ruthenica. Based on the genetic data, the selfing rates of M. lupulina and M. ruthenica were estimated at 95·8 % and 29·5 %, respectively. The genetic differentiation among populations of both species was positively correlated with geographical distance.
The mating system differentiation estimated from the genetic data is consistent with floral morphology and observed pollinator visitation. There was a much higher historical gene flow in M. ruthenica than in M. lupulina, despite more effective seed dispersal mechanisms in M. lupulina. The population genetic structure and geographical distribution of the two Medicago species have been shaped by life form, mating systems and seed dispersal mechanisms.
PMCID: PMC2707894  PMID: 19174379
Medicago lupulina; Medicago ruthenica; microsatellite; genetic diversity; gene flow; forage legume
2.  Magnitude and Timing of Leaf Damage Affect Seed Production in a Natural Population of Arabidopsis thaliana (Brassicaceae) 
PLoS ONE  2012;7(1):e30015.
The effect of herbivory on plant fitness varies widely. Understanding the causes of this variation is of considerable interest because of its implications for plant population dynamics and trait evolution. We experimentally defoliated the annual herb Arabidopsis thaliana in a natural population in Sweden to test the hypotheses that (a) plant fitness decreases with increasing damage, (b) tolerance to defoliation is lower before flowering than during flowering, and (c) defoliation before flowering reduces number of seeds more strongly than defoliation during flowering, but the opposite is true for effects on seed size.
Methodology/Principal Findings
In a first experiment, between 0 and 75% of the leaf area was removed in May from plants that flowered or were about to start flowering. In a second experiment, 0, 25%, or 50% of the leaf area was removed from plants on one of two occasions, in mid April when plants were either in the vegetative rosette or bolting stage, or in mid May when plants were flowering. In the first experiment, seed production was negatively related to leaf area removed, and at the highest damage level, also mean seed size was reduced. In the second experiment, removal of 50% of the leaf area reduced seed production by 60% among plants defoliated early in the season at the vegetative rosettes, and by 22% among plants defoliated early in the season at the bolting stage, but did not reduce seed output of plants defoliated one month later. No seasonal shift in the effect of defoliation on seed size was detected.
The results show that leaf damage may reduce the fitness of A. thaliana, and suggest that in this population leaf herbivores feeding on plants before flowering should exert stronger selection on defence traits than those feeding on plants during flowering, given similar damage levels.
PMCID: PMC3261866  PMID: 22276140
3.  The activity of SnRK1 is increased in Phaseolus vulgaris seeds in response to a reduced nutrient supply 
Phaseolus vulgaris seeds can grow and develop at the expense of the pod reserves after the fruits have been removed from the plant (Fountain etal., 1989). Because this process involves sensing the reduction of nutrients and the remobilisation of pod reserves, we investigated the effect on sucrose non-fermenting related kinase 1 (SnRK1) activity during this process. Bean fruits removed from the plant at 20 days after flowering (DAF) demonstrated active remobilisation of nutrients from the pod to the seeds. After 5 days, the pod dry weight was reduced by 50%. The process was characterized by a rapid degradation of starch, with the greatest decrease observed on day 1 after the fruits were removed. The pod nutrients were insufficient for the needs of all the seeds, and only some seeds continued their development. Those seeds exhibited a transient reduction in sucrose levels on day 1 after the fruits were removed. However, the normal level of sucrose was recovered, and the rate of starch synthesis was identical to that of a seed developed under normal conditions. Removing the fruits from the plant had no effect on the activity of SnRK1 in the pods, whereas in the seeds, the activity was increased by 35%. Simultaneously, a large reduction in seed sucrose levels was observed. The increase in SnRK1 activity was observed in both the cotyledon and embryo axes, but it was higher in the cotyledon. At 20–25 DAF, cotyledons actively accumulate storage materials. It is possible that the increase in SnRK1 activity observed in seeds developed in fruits that have been removed from the plant is part of the mechanism required for nutrient remobilisation under conditions of stress.
PMCID: PMC4030202  PMID: 24860586
nutrient remobilisation; SnRK1; bean seed development
4.  Inherited variability in multiple traits determines fitness in populations of an annual legume from contrasting latitudinal origins 
Annals of Botany  2009;103(8):1279-1289.
Background and Aims
Variation in fitness depends on corresponding variation in multiple traits which have both genetically controlled and plastic components. These traits are subjected to varying degrees of local adaptation in specific populations and, consequently, are genetically controlled to different extents. In this study it is hypothesized that modulation of different traits would have contrasting relevance for the fitness of populations of diverse origins. Specifically, assuming that environmental pressures vary across a latitudinal gradient, it is suggested that inherited variation in traits differentially determines fitness in annual Lupinus angustifolius populations from contrasting latitudinal origins in western Spain.
Seeds of L. angustifolius from three contrasting origins were grown in a common garden. Traits related to more plastic vegetative growth and more genetically conserved phenology were measured, together with estimates of reproductive success. Fitness was estimated by the number of viable seeds per plant. Structural Equation Models were used to infer causal relationships among multiple traits and fitness, separating the direct and indirect effects of morphological, phenological and reproductive traits.
Key Results
Phenological, vegetative and reproductive traits accounted for most of the fitness variation. Fitness was highest in plants of southernmost origin, mainly due to earlier flowering. Fitness within each seed origin was controlled by variation in different traits. Southern origin plants that grew to a larger size achieved higher fitness. However, plant size in plants of northernmost origin was irrelevant, but early flowering promoted higher fitness. Variation in fruit and seed set had a greater effect on the fitness of plants of central origin than phenological and size variation.
It is concluded that modulation of a functional trait can be relevant to fitness in a given population (i.e. affecting intensity and direction), but irrelevant in other populations. This points to the need to consider integrated phenotypes when trying to unravel local adaptation effects over single traits.
PMCID: PMC2685322  PMID: 19318383
Lupinus; Structural Equation Models; fitness; phenology; functional traits; reproductive success; SLA; seed size
5.  Acorn cotyledons are larger than their seedlings' need: evidence from artificial cutting experiments 
Scientific Reports  2015;5:8112.
Although the consequences of cotyledon removal have been widely studied in oaks producing large acorns, we have little knowledge of at what level cotyledons can be removed without affecting acorn survival and seedling development. In this study, we aimed to test the hypothesis that the amount of energy reserves in cotyledons is more than the demands of seedlings and that large acorns can tolerate seed predation and/or attract seed predators for seed dispersal. Acorn germination rates were not affected even when 60% of cotyledons were cut off at the basal end, suggesting that the energy reserves contained in cotyledons are not essential for acorn survival. Post-cut acorn mass, more than initial acorn mass, appear to be a better predictor of seedling performance, indicating that the energy reserves in cotyledons are sufficient for seedlings. Acorns with large masses sustained cotyledon damage better than small ones with respect to seedling performance. Large acorns were more likely to be dispersed and cached by animals, implying that producing large acorns is more important for oaks to manipulate seed predators and dispersers rather than provide a seedling with cotyledonary reserves.
PMCID: PMC4309963  PMID: 25630843
6.  Germination Season and Watering Regime, but Not Seed Morph, Affect Life History Traits in a Cold Desert Diaspore-Heteromorphic Annual 
PLoS ONE  2014;9(7):e102018.
Seed morph, abiotic conditions and time of germination can affect plant fitness, but few studies have tested their combined effects on plasticity of plant life history traits. Thus, we tested the hypothesis that seed morph, germination season and watering regime influence phenotypic expression of post-germination life history traits in the diaspore-heteromorphic cold desert winter annual/spring ephemeral Diptychocarpus strictus. The two seed morphs were sown in watered and non-watered plots in late summer, and plants derived from them were watered or not-watered throughout the study. Seed morph did not affect phenology, growth and morphology, survival, dry mass accumulation and allocation or silique and seed production. Seeds in watered plots germinated in autumn (AW) and spring (SW) but only in spring for non-watered plots (SNW). A high percentage of AW, SW and SNW plants survived and reproduced, but flowering date and flowering period of autumn- vs. spring-germinated plants differed. Dry mass also differed with germination season/watering regime (AW > SW > SNW). Number of siliques and seeds increased with plant size (AW > SW > SNW), whereas percent dry mass allocated to reproduction was higher in small plants: SNW > SW > AW. Thus, although seed morph did not affect the expression of life history traits, germination season and watering regime significantly affected phenology, plant size and accumulation and allocation of biomass to reproduction. Flexibility throughout the life cycle of D. strictus is an adaptation to the variation in timing and amount of rainfall in its cold desert habitat.
PMCID: PMC4094427  PMID: 25013967
7.  Effects of pollination limitation and seed predation on female reproductive success of a deceptive orchid 
AoB Plants  2014;6:plu031.
This research examines the contribution of plant height, number of flowers, number of stems, as well the joint impacts of mutualists and antagonists on the pollination biology and seed production of the imperiled, deceptive orchid, Cypripedium candidum. We found flowering stem height to be the only morphological feature significant in reproduction, with taller flowering stems simultaneously receiving increased pollination and decreased seed predation. Furthermore we found decreased seed mass in individuals subjected to hand-self pollination treatments. Our results may help explain the factors limiting seed production in other Cypripedium and further emphasize the importance of management in orchid conservation.
For many species of conservation significance, multiple factors limit reproduction. This research examines the contributions of plant height, number of flowers, number of stems, pollen limitation and seed predation to female reproductive success in the deceit-pollinated orchid, Cypripedium candidum. The deceptive pollination strategy employed by many orchids often results in high levels of pollen limitation. While increased floral display size may attract pollinators, C. candidum's multiple, synchronously flowering stems could promote selfing and also increase attack by weevil seed predators. To understand the joint impacts of mutualists and antagonists, we examined pollen limitation, seed predation and the effects of pollen source over two flowering seasons (2009 and 2011) in Ohio. In 2009, 36 pairs of plants size-matched by flower number, receiving either supplemental hand or open pollination, were scored for fruit maturation, mass of seeds and seed predation. Pollen supplementation increased proportion of flowers maturing into fruit, with 87 % fruit set when hand pollinated compared with 46 % for naturally pollinated flowers. Inflorescence height had a strong effect, as taller inflorescences had higher initial fruit set, while shorter stems had higher predation. Seed predation was seen in 73 % of all fruits. A parallel 2011 experiment that included a self-pollination treatment and excluded seed predators found initial and final fruit set were higher in the self and outcross pollination treatments than in the open-pollinated treatment. However, seed mass was higher in both open pollinated and outcross pollination treatments compared with hand self-pollinated. We found greater female reproductive success for taller flowering stems that simultaneously benefited from increased pollination and reduced seed predation. These studies suggest that this species is under strong reinforcing selection to increase allocation to flowering stem height. Our results may help explain the factors limiting seed production in other Cypripedium and further emphasize the importance of management in orchid conservation.
PMCID: PMC4094650  PMID: 24916060
Conservation; orchid; plant reproduction; plant–insect interactions; pollen limitation; pollination ecology; reproductive trade-offs; seed predation; supplemental pollination.
8.  Implications of a long-term, pollinator-mediated selection on floral traits in a generalist herb 
Annals of Botany  2009;104(4):689-701.
Background and Aims
The phenotypic selection of a diverse insect assemblage was studied on a generalist plant species (Paeonia broteroi) in ten flowering seasons, with tests for whether visitor preferences for plants with larger flowers eventually translated into significant differences among plants in visitation rates, seed production, seed mass, seed germination and seedling survival.
Selection gradients were used to assess if selection on flower size contributed to explain differences in visitation rates, seed production and seed mass. First, independent analyses were carried out for each season; then for the ten season as a whole. Seedling emergence and survival were assessed by generalized linear models.
Key Results
Directional selection was found on flower size through visitation rates and seed production, and stabilizing selection through seed mass. Thus, larger flowers were more visited, and produced more, but lighter seeds, than smaller flowers. The results suggest a conflicting selection on flower size through seed number and size. Floral integration found in the study populations was larger than that in populations of a distant region. Finally, seed size did not influence seedling emergence and survival; thus, any advantages of seed size may be constrained under natural conditions before plants become reproductive individuals.
Plants with larger flowers may be benefited by producing more lighter seeds than fewer heavier ones, as they may contribute disproportionately to the seed bank, and have better chances that any descendant could eventually recruit. However, it seems unlikely that differences in flower size and integration found among populations in different regions could have been originated by rapid evolutionary change. First, because of the conflicting selection described; second, because of the remarkably low seedling survival found under natural conditions. Consequently, the influence of pollinator selection alone does not seem to explain differences in flower size and integration.
PMCID: PMC2729625  PMID: 19508980
Paeonia broteroi; long-term selection; conflicting selection; flower size; seed production; generalist pollination
9.  Differences in Plastic Responses to Defoliation due to Variation in the Timing of Treatments for Two Species of Sesbania (Fabaceae) 
Annals of Botany  2005;95(6):1049-1058.
• Background and Aims Plastic responses to stress in components of reproduction can have important effects on plant fitness and can vary both within and between species. Responses may also depend on when in the life cycle stress occurs. Here, it is predicted that the timing of initiation of a stress, defoliation, would affect the pattern of plastic responses. These differences should occur because some components of reproduction, such as flower number, are determined earlier in a plant's life than others, such as individual seed mass.
• Methods To test this prediction, 50 % artificial defoliation treatments were initiated at four different times for Sesbania macrocarpa and S. vesicaria. Responses were measured in plant size, number of flowers, number of flowers/plant size, fruit set, number of seeds per fruit, individual seed mass and total seed mass per plant.
• Key Results For S. vesicaria, changes in the timing of stress changed the severity, but not the pattern of response. For S. macrocarpa, plastic responses to defoliation varied strikingly between early and late treatments. Late treatments resulted in over-compensation in this species. Sesbania macrocarpa was generally more plastic than S. vesicaria and the species showed opposite responses for most components of reproduction.
• Conclusions While there were effects of timing of defoliation and differences between species, the nature of these effects did not precisely fit our predictions. Our results suggest that differences in the length and flexibility of the life cycles of the two species allowed for unexpected variation in responses. For example, because flower production continued after the last treatment in S. vesicaria, responses were not constrained to reductions in individual seed mass.
PMCID: PMC4246763  PMID: 15753116
Phenotypic plasticity; components of reproduction; artificial defoliation; reproductive allocation; overcompensation; Sesbania macrocarpa; Sesbania vesicaria
10.  Role of Seed Coat in Imbibing Soybean Seeds Observed by Micro-magnetic Resonance Imaging 
Annals of Botany  2008;102(3):343-352.
Background and Aims
Imbibition of Japanese soybean (Glycine max) cultivars was studied using micro-magnetic resonance imaging (MRI) in order to elucidate the mechanism of soaking injury and the protective role of the seed coat.
Time-lapse images during water uptake were acquired by the single-point imaging (SPI) method at 15-min intervals, for 20 h in the dry seed with seed coat, and for 2 h in seeds with the seed coat removed. The technique visualized water migration within the testa and demonstrated the distortion associated with cotyledon swelling during the very early stages of water uptake.
Key Results
Water soon appeared in the testa and went around the dorsal surface of the seed from near the raphe, then migrated to the hilum region. An obvious protrusion was noted when water reached the hypocotyl and the radicle, followed by swelling of the cotyledons. A convex area was observed around the raphe with the enlargement of the seed. Water was always incorporated into the cotyledons from the abaxial surfaces, leading to swelling and generating a large air space between the adaxial surfaces. Water uptake greatly slowed, and the internal structures, veins and oil-accumulating tissues in the cotyledons developed after the seed stopped expanding. When the testa was removed from the dry seeds before imbibition, the cotyledons were severely damaged within 1·5 h of water uptake.
The activation of the water channel seemed unnecessary for water entry into soybean seeds, and the testa rapidly swelled with steeping in water. However, the testa did not regulate the water incorporation in itself, but rather the rate at which water encountered the hypocotyl, the radicle, and the cotyledons through the inner layer of the seed coat, and thus prevented the destruction of the seed tissues at the beginning of imbibition.
PMCID: PMC2516911  PMID: 18565982
Dry seeds; Glycine max; MRI; seed coat; soaking injury; soybean; testa; role of inner layer of seed coat; water uptake
11.  Sexual Dimorphism of Staminate- and Pistillate-Phase Flowers of Saponaria officinalis (Bouncing Bet) Affects Pollinator Behavior and Seed Set 
PLoS ONE  2014;9(4):e93615.
The sequential separation of male and female function in flowers of dichogamous species allows for the evolution of differing morphologies that maximize fitness through seed siring and seed set. We examined staminate- and pistillate-phase flowers of protandrous Saponaria officinalis for dimorphism in floral traits and their effects on pollinator attraction and seed set. Pistillate-phase flowers have larger petals, greater mass, and are pinker in color, but due to a shape change, pistillate-phase flowers have smaller corolla diameters than staminate-phase flowers. There was no difference in nectar volume or sugar content one day after anthesis, and minimal evidence for UV nectar guide patterns in staminate- and pistillate-phase flowers. When presented with choice arrays, pollinators discriminated against pistillate-phase flowers based on their pink color. Finally, in an experimental garden, in 2012 there was a negative correlation between seed set of an open-pollinated, emasculated flower and pinkness (as measured by reflectance spectrometry) of a pistillate-phase flower on the same plant in plots covered with shade cloth. In 2013, clones of genotypes chosen from the 2012 plants that produced pinker flowers had lower seed set than those from genotypes with paler flowers. Lower seed set of pink genotypes was found in open-pollinated and hand-pollinated flowers, indicating the lower seed set might be due to other differences between pink and pale genotypes in addition to pollinator discrimination against pink flowers. In conclusion, staminate- and pistillate-phase flowers of S. officinalis are dimorphic in shape and color. Pollinators discriminate among flowers based on these differences, and individuals whose pistillate-phase flowers are most different in color from their staminate-phase flowers make fewer seeds. We suggest morphological studies of the two sex phases in dichogamous, hermaphroditic species can contribute to understanding the evolution of sexual dimorphism in plants without the confounding effects of genetic differences between separate male and female individuals.
PMCID: PMC3972141  PMID: 24690875
12.  The Role of the Storage Carbon of Cotyledons in the Establishment of Seedlings of Hymenaea courbaril Under Different Light Conditions 
Annals of Botany  2004;94(6):819-830.
• Background and Aims Hymenaea courbaril (Leguminosae-Caesalpinioideae) is a tree species with wide distribution through all of the Neotropics. It has large seeds (approx. 5 g) with non-photosynthetic storage cotyledons rich (40 %) in a cell wall polysaccharide (xyloglucan) as a carbon reserve. Because it is found in the understorey of tropical forests, it has been considered as a shade-tolerant, late-secondary species. However, the physiological mechanisms involved in seedling establishment, especially regarding the interplay between storage and light intensity, are not understood. In this work, the ecophysiological role of this carbon cotyledon reserve (xyloglucan) is characterized, emphasizing its effects on seedling growth and development during the transition from heterotrophy to autotrophy under different light conditions.
• Methods Seedlings of H. courbaril were grown in environments with different light intensities, and with or without cotyledons detached before xyloglucan mobilization. Development, growth, photosynthesis and carbon partitioning (dry mass and [14C]sucrose) were analysed in each treatment.
• Key Results The detachment of cotyledons was not important for seedling survival, but resulted in a strong restriction (50 % less) of shoot growth, which was the main sink for the cotyledon carbon reserves. Carbon restriction promoted an early maturation of the photosynthetic apparatus without changes in the net CO2 fixation per unit area. The reduced surface area of the first leaves in seedlings without cotyledons was evidence of limited growth and development of seedlings in low light conditions (22 µmol m−2 s−1 photon flux).
• Conclusions There is an increase in the importance of storage xyloglucan in cotyledons for H. courbaril seedling development as light intensity decreases, confirming that this polymer plays a key role in the adaptation of this species to establish successfully in the shadowed understorey of the forest.
PMCID: PMC4242276  PMID: 15514028
Carbon partitioning; forest; light; growth; cell wall; Hymenaea courbaril; photosynthesis; seedling; xyloglucan; storage
13.  Herbivore and Fungal Pathogen Exclusion Affects the Seed Production of Four Common Grassland Species 
PLoS ONE  2010;5(8):e12022.
Insect herbivores and fungal pathogens can independently affect plant fitness, and may have interactive effects. However, few studies have experimentally quantified the joint effects of insects and fungal pathogens on seed production in non-agricultural populations. We examined the factorial effects of insect herbivore exclusion (via insecticide) and fungal pathogen exclusion (via fungicide) on the population-level seed production of four common graminoid species (Andropogon gerardii, Schizachyrium scoparium, Poa pratensis, and Carex siccata) over two growing seasons in Minnesota, USA. We detected no interactive effects of herbivores and pathogens on seed production. However, the seed production of all four species was affected by either insecticide or fungicide in at least one year of the study. Insecticide consistently doubled the seed production of the historically most common species in the North American tallgrass prairie, A. gerardii (big bluestem). This is the first report of insect removal increasing seed production in this species. Insecticide increased A. gerardii number of seeds per seed head in one year, and mass per seed in both years, suggesting that consumption of flowers and seed embryos contributed to the effect on seed production. One of the primary insect species consuming A. gerardii flowers and seed embryos was likely the Cecidomyiid midge, Contarinia wattsi. Effects on all other plant species varied among years. Herbivores and pathogens likely reduce the dispersal and colonization ability of plants when they reduce seed output. Therefore, impacts on seed production of competitive dominant species may help to explain their relatively poor colonization abilities. Reduced seed output by dominant graminoids may thereby promote coexistence with subdominant species through competition-colonization tradeoffs.
PMCID: PMC2920334  PMID: 20711408
14.  LEA polypeptide profiling of recalcitrant and orthodox legume seeds reveals ABI3-regulated LEA protein abundance linked to desiccation tolerance 
Journal of Experimental Botany  2013;64(14):4559-4573.
In contrast to orthodox seeds that acquire desiccation tolerance during maturation, recalcitrant seeds are unable to survive drying. These desiccation-sensitive seeds constitute an interesting model for comparative analysis with phylogenetically close species that are desiccation tolerant. Considering the importance of LEA (late embryogenesis abundant) proteins as protective molecules both in drought and in desiccation tolerance, the heat-stable proteome was characterized in cotyledons of the legume Castanospermum australe and it was compared with that of the orthodox model legume Medicago truncatula. RNA sequencing identified transcripts of 16 homologues out of 17 LEA genes for which polypeptides are detected in M. truncatula seeds. It is shown that for 12 LEA genes, polypeptides were either absent or strongly reduced in C. australe cotyledons compared with M. truncatula seeds. Instead, osmotically responsive, non-seed-specific dehydrins accumulated to high levels in the recalcitrant cotyledons compared with orthodox seeds. Next, M. truncatula mutants of the ABSCISIC ACID INSENSITIVE3 (ABI3) gene were characterized. Mature Mtabi3 seeds were found to be desiccation sensitive when dried below a critical water content of 0.4g H2O g DW–1. Characterization of the LEA proteome of the Mtabi3 seeds revealed a subset of LEA proteins with severely reduced abundance that were also found to be reduced or absent in C. australe cotyledons. Transcripts of these genes were indeed shown to be ABI3 responsive. The results highlight those LEA proteins that are critical to desiccation tolerance and suggest that comparable regulatory pathways responsible for their accumulation are missing in both desiccation-sensitive genotypes, revealing new insights into the mechanistic basis of the recalcitrant trait in seeds.
PMCID: PMC3808335  PMID: 24043848
abi3; Castanospermum australe; desiccation tolerance; late embryogenesis abundant proteins; Medicago truncatula; proteomics; recalcitrant seed; RNAseq.
15.  Spatially Quantitative Control of the Number of Cotyledons in a Clonal Population of Somatic Embryos of Hybrid Larch Larix × leptoeuropaea 
Annals of Botany  2004;93(4):423-434.
• Background and Aims Many conifer embryos, both in natural seeds and in clonal populations of somatic embryos, display variability in the number of cotyledons. In hybrid larch, Larix × leptoeuropaea (synonymous with L. × marschlinsii Coaz), such variability has previously been reported in somatic embryos, together with a decrease in the average cotyledon number when benzyladenine (BA) is applied exogenously. Described here is a spatially quantitative study with the aim of throwing some light on the way cotyledon number is determined, and hence the mechanism of cotyledon formation.
• Methods Stock cultures of embryogenic tissue were maintained and later made embryogenically active by standard methods. Development through cotyledon formation was followed by optical microscopy with quantitative measurement of embryo diameter and number of cotyledons. SEMs of representative stages and cotyledon numbers were done for purposes of illustration in this account. Existing mathematics of waveforms on a disc were cast into a form suitable to compare with the quantitative data.
• Key Results The number of cotyledons is linearly related to the diameter of the apical surface of the embryo (which approximates a circular disc) at the time of first appearance of the cotyledon primordia. This linearity is a constant‐spacing phenomenon between adjacent primordia. Addition of BA to the medium restricts the range of apical diameters without changing inter‐cotyledon spacing. Slope/intercept ratio of the linear plot matches expectation for initiation of cotyledon pattern as a harmonic waveform on a circular disc.
• Conclusions The entire pattern of cotyledon primordia arises as a single entity coordinated by a mechanism with wave‐forming properties. This is explicable by diverse mechanisms, especially either mechanical buckling (‘biophysical’) or reaction–diffusion kinetics (‘physicochemical’).
PMCID: PMC4242340  PMID: 15023703
Larix × leptoeuropaea; larch; cotyledon formation; somatic embryos; pattern formation; spatial quantitation; disc waveforms
16.  Seed colour loci, homoeology and linkage groups of the C genome chromosomes revealed in Brassica rapa–B. oleracea monosomic alien addition lines 
Annals of Botany  2012;109(7):1227-1242.
Background and Aims
Brassica rapa and B. oleracea are the progenitors of oilseed rape B. napus. The addition of each chromosome of B. oleracea to the chromosome complement of B. rapa results in a series of monosomic alien addition lines (MAALs). Analysis of MAALs determines which B. oleracea chromosomes carry genes controlling specific phenotypic traits, such as seed colour. Yellow-seeded oilseed rape is a desirable breeding goal both for food and livestock feed end-uses that relate to oil, protein and fibre contents. The aims of this study included developing a missing MAAL to complement an available series, for studies on seed colour control, chromosome homoeology and assignment of linkage groups to B. oleracea chromosomes.
A new batch of B. rapa–B. oleracea aneuploids was produced to generate the missing MAAL. Seed colour and other plant morphological features relevant to differentiation of MAALs were recorded. For chromosome characterization, Snow's carmine, fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH) were used.
Key Results
The final MAAL was developed. Morphological traits that differentiated the MAALs comprised cotyledon number, leaf morphology, flower colour and seed colour. Seed colour was controlled by major genes on two B. oleracea chromosomes and minor genes on five other chromosomes of this species. Homoeologous pairing was largely between chromosomes with similar centromeric positions. FISH, GISH and a parallel microsatellite marker analysis defined the chromosomes in terms of their linkage groups.
A complete set of MAALs is now available for genetic, genomic, evolutionary and breeding perspectives. Defining chromosomes that carry specific genes, physical localization of DNA markers and access to established genetic linkage maps contribute to the integration of these approaches, manifested in the confirmed correspondence of linkage groups with specific chromosomes. Applications include marker-assisted selection and breeding for yellow seeds.
PMCID: PMC3359914  PMID: 22628364
Brassica rapa var. trilocularis; B. oleracea var. alboglabra; MAALs; characterization of C chromosomes; plant morphology; seed colour control; FISH; GISH; chromosome homoeology; chromosome structural changes; linkage groups; crop plant breeding
17.  Sex Allocation of Females and Hermaphrodites in the Gynodioecious Geranium sylvaticum 
Annals of Botany  2003;92(2):207-213.
Seed production and patterns of sex allocation were studied in female and hermaphroditic plants in two gynodioecious populations of Geranium sylvaticum (Geraniaceae). Females produced more flower buds and seeds than hermaphrodites in one of the two study populations. The other female traits measured (pistil biomass, seed number per fruit, individual seed mass) did not differ between the gender morphs. The relative seed fitness of hermaphrodites differed between the study populations, with hermaphrodites gaining less of their fitness through female function in the population with a high frequency of females. However, the amount and size of pollen produced by hermaphrodites did not differ between populations. The number of flower buds was positively correlated with seed production in females, whereas in hermaphrodites a positive correlation between number of buds and seed production was found in only one of the two study populations. These results suggest that fitness gain through female function is labile in hermaphrodites of this species, and is probably affected by environmental factors such as the sex ratio of the population.
PMCID: PMC4243648  PMID: 12814954
Geranium sylvaticum; Geraniaceae; gynodioecy; sex allocation; pollen production
18.  Effect of seed position in spikelet on life history of Eremopyrum distans (Poaceae) from the cold desert of north-west China 
Annals of Botany  2010;106(1):95-105.
Background and Aims
Most studies on seed position-dependent effects have focused on germination characteristics. Our aim was to determine the effects of seed position in the spikelet on differences in timing of germination and on the ecological life history of the grass Eremopyrum distans in its cold desert habitat.
For seeds in three spikelet positions, morphology, mass and dormancy/germination characteristics were determined in the laboratory, and seeds planted in field plots with and without watering were followed to reproduction to investigate seedling emergence and survival, plant size and seed production.
Key Results
After maturation, of the seeds within the spikelet, basal ones (group 1) are the largest and have the highest proportion with physiological dormancy, while distal ones (group 3) are the smallest and have the highest proportion of non-dormant seeds. A higher percentage of seeds after-ripened in groups 2 and 3 than in group 1. Seeds sown in the field in early summer and watered at short, regular intervals germinated primarily in autumn, while those under natural soil moisture conditions germinated only in spring. Both cohorts completed their life cycle in early summer. Seeds in group 1 had lower percentages of seedling emergence and higher percentages of seedling survival than those in groups 2 and 3. Also, plants from group 1 seeds were larger and produced more seeds per plant than those from groups 2 and 3.
Seed position-dependent mass was associated with quantitative differences in several life history traits of E. distans. The environmentally enforced (low soil moisture) delay of germination from autumn to spring results in a reduction in fitness via reduction in number of seeds produced per plant.
PMCID: PMC2889797  PMID: 20460387
Eremopyrum distans; physiological dormancy; plant size; seed mass; seed position-dependent effects; seed production; seedling survival
19.  Effects of herbivory on the reproductive effort of 4 prairie perennials 
BMC Ecology  2002;2:2.
Herbivory can affect every aspect of a plant's life. Damaged individuals may show decreased survivorship and reproductive output. Additionally, specific plant species (legumes) and tissues (flowers) are often selectively targeted by herbivores, like deer. These types of herbivory influence a plant's growth and abundance. The objective of this study was to identify the effects of leaf and meristem removal (simulated herbivory within an exclosure) on fruit and flower production in four species (Rhus glabra, Rosa arkansana, Lathyrus venosus, and Phlox pilosa) which are known targets of deer herbivory.
Lathyrus never flowered or went to seed, so we were unable to detect any treatment effects. Leaf removal did not affect flower number in the other three species. However, Phlox, Rosa, and Rhus all showed significant negative correlations between seed mass and leaf removal. Meristem removal had a more negative effect than leaf removal on flower number in Phlox and on both flower number and seed mass in Rosa.
Meristem removal caused a greater response than defoliation alone in both Phlox and Rosa, which suggests that meristem loss has a greater effect on reproduction. The combination of leaf and meristem removal as well as recruitment limitation by deer, which selectively browse for these species, is likely to be one factor contributing to their low abundance in prairies.
PMCID: PMC77412  PMID: 11876828
20.  Natural Variation in an ABC Transporter Gene Associated with Seed Size Evolution in Tomato Species 
PLoS Genetics  2009;5(1):e1000347.
Seed size is a key determinant of evolutionary fitness in plants and is a trait that often undergoes tremendous changes during crop domestication. Seed size is most often quantitatively inherited, and it has been shown that Sw4.1 is one of the most significant quantitative trait loci (QTLs) underlying the evolution of seed size in the genus Solanum—especially in species related to the cultivated tomato. Using a combination of genetic, developmental, molecular, and transgenic techniques, we have pinpointed the cause of the Sw4.1 QTL to a gene encoding an ABC transporter gene. This gene exerts its control on seed size, not through the maternal plant, but rather via gene expression in the developing zygote. Phenotypic effects of allelic variation at Sw4.1 are manifested early in seed development at stages corresponding to the rapid deposition of starch and lipids into the endospermic cells. Through synteny, we have identified the Arabidopsis Sw4.1 ortholog. Mutagenesis has revealed that this ortholog is associated with seed length variation and fatty acid deposition in seeds, raising the possibility that the ABC transporter may modulate seed size variation in other species. Transcription studies show that the ABC transporter gene is expressed not only in seeds, but also in other tissues (leaves and roots) and, thus, may perform functions in parts of the plants other than developing seeds. Cloning and characterization of the Sw4.1 QTL gives new insight into how plants change seed during evolution and may open future opportunities for modulating seed size in crop plants for human purposes.
Author Summary
Given fixed resources, plants have a choice whether to produce many small seeds or a few large seeds. In terms of reproductive fitness, there are costs and benefits to both strategies. As a result, plant species vary more than 100,000-fold in both seed size and seed output. The current study focuses on understanding the molecular and developmental basis of a single genetic locus (or quantitative trait locus) that determines seed size between the cultivated tomato and its wild relatives. We show that the cause of size variation can be traced to a gene encoding an ABC transporter protein. The gene apparently exercises its control on seed size through expression in the developing seeds and not the mother plant that nurtures those seeds. A comparison with the model plant Arabidopsis thaliana suggests that the ABC transporter identified in tomato may also control seed size in other plants, opening research opportunities for understanding plant adaptation and for potentially modulating seed size in crop plants for human purposes.
PMCID: PMC2617763  PMID: 19165318
21.  Cost of Reproduction in a Spring Ephemeral Species, Adonis ramosa (Ranunculaceae): Carbon Budget for Seed Production 
Annals of Botany  2007;100(3):565-571.
Background and Aims
Spring ephemerals have a specific life-history trait, i.e. shoot growth and sexual reproduction occur simultaneously during a short period from snowmelt to canopy closure in deciduous forests. The aim of this study is to clarify how spring ephemerals invest resources for seed production within a restricted period.
In order to evaluate the cost of reproduction of a typical spring ephemeral species, Adonis ramosa, an experiment was conducted comprising defoliation treatments (intact, one-third and two-thirds leaf-cutting) and fruit manipulations (control, shading and removal) over two growing seasons. In addition, measurements were made of the movements of carbon assimilated via 13C tracing.
Key Results
Survival rate was high irrespective of treatments and manipulations. The proportion of flowering plants and plant size decreased as a result of the defoliation treatments over 2 years, but the fruit manipulations did not affect flowering activity or plant size. Seed set and seed number decreased as a result of fruit shading treatment, but the defoliation treatments did not affect current seed production. Individual seed weight also decreased in the second year due to fruit shading. The 13C tracing experiment revealed that young fruits had photosynthetic ability and current photosynthetic products from leaves were mainly transferred to the below-ground parts, while translocation to fruit was very small even when fruit photosynthesis was restricted by the shading treatment.
Current foliage photosynthetic products are largely stored in the below-ground parts for survival and future growth, and about one-third of the resources for seed production may be attained by fruit photosynthesis. Therefore, the trade-off between current seed production and subsequent growth is weak. The cost of seed production may be buffered by sufficient storage in the below-ground organs, effective photosynthesis under high irradiation and self-assimilation ability of fruits.
PMCID: PMC2533605  PMID: 17611190
Adonis ramosa; carbon transfer; cost of reproduction; defoliation; non-foliar photosynthesis; resource allocation; seed production; spring ephemeral
22.  Co-adaptation of seed dormancy and flowering time in the arable weed Capsella bursa-pastoris (shepherd's purse) 
Annals of Botany  2011;109(2):481-489.
Background and Aims
The duration of the plant life cycle is an important attribute that determines fitness and coexistence of weeds in arable fields. It depends on the timing of two key life-history traits: time from seed dispersal to germination and time from germination to flowering. These traits are components of the time to reproduction. Dormancy results in reduced and delayed germination, thus increasing time to reproduction. Genotypes in the arable seedbank predominantly have short time to flowering. Synergy between reduced seed dormancy and reduced flowering time would create stronger contrasts between genotypes, offering greater adaptation in-field. Therefore, we studied differences in seed dormancy between in-field flowering time genotypes of shepherd's purse.
Genotypes with early, intermediate or late flowering time were grown in a glasshouse to provide seed stock for germination tests. Secondary dormancy was assessed by comparing germination before and after dark-incubation. Dormancy was characterized separately for seed myxospermy heteromorphs, observed in each genotype. Seed carbon and nitrogen content and seed mass were determined as indicators of seed filling and resource partitioning associated with dormancy.
Key Results
Although no differences were observed in primary dormancy, secondary dormancy was weaker among the seeds of early-flowering genotypes. On average, myxospermous seeds showed stronger secondary dormancy than non-myxospermous seeds in all genotypes. Seed filling was similar between the genotypes, but nitrogen partitioning was higher in early-flowering genotypes and in non-myxospermous seeds.
In shepherd's purse, early flowering and reduced seed dormancy coincide and appear to be linked. The seed heteromorphism contributes to variation in dormancy. Three functional groups of seed dormancy were identified, varying in dormancy depth and nitrate response. One of these groups (FG-III) was distinct for early-flowering genotypes. The weaker secondary dormancy of early-flowering genotypes confers a selective advantage in arable fields.
PMCID: PMC3268546  PMID: 22147546
Co-adaptation; Capsella bursa-pastoris; shepherd's purse; seedbank; flowering time; seed heteromorphism; light; nitrate; primary dormancy; secondary dormancy; weed; myxospermy; mucilage
23.  Gene expression analysis of flax seed development 
BMC Plant Biology  2011;11:74.
Flax, Linum usitatissimum L., is an important crop whose seed oil and stem fiber have multiple industrial applications. Flax seeds are also well-known for their nutritional attributes, viz., omega-3 fatty acids in the oil and lignans and mucilage from the seed coat. In spite of the importance of this crop, there are few molecular resources that can be utilized toward improving seed traits. Here, we describe flax embryo and seed development and generation of comprehensive genomic resources for the flax seed.
We describe a large-scale generation and analysis of expressed sequences in various tissues. Collectively, the 13 libraries we have used provide a broad representation of genes active in developing embryos (globular, heart, torpedo, cotyledon and mature stages) seed coats (globular and torpedo stages) and endosperm (pooled globular to torpedo stages) and genes expressed in flowers, etiolated seedlings, leaves, and stem tissue. A total of 261,272 expressed sequence tags (EST) (GenBank accessions LIBEST_026995 to LIBEST_027011) were generated. These EST libraries included transcription factor genes that are typically expressed at low levels, indicating that the depth is adequate for in silico expression analysis. Assembly of the ESTs resulted in 30,640 unigenes and 82% of these could be identified on the basis of homology to known and hypothetical genes from other plants. When compared with fully sequenced plant genomes, the flax unigenes resembled poplar and castor bean more than grape, sorghum, rice or Arabidopsis. Nearly one-fifth of these (5,152) had no homologs in sequences reported for any organism, suggesting that this category represents genes that are likely unique to flax. Digital analyses revealed gene expression dynamics for the biosynthesis of a number of important seed constituents during seed development.
We have developed a foundational database of expressed sequences and collection of plasmid clones that comprise even low-expressed genes such as those encoding transcription factors. This has allowed us to delineate the spatio-temporal aspects of gene expression underlying the biosynthesis of a number of important seed constituents in flax. Flax belongs to a taxonomic group of diverse plants and the large sequence database will allow for evolutionary studies as well.
PMCID: PMC3107784  PMID: 21529361
24.  Hanging by a coastal strand: breeding system of a federally endangered morning-glory of the south-eastern Florida coast, Jacquemontia reclinata 
Annals of Botany  2009;104(7):1301-1311.
Background and Aims
Coastal development has led to extensive habitat destruction and the near extinction of the beach clustervine, Jacquemontia reclinata (Convolvulaceae), an endangered, perennial vine endemic to dune and coastal strand communities in south-eastern Florida. We examined the breeding system of this rare species, and observed visitors to its flowers, as part of a larger effort to document its status and facilitate its recovery.
Reproductively mature experimental plants were grown from seed collected from wild plants in two of the largest remaining populations. Controlled hand pollinations on potted plants were conducted to determine the level of compatibility of the species and to investigate compatibility within and between populations. Seeds from the hand pollinations were planted in soil, and they were monitored individually, recording time to seed germination (cotyledon emergence). Wild plants were observed in several of the remaining populations to determine which species visited the flowers.
Key Results
Hand pollination and seed planting experiments indicate that J. reclinata has a mixed mating system: flowers are able to set fruit with viable seeds with self-pollen, but outcross pollen produces significantly greater fruit and seed set than self-pollen (≥50 % for crosses vs. <25 % for self-pollinations). Visitors included a wide array of insect species, primarily of the orders Diptera, Hymenoptera and Lepidoptera. All visitors captured and examined carried J. reclinata pollen, and usually several other types of pollen.
Remnant populations of beach clustervine will have greater reproductive success not only if floral visitor populations are maintained, but also if movement of either pollen or seed takes place between populations. Restoration efforts should include provisions for the establishment and maintenance of pollinator populations.
PMCID: PMC2778389  PMID: 19797424
Breeding system; conservation; beach clustervine; Jacquemontia reclinata; Convolvulaceae; endangered species; floral visitors; coastal dunes; pollination; reproductive biology; Florida; Caribbean; bees; butterflies
25.  Reprogramming of H3K27me3 Is Critical for Acquisition of Pluripotency from Cultured Arabidopsis Tissues 
PLoS Genetics  2012;8(8):e1002911.
In plants, multiple detached tissues are capable of forming a pluripotent cell mass, termed callus, when cultured on media containing appropriate plant hormones. Recent studies demonstrated that callus resembles the root-tip meristem, even if it is derived from aerial organs. This finding improves our understanding of the regeneration process of plant cells; however, the molecular mechanism that guides cells of different tissue types to form a callus still remains elusive. Here, we show that genome-wide reprogramming of histone H3 lysine 27 trimethylation (H3K27me3) is a critical step in the leaf-to-callus transition. The Polycomb Repressive Complex 2 (PRC2) is known to function in establishing H3K27me3. By analyzing callus formation of mutants corresponding to different histone modification pathways, we found that leaf blades and/or cotyledons of the PRC2 mutants curly leaf swinger (clf swn) and embryonic flower2 (emf2) were defective in callus formation. We identified the H3K27me3-covered loci in leaves and calli by a ChIP–chip assay, and we found that in the callus H3K27me3 levels decreased first at certain auxin-pathway genes. The levels were then increased at specific leaf genes but decreased at a number of root-regulatory genes. Changes in H3K27me3 levels were negatively correlated with expression levels of the corresponding genes. One possible role of PRC2-mediated H3K27me3 in the leaf-to-callus transition might relate to elimination of leaf features by silencing leaf-regulatory genes, as most leaf-preferentially expressed regulatory genes could not be silenced in the leaf explants of clf swn. In contrast to the leaf explants, the root explants of both clf swn and emf2 formed calli normally, possibly because the root-to-callus transition bypasses the leaf gene silencing process. Furthermore, our data show that PRC2-mediated H3K27me3 and H3K27 demethylation act in parallel in the reprogramming of H3K27me3 during the leaf-to-callus transition, suggesting a general mechanism for cell fate transition in plants.
Author Summary
Callus formation is a necessary step in regenerating a new plant from detached plant tissues, and the nature of the callus is similar to that of the root meristem. In this study, we intended to address the molecular basis that directs different plant tissues to form the root-meristem-like callus. We found that leaves and cotyledons, but not roots, of PRC2 mutants curly leaf-50 swinger-1 and embryonic flower2 lost the ability to form a callus. Using ChIP–chip analysis, we identified genes that were changed markedly in the histone H3 lysine 27 trimethylation (H3K27me3) levels during callus formation from leaf blades. Among these genes, a number of leaf-regulatory genes were repressed through PRC2-mediated H3K27me3. Conversely, certain auxin pathway genes and many root-regulatory genes were derepressed through H3K27 demethylation. Our data indicate that genome-wide H3K27me3 reprogramming, through the PRC2-mediated H3K27me3 and the H3K27 demethylation pathways, is critical in directing cell fate transition.
PMCID: PMC3426549  PMID: 22927830

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