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1.  Phenological niches and the future of invaded ecosystems with climate change 
AoB Plants  2014;6:plu013.
We review recent evidence that non-native and invasive plant species may have distinct timings of their seasonal life history characteristics (such as date of leaf out or flowering, that is, their phenology) that allow them to establish in new communities. In particular we examine how invasions may be bolstered by the longer growing seasons associated with climate change. Based on our current of plant phenology and growth strategies—especially rapid growing, early-flowering species versus later-flowering species that make slower-return investments in growth—we project optimal periods for invasions across three distinct systems under current climate change scenarios.
In recent years, research in invasion biology has focused increasing attention on understanding the role of phenology in shaping plant invasions. Multiple studies have found non-native species that tend to flower distinctly early or late in the growing season, advance more with warming or have shifted earlier with climate change compared with native species. This growing body of literature has focused on patterns of phenological differences, but there is a need now for mechanistic studies of how phenology contributes to invasions. To do this, however, requires understanding how phenology fits within complex functional trait relationships. Towards this goal, we review recent literature linking phenology with other functional traits, and discuss the role of phenology in mediating how plants experience disturbance and stress—via climate, herbivory and competition—across the growing season. Because climate change may alter the timing and severity of stress and disturbance in many systems, it could provide novel opportunities for invasion—depending upon the dominant climate controller of the system, the projected climate change, and the traits of native and non-native species. Based on our current understanding of plant phenological and growth strategies—especially rapid growing, early-flowering species versus later-flowering species that make slower-return investments in growth—we project optimal periods for invasions across three distinct systems under current climate change scenarios. Research on plant invasions and phenology within this predictive framework would provide a more rigorous test of what drives invader success, while at the same time testing basic plant ecological theory. Additionally, extensions could provide the basis to model how ecosystem processes may shift in the future with continued climate change.
doi:10.1093/aobpla/plu013
PMCID: PMC4025191  PMID: 24876295
Alien or exotic species; climate change; invasions; non-native; phenology; plasticity; temperate systems.
2.  Floral specialization and angiosperm diversity: phenotypic divergence, fitness trade-offs and realized pollination accuracy 
AoB Plants  2014;6:plu003.
This review considers the role of reproductive factors in the evolutionary success of flowering plants, with emphasis on flowers and pollination. Flowers are complex structures that have varying degrees of integration of parts and surprising evolutionary lability. Diversification of floral form usually accompanies plant diversification by speciation. This correlation has traditionally been interpreted as the result of floral specialization increasing speciation rates. However, another possibility is that species diversity generates selection for divergent specialized flowers when related species occur together, thereby reducing extinction rates.
Plant reproduction by means of flowers has long been thought to promote the success and diversification of angiosperms. It remains unclear, however, how this success has come about. Do flowers, and their capacity to have specialized functions, increase speciation rates or decrease extinction rates? Is floral specialization fundamental or incidental to the diversification? Some studies suggest that the conclusions we draw about the role of flowers in the diversification and increased phenotypic disparity (phenotypic diversity) of angiosperms depends on the system. For orchids, for example, specialized pollination may have increased speciation rates, in part because in most orchids pollen is packed in discrete units so that pollination is precise enough to contribute to reproductive isolation. In most plants, however, granular pollen results in low realized pollination precision, and thus key innovations involving flowers more likely reflect reduced extinction rates combined with opportunities for evolution of greater phenotypic disparity (phenotypic diversity) and occupation of new niches. Understanding the causes and consequences of the evolution of specialized flowers requires knowledge of both the selective regimes and the potential fitness trade-offs in using more than one pollinator functional group. The study of floral function and flowering-plant diversification remains a vibrant evolutionary field. Application of new methods, from measuring natural selection to estimating speciation rates, holds much promise for improving our understanding of the relationship between floral specialization and evolutionary success.
doi:10.1093/aobpla/plu003
PMCID: PMC4038416  PMID: 24790124
Adaptive accuracy; Collinsia; Dalechampia; fitness trade-offs; Pedicularis; pollination; realized precision; Stylidium.
3.  Phragmites australis management in the United States: 40 years of methods and outcomes 
AoB Plants  2014;6:plu001.
We reviewed all available studies on Phragmites australis management in the United States. Our results show that there is a heavy emphasis on herbicides to manage Phragmites, relative to other methods, and a lack of information on what types of plant communities establish once Phragmites is removed. Our model of Phragmites establishment and reproduction describes the invasion as a symptom of watershed-scale land use and disturbance. We advocate more holistic approaches to control and management that focus on improving water quality and minimizing human disturbance to deter future invasion and improve resilience of native plant communities.
Studies on invasive plant management are often short in duration and limited in the methods tested, and lack an adequate description of plant communities that replace the invader following removal. Here we present a comprehensive review of management studies on a single species, in an effort to elucidate future directions for research in invasive plant management. We reviewed the literature on Phragmites management in North America in an effort to synthesize our understanding of management efforts, identify gaps in knowledge and improve the efficacy of management. Additionally, we assessed recent ecological findings concerning Phragmites mechanisms of invasion and integrated these findings into our recommendations for more effective management. Our overall goal is to examine whether or not current management approaches can be improved and whether they promote reestablishment of native plant communities. We found: (i) little information on community-level recovery of vegetation following removal of Phragmites; and (ii) most management approaches focus on the removal of Phragmites from individual stands or groups of stands over a relatively small area. With a few exceptions, recovery studies did not monitor vegetation for substantial durations, thus limiting adequate evaluation of the recovery trajectory. We also found that none of the recovery studies were conducted in a landscape context, even though it is now well documented that land-use patterns on adjacent habitats influence the structure and function of wetlands, including the expansion of Phragmites. We suggest that Phragmites management needs to shift to watershed-scale efforts in coastal regions, or larger management units inland. In addition, management efforts should focus on restoring native plant communities, rather than simply eradicating Phragmites stands. Wetlands and watersheds should be prioritized to identify ecosystems that would benefit most from Phragmites management and those where the negative impact of management would be minimal.
doi:10.1093/aobpla/plu001
PMCID: PMC4038441  PMID: 24790122
Common reed; ecological restoration; herbicide; invasive plant; invasive species; management; Phragmites australis; watershed restoration.
4.  Network epidemiology and plant trade networks 
AoB Plants  2014;6:plu007.
Epidemic models in complex networks are helping us better understand infectious disease outbreaks. This review focuses on the application of new developments in network epidemiology to the study and management of plant diseases. The main aspects covered are: 1) surveys of social networks, 2) models and data about human mobility, 3) epidemic models in directed and hierarchical networks, 4) studies of dynamic networks, and 5) spatial epidemic simulations integrating network data. Because of the increasing amounts of traded plant commodities and the associated rise in introduced plant pests and pathogens, network theory has a great potential in plant science.
Models of epidemics in complex networks are improving our predictive understanding of infectious disease outbreaks. Nonetheless, applying network theory to plant pathology is still a challenge. This overview summarizes some key developments in network epidemiology that are likely to facilitate its application in the study and management of plant diseases. Recent surveys have provided much-needed datasets on contact patterns and human mobility in social networks, but plant trade networks are still understudied. Human (and plant) mobility levels across the planet are unprecedented—there is thus much potential in the use of network theory by plant health authorities and researchers. Given the directed and hierarchical nature of plant trade networks, there is a need for plant epidemiologists to further develop models based on undirected and homogeneous networks. More realistic plant health scenarios would also be obtained by developing epidemic models in dynamic, rather than static, networks. For plant diseases spread by the horticultural and ornamental trade, there is the challenge of developing spatio-temporal epidemic simulations integrating network data. The use of network theory in plant epidemiology is a promising avenue and could contribute to anticipating and preventing plant health emergencies such as European ash dieback.
doi:10.1093/aobpla/plu007
PMCID: PMC4038442  PMID: 24790128
Complex networks; epidemic threshold; global change; Hymenoscyphus pseudoalbidus; infectious diseases; information diffusion; network structure; Phytophthora ramorum; scale-free; small-world.
5.  Prosopis: a global assessment of the biogeography, benefits, impacts and management of one of the world's worst woody invasive plant taxa 
AoB Plants  2014;6:plu027.
Taxa from the genus Prosopis are widespread invasive aliens across the globe. Numerous species have contentious issues surrounding them as they provide both benefits and harm. Prosopis taxa are currently naturalised or invasive in 103 countries and are bioclimatically suitable for many more. There are numerous management practices available to control Prosopis invasions, each with their benefits and costs, however, in most areas management has had only limited success. There is need for more research to improve understanding and management success and for countries to develop strategic plants to guide managed in the future.
Invasive species cause ecological, economic and social impacts and are key drivers of global change. This is the case for the genus Prosopis (mesquite; Fabaceae) where several taxa are among the world's most damaging invasive species. Many contentious issues (‘conflicts of interest’) surround these taxa, and management interventions have not yet sustainably reduced the negative impacts. There is an urgent need to better understand the factors that drive invasions and shape management actions, and to compare the effectiveness of different management approaches. This paper presents a global review of Prosopis, focusing on its distribution, impacts, benefits and approaches to management. Prosopis was found to occur in a 129 countries globally and many more countries are climatically suitable. All areas with naturalized or invasive Prosopis species at present are suitable for more taxa and many Asian and Mediterranean countries with no records of Prosopis are bioclimatically suitable. Several Prosopis species have substantial impacts on biodiversity, ecosystem services, and local and regional economies in their native and even more so in their invasive ranges; others provide multiple benefits to local communities. Management efforts are underway in only a small part of the invaded range. Countries where more research has been done are more likely to implement formal management than those where little published research is available. Management strategies differ among countries; developed nations use mainly mechanical and chemical control whereas developing nations tend to apply control through utilization approaches. A range of countries are also using biological control. Key gaps in knowledge and promising options for management are highlighted.
doi:10.1093/aobpla/plu027
PMCID: PMC4086457  PMID: 24899150
Classification and regression tree; distribution; global review; impacts; logistic regression; management; mesquite; tree invasions.
6.  Wheat production in Bangladesh: its future in the light of global warming 
AoB Plants  2013;5:pls042.
Global warming has already seen a radical change in temperature regimes in Bangladesh. This review provides the first up-to-date perspective and detailed analysis of wheat research in Bangladesh and the impact that global warming will have on its agriculture, especially wheat farming.
Background and aims
The most fundamental activity of the people of Bangladesh is agriculture. Modelling projections for Bangladesh indicate that warmer temperatures linked to climate change will severely reduce the growth of various winter crops (wheat, boro rice, potato and winter vegetables) in the north and central parts. In summer, crops in south-eastern parts of the country are at risk from increased flooding as sea levels increase.
Key facts
Wheat is one of the most important winter crops and is temperature sensitive and the second most important grain crop after rice. In this review, we provide an up-to-date and detailed account of wheat research of Bangladesh and the impact that global warming may have on agriculture, especially wheat production. Although flooding is not of major importance or consequence to the wheat crop at present, some perspectives are provided on this stress since wheat is flood sensitive and the incidence of flooding is likely to increase.
Projections
This information and projections will allow wheat breeders to devise new breeding programmes to attempt to mitigate future global warming. We discuss what this implies for food security in the broader context of South Asia.
doi:10.1093/aobpla/pls042
PMCID: PMC3540706  PMID: 23304431
7.  Mineral nutrient remobilization during corolla senescence in ethylene-sensitive and -insensitive flowers 
AoB Plants  2013;5:plt023.
The flower has a finite lifespan that is controlled largely by its role in sexual reproduction. The programmed senescence of flowers allows the plant to systematically degrade the petal cells and remobilize nutrients to developing tissues, including the seeds. This senescence program is tightly controlled by the plant hormone ethylene in some flowers, while in some species the senescence signals are unknown. This review article will examine the role of nutrient remobilization during petal senescence and how this differs among flowers with different flower termination phenotypes.
The flower has a finite lifespan that is controlled largely by its role in sexual reproduction. Once the flower has been pollinated or is no longer receptive to pollination, the petals are programmed to senesce. A majority of the genes that are up-regulated during petal senescence, in both ethylene-sensitive and -insensitive flowers, encode proteins involved in the degradation of nucleic acids, proteins, lipids, fatty acids, and cell wall and membrane components. A smaller subset of these genes has a putative role in remobilizing nutrients, and only a few of these have been studied in detail. During senescence, carbohydrates (primarily sucrose) are transported from petals, and the degradation of macromolecules and organelles also allows the plant to salvage mineral nutrients from the petals before cell death. The remobilization of mineral nutrients from a few species has been investigated and will be reviewed in this article. Ethylene's role in nutrient remobilization is discussed by comparing nutrient changes during the senescence of ethylene-sensitive and -insensitive flowers, and by studies in transgenic petunias (Petunia × hybrida) that are insensitive to ethylene. Gene expression studies indicate that remobilization is a key feature of senescence, but some senescence-associated genes have different expression in leaves and petals. These gene expression patterns, along with differences in the nutrient content of leaves and petals, suggest that there are differences in the mechanisms of cellular degradation and nutrient transport in vegetative and floral organs. Autophagy may be the mechanism for large-scale degradation that allows for recycling during senescence, but it is unclear if this causes cell death. Future research should focus on autophagy and the regulation of ATG genes by ethylene during both leaf and petal senescence. We must identify the mechanisms by which individual mineral nutrients are transported out of senescing corollas in both ethylene-sensitive and -insensitive species.
doi:10.1093/aobpla/plt023
PMCID: PMC3648795  PMID: 23671789
Abscission; autophagy; cell death; flowers; nitrogen; petals; petunias; phosphorus
8.  Conserved versatile master regulators in signalling pathways in response to stress in plants 
AoB Plants  2013;5:plt033.
Environmental conditions have forced plants to develop elaborated molecular strategies to surpass natural obstacles to growth and proliferation. Elements in multiple signaling cascades allow plants to sense multiple and simultaneous ambient cues, and establish an opportune defensive response. A group of versatile master regulators of gene expression are decisive to control plant responses to stressing conditions. For crop breeding purposes, the task is to determine how to activate these key regulators to enable accurate and optimal responses to stressing conditions. In this review, we discuss how and which master regulators are implied in the responses to biotic and stresses, their evolution in the life kingdoms, and the interaction with other molecular factors that lead to a proper and efficient plant response.
From the first land plants to the complex gymnosperms and angiosperms of today, environmental conditions have forced plants to develop molecular strategies to surpass natural obstacles to growth and proliferation, and these genetic gains have been transmitted to the following generations. In this long natural process, novel and elaborate mechanisms have evolved to enable plants to cope with environmental limitations. Elements in many signalling cascades enable plants to sense different, multiple and simultaneous ambient cues. A group of versatile master regulators of gene expression control plant responses to stressing conditions. For crop breeding purposes, the task is to determine how to activate these key regulators to enable accurate and optimal reactions to common stresses. In this review, we discuss how plants sense biotic and abiotic stresses, how and which master regulators are implied in the responses to these stresses, their evolution in the life kingdoms, and the domains in these proteins that interact with other factors to lead to a proper and efficient plant response.
doi:10.1093/aobpla/plt033
PMCID: PMC3800984  PMID: 24147216
Biotic/abiotic stress; co-activators; gene expression regulation; integrators; key regulators; plant stress response.
9.  Adaptation to flooding during emergence and seedling growth in rice and weeds, and implications for crop establishment 
AoB Plants  2012;2012:pls019.
Direct seeding is replacing transplanting in rice. Early flooding suppresses weeds but selective action is compromised by the sharing of flood-tolerance traits. Understanding adaptive traits in both species is therefore a prerequisite for developing direct seeding systems that control weeds while leaving rice seedlings relatively unharmed.
Background and aims
Direct seeding of rice is being adopted in rainfed and irrigated lowland ecosystems because it reduces labour costs in addition to other benefits. However, early flooding due to uneven fields or rainfall slows down seed germination and hinders crop establishment. Conversely, early flooding helps suppress weeds and reduces the costs of manual weeding and/or dependence on herbicides; however, numerous weed species are adapted to lowlands and present challenges for the use of flooding to control weeds. Advancing knowledge on the mechanisms of tolerance of flooding during germination and early growth in rice and weeds could facilitate the development of improved rice varieties and effective weed management practices for direct-seeded rice.
Principal results
Rice genotypes with a greater ability to germinate and establish in flooded soils were identified, providing opportunities to develop varieties suitable for direct seeding in flooded soils. Tolerance of flooding in these genotypes was mostly attributed to traits associated with better ability to mobilize stored carbohydrates and anaerobic metabolism. Limited studies were undertaken in weeds associated with lowland rice systems. Remaining studies compared rice and weeds and related weed species such as Echinochloa crus-galli and E. colona or compared ecotypes of the same species of Cyperus rotundus adapted to either aerobic or flooded soils.
Conclusions
Tolerant weeds and rice genotypes mostly developed similar adaptive traits that allow them to establish in flooded fields, including the ability to germinate and elongate faster under hypoxia, mobilize stored starch reserves and generate energy through fermentation pathways. Remarkably, some weeds developed additional traits such as larger storage tubers that enlarge further in deeper flooded soils (C. rotundus). Unravelling the mechanisms involved in adaptation to flooding will help design management options that will allow tolerant rice genotypes to adequately establish in flooded soils while simultaneously suppressing weeds.
doi:10.1093/aobpla/pls019
PMCID: PMC3434364  PMID: 22957137
10.  Hybridization of common reed in North America? The answer is blowing in the wind 
AoB Plants  2012;2012:pls022.
Hybridization of Phragmites has occurred in the Gulf Coast and likely is occurring elsewhere in North America. However, detection failure may be due to limited genetic tools. Additionally, nomenclature confusion necessitates a revision of the current classification system.
Background and aims
We review evidence for hybridization of Phragmites australis in North America and the implications for the persistence of native P. australis ssp. americanus populations in North America. We also highlight the need for an updated classification system, which takes P. australis intraspecific variation and hybridization into account.
Methodology
We reviewed available published, in press and in preparation literature to assess the likelihood of hybridization and interbreeding in genotypes of P. australis present in North America.
Principal results
Experimental results demonstrate that hybridization among introduced and native haplotypes is possible within the genus Phragmites, yet evidence that hybridization has occurred naturally is only starting to emerge. The lag in identifying hybridization in Phragmites in North America may be related to under-sampling in some parts of North America and to a lack of molecular tools that provide the capability to recognize hybrids.
Conclusions
Our understanding of the gene flow within and between species in the genus Phragmites is moving at a fast pace, especially on the east and Gulf coasts of North America. More attention should also be focused on the Great Lakes region, the southwestern and the west coast of the USA, where sympatry has created opportunities for hybridization. Where hybridizations have been detected, there are currently no published data on how hybridization affects plant vigour, morphology, invasiveness or conservation of the genetic integrity of the North American native subspecies. We conclude that the detection of more hybridization is highly likely and that there is a need to develop new markers for the different Phragmites species and lineages to fill current knowledge gaps. Finally, we suggest that the classification system for P. australis should be updated and published to help clarify the nomenclature.
doi:10.1093/aobpla/pls022
PMCID: PMC3444738  PMID: 22993684
11.  Approaches towards nitrogen- and phosphorus-efficient rice 
AoB Plants  2012;2012:pls028.
Crop tolerance to lowered availability of nutrients is a major breeding objective in rice. Current understanding of complex genetic control of N and P utilisation is being converged towards precision breeding such as marker assisted breeding for nutrient efficient varieties.
Background and aims
Food production has to increase to meet the demand of a growing population. In light of the high energy costs and increasingly scarce resources, future agricultural systems have to be more productive and more efficient in terms of inputs such as fertilizer and water. The development of rice varieties with high yield under low-nutrient conditions has therefore become a breeding priority. The rapid progress made in sequencing and molecular-marker technology is now beginning to change the way breeding is done, providing new opportunities.
Scope
Nitrogen (N) and phosphorus (P) are applied to agricultural systems in large quantities and a deficiency of either nutrient leads to yield losses and triggers complex molecular and physiological responses. The underlying genes are now being identified and studied in detail, and an increasing number of quantitative trait loci (QTLs) related to N and P uptake and utilization are being reported. Here, we provide an overview of the different aspects related to N and P in rice production systems, and apply a breeder's perspective on the potential of relevant genes and pathways for breeding applications.
Main points
For the development of nutrient-efficient rice, a holistic approach should be followed combining optimized fertilizer management with enhanced nutrient uptake via a vigorous root system, leading to increased grain filling and yield. Despite an increasing number of N- and P-related genes and QTLs being reported, very few are actively used in molecular breeding programmes. The complex regulation of N- and P-related pathways challenges breeders and the research community to identify large-effect genes/QTLs. For this it will be important to focus more on the analysis of tolerant genotypes rather than model plants, since tolerance pathways may employ a different set of genes.
doi:10.1093/aobpla/pls028
PMCID: PMC3484362  PMID: 23115710
12.  Germination rate is the significant characteristic determining coconut palm diversity 
AoB Plants  2012;2012:pls045.
Using information and DNA analysis data accessable on the internet, this review builds on a germination and taxonomy study of the coconut palm published in Annals of Botany in 1981, resolves earlier issues, and opens up new lines of investigation.
Rationale
This review comes at a time when in vitro embryo culture techniques are being adopted for the safe exchange and cryo-conservation of coconut germplasm. In due course, laboratory procedures may replace the options that exist among standard commercial nursery germination techniques. These, in their turn, have supplanted traditional methods that are now forgotten or misunderstood. Knowledge of all germination options should help to ensure the safe regeneration of conserved material.
Scope
This review outlines the many options for commercial propagation, recognizes the full significance of one particular traditional method and suggests that the diversity of modern cultivated coconut varieties has arisen because natural selection and domestic selection were associated with different rates of germination and other morphologically recognizable phenotypic characteristics. The review takes into account both the recalcitrant and the viviparous nature of the coconut. The ripe fruits that fall but do not germinate immediately and lose viability if dried for storage are contrasted with the bunches of fruit retained in the crown of the palm that may, in certain circumstances, germinate to produce seedlings high above ground level.
Significance
Slow-germinating and quick-germinating coconuts have different patterns of distribution. The former predominate on tropical islands and coastlines that could be reached by floating when natural dispersal originally spread coconuts widely—but only where tides and currents were favourable—and then only to sea-level locations. Human settlers disseminated the domestic types even more widely—to otherwise inaccessible coastal sites not reached by floating—and particularly to inland and upland locations on large islands and continental land masses. This review suggests four regions where diversity has been determined by germination rates. Although recent DNA studies support these distinctions, further analyses of genetic markers related to fruit abscission and germination are recommended.
doi:10.1093/aobpla/pls045
PMCID: PMC3532018  PMID: 23275832
13.  Image use in field guides and identification keys: review and recommendations 
AoB Plants  2011;2011:plr004.
We review image use in field guides and keys, and formulate a set of best practices for image use. The review covers the full range of guides, from those that consist only of species descriptions, to lavishly illustrated technical guides.
Background and aims
Although illustrations have played an important role in identification keys and guides since the 18th century, their use has varied widely. Some keys lack all illustrations, while others are heavily illustrated. Even within illustrated guides, the way in which images are used varies considerably. Here, we review image use in paper and electronic guides, and establish a set of best practices for image use in illustrated keys and guides.
Scope
Our review covers image use in both paper and electronic guides, though we only briefly cover apps for mobile devices. With this one exception, we cover the full range of guides, from those that consist only of species descriptions with no keys, to lavishly illustrated technical keys. Emphasis is placed on how images are used, not on the operation of the guides and key, which has been reviewed by others. We only deal with operation when it impacts image use.
Main points
Few illustrated keys or guides use images in optimal ways. Most include too few images to show taxonomic variation or variation in characters and character states. The use of multiple images allows easier taxon identification and facilitates the understanding of characters. Most images are usually not standardized, making comparison between images difficult. Although some electronic guides allow images to be enlarged, many do not.
Conclusions
The best keys and guides use standardized images, displayed at sizes that are easy to see and arranged in a standardized manner so that similar images can be compared across species. Illustrated keys and glossaries should contain multiple images for each character state so that the user can judge variation in the state. Photographic backgrounds should not distract from the subject and, where possible, should be of a standard colour. When used, drawings should be prepared by professional botanical illustrators, and clearly labelled. Electronic keys and guides should allow images to be enlarged so that their details can be seen.
doi:10.1093/aobpla/plr004
PMCID: PMC3077818  PMID: 22476475
14.  Expanding the docosahexaenoic acid food web for sustainable production: engineering lower plant pathways into higher plants 
AoB Plants  2011;2011:plr011.
This article describes current progress in the engineering of oilseed crops for the production of long-chain omega-3 fatty acids such as DHA. This example highlights the importance of algal genetic resources to the future of agricultural biotechnology.
Background
Algae are becoming an increasingly important component of land plant metabolic engineering projects. Land plants and algae have similar enough genetics to allow relatively straightforward gene transfer and they also share enough metabolic similarities that algal enzymes often function in a plant cell environment. Understanding metabolic systems in algae can provide insights into homologous systems in land plants. As examples, algal models are currently being used by several groups to better understand starch and lipid metabolism and catabolism, fields which have relevance in land plants. Importantly, land plants and algae also have enough metabolic divergence that algal genes can often provide new metabolic traits to plants. Furthermore, many algal genomes have now been sequenced, with many more in progress, and this easy access to genome-wide information has revealed that algal genomes are often relatively simple when compared with plants.
Scope
One example of the importance of algal, and in particular microalgal, resources to land plant research is the metabolic engineering of long-chain polyunsaturated fatty acids into oilseed crops which typically uses microalgal genes to extend existing natural plant biosynthetic pathways. This review describes both recent progress and remaining challenges in this field.
doi:10.1093/aobpla/plr011
PMCID: PMC3114564  PMID: 22476481
15.  Phenotypic variation in heteroblastic woody species does not contribute to shade survival 
AoB Plants  2011;2011:plr013.
Heteroblastic species change their leaf morphology due to changes in light environment. However, growth and biomass allocation pattern do not contribute to their better survival relative to homoblastic congeners in low light. Thus, shade does not select for leaf heteroblasty.
Background and aims
Leaf heteroblasty involves dramatic phenotypic differences between adult and seedling leaves while leaves of homoblastic plants display only small differences. This study tested whether, in low-light environments, the marked difference in the morphology of seedling leaves that characterizes heteroblastic species confers advantages for seedling survival and growth compared with homoblastic congeners.
Methodology
Four pairs of heteroblastic and homoblastic species in genera Hoheria, Aristotelia, Pseudopanax and Melicope were grown in simulated full sunlight (100 % of light, red:far red ratio (R:FR) = 1.25) or in simulated forest understorey shade (5 % of full sunlight, R:FR ratio = 0.25) in a glasshouse.
Principal results
After 9 months, 100 % of seedlings of both homoblastic and heteroblastic species survived in full sun while in the understorey treatment there were 25 % fewer heteroblastic survivors than homoblastic congeners. Compared with homoblastic congeners, all heteroblastic species except for Pseudopanax crassifolius produced more and smaller leaves and branches, but grew more slowly in height, root collar diameter and total biomass both in full sun and in forest understorey treatments.
Conclusions
Homoblastic species survive and grow better in the forest understorey light treatment, suggesting that heteroblastic seedling leaf morphology does not give an advantage over homoblastic congeners under low light intensities.
doi:10.1093/aobpla/plr013
PMCID: PMC3129537  PMID: 22476483
16.  Reproductive phenology of 233 species from four herbaceous–shrubby communities in the Gran Sabana Plateau of Venezuela 
AoB Plants  2011;2011:plr014.
The reproductive phenology of 233 species from four herbaceous-shrubby communities in the Venezuelan Guayana Highlands (shrublands, secondary bush, savanna, and broad-leaved meadow) exhibited non-seasonal patterns of variability These were found to be related to composition of life-forms, precipitation regime and soil type.
Background and aims
Herbaceous–shrubby communities in the Gran Sabana (Great Savanna) Plateau of Venezuela grow under non-zonal conditions. We speculated that this would produce specific patterns of reproductive phenology within these different soil–climate–vegetation associations. Specifically, we tested the hypothesis that the reproductive phenology patterns of four herbaceous–shrubby communities are determined by climate, plant life-forms and soil properties.
Methodology
The reproductive phenology of 233 plant species of the Gran Sabana Plateau of the Venezuelan Guayana Highlands was studied taking into account their life-forms (i.e. trees, shrubs, climbers, annual herbs, perennial herbs, epiphytes and parasites/hemiparasites) in four herbaceous–shrubby communities: (i) shrubland, (ii) secondary bush, (iii) savanna and (iv) broad-leaved meadow. Patterns of flowering, and occurrence of unripe fruit and ripe fruit were studied at two levels of intensity for 24 months within a 5-year span. Two phenological records for each month of the year and between two and four replicates for each community type were made. Randomly selected 2–3 ha plots were used. General phenological patterns were established using <25% of the plants of each species in each plot to give the total duration of each phenological phase. High-intensity phenological patterns were established using >25% of individuals in each plot to establish times of high abundance of flowers, and presence of unripe fruit and/or ripe fruit on individual plants. This generated phenological peaks for each species.
Principal results
Non-seasonality of general flowering and unripe fruiting in each of the four communities was related to non-seasonal flowering and unripe fruiting patterns in the plant life-forms studied and to low variation in precipitation throughout the year. Flowering activity in the shrubland and broad-leaved meadow peaked twice. The bush community had only one flowering peak while the savanna gave a non-seasonal flowering peak. The peak unripe fruiting pattern was not clearly related to unripe fruit phenological patterns of the most abundant life-forms. Unripe fruit patterns and precipitation were only correlated for shrubs, climbers and trees in the shrubland. Ripe fruiting patterns peaked during the short-dry season in the bush and shrubland, and were negatively correlated with precipitation in the shrubland. General and peak ripe fruiting patterns were non-seasonal in the savanna and broad-leaved meadow and related to the dominance of herbaceous species with prolonged ripe fruiting times, low climate seasonality, high plant species richness and diversity, and dispersal syndromes.
Conclusions
The reproductive phenology of the herbaceous–shrubby communities is mainly influenced by the composition of the life-forms, the precipitation regime and soil type.
doi:10.1093/aobpla/plr014
PMCID: PMC3144378  PMID: 22476484
17.  Green love talks; cell–cell communication during double fertilization in flowering plants 
AoB Plants  2011;2011:plr015.
A major breakthrough in understanding double fertilization has been made by high resolution live-imaging. This has helped resolve several disputed issues such as preferential fertilization and polyspermy block. Cumulated information of molecular components involved in double fertilization highlights the importance of cell-cell communication between male and female gametophytes.
Background
Flowering plant seeds originate from a unique double-fertilization event, which involves two sperm cells and two female gametes, the egg cell and the central cell. For many years our knowledge of mechanisms involved in angiosperm fertilization remained minimal. It was obvious that several signals were required to explain how the male gametes are delivered inside the maternal reproductive tissues to the two female gametes but their molecular nature remained unknown. The difficulties in imaging the double-fertilization process prevented the identification of the mode of sperm cell delivery. It was believed that the two sperm cells were not functionally equivalent.
Scope
We review recent studies that have significantly improved our understanding of the early steps of double fertilization. The attractants of the pollen tube have been identified as small proteins produced by the synergid cells that surround the egg cell. Genetic studies have identified the signalling pathways required for the release of male gametes from the pollen tube. High-resolution imaging of the trajectory of the two male gametes showed that their transport does not involve the synergid cells directly and that isomorphic male gametes are functionally equivalent. We also outline major outstanding issues in the field concerned with the barrier against polyspermy, gamete recognition and mechanisms that prevent interspecies crosses.
doi:10.1093/aobpla/plr015
PMCID: PMC3144379  PMID: 22476485
18.  Receptor-like kinases as surface regulators for RAC/ROP-mediated pollen tube growth and interaction with the pistil 
AoB Plants  2011;2011:plr017.
Pollen tube growth is regulated by female tissue-produced factors that facilitate growth and provide directional guidance. We discuss here signal perception and transduction molecules on the male and the female cell surfaces mediate male-female interactions that underlie successful reproduction.
Background
RAC/ROPs are RHO-type GTPases and are known to play diverse signalling roles in plants. Cytoplasmic RAC/ROPs are recruited to the cell membrane and activated in response to extracellular signals perceived and mediated by cell surface-located signalling assemblies, transducing the signals to regulate cellular processes. More than any other cell types in plants, pollen tubes depend on continuous interactions with an extracellular environment produced by their surrounding tissues as they grow within the female organ pistil to deliver sperm to the female gametophyte for fertilization.
Scope
We review studies on pollen tube growth that provide compelling evidence indicating that RAC/ROPs are crucial for regulating the cellular processes that underlie the polarized cell growth process. Efforts to identify cell surface regulators that mediate extracellular signals also point to RAC/ROPs being the molecular switches targeted by growth-regulating female factors for modulation to mediate pollination and fertilization. We discuss a large volume of work spanning more than two decades on a family of pollen-specific receptor kinases and some recent studies on members of the FERONIA family of receptor-like kinases (RLKs).
Significance
The research described shows the crucial roles that two RLK families play in transducing signals from growth regulatory factors to the RAC/ROP switch at the pollen tube apex to mediate and target pollen tube growth to the female gametophyte and signal its disintegration to achieve fertilization once inside the female chamber.
doi:10.1093/aobpla/plr017
PMCID: PMC3158858  PMID: 22476487
19.  Pollen tube energetics: respiration, fermentation and the race to the ovule 
AoB Plants  2011;2011:plr019.
This review covers historical and recent progress in understanding how respiration, fermentation and mitochondria contribute to pollen tube growth. It also summarizes what is known about the energetic requirements of this growth. Molecular mechanisms are viewed in the context of pollen tube physiology, a necessary perspective to understanding pollen tube growth.
Background
Pollen tubes grow by transferring chemical energy from stored cellular starch and newly assimilated sugars into ATP. This drives myriad processes essential for cell elongation, directly or through the creation of ion gradients. Respiration plays a central role in generating and regulating this energy flow and thus in the success of plant reproduction. Pollen tubes are easily grown in vitro and have become an excellent model for investigating the contributions of respiration to plant cellular growth and morphogenesis at the molecular, biochemical and physiological levels.
Scope
In recent decades, pollen tube research has become increasingly focused on the molecular mechanisms involved in cellular processes. Yet, effective growth and development requires an intact, integrated set of cellular processes, all supplied with a constant flow of energy. Here we bring together information from the current and historical literature concerning respiration, fermentation and mitochondrial physiology in pollen tubes, and assess the significance of more recent molecular and genetic investigations in a physiological context.
Conclusions
The rapid growth of the pollen tube down the style has led to the evolution of high rates of pollen tube respiration. Respiration rates in lily predict a total energy turnover of 40–50 fmol ATP s−1 per pollen grain. Within this context we examine the energetic requirements of cell wall synthesis, osmoregulation, actin dynamics and cyclosis. At present, we can only estimate the amount of energy required, because data from growing pollen tubes are not available. In addition to respiration, we discuss fermentation and mitochondrial localization. We argue that the molecular pathways need to be examined within the physiological context to understand better the mechanisms that control tip growth in pollen tubes.
doi:10.1093/aobpla/plr019
PMCID: PMC3169925  PMID: 22476489
20.  Isolated history of the coastal plant Lathyrus japonicus (Leguminosae) in Lake Biwa, an ancient freshwater lake 
AoB Plants  2011;2011:plr021.
Lathyrus japonicus commonly inhabits seashores. However it also grows near the shores of an inland lake (Lake Biwa, an ancient japanese freshwater lake) where it is assumed to have been isolated for a long time. The impact of this long-term isolation on phylogeographic and population structures is described. This reveals low genetic diversity due to the bottleneck effect. Implications for these dwindling inland populations and their conservation are discussed
Background and aims
Lake Biwa is one of the world's few ancient lakes. Formed ∼4 million years ago, the lake harbours many coastal species that commonly inhabit seashores. The beach pea Lathyrus japonicus is a typical coastal species of this freshwater lake, but its inland populations are faced with the threat of extinction. Here, we investigated the phylogeographical and population structures of both inland and coastal populations of L. japonicus. We also elucidated the historical isolation of the Lake Biwa population.
Methodology
In total, 520 individuals from 50 L. japonicus populations were sampled throughout the species distribution in Japan. Chloroplast haplotyping using intergenic spacers psbA–trnH and atpI–atpH was performed to investigate the phylogeographical structure as well as the genetic diversity of L. japonicus. Six nuclear microsatellite markers were also used to analyse the population structure.
Principal results
Population structure analyses of chloroplast DNA (cpDNA) and nuclear DNA (nDNA) identified inland and coastal groups. Based on the genetic differentiation, inland populations exhibited a single cpDNA haplotype and significantly lower values of HS, AR and FIS than coastal populations. In addition to the presence of a bottleneck, the lack of gene flow among inland populations was supported by estimates of recent migration rates between subpopulations.
Conclusions
Our data revealed that inland populations have been isolated in Lake Biwa as ‘landlocked’ populations since the predecessor lake was isolated from sea. This was also seen in a previous study of Calystegia soldanella. However, the high genetic differentiation, accompanied by a lack of gene flow among the Lake Biwa populations (according to the BAYESASS+ analysis), contradicts the results with C. soldanella. We conclude that because of the presence of a bottleneck and low genetic diversity of the inland populations, self-sustaining population persistence may be difficult in the future. Conservation strategies must consider the genetic properties of such isolated populations.
doi:10.1093/aobpla/plr021
PMCID: PMC3176521  PMID: 22476491
21.  Salinity tolerance ecophysiology of Equisetum giganteum in South America: a study of 11 sites providing a natural gradient of salinity stress 
AoB Plants  2011;2011:plr022.
In river valleys of the world's driest desert (The Atacama of South America) large stands of giant horsetail (Equisetum giganteum) are found to tolerate soil water salinity up to at least half that of seawater. The roots selectively exclude Na and take-up K in response to salinity while stomatal conductances and photochemical efficiency of Photosystem II remain unaffected.
Background and aims
The basic set of adaptations necessary for salinity tolerance in vascular plants remains unknown. Although much has been published on salinity stress, almost all studies deal with spermatophytes. Studies of salinity tolerance in pteridophytes are relatively rare but hold promise for revealing the fundamental adaptations that all salt-tolerant vascular plants may share. The most basal pteridophytes to exhibit salinity tolerance are members of the genus Equisetum, including the giant horsetail, Equisetum giganteum, the only pteridophyte to occur in salinity-affected regions of the Atacama Desert valleys of northern Chile. Here it can constitute a significant vegetation component, forming dense stands of shoots >4 m high.
Methodology
Physiological parameters (stomatal conductances; efficiency of photosystem II; sap osmotic potential) were measured in E. giganteum populations in northern Chile across a range of groundwater salinities at 11 sites. In addition, Na, K, electrical conductivity and total plant water potential were measured in the plants and groundwater from each site.
Principal results
Equisetum giganteum exhibits similar stomatal conductances and photochemical efficiencies of photosystem II across a wide range of groundwater salinities. It lowers cell sap osmotic potential with increasing salinity and produces positive root pressure, as evidenced by guttation, at the full range of salinities experienced in the Atacama Desert. Equisetum giganteum maintains low Na concentrations in its xylem fluid and cell sap when soil water Na is high. It also maintains high K/Na ratios in xylem fluid and cell sap when soil water has low K/Na ratios.
Conclusions
Equisetum giganteum is well adapted to salinity stress. Efficient K uptake and Na exclusion are important adaptations and closely similar to those of the facultative halophyte fern Acrostichum aureum.
doi:10.1093/aobpla/plr022
PMCID: PMC3178842  PMID: 22476492
22.  A platform for efficient genotyping in Musa using microsatellite markers 
AoB Plants  2011;2011:plr024.
Establishment of a standardized platform for genotyping banana (Musa spp.) using a set of previously published SSR markers is described. The platform will serve a broad Musa research and breeding community and support the conservation and use of genetic diversity.
Background and aims
Bananas and plantains (Musa spp.) are one of the major fruit crops worldwide with acknowledged importance as a staple food for millions of people. The rich genetic diversity of this crop is, however, endangered by diseases, adverse environmental conditions and changed farming practices, and the need for its characterization and preservation is urgent. With the aim of providing a simple and robust approach for molecular characterization of Musa species, we developed an optimized genotyping platform using 19 published simple sequence repeat markers.
Methodology
The genotyping system is based on 19 microsatellite loci, which are scored using fluorescently labelled primers and high-throughput capillary electrophoresis separation with high resolution. This genotyping platform was tested and optimized on a set of 70 diploid and 38 triploid banana accessions.
Principal results
The marker set used in this study provided enough polymorphism to discriminate between individual species, subspecies and subgroups of all accessions of Musa. Likewise, the capability of identifying duplicate samples was confirmed. Based on the results of a blind test, the genotyping system was confirmed to be suitable for characterization of unknown accessions.
Conclusions
Here we report on the first complex and standardized platform for molecular characterization of Musa germplasm that is ready to use for the wider Musa research and breeding community. We believe that this genotyping system offers a versatile tool that can accommodate all possible requirements for characterizing Musa diversity, and is economical for samples ranging from one to many accessions.
doi:10.1093/aobpla/plr024
PMCID: PMC3185971  PMID: 22476494
23.  Evolutionary development of the plant and spore wall 
AoB Plants  2011;2011:plr027.
The article provides an overview of the development and structure of spore and pollen walls in the major plant groups and summarises progress in our understanding of the molecular genetics underpinning spore/pollen evolution and development.
Background and aims
Many key innovations were required to enable plants to colonize terrestrial habitats successfully. One of these was the acquisition of a durable spore/pollen wall capable of withstanding the harsh desiccating and UV-B-rich environment encountered on land. The spores of ‘lower’ spore-bearing plants and the pollen of ‘higher’ seed plants are homologous. In recent years, researchers have begun to investigate the molecular genetics of pollen wall development in angiosperms (including the model organism Arabidopsis thaliana). However, research into the molecular genetics of spore wall development in more basal plants has thus far been extremely limited. This review summarizes the literature on spore/pollen wall development, including the molecular genetics associated with pollen wall development in angiosperms, in a preliminary attempt to identify possible candidate genes involved in spore wall development in more basal plants.
Presence in moss of genes involved in pollen wall development
Bioinformatic studies have suggested that genes implicated in pollen wall development in angiosperms are also present in moss and lycopsids, and may therefore be involved in spore wall development in basal plants. This suggests that the molecular genetics of spore/pollen development are highly conserved, despite the large morphological and functional differences between spores and pollen.
Future work
The use of high-throughput sequencing strategies and/or microarray experiments at an appropriate stage of ‘lower’ land plant sporogenesis will allow the identification of candidate genes likely to be involved in the development of the spore wall by way of comparison with those genes known to be involved in pollen wall development. Additionally, by conducting gene knock-out and gene swap experiments between ‘lower’ land plant species, such as the moss model species Physcomitrella patens, and the angiosperm model species arabidopsis it will be possible to test the role of these candidate genes.
doi:10.1093/aobpla/plr027
PMCID: PMC3220415  PMID: 22476497
24.  A perspective on underwater photosynthesis in submerged terrestrial wetland plants 
AoB Plants  2011;2011:plr030.
Submergence inhibits photosynthesis by terrestrial wetland plants, but less so in species that possess leaf gas films when submerged. Floodwaters are often supersaturated with dissolved CO2 enabling photosynthesis by submerged terrestrial plants, although rates remain well-below those in air. This important adaptation that enhances survival in submerged conditions is reviewed.
Background and aims
Wetland plants inhabit flood-prone areas and therefore can experience episodes of complete submergence. Submergence impedes exchange of O2 and CO2 between leaves and the environment, and light availability is also reduced. The present review examines limitations to underwater net photosynthesis (PN) by terrestrial (i.e. usually emergent) wetland plants, as compared with submerged aquatic plants, with focus on leaf traits for enhanced CO2 acquisition.
Scope
Floodwaters are variable in dissolved O2, CO2, light and temperature, and these parameters influence underwater PN and the growth and survival of submerged plants. Aquatic species possess morphological and anatomical leaf traits that reduce diffusion limitations to CO2 uptake and thus aid PN under water. Many aquatic plants also have carbon-concentrating mechanisms to increase CO2 at Rubisco. Terrestrial wetland plants generally lack the numerous beneficial leaf traits possessed by aquatic plants, so submergence markedly reduces PN. Some terrestrial species, however, produce new leaves with a thinner cuticle and higher specific leaf area, whereas others have leaves with hydrophobic surfaces so that gas films are retained when submerged; both improve CO2 entry.
Conclusions
Submergence inhibits PN by terrestrial wetland plants, but less so in species that produce new leaves under water or in those with leaf gas films. Leaves with a thinner cuticle, or those with gas films, have improved gas diffusion with floodwaters, so that underwater PN is enhanced. Underwater PN provides sugars and O2 to submerged plants. Floodwaters often contain dissolved CO2 above levels in equilibrium with air, enabling at least some PN by terrestrial species when submerged, although rates remain well below those in air.
doi:10.1093/aobpla/plr030
PMCID: PMC3249690  PMID: 22476500
25.  Petiole hyponasty: an ethylene-driven, adaptive response to changes in the environment 
AoB Plants  2011;2011:plr031.
Hyponastic (upwardly bending) growth by leaves is a response of numerous plant species to adverse environmental conditions. This review summarises current knowledge on hyponasty with a particular focus on the role of ethylene in regulating this phenomenon and its possible adaptive significance.
Background
Many plant species can actively reorient their organs in response to dynamic environmental conditions. Organ movement can be an integral part of plant development or can occur in response to unfavourable external circumstances. These active reactions take place with or without a directional stimulus and can be driven either by changes in turgor pressure or by asymmetric growth. Petiole hyponasty is upward movement driven by a higher rate of cell expansion on the lower (abaxial) compared with the upper (adaxial) side. Hyponasty is common among rosette species facing environmental stresses such as flooding, proximity of neighbours or elevated ambient temperature. The complex regulatory mechanism of hyponasty involves activation of pathways at molecular and developmental levels, with ethylene playing a crucial role.
Scope
We present current knowledge on the mechanisms that promote hyponasty in the context of other organ movements, including tropic and nastic reactions together with circumnutation. We describe major environmental cues resulting in hyponasty and briefly discuss their perception and signal transduction. Since ethylene is a central agent triggering hyponasty, we focus on ethylene in controlling different stages during plant development and summarize current knowledge on the relationship between ethylene and cell growth.
doi:10.1093/aobpla/plr031
PMCID: PMC3249691  PMID: 22476501

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