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Key message Mapping combined with expression and variant analyses in switchgrass, a crop with complex genetics, identified a cluster of candidate genes for leaf wax in a fast-evolving region of chromosome 7K. Abstract Switchgrass (Panicum virgatum L.) is a promising warm-season candidate energy crop. It occurs in two ecotypes, upland and lowland, which vary in a number of phenotypic traits, including leaf glaucousness. To initiate trait mapping, two F2 mapping populations were developed by crossing two different F1 sibs derived from a cross between the tetraploid lowland genotype AP13 and the tetraploid upland genotype VS16, and high-density linkage maps were generated. Quantitative trait locus (QTL) analyses of visually scored leaf glaucousness and of hydrophobicity of the abaxial leaf surface measured using a drop shape analyzer identified highly significant colocalizing QTL on chromosome 7K (Chr07K). Using a multipronged approach, we identified a cluster of genes including Pavir.7KG077009, which encodes a Type III polyketide synthase-like protein, and Pavir.7KG013754 and Pavir.7KG030500, two highly similar genes that encode putative acyl-acyl carrier protein (ACP) thioesterases, as strong candidates underlying the QTL. The lack of homoeologs for any of the three genes on Chr07N, the relatively low level of identity with other switchgrass KCS proteins and thioesterases, as well as the organization of the surrounding region suggest that Pavir.7KG077009 and Pavir.7KG013754/Pavir.7KG030500 were duplicated into a fast-evolving chromosome region, which led to their neofunctionalization. Furthermore, sequence analyses showed all three genes to be absent in the two upland compared to the two lowland accessions analyzed. This study provides an example of and practical guide for trait mapping and candidate gene identification in a complex genetic system by combining QTL mapping, transcriptomics and variant analysis.

Background MicroRNAs (miRNAs) are important post-transcriptional regulators involved in the control of a range of processes, including symbiotic interactions in plants. MiRNA involvement in arbuscular mycorrhizae (AM) symbiosis has been mainly studied in model species, and our study is the first to analyze global miRNA expression in the roots of AM colonized switchgrass (Panicum virgatum), an emerging biofuel feedstock. AM symbiosis helps plants gain mineral nutrition from the soil and may enhance switchgrass biomass production on marginal lands. Our goals were to identify miRNAs and their corresponding target genes that are controlling AM symbiosis in switchgrass. Results Through genome-wide analysis of next-generation miRNA sequencing reads generated from switchgrass roots, we identified 122 mature miRNAs, including 28 novel miRNAs. By comparing miRNA expression profiles of AM-inoculated and control switchgrass roots, we identified 15 AM-responsive miRNAs across lowland accession “Alamo”, upland accession “Dacotah”, and two upland/lowland F1 hybrids. We used degradome sequencing to identify target genes of the AM-responsive miRNAs revealing targets of miRNAs residing on both K and N subgenomes. Notably, genes involved in copper ion binding were targeted by downregulated miRNAs, while upregulated miRNAs mainly targeted GRAS family transcription factors. Conclusion Through miRNA analysis and degradome sequencing, we revealed that both upland and lowland switchgrass genotypes as well as upland-lowland hybrids respond to AM by altering miRNA expression. We demonstrated complex GRAS transcription factor regulation by the miR171 family, with some miR171 family members being AM responsive while others remained static. Copper miRNA downregulation was common amongst the genotypes tested and we identified superoxide dismutases and laccases as targets, suggesting that these Cu-miRNAs are likely involved in ROS detoxification and lignin deposition, respectively. Other prominent targets of the Cu miRNAs were blue copper proteins. Overall, the potential effect of AM colonization on lignin deposition pathways in this biofuel crop highlights the importance of considering AM and miRNA in future biofuel crop development strategies.

Finger millet [Eleusine coracana (L.) Gaertn.] is a critical subsistence crop in eastern Africa and southern Asia but has few genomic resources and modern breeding programs. To aid in the understanding of finger millet genomic organization and genes underlying disease resistance and agronomically important traits, we generated a F

Long-term climate change and periodic environmental extremes threaten food and fuel security1 and global crop productivity2–4. Although molecular and adaptive breeding strategies can buffer the effects of climatic stress and improve crop resilience5, these approaches require sufficient knowledge of the genes that underlie productivity and adaptation6—knowledge that has been limited to a small number of well-studied model systems. Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass (Panicum virgatum). Analysis of biomass and survival among 732 resequenced genotypes, which were grown across 10 common gardens that span 1,800 km of latitude, jointly revealed extensive genomic evidence of climate adaptation. Climate–gene–biomass associations were abundant but varied considerably among deeply diverged gene pools. Furthermore, we found that gene flow accelerated climate adaptation during the postglacial colonization of northern habitats through introgression of alleles from a pre-adapted northern gene pool. The polyploid nature of switchgrass also enhanced adaptive potential through the fractionation of gene function, as there was an increased level of heritable genetic diversity on the nondominant subgenome. In addition to investigating patterns of climate adaptation, the genome resources and gene–trait associations developed here provide breeders with the necessary tools to increase switchgrass yield for the sustainable production of bioenergy., The genome of the biofuel crop switchgrass (Panicum virgatum) reveals climate–gene–biomass associations that underlie adaptation in nature and will facilitate improvements of the yield of this crop for bioenergy production.

BackgroundBiomass composition varies from plant to plant and greatly affects biomass utilization. Lignin is a heterogeneous phenolic polymer derived mainly fromp-coumaryl, coniferyl, and sinapyl alcohols and makes up to 10–25% of lignocellulosic biomass. Recently, tricin, anO-methylated flavone, was identified as a lignin monomer in many grass species. Tricin may function as a nucleation site for lignification and is advocated as a novel target for lignin engineering to reduce lignin content and improve biomass digestibility in grasses. Thioacidolysis is an analytical method that can be adapted to analyze both lignin monomeric composition and tricin content in the lignin polymer. However, the original thioacidolysis procedure is complex, laborious, and time consuming, making it difficult to be adopted for large-scale screening in biomass research. In this study, a modified, rapid higher throughput thioacidolysis method was developed.ResultsIn combination with gas chromatography–mass spectrometry (GC–MS) and liquid chromatography–mass spectrometry (LC–MS), the modified thioacidolysis method can be used to simultaneously characterize the lignin composition and tricin content using 2–5 mg of dry samples. The modified method eliminates the solvent extraction and drastically improves the throughput; 80 samples can be processed in one day per person. Our results indicate that there is no significant difference in the determination of lignin S/G ratio and tricin content between the original and modified methods.ConclusionsA modified thioacidolysis protocol was established. The results demonstrate that the modified method can be used for rapid, high-throughput, and reliable lignin composition and tricin content analyses for screening transgenic plants for cell wall modifications or in large-scale genome-wide association studies (GWAS).

While both plant-soil feedbacks and allelochemical interactions are key drivers of plant community dynamics, the potential for these two drivers to interact with each other remains largely unexplored. If soil microbes influence allelochemical production, this would represent a novel dimension of heterogeneity in plant-soil feedbacks. To explore the linkage between soil microbial communities and plant chemistry, we experimentally generated soil microbial communities and evaluated their impact on leaf chemical composition and allelopathic potential. Four native perennial old-field species (two each of Aster and Solidago) were grown in pairwise combination with each species' soil microbial community as well as a sterilized inoculum. We demonstrated unequivocally that variation in soil microbial communities altered leaf chemical fingerprints for all focal plant species and also changed their allelopathic potential. Soil microbes reduced allelopathic potential in bioassays by increasing germination 25-54% relative to sterile control soils in all four species. Plants grown with their own microbial communities had the lowest allelopathic potential, suggesting that allelochemical production may be lessened when growing with microbes from conspecifics. The allelopathic potential of plants grown in congener and confamilial soils was indistinguishable from each other, indicating an equivalent response to all non-conspecific microbial communities within these closely related genera. Our results clearly demonstrated that soil microbial communities cause changes in leaf tissue chemistry that altered their allelopathic properties. These findings represent a new mechanism of plant-soil feedbacks that may structure perennial plant communities over very small spatial scales that must be explored in much more detail.

Decades of white-tailed deer (Odocoileus virginianus (Zimmermann, 1780)) overpopulation have dramatically homogenized forests across much of the eastern United States, creating depauperate forest understory communities. The rate at which these communities recover once deer browsing has been reduced remains an open question. We evaluate overbrowsing legacy effects by examining how forest herbaceous layers respond in terms of biodiversity, density, and community composition over 11 years using exclosures and control plots within a mature beech–maple forest. Although little recovery occurred in the first 5 years, total density and preferred browse density rebounded substantially during the final years of the study. Although community composition began to diverge between exclosure and control plots after 5 years, diversity failed to recover even after 11 years of excluding browsers. Our findings show that vulnerable species can increase after excluding browsers but only if those species were initially present. Biodiversity recovery may be extremely slow because preferred browse species have been nearly extirpated from many forests and thus are unable to recruit into refugia. We empirically demonstrate the extent of the ghost of herbivory past or legacy effect of browsing, i.e., the substantial time delay between herbivore abatement and community response after decades of high deer densities.

Plants form belowground associations with mycorrhizal fungi in one of the most common symbioses on Earth. However, few large-scale generalizations exist for the structure and function of mycorrhizal symbioses, as the nature of this relationship varies from mutualistic to parasitic and is largely context-dependent. We announce the public release of MycoDB, a database of 4,010 studies (from 438 unique publications) to aid in multi-factor meta-analyses elucidating the ecological and evolutionary context in which mycorrhizal fungi alter plant productivity. Over 10 years with nearly 80 collaborators, we compiled data on the response of plant biomass to mycorrhizal fungal inoculation, including meta-analysis metrics and 24 additional explanatory variables that describe the biotic and abiotic context of each study. We also include phylogenetic trees for all plants and fungi in the database. To our knowledge, MycoDB is the largest ecological meta-analysis database. We aim to share these data to highlight significant gaps in mycorrhizal research and encourage synthesis to explore the ecological and evolutionary generalities that govern mycorrhizal functioning in ecosystems. ispartof: Scientific Data vol:10 issue:3 ispartof: location:England status: published

We propose a comprehensive program to evaluate the post-release phase of biocontrol programs that use insect herbivores to control invasive plant species. We argue that any release should be done in randomized release and non-release sites and should be followed up by well-replicated sampling and experimental protocols that evaluate the degree of success or failure. These follow-up studies should include landscape scale monitoring across relevant habitat gradients of (1) the abundance of the biocontrol agent, (2) the impact of the biocontrol agent on the target plant species, (3) the potential for non-target effects, and (4) the response of native species and communities to a reduction in the invasive species. We also argue that (5) experimental reductions of the biocontrol agent are required to eliminate the chance that the putative impact of the biocontrol agent is not confounded with other causes. Finally, we describe six scenarios, informed largely by a community ecology perspective, in which a biocontrol agent may decrease the abundance or vigor of the target plant species but not lead to successful control where native communities re-establish. We classify these failure scenarios as either direct or indirect effects of the invasive plant species: Native Source Limitation, Static Competitive Hierarchies, Novel Weapons, Trophic Shifts, Invasive Engineering and Associated Invasives. Overall, we argue that well replicated and landscape-scale post release monitoring programs are required not only to evaluate critically the degree of success and failure of biocontrol programs worldwide but also to provide insights into improving future biocontrol efforts.

Here we investigate the long-cited pattern that throughout the eastern United States, Solidago species (goldenrods), and in particular S. canadensis displace Aster species and dominate old-field communities. Theory predicts that such a ubiquitous pattern of repeated dominance should be linked to competitive ability for a limiting resource. However, no one has investigated this possibility in old-fields, representing a potentially significant gap in our understanding of a common human-altered environment. We tested the hypothesis that S. canadensis is the superior competitor for light compared to other common co-occurring goldenrod species, and that the goldenrods in general are the superior competitors for light compared to coexisting aster species, which are typically less abundant. We tested this hypothesis by comparing the light attenuation abilities of four goldenrod species, S. canadensis, S. rugosa, S. gigantea, and Euthamia graminifolia, and three aster species, Aster novae-angliae, A. pilosus, and A. prenanthoides. Consistent with our hypothesis, S. canadensis had a greater ability to attenuate light than any of the other goldenrods at higher densities, and the goldenrods overall had a greater ability to attenuate light than the asters. By conducting a census in our study area, we verified that S. canadensis is locally the most abundant goldenrod and that goldenrods are more locally abundant than asters. Furthermore, by conducting a literature survey we found evidence that S. canadensis replaces A. pilosus through time. Thus we found a close correspondence between relative abundance in the field and light attenuation ability in field experiments. These results are consistent with theory predicting that competition for limiting resources, in this case light, explains patterns of dominance and relative abundance in old-field plant communities.

White-tailed deer have been at high levels in the northeastern forests of the United States for decades and have strongly influenced forest dynamics. In this long-term study, we found that the composition of the overstory and understory assemblages of an old-growth beech-maple forest differed significantly. We used exclosures to test the hypothesis that deer contributed to these differences by differentially influencing the relationship between growth and mortality among seedlings of the six most abundant tree species. In the absence of deer, we found that the mortality of the six species decreased with increased growth and that interspecific differences in the relationships between growth and mortality coincided with previously observed shade-tolerance rankings. In the presence of deer, mortality decreased with growth only for the browse tolerant species (American beech, black cherry, and sugar maple). Mortality did not decrease with growth for preferred browse species (oak species, ash species, and red maple), rather, this relationship was eliminated in the presence of deer. The changes in growth and mortality relationships in the presence of browsing generally corresponded to observed changes in seedling density following the removal of deer. Sugar maple, ash, black cherry, and total stem density increased in the absence of deer. Our results suggest that the relationship between survival and growth in the understory, a metric of shade tolerance, is a fairly plastic response that varies depending upon the presence and absence of herbivores. Our results indicate that deer have contributed to the differences between understory and overstory vegetation, with browse tolerant species increasing in abundance at the expense of preferred browse species.

To understand the potential for facultative sugar feeding by Aedes aegypti, an important vector of dengue viruses, we evaluated seasonal and villagewide variation in sugar feeding during high- and low-dengue transmission seasons (rainy and dry seasons, respectively) in the Mae Sot region of Thailand. These seasons in Thailand are represented by different periods of flowering plant phenology. Although overall sugar feeding among female and male mosquitoes was low (ranging from 0.60 to 7.53 microg fructose per mosquito), sugar feeding among females was significantly greater during the dry, low-dengue transmission season. This variation could reflect specific preferences for flowering plants that were abundant in and around village homes during the dry season, such as Bougainvillea, Hibiscus, and Euphorbia.

Few studies have tested whether mutualisms may affect species distributions by altering the niches of partner species. We show that a fungal endophyte is associated with a shift in the soil moisture niche of its host plant relative to a co-occurring, endophyte-free congener. The endophyte appeared to initially restrict its host's distribution to wetter microsites before positively affecting its growth, suggesting the value of considering symbiont effects at different partner life stages. Our study identifies a symbiotic relationship as a potential mechanism facilitating the coexistence of two species, suggesting that symbiont effects on host niche may have community-level consequences., Mutualisms can play important roles in influencing species coexistence and determining community composition. However, few studies have tested whether such interactions can affect species distributions by altering the niches of partner species. In subalpine meadows of the Rocky Mountains, USA, we explored whether the presence of a fungal endophyte (genus Epichloë) may shift the niche of its partner plant, marsh bluegrass (Poa leptocoma) relative to a closely related but endophyte-free grass species, nodding bluegrass (Poa reflexa). Using observations and a 3-year field experiment, we tested two questions: (i) Do P. leptocoma and P. reflexa occupy different ecological niches? and (ii) Does endophyte presence affect the relative fitness of P. leptocoma versus P. reflexa in the putative niches of these grass species? The two species were less likely to co-occur than expected by chance. Specifically, P. leptocoma grew closer to water sources and in wetter soils than P. reflexa, and also had higher root colonization by mycorrhizal fungi. Endophyte-symbiotic P. leptocoma seeds germinated with greater frequency in P. leptocoma niches relative to P. reflexa niches, whereas neither endophyte-free (experimentally removed) P. leptocoma seeds nor P. reflexa seeds showed differential germination between the two niche types. Thus, endophyte presence constrained the germination and early survival of host plants to microsites occupied by P. leptocoma. However, endophyte-symbiotic P. leptocoma ultimately showed greater growth than endophyte-free plants across all microsites, indicating a net benefit of the symbiosis at this life history stage. Differential effects of endophyte symbiosis on different host life history stages may thus contribute to niche partitioning between the two congeneric plant species. Our study therefore identifies a symbiotic relationship as a potential mechanism facilitating the coexistence of two species, suggesting that symbiont effects on host niche may have community-level consequences.

Feedbacks between soil communities and plants may determine abundance and diversity in plant communities by influencing fitness and competitive outcomes. We tested the core hypotheses of soil community feedback theory: plant species culture distinct soil communities that alter plant performance and the outcome of interspecific competition. We applied this framework to inform the repeated dominance of Solidago canadensis in old-field communities. In glasshouse experiments, we examined the effects of soil communities on four plant species' performance in monoculture and outcomes of interspecific competition. We used terminal restriction fragment length polymorphism (TRFLP) analysis to infer differences in the soil communities associated with these plant species. Soil community origin had strong effects on plant performance, changed the intensity of interspecific competition and even reversed whether plant species were limited by conspecifics or heterospecifics. These plant-soil feedbacks are strong enough to upend winners and losers in classic competition models. Plant species cultured significantly different mycorrhizal fungal and bacterial soil communities, indicating that these feedbacks are likely microbiotic in nature. In old-fields and other plant communities, these soil feedbacks appear common, fundamentally alter the intensity and nature of plant competition and potentially maintain diversity while facilitating the dominance of So. canadensis.

Throughout Amazonia, overfishing has decimated populations of fruit-eating fishes, especially the large-bodied characid, Colossoma macropomum . During lengthy annual floods, frugivorous fishes enter vast Amazonian floodplains, consume massive quantities of fallen fruits and egest viable seeds. Many tree and liana species are clearly specialized for icthyochory, and seed dispersal by fish may be crucial for the maintenance of Amazonian wetland forests. Unlike frugivorous mammals and birds, little is known about seed dispersal effectiveness of fishes. Extensive mobility of frugivorous fish could result in extremely effective, multi-directional, long-distance seed dispersal. Over three annual flood seasons, we tracked fine-scale movement patterns and habitat use of wild Colossoma , and seed retention in the digestive tracts of captive individuals. Our mechanistic model predicts that Colossoma disperses seeds extremely long distances to favourable habitats. Modelled mean dispersal distances of 337–552 m and maximum of 5495 m are among the longest ever reported. At least 5 per cent of seeds are predicted to disperse 1700–2110 m, farther than dispersal by almost all other frugivores reported in the literature. Additionally, seed dispersal distances increased with fish size, but overfishing has biased Colossoma populations to smaller individuals. Thus, overexploitation probably disrupts an ancient coevolutionary relationship between Colossoma and Amazonian plants.

Primack, Richard, and Richard Corlett. 2005. Tropical rain forests: an ecological and biogeographical comparison. Blackwell, Malden, Massachusetts. ix + 319 p. $74.95, ISBN: 0-632-04513-2 (alk. paper).

WEBB, S. L., T H. PENDERGAST IV, AND M. E. DWYER (Drew University, Biology Department, Madison, NJ 07940.) Response of native and invasive maple seedling banks to removal of the exotic, invasive Norway maple (Acer platanoides). J. Torrey Bot. Soc. 128:000-000. 2001.-Acer platanoides is an exotic, invasive tree in eastern deciduous forests of North America where past research shows it to thrive in the forest interior and to suppress understory diversity. To test the efficacy of restoration strategies and to probe dynamics of this tree's seedling bank, trees and seedlings of Acer platanoides were removed in 1997 from a mixed maple forest carpeted by an even mix of exotic Acer platanoides and native Acer saccharum seedlings. The treatments were removal of trees (height > 1.5 m) and removal of small seedlings (height < 1.5 m), using a crossed design with a total of 80 permanent plots, all sampled before removals and two years later. After two years, removal of Acer platanoides trees had caused an increase in native Acer saccharum seedling densities over those in control areas and had caused a decrease of new Acer platanoides recruitment. Conversely, removal of Acer platanoides seedlings initiated far more new Acer platanoides than Acer saccharum seedlings. The Acer platanoides seedling bank was partially, but not fully, replenished two years after its removal. Although removal of canopy trees appears effective as a restoration tool, other exotic species (especially Lonicera japonica, Alliaria petiolata, and Robinia pseudoacacia) proliferated where tree removals opened the canopy. Restoring the pre-invasion community will thus require future intervention.