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1.  An effective nutrient medium for asymbiotic seed germination and large-scale in vitro regeneration of Dendrobium hookerianum, a threatened orchid of northeast India 
AoB Plants  2011;2012:plr032.
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
Dendrobium hookerianum is a rare and threatened epiphytic orchid of northeast India. Prospects for conservation would be strengthened by developing an in vitro method for mass propagation. Seeds are minute and difficult to use directly in the field for this purpose, being non-endospermous with a low nutrient content and dependent on a specific fungus for germination and early seedling development. Although produced in large numbers (2–3 million per capsule), <5 % germinate naturally in the wild. Our objective was to develop a rapid and successful method for in vitro propagation based on an initial in vitro asymbiotic seed germination step that achieved high percentages.
Effects of four different media, i.e. (i) Murashige and Skoog (MS), (ii) Mitra et al., (iii) Knudson (KC) and (iv) Gamborg et al. (B5), were evaluated for large-scale multiplication by asymbiotic seed germination. Seedling leaf number, shoot number, shoot length, root number and root length were scored. After 7–8 months, large numbers of well-rooted plantlets were transferred to a glasshouse in thermocol pots containing compost. Six different composts based on broken brick and charcoal were compared for their ability to support further development over 90 days of hardening.
Principal results
The fastest and highest percentage seed germination was achieved using MS medium. Seeds on MS medium germinated in 3–4 weeks compared with 7–8 weeks on B5 medium. Seedling development was also superior on MS medium. The inclusion of plant growth regulators was unnecessary. Compost comprising broken brick and charcoal with an upper layer of moss was found to be the most suitable for the survival of transferred plantlets. Ninety per cent survival of plantlets was achieved 90 days after transfer to a glasshouse.
The use of MS culture medium is well suited for the mass multiplication of D. hookerianum plants intended for re-introducing this threatened orchid into the wild.
PMCID: PMC3260561
2.  Estimates of nuclear DNA content in 98 species of brown algae (Phaeophyta) 
AoB Plants  2011;2011:plr001.
Despite the fact that brown algae are critical components of marine ecosystems around the world only one species has had its genome sequenced. To facilitate genome studies in the class we report data for 12 of the 19 recognized orders.
Background and aims
Brown algae are critical components of marine ecosystems around the world. However, the genome of only one species of the class has so far been sequenced. This contrasts with numerous sequences available for model organisms such as higher plants, flies or worms. The present communication expands our coverage of DNA content information to 98 species of brown algae with a view to facilitating further genomic investigations of the class.
The DNA-localizing fluorochrome DAPI (4′,6-diamidino-2-phenylindole) and the red blood cell (chicken erythrocyte) standard were used to estimate 2C values by static microspectrophotometry.
Principal results
2C DNA contents are reported for 98 species of brown algae, almost doubling the number of estimates available for the class. The present results also expand the reported DNA content range to 0.2–3.6 pg, with several species of Fucales and Laminariales containing apparent polyploid genomes with 2C = 1.8–3.6 pg.
The data provide DNA content values for 12 of the 19 recognized orders of brown algae spanning the breadth of the class. Despite earlier contentions concerning DNA content and the presence of oogamy, the present results do not support a correlation between phylogenetic placement and genome size. The closest sister groups to the brown algae have genome sizes on the order of 0.3 pg (e.g. Schizocladiophyceae), suggesting that this may be the ancestral genome size. However, DNA content ranges widely across the class.
PMCID: PMC3064507  PMID: 22476472
3.  High genetic diversity with moderate differentiation in Juniperus excelsa from Lebanon and the eastern Mediterranean region 
AoB Plants  2011;2011:plr003.
Juniperus excelsa constitutes a precious woody species of high ecological value able to grow up to Mountain treeline around the Mediterranean. Nuclear microsatellites were used to shed light on genetic diversity and differentiation of different Mediterranean populations. This information is essential in planning conservation strategies and reforestation programs.
Background and aims
Juniperus excelsa is an important woody species in the high mountain ecosystems of the eastern Mediterranean Basin where it constitutes the only coniferous species found at the tree line. The genetic diversity within and among J. excelsa populations of the eastern Mediterranean Basin is studied in the light of their historical fragmentation.
Nuclear microsatellites originally developed for Juniperus communis and J. przewalskii were tested on 320 individuals from 12 different populations originating from Lebanon, Turkey, Cyprus, Greece and the Ukraine.
Principal results
Among the 31 nuclear microsatellite primers tested, only three produced specific amplification products, with orthology confirmed by sequence analysis. They were then used for genetic diversity studies. The mean number of alleles and the expected heterozygosity means were Na=8.78 and He=0.76, respectively. The fixation index showed a significant deviation from Hardy–Weinberg equilibrium and an excess of homozygotes (FIS=0.27–0.56). A moderate level of genetic differentiation was observed among the populations (FST=0.075, P<0.001). The most differentiated populations corresponded to old vestigial stands found at the tree line (>2000 m) in Lebanon. These populations were differentiated from the other populations that are grouped into three sub-clusters.
High levels of genetic diversity were observed at species and population levels. The high level of differentiation in the high-mountain Lebanese populations reflects a long period of isolation or possibly a different origin. The admixture observed in other populations from Lebanon suggests a more recent separation from the Turkish–southeastern European populations.
PMCID: PMC3064508  PMID: 22476474
4.  Principles of visual key construction―with a visual identification key to the Fagaceae of the southeastern United States 
AoB Plants  2011;2011:plr005.
We present the first visual, as opposed to illustrated, keys to a group of taxa. The creation of four visual keys to the Fagaceae of the southeastern United States are described, one for each of the following characteristics: leaves, buds, fruits, bark.
Background and aims
Advances in digital imaging have made possible the creation of completely visual keys. By a visual key we mean a key based primarily on images, and that contains a minimal amount of text. Characters in visual keys are visually, not verbally defined. In this paper we create the first primarily visual key to a group of taxa, in this case the Fagaceae of the southeastern USA. We also modify our recently published set of best practices for image use in illustrated keys to make them applicable to visual keys.
Photographs of the Fagaceae were obtained from internet and herbarium databases or were taken specifically for this project. The images were printed and then sorted into hierarchical groups. These hierarchical groups of images were used to create the ‘couplets’ in the key. A reciprocal process of key creation and testing was used to produce the final keys.
Principal results
Four keys were created, one for each of the parts—leaves, buds, fruits and bark. Species description pages consisting of multiple images were also created for each of the species in the key. Creation and testing of the key resulted in a modified list of best practices for image use visual keys.
The inclusion of images into paper and electronic keys has greatly increased their ease of use. However, virtually all of these keys are still based upon verbally defined, atomistic characters. The creation of primarily visual keys allows us to overcome the well-known limitations of linguistic-based characters and create keys that are much easier to use, especially for botanical novices.
PMCID: PMC3072766  PMID: 22476476
5.  How much detail and accuracy is required in plant growth sub-models to address questions about optimal management strategies in agricultural systems? 
AoB Plants  2011;2011:plr006.
The amount of detail and accuracy required in plant growth sub-models within agricultural systems management models depends strongly on the question being addressed. Taking an ‘as-simple-as-possible’ approach has advantages such as keeping models transparent and easy to analyse while remaining appropriate to the question of interest.
Background and aims
Simulations that integrate sub-models of important biological processes can be used to ask questions about optimal management strategies in agricultural and ecological systems. Building sub-models with more detail and aiming for greater accuracy and realism may seem attractive, but is likely to be more expensive and time-consuming and result in more complicated models that lack transparency. This paper illustrates a general integrated approach for constructing models of agricultural and ecological systems that is based on the principle of starting simple and then directly testing for the need to add additional detail and complexity.
The approach is demonstrated using LUSO (Land Use Sequence Optimizer), an agricultural system analysis framework based on simulation and optimization. A simple sensitivity analysis and functional perturbation analysis is used to test to what extent LUSO's crop–weed competition sub-model affects the answers to a number of questions at the scale of the whole farming system regarding optimal land-use sequencing strategies and resulting profitability.
Principal results
The need for accuracy in the crop–weed competition sub-model within LUSO depended to a small extent on the parameter being varied, but more importantly and interestingly on the type of question being addressed with the model. Only a small part of the crop–weed competition model actually affects the answers to these questions.
This study illustrates an example application of the proposed integrated approach for constructing models of agricultural and ecological systems based on testing whether complexity needs to be added to address particular questions of interest. We conclude that this example clearly demonstrates the potential value of the general approach. Advantages of this approach include minimizing costs and resources required for model construction, keeping models transparent and easy to analyse, and ensuring the model is well suited to address the question of interest.
PMCID: PMC3072767  PMID: 22476477
6.  Seed pre-treatment in rice reduces damage, enhances carbohydrate mobilization and improves emergence and seedling establishment under flooded conditions 
AoB Plants  2011;2011:plr007.
Priming rice seeds (soaking followed by drying) or soaking just before sowing improved emergence from flooded soil, reduced membrane damage from ROS and hastened carbohydrate mobilization. Most benefit was to lines with a superior ability to germinate in flooded soil even when untreated.
Background and aims
Early flooding helps control weeds but reduces seedling establishment in direct-seeded rice (Oryza sativa). When combined with appropriate management practices, the use of genotypes that better tolerate flooding during emergence can enhance crop establishment in flood-prone areas. Management options include seed pre-treatment and we tested the influence of pre-soaking for 24 h prior to sowing or of priming (soaking for 24 or 48 h followed by drying).
The effects on seedling establishment after 21-day flooding of pre-soaking seeds for 24 h before sowing and/or of priming seeds were examined together with physiological responses connected with reactive oxygen scavenging. Seeds of four lines with contrasting abilities to tolerate flooding at the germination stage were compared. Seeds were primed using KCl solutions (48 h) or water (24 h) and pre-soaked using water. Lipid peroxidation and activities of reactive oxygen-scavenging enzymes were measured in seeds before sowing. Carbohydrate mobilization in germinating seeds and seedling growth were also monitored at intervals.
Principal results
Seed pre-treatment by pre-soaking or by priming increased survival of flooding and accelerated and improved seedling establishment, especially in tolerant genotypes. Primed seeds had less lipid peroxidation and higher superoxide dismutase (SOD) and catalase (CAT) activities than non-primed seeds. Amylase activities and starch breakdown were also hastened in primed seeds. Survival after flooding was positively correlated with amylase activity but negatively correlated with the extent of lipid peroxidation.
Pre-soaking and priming improved seedling establishment in flooded soil, enhanced the capacity to scavenge reactive oxygen species in seeds by increasing SOD and CAT activities, and hastened carbohydrate mobilization. Tolerant genotypes responded better to these treatments, emphasizing the effectiveness of combining genetic tolerance with appropriate seed pre-treatment to improve seedling establishment of rice sown in flooded soils.
PMCID: PMC3072768  PMID: 22476478
7.  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.
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.
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.
PMCID: PMC3077818  PMID: 22476475
8.  Equisetum species show uniform epicuticular wax structures but diverse composition patterns 
AoB Plants  2011;2011:plr009.
In the Equisetopsida, different wax distribution and composition patterns in the plant organs indicate a close relationship between wax structure and chemistry and the assimilatory function of these organs. Diverging wax compound classes show the two subgenera of Equisetum to be well separated.
Background and aims
Only few data on the epicuticular waxes (EWs) of horsetails are available. This contribution therefore focuses on the wax micromorphology and chemical composition of Equisetum species of the subgenera Equisetum and Hippochaete.
Distribution patterns and structural details of EW on the shoots were studied by scanning electron microscopy. After extraction with chloroform, the chemical composition of wax isolates was analysed by gas chromatography.
Principal results
Epicuticular wax crystals were non-oriented platelets or membraneous platelets. They were usually located on subsidiary cells of stomata and adjacent cells. Other parts of the shoots were covered mainly with a smooth wax film or small granules only. The chemical constituents found were alkanes, esters, aldehydes, primary alcohols and free fatty acids in a range of C20–C36 (in esters C36–C56). All species of the subgenus Hippochaete showed a similar pattern of fractions with high percentages of alkanes and aldehydes, whereas the subgenus Equisetum species had distinctly different wax compositions. Extracts from the internodes—surfaces without well-developed EW crystals and only few stomata—showed the lowest contents of aldehydes.
The covering with EW crystals will provide unhindered gas exchange and, combined with intracuticular wax, may prevent excess water loss during winter in the evergreen shoots of the subgenus Hippochaete. The results indicate that the Equisetum wax micromorphology and biosynthesis are comparable to EW of other pteridophyte classes and mosses.
PMCID: PMC3096319  PMID: 22476480
9.  Detection and analysis of endogenous badnaviruses in the New Zealand flora 
AoB Plants  2011;2011:plr008.
Discovery of badnavirus reverse transcriptase sequences in species from the New Zealand flora upsets conventional wisdom that badnaviruses are of tropical origin. Although no freely replicating badnaviruses were detected, the sequences help in the study of phylogeny, systematics and reproductive biology.
Background and aims
Badnaviruses and their host-integrated DNA occur in tropical crops and a few northern temperate species. Following the discovery of a badnavirus on a subantarctic island with floristic links to New Zealand, we postulated that badnaviruses exist in the New Zealand flora. Badnavirus reverse transcriptase (RT) sequences consist of variable regions flanked by highly conserved regions. This study used RT sequences to detect and characterize badnavirus sequences in the New Zealand flora and to investigate their utility for the study of broader aspects of plant biology.
Molecular diversity of RT sequences was analysed using polymerase chain reaction and denaturing gradient gel electrophoresis (DGGE). In a study of the genus Melicytus, internal transcribed spacer (ITS) sequences were compared with the RT data.
Principal results
No freely replicating badnaviruses were detected but more than half of the species (37/60) contained RT sequences. Phylogenetic analysis of 21 RT sequences formed monophyletic groups distinct from other species and from badnaviruses. No frameshift mutations occurred in any of the sequences translated in silico. More detailed study of the genus Melicytus indicated broader applications for our approach. Analysis of RT sequences revealed the presence of a previously unrecognized species (confirmed using ITS). Inheritance of DGGE profiles by Melicytus ramiflorus seedlings suggested that this species may undergo apomixis.
The presence of integrated badnavirus sequences in a wide range of taxa from this Southern Hemisphere flora indicates that these sequences may be common in many temperate regions. Potential to activate viruses from these sequences should be considered when placing these species in tissue culture or under other forms of abiotic or genomic stress. Analysis of endogenous RT sequences shows potential for the study of systematics, phylogenetics and plant reproductive biology.
PMCID: PMC3104934  PMID: 22476479
10.  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.
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.
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.
PMCID: PMC3114564  PMID: 22476481
11.  Micropropagation of Ilex khasiana, a critically endangered and endemic holly of Northeast India 
AoB Plants  2011;2011:plr012.
The paper describes in vitro techniques for mass propagation of IIex khasiana, a rare and critically endangered holly endemic to Khasi Hills Hills of Meghalaya, India. The approach will help conserve I. khasiana and other endangered species.
Background and aims
Ilex khasiana is a rare and critically endangered holly endemic to the Khasi Hills of Meghalaya, India, and confined to a small number of pocket areas. In addition to conventional methods of propagation, endemic and threatened plants such as this could be more effectively multiplied and conserved using in vitro methods. Such techniques have the additional advantage of having a low impact on wild populations because they require a minimum of starting material. Our objective was to develop methodologies for the successful in vitro mass propagation of I. khasiana.
Seedlings were germinated in vitro under sterile conditions and nodal explants from these were transferred to Murashige and Skoog (MS) medium supplemented with 8.88 µM 6-benzyladenine and 4.64 µM kinetin.
Principal results
This generated ∼10 shoots per explant. In a second approach, callus was obtained from seedling-derived leaf discs cultured on MS medium supplemented with 2,4-dichlorophenoxyacetic acid and 6-benzyladenine. Approximately 12 adventitious shoots per callus were regenerated from 83.33 % of the calli after transfer to MS medium supplemented with 6.63 µM 6-benzyladenine. The most effective treatment for inducing root formation on the shoots was transfer of shoots to half-strength MS medium with 9.84 µM indole-3-butyric acid. Regenerated plantlets with well-developed shoots and roots were hardened and transferred to open soil with 70 % survival after 4 weeks.
Both the methods described here are well suited for the mass multiplication of this critically endangered tree species.
PMCID: PMC3129536  PMID: 22476482
12.  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.
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.
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.
PMCID: PMC3129537  PMID: 22476483
13.  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.
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.
The reproductive phenology of the herbaceous–shrubby communities is mainly influenced by the composition of the life-forms, the precipitation regime and soil type.
PMCID: PMC3144378  PMID: 22476484
14.  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.
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.
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.
PMCID: PMC3144379  PMID: 22476485
15.  Parentage determination of Vanda Miss Joaquim (Orchidaceae) through two chloroplast genes rbcL and matK 
AoB Plants  2011;2011:plr018.
This manuscript describes the use of the DNA barcoding regions matK and rbcL to determine the seed parent of the popular orchid hybrid and Singapore's national flower, Vanda Miss Joaquim. The pollen parent was inferred by exclusion to be V. hookeriana and the pod parent V. teres var. andersonii.
Background and aims
The popular hybrid orchid Vanda Miss Joaquim was made Singapore's national flower in 1981. It was originally described in the Gardeners’ Chronicle in 1893, as a cross between Vanda hookeriana and Vanda teres. However, no record had been kept as to which parent contributed the pollen. This study was conducted using DNA barcoding techniques to determine the pod parent of V. Miss Joaquim, thereby inferring the pollen parent of the hybrid by exclusion.
Two chloroplast genes, matK and rbcL, from five related taxa, V. hookeriana, V. teres var. alba, V. teres var. andersonii, V. teres var. aurorea and V. Miss Joaquim ‘Agnes’, were sequenced. The matK gene from herbarium specimens of V. teres and V. Miss Joaquim, both collected in 1893, was also sequenced.
Principal results
No sequence variation was found in the 600-bp region of rbcL sequenced. Sequence variation was found in the matK gene of V. hookeriana, V. teres var. alba, V. teres var. aurorea and V. Miss Joaquim ‘Agnes’. Complete sequence identity was established between V. teres var. andersonii and V. Miss Joaquim ‘Agnes’. The matK sequences obtained from the herbarium specimens of V. teres and V. Miss Joaquim were completely identical to the sequences obtained from the fresh samples of V. teres var. andersonii and V. Miss Joaquim ‘Agnes’.
The pod parent of V. Miss Joaquim ‘Agnes’ is V. teres var. andersonii and, by exclusion, the pollen parent is V. hookeriana. The herbarium and fresh samples of V. teres var. andersonii and V. Miss Joaquim share the same inferred maternity. The matK gene was more informative than rbcL and facilitated differentiation of varieties of V. teres.
PMCID: PMC3156982  PMID: 22476488
16.  The amino terminal F-box domain of Petunia inflata S-locus F-box protein is involved in the S-RNase-based self-incompatibility mechanism 
AoB Plants  2011;2011:plr016.
We showed that the F-box domain of PiSLF, Petunia inflata S-locus F-box protein, is essential for SI function and that a P. inflata ortholog of Antirrhinum SSK1 does not interact with PiSLF, consistent with our previous finding that PiSLF might be in a novel E3 complex.
Background and aims
Pistils of flowering plants possessing self-incompatibility (SI) can distinguish between self and non-self pollen, and only allow non-self pollen to effect fertilization. For Petunia inflata, the S-RNase gene encodes pistil specificity and multiple S-locus F-box (SLF) genes encode pollen specificity. Each SLF produced in pollen interacts with a subset of non-self S-RNases to mediate their ubiquitination and degradation by the 26S proteasome.
S-locus F-box has been proposed to function as a component of the conventional SCF (SKP1-CULLIN-F-box protein) complex, based on the finding that two SKP1-like proteins, AhSSK1 (Antirrhinum hispanicum SLF-interacting SKP1-like1) and PhSSK1 (Petunia hybrida SSK1), interact with the F-box domain of some allelic variants of SLF. However, we previously showed that PiSLF (P. inflata SLF) did not interact with any SKP1 of P. inflata or Arabidopsis thaliana, but instead interacted with a RING-finger protein, PiSBP1 (P. inflata S-RNase-Binding Protein1), which may also play the role of SKP1. Thus, the biochemical nature of the SLF-containing complex is as yet unclear.
Principal results
To examine whether the F-box domain of PiSLF is required for SI function, we expressed a truncated PiSLF2 (S2 allelic variant) without this domain in S2S3 plants and showed that, unlike the full-length PiSLF2, it did not cause breakdown of SI in S3 pollen. We identified PiSSK1 (P. inflata SSK1) and found that it did not interact with PiSLF1, PiSLF2 or PiSLF3.
The finding that the truncated PiSLF2 did not cause breakdown of SI in S3 transgenic pollen suggests that the F-box domain of PiSLF2 is required for mediating degradation of S3-RNase, a non-self S-RNase, in S3 pollen, and thus is required for SI function. The finding that PiSSK1 did not interact with three allelic variants of PiSLF is consistent with our previous finding that PiSLF might not be in a conventional SCF complex.
PMCID: PMC3158857  PMID: 22476486
17.  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.
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.
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).
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.
PMCID: PMC3158858  PMID: 22476487
18.  Chromosome number variation in two antipodean floras 
AoB Plants  2011;2011:plr020.
Italy and New Zealand are very similar in shape, extension, altitudinal and latitudinal range but located in opposite hemispheres. This paper compares variation in chromosome number in these two hotspot regions. The results challenge previous ideas concerning links between geography and patterns of chromosome number variation.
Background and aims
We compared chromosome number (CN) variation in the nearly antipodean Italian and New Zealand floras to verify (i) whether patterns of variation reflect their similar latitudinal ranges or their different biogeographic/taxonomic contexts, (ii) if any differences are equally distributed across major taxa/lineages and (iii) if the frequency, number and taxonomic distribution of B-chromosomes differ between the two countries.
We compared two datasets comprising 3426 (Italy) and 2525 (New Zealand) distinct cytotypes. We also compared a subset based on taxonomic orders and superimposed them onto a phylogeny of vascular plants. We used standard statistics, histograms, and either analysis of variance or Kruskal–Wallis tests to analyse the data.
Principal results
Mean CN of the vascular New Zealand flora is about twice that of Italy. For most orders, mean CN values for New Zealand are higher than those of the Italian flora and the differences are statistically significant. Further differences in CN variation among the orders and main clades that we studied, irrespective of geographical distinctions, are revealed. No correlation was found between chromosome and B-chromosome number.
Mean CN of the whole New Zealand dataset is about twice that of the Italian flora. This suggests that extensive polyploidization played a major role in the evolution of the New Zealand vascular flora that is characterized by a rate of high endemism. Our results show that the hypothesis of a polyploid increase proportional to distance from the Equator cannot be applied to territories with the same latitudinal ranges but placed in different hemispheres. We suggest that bioclimatic gradients, rather than or in addition to latitudinal gradients, might account for a polyploidy increase. Our data also suggest that any adaptive role of B-chromosomes at geographic scale may be sought in their frequency rather than in their number.
PMCID: PMC3166199  PMID: 22476490
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.
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.
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.
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.
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.
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.
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.
PMCID: PMC3176521  PMID: 22476491
21.  Reductions in biomass accumulation, photosynthesis in situ and net carbon balance are the costs of protecting Vitis vinifera ‘Semillon’ grapevines from heat stress with shade covering 
AoB Plants  2011;2011:plr023.
Shade cloth can be used to protect grapevines from high temperatures. However, the resulting low light intensity is shown to reduce photosynthesis, leading to lower carbon allocation to vegetative growth and sugar accumulation. Protection from heat by shading is, therefore, costly for the carbon economy of the vines.
Background and aims
Covering whole vines with shade cloth is used to protect the vines from heat stress, but may have costs on vine productivity through reduced light availability. Our aim was to assess the carbon balance of vines growing with and without shade to quantify the impact of the covering.
Whole vines were covered with 70 % shade cloth, and shoot leaf area and leaf, stem and bunch growth were followed over two growing seasons. Photosynthesis was measured in situ in all leaves along selected shoots over the growing season. A carbon balance was constructed from the difference in acquisition of carbon and the sequestration of carbon as biomass across the growing seasons.
Principal results
Shade covering had no initial impact on shoot growth but later reduced leaf growth and later still bunch growth. Stem growth was unaffected. Photosynthetic properties were characteristic of shade leaves, with lower rates and lower light saturation compared with well-exposed leaves. Overall, net photosynthesis was reduced by 40 % by the shade covering and was attributed to the reduced photon flux densities. From the carbon balance, vines were reliant on carbon reserves over 6 weeks after budbreak until current photosynthate increased sufficiently to supply the growth. Shade covering impacted most on biomass accumulation to leaves and bunches at the stage when the vines became autotrophic, consistent with the reduction in carbon acquisition. The markedly high carbon demand by bunches caused a mid-season negative carbon balance, implying that shoots had to draw further on reserves to supply the carbon.
Shade covering over whole grapevines exacerbated the imbalance between the supply of and demand for carbon and greatly reduced vine biomass, especially reproductive allocation. Covering vines with shade cloth to protect the vines from heat events, therefore, had major costs in the carbon economy.
PMCID: PMC3176522  PMID: 22476493
22.  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.
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.
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.
PMCID: PMC3178842  PMID: 22476492
23.  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.
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.
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.
PMCID: PMC3185971  PMID: 22476494
24.  Phylogeny and divergence times inferred from rps16 sequence data analyses for Tricyrtis (Liliaceae), an endemic genus of north-east Asia 
AoB Plants  2011;2011:plr025.
The rate of molecular evolution of Tricyrtis plant groups as a model system was estimated. The outcome further highlights the importance of conserving biodiversity in a rapidly changing Earth environment. This phylogenetic analyses of Tricyrtis with its high endemism in north-east Asia sheds light on processes of speciation processes.
Background and aims
Tricyrtis is a genus of monocots with attractive and sophisticated flower shapes and colours, endemic to north-east Asia. There are 18 known species. The highly restricted geographical distribution of the genus is of great interest in terms of both abiotic (continental drift) and biotic (long-distance dispersal) impacts on monocot plant speciation events and their timing, and of evolutionary patterns of diversification leading to the extant taxa. The aims of this study were to (i) predict the time of speciation (divergence) events at infraspecific levels of Tricyrtis, (ii) estimate the rate of evolution of the genus and (iii) provide information on an excellent plant model system in terms of studying loss of biodiversity or extinction of organisms in the dynamic earth environment.
To investigate the divergence time and evolution rate of Tricyrtis, Bayesian Markov chain Monte Carlo (MCMC) analyses were performed by calculating the mean branch lengths of evolutionary paths based on base substitution variations between rps16 intron nucleotide sequences from the 18 known species.
Principal results
Based upon the relaxed molecular clock model test data, a Bayesian phylogenetic inference tree is presented, and the divergence times and rate of evolution of Tricyrtis were estimated. The analyses also suggest that evolution is occurring at the infraspecific level of the genus in a manner that is not strictly clock bound.
Continental drift may have been the main speciation process giving rise to the current distribution of the taxa of Tricyrtis. The single-locus gene sequence data presented here are a significant step towards an improved future understanding of the molecular evolution of Tricyrtis via multi-locus evaluation.
PMCID: PMC3186281  PMID: 22476495
25.  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.
PMCID: PMC3220415  PMID: 22476497

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