Host plant genetic control of associated fungal and insect species in a Populus hybrid cross

Plants employ a diverse set of defense mechanisms to mediate interactions with insects and fungi. These relationships can leave lasting impacts on host plant genome structure such as rapid expansion of gene families through tandem duplication. These genomic signatures provide important clues about the complexities of plant/biotic stress interactions and evolution. We used a pseudo‐backcross hybrid family to identify quantitative trait loci (QTL) controlling associations between Populus trees and several common Populus diseases and insects. Using whole‐genome sequences from each parent, we identified candidate genes that may mediate these interactions. Candidates were partially validated using mass spectrometry to identify corresponding QTL for defensive compounds. We detected significant QTL for two interacting fungal pathogens and three insects. The QTL intervals contained candidate genes potentially involved in physical and chemical mechanisms of host–plant resistance and susceptibility. In particular, we identified adjoining QTLs for a phenolic glycoside and Phyllocolpa sawfly abundance. There was also significant enrichment of recent tandem duplications in the genomic intervals of the native parent, but not the exotic parent. Tandem gene duplication may be an important mechanism for rapid response to biotic stressors, enabling trees with long juvenile periods to reach maturity despite many coevolving biotic stressors.     

Genomic evidence of genetic variation with pleiotropic effects on caterpillar fitness and plant traits in a model legume

Plant–insect interactions are ubiquitous, and have been studied intensely because of their relevance to damage and pollination in agricultural plants, and to the ecology and evolution of biodiversity. Variation within species can affect the outcome of these interactions. Specific genes and chemicals that mediate these interactions have been identified, but genome‐ or metabolome‐scale studies might be necessary to better understand the ecological and evolutionary consequences of intraspecific variation for plant–insect interactions. Here, we present such a study. Specifically, we assess the consequences of genome‐wide genetic variation in the model plant Medicago truncatula for Lycaeides melissa caterpillar growth and survival (larval performance). Using a rearing experiment and a whole‐genome SNP data set (>5 million SNPs), we found that polygenic variation in M. truncatula explains 9%–41% of the observed variation in caterpillar growth and survival. Genetic correlations among caterpillar performance and other plant traits, including structural defences and some anonymous chemical features, suggest that multiple M. truncatula alleles have pleiotropic effects on plant traits and caterpillar performance (or that substantial linkage disequilibrium exists among distinct loci affecting subsets of these traits). A moderate proportion of the genetic effect of M. truncatula alleles on L. melissa performance can be explained by the effect of these alleles on the plant traits we measured, especially leaf toughness. Taken together, our results show that intraspecific genetic variation in M. truncatula has a substantial effect on the successful development of L. melissa caterpillars (i.e., on a plant–insect interaction), and further point toward traits potentially mediating this genetic effect.     

Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations

Currently, there is much debate on the genetic architecture of quantitative traits in wild populations. Is trait variation influenced by many genes of small effect or by a few genes of major effect? Where is additive genetic variation located in the genome? Do the same loci cause similar phenotypic variation in different populations? Great tits (Parus major) have been studied extensively in long‐term studies across Europe and consequently are considered an ecological ‘model organism’. Recently, genomic resources have been developed for the great tit, including a custom SNP chip and genetic linkage map. In this study, we used a suite of approaches to investigate the genetic architecture of eight quantitative traits in two long‐term study populations of great tits—one in the Netherlands and the other in the United Kingdom. Overall, we found little evidence for the presence of genes of large effects in either population. Instead, traits appeared to be influenced by many genes of small effect, with conservative estimates of the number of contributing loci ranging from 31 to 310. Despite concordance between population‐specific heritabilities, we found no evidence for the presence of loci having similar effects in both populations. While population‐specific genetic architectures are possible, an undetected shared architecture cannot be rejected because of limited power to map loci of small and moderate effects. This study is one of few examples of genetic architecture analysis in replicated wild populations and highlights some of the challenges and limitations researchers will face when attempting similar molecular quantitative genetic studies in free‐living populations.     

Variation in the guild composition of herbivorous insect assemblages among co‐occurring plant species

Variation in plant traits among plant species may promote the development of a characteristic functional assemblage of insect herbivores associated with each plant species. However, only a small number of studies have detailed the representation of several herbivore guilds among co‐occurring plant species to determine whether the functional structure of herbivorous insect assemblages varies widely and consistently among plant species. The present study provides one of the few published data sets reporting on the density of several guilds of insect herbivores among numerous plant species. Variation in guild associations with plant phenology and season are also described. Insect herbivores were divided into 10 guilds, and the representation of these guilds was examined for 18 co‐occurring plant species. Guild densities and assemblage composition varied significantly among plant species, even when variation over time was taken into account. Variation in guild densities and assemblage composition were not strongly related to the taxonomic relationships of the plants. The highest densities of several guilds occurred in spring and summer, although other guilds were not strongly seasonal. Certain guilds were strongly associated with the presence of new leaves, whereas other guilds appeared to prefer mature leaves. This resulted in assemblage differences between samples containing new and mature leaves and samples containing mature leaves only. Even though the timing and duration of leaf and flower production varied among plant species, this did not explain all variation in guild densities among plant species. It is suggested that additional factors, including plant traits, are contributing to the wide and consistent variation in herbivore assemblage composition among plant species.     

Geographic structure in metabolome and herbivore community co‐occurs with genetic structure in plant defence genes

Plant–herbivore interactions vary across the landscape and have been hypothesised to promote local adaption in plants to the prevailing herbivore regime. Herbivores that feed on European aspen (Populus tremula) change across regional scales and selection on host defence genes may thus change at comparable scales. We have previously observed strong population differentiation in a set of inducible defence genes in Swedish P. tremula. Here, we study the geographic patterns of abundance and diversity of herbivorous insects, the untargeted metabolome of the foliage and genetic variation in a set of wound‐induced genes and show that the geographic structure co‐occurs in all three data sets. In response to this structure, we observe local maladaptation of herbivores, with fewer herbivores on local trees than on trees originated from more distant localities. Finally, we also identify 28 significant associations between single nucleotide polymorphisms SNPs from defence genes and a number of the herbivore traits and metabolic profiles.     

Variation in composition of two bumble bee species across communities affects nectar robbing but maintains pollinator visitation rate to an alpine plant,Salvia przewalskii

1. In many flowering plants, bumble bees may forage as both pollinators and nectar robbers. This mixed foraging behaviour may be influenced by community context and consequently, potentially affect pollination of the focal plant. 2. Salvia przewalskii is both pollinated and robbed exclusively by bumble bees. In the present study area, it was legitimately visited by two species of bumble bees with different tongue length, Bombus friseanus and Bombus religiosus, but it was only robbed by Bombus friseanus, the shorter‐tongued bumble bee. The intensity of nectar robbing and pollinator visitation rate to the plant were investigated across 26 communities in the Hengduan Mountains in East Himalaya during a 2‐year project. For each of these communities, the floral diversity, and the population size and floral resource of S. przewalskii were quantified. The abundances of the two bumble bee species were also recorded. 3. Both nectar robbing and pollinator visitation rate were influenced by floral diversity. However, pollinator visitation rate was not affected by nectar robbing. The results revealed that relative abundance of the two bumble bee species significantly influenced the incidence of nectar robbing but not the pollinator visitation rate. Increased abundance of B. religiosus, the legitimate visitors, exacerbated nectar robbing, possibly by causing B. friseanus to shift to robbing; however, pollinator visitation remained at a relatively high level. 4. The results may help to explain the persistence of both nectar robbing and pollination, and suggest that, in comparison to pollination, nectar robbing is a more unstable event in a community.     

Entrapped sand as a plant defence: effects on herbivore performance and preference

1. Abrasive material in the diet of herbivorous organisms comes from a variety of sources, including crystalline silica or calcium in plant tissues, accidentally ingested soil while digging or grazing, and entrapped substrate on the surfaces of plants. A wide variety of plants entrap substrate, usually with glandular trichomes. 2. A previous study demonstrated that entrapped sand provided resistance to herbivory in the field. In this study, the following questions were addressed: how does entrapped sand on Abronia latifolia (Nyctaginaceae) leaves and stems affect preference and performance of a common herbivore, the large‐bodied caterpillar Hyles lineata (Sphingidae); does this effect differ from those experienced by an internally feeding leaf miner? 3. Using a combination of experimental and observational approaches, it was found that sand comprised ～4–5% of ingested weight during normal feeding of H. lineata caterpillars. This entrapped sand caused extensive wear to their mandibles, they avoided sand‐covered plants when given the choice, and the sand negatively impacted performance metrics, including pupal weight, development time, and growth rate. In contrast, a leaf‐mining caterpillar did not have a preference for or against feeding on sandy plants. 4. These results are similar to studies on mandibular wear due to grasses, and herbivorous insects that feed on these two plant groups may have similar morphologies. It is hypothesised that increased wear potential may be a convergent solution to abrasive plants in both mammals (hypsodonty) and insects.     

Interactions between a pollinating seed predator and its host plant: the role of environmental context within a population

Plant–insect interactions often are important for plant reproduction, but the outcome of these interactions may vary with environmental context. Pollinating seed predators have positive and negative effects on host plant reproduction, and the interaction outcome is predicted to vary with density or abundance of the partners. We studied the interaction between Silene stellata, an herbaceous perennial, and Hadena ectypa, its specialized pollinating seed predator. Silene stellata is only facultatively dependent upon H. ectypa for pollination because other nocturnal moth co‐pollinators are equally effective at pollen transfer. We hypothesized that for plants without conspecific neighbors, H. ectypa would have higher visitation rates compared to co‐pollinators, and the plants would experience lower levels of H. ectypa pollen deposition. We predicted similar oviposition throughout the study site but greater H. ectypa predation in the area without conspecific neighbors compared to plants embedded in a naturally high density area. We found that H. ectypa had consistently higher visitation than moth co‐pollinators in all host plant contexts. However, H. ectypa pollinator importance declined in areas with low conspecific density because of reduced pollen deposition, resulting in lower seed set. Conversely, oviposition was similar across the study site independent of host plant density. Greater likelihood of very high fruit predation combined with lower pollination by H. ectypa resulted in reduced S. stellata female reproductive success in areas with low conspecific density. Our results demonstrate local context dependency of the outcomes of pollinating seed predator interactions with conspecific host plant density within a population.     

Genome‐wide association study of insect bite hypersensitivity in Dutch Shetland pony mares

Insect bite hypersensitivity (IBH) is the most common allergic disease present in horses worldwide. It has been shown that IBH is under genetic control, but the knowledge of associated genes is limited. We conducted a genome‐wide association study to identify and quantify genomic regions contributing to IBH in the Dutch Shetland pony population. A total of 97 cases and 91 controls were selected and matched on withers height, coat colour and pedigree to minimise the population stratification. A blood sample was collected from participating Shetland pony mares, their IBH phenotype was scored and the owner filled in a questionnaire. A total of 40 021 single‐nucleotide polymorphisms (SNPs) were fitted in a univariable logistic model fitting an additive effect. Analysis revealed no effects of population stratification. Significant associations with IBH were detected for 24 SNPs on 12 chromosomes [?log₁₀(P‐value) > 2.5]. Odds ratios of allele substitution effects of the unfavourable allele were between 1.94 and 5.95. The most significant SNP was found on chromosome 27, with an odds ratio of 2.31 and with an allele frequency of the unfavourable allele of 0.72 in cases and 0.53 in controls. Genome‐wide association studies on additional horse populations are desired to validate the identified associations, to identify the genes involved in IBH and to develop genomic tools to decrease IBH prevalence.     

Specific herbivore-induced volatiles defend plants and determine insect community composition in the field

In response to insect attack, plants release complex blends of volatile compounds. These volatiles serve as foraging cues for herbivores, predators and parasitoids, leading to plant-mediated interactions within and between trophic levels. Hence, plant volatiles may be important determinants of insect community composition. To test this, we created rice lines that are impaired in the emission of two major signals, S-linalool and (E)-β-caryophyllene. We found that inducible S-linalool attracted predators and parasitoids as well as chewing herbivores, but repelled the rice brown planthopper Nilaparvata lugens, a major pest. The constitutively produced (E)-β-caryophyllene on the other hand attracted both parasitoids and planthoppers, resulting in an increased herbivore load. Thus, silencing either signal resulted in specific insect assemblages in the field, highlighting the importance of plant volatiles in determining insect community structures. Moreover, the results imply that the manipulation of volatile emissions in crops has great potential for the control of pest populations.     

Trees to treehoppers: genetic variation in host plants contributes to variation in the mating signals of a plant‐feeding insect

Community genetics research has demonstrated ‘bottom‐up’ effects of genetic variation within a plant species in shaping the larger community with which it interacts, such as compositions of arthropod faunas. We demonstrate that such cross‐trophic interactions also influence sexually selected traits. We used a member of the Enchenopa binotata species complex of treehoppers (Hemiptera: Membracidae) to ask whether male mating signals are influenced by host plant genetic variation. We reared a random sample of the treehoppers on potted replicates of a sample of host plant clone lines. We found that treehopper male signals varied according to the clone line on which they developed, showing that genetic variation in host plants affects male treehoppers' behavioural phenotypes. This is the first demonstration of cross‐trophic indirect genetic effects on a sexually selected trait. We discuss how such effects may play an important role in the maintenance of variation and within‐population phenotypic differentiation, thereby promoting evolutionary divergence.     

Fine‐scale substrate heterogeneity in green roof plant communities: The constraint of size

Heterogeneity–diversity relationship (HDR) is commonly shown to be positive in accordance with classic niche processes. However, recent soil‐based studies have often found neutral and even negative HDRs. Some of the suggested reasons for this discrepancy include the lack of resemblance between manipulated substrate and natural settings, the treated areas not being large enough to contain species' root span, and finally limited‐sized plots may not sustain focal species’ populations over time. Vegetated green roofs are a growing phenomenon in many cities that could be an ideal testing ground for this problem. Recent studies have focused on the ability of these roofs to sustain stable and diverse plant communities and substrate heterogeneity that would increase niches on the roof has been proposed as a method to attain this goal. We constructed an experimental design using green roof experimental modules (4 m²) where we manipulated mineral and organic substrate component heterogeneity in different subplots (0.25 m²) within the experimental module while maintaining the total sum of mineral and organic components. A local annual plant community was seeded in the modules and monitored over three growing seasons. We found that plant diversity and biomass were not affected by experimentally created substrate heterogeneity. In addition, we found that different treatments, as well as specific subplot substrates, had an effect on plant community assemblages during the first year but not during the second and third years. Substrate heterogeneity levels were mostly unchanged over time. The inability to retain plant community composition over the years despite the maintenance of substrate differences supports the hypothesis that maintenance of diversity is constrained at these spatial scales by unfavorable dispersal and increased stochastic events as opposed to predictions of classic niche processes.     

Host and symbiont genetic determinants of nutritional phenotype in a natural population of the pea aphid

A defining feature of the nutritional ecology of plant sap‐feeding insects is that the dietary deficit of essential amino acids (EAAs) in plant sap is supplemented by EAA‐provisioning microbial symbionts in the insect. Here, we demonstrated substantial variation in the nutritional phenotype of 208 genotypes of the pea aphid Acyrthosiphon pisum collected from a natural population. Specifically, the genotypes varied in performance (larval growth rates) on four test diets lacking the EAAs arginine, histidine and methionine or aromatic EAAs (phenylalanine and tryptophan), relative to the diet containing all EAAs. These data indicate that EAA supply from the symbiotic bacteria Buchnera can meet total aphid nutritional demand for only a subset of the EAA/aphid genotype combinations. We then correlated single nucleotide polymorphisms (SNPs) identified in the aphid and Buchnera genomes by reduced genome sequencing against aphid performance for each EAA deletion diet. This yielded significant associations between performance on the histidine‐free diet and Buchnera SNPs, including metabolism genes predicted to influence histidine biosynthesis. Aphid genetic correlates of performance were obtained for all four deletion diets, with associations on the arginine‐free diet and aromatic‐free diets dominated by genes functioning in the regulation of metabolic and cellular processes. The specific aphid genes associated with performance on different EAA deletion diets are largely nonoverlapping, indicating some independence in the regulatory circuits determining aphid phenotype for the different EAAs. This study demonstrates how variation in the phenotype of associations collected from natural populations can be applied to elucidate the genetic basis of ecologically important traits in systems intractable to traditional forward/reverse genetic techniques.     

Terrestrial deposition of aquatic insects increases plant quality for insect herbivores and herbivore density

1. Mobile organisms such as emergent aquatic insects can subsidise land with aquatic nutrients, creating a link between terrestrial and aquatic ecosystems. 2. Deposition of aquatic insects on land produces bottom‐up effects in arthropod detritivore communities and may also affect plants and plant–herbivore interactions. 3. To investigate the effects of insect deposition on plant–herbivore interactions, we conducted a field experiment and surveys of tealeaf willow (Salicaceae; Salix phylicifolia Coste) and July highflyer caterpillars (Geometridae; Hydriomena furcata Thunberg) at lakes in Northeast Iceland with either high‐ or low‐midge density and deposition to land. 4. It was found that willow at high‐midge lakes had 8–11% higher nitrogen content compared with willow at low‐midge lakes. In addition, natural caterpillar density was 4–6 times higher and caterpillars were 72% heavier at high‐midge lakes than low‐midge lakes. 5. A fully reciprocal caterpillar transplant experiment among willow at high‐ and low‐midge lakes was performed to separate the influence of habitat and midge effects on caterpillar performance. 6. After transplant, pupae of July Highflyer caterpillars were on average 11% heavier at high‐midge sites compared with low‐midge sites. However, this difference was not statistically significant. 7. The present findings indicate that cross‐ecosystem subsidies in the form of aquatic insects can increase plant foliar quality and the abundance of insect herbivores in recipient ecosystems.     

Future directions in the ontogeny of plant defence: understanding the evolutionary causes and consequences

Plant defence often varies by orders of magnitude as plants develop from the seedling to juvenile to mature and senescent stages. Ontogenetic trajectories can involve switches among defence traits, leading to complex shifting phenotypes across plant lifetimes. While considerable research has characterised ontogenetic trajectories for now hundreds of plant species, we still lack a clear understanding of the molecular, ecological and evolutionary factors driving these patterns. In this study, we identify several non‐mutually exclusive factors that may have led to the evolution of ontogenetic trajectories in plant defence, including developmental constraints, resource allocation costs, multi‐functionality of defence traits, and herbivore selection pressure. Evidence from recent physiological studies is highlighted to shed light on the underlying molecular mechanisms involved in the regulation and activation of these developmental changes. Overall, our goal is to promote new research avenues that would provide evidence for the factors that have promoted the evolution of this complex lifetime phenotype. Future research focusing on the questions and approaches identified here will advance the field and shed light on why defence traits shift so dramatically across plant ontogeny, a widespread but poorly understood ecological pattern.     

Evolutionary consequences of ecological factors: pollinator reliability predicts mating‐system traits of a perennial plant

The reproductive‐assurance hypothesis predicts that mating‐system traits will evolve towards increased autonomous self‐pollination in plant populations experiencing unreliable pollinator service. We tested this long‐standing hypothesis by assessing geographic covariation among pollinator reliability, outcrossing rates, heterozygosity and relevant floral traits across populations of Dalechampia scandens in Costa Rica. Mean outcrossing rates ranged from 0.16 to 0.49 across four populations, and covaried with the average rates of pollen arrival on stigmas, a measure of pollinator reliability. Across populations, genetically based differences in herkogamy (anther–stigma distance) were associated with variation in stigmatic pollen loads, outcrossing rates and heterozygosity. These observations are consistent with the hypothesis that, when pollinators are unreliable, floral traits promoting autonomous selfing evolve as a mechanism of reproductive assurance. Extensive covariation between floral traits and mating system among closely related populations further suggests that floral traits influencing mating systems track variation in adaptive optima generated by variation in pollinator reliability.     

Analysis of the genetic architecture of maize kernel size traits by combined linkage and association mapping

Kernel size‐related traits are the most direct traits correlating with grain yield. The genetic basis of three kernel traits of maize, kernel length (KL), kernel width (KW) and kernel thickness (KT), was investigated in an association panel and a biparental population. A total of 21 single nucleotide polymorphisms (SNPs) were detected to be most significantly (P < 2.25 × 10^?6) associated with these three traits in the association panel under four environments. Furthermore, 50 quantitative trait loci (QTL) controlling these traits were detected in seven environments in the intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population, of which eight were repetitively identified in at least three environments. Combining the two mapping populations revealed that 56 SNPs (P < 1 × 10^?3) fell within 18 of the QTL confidence intervals. According to the top significant SNPs, stable‐effect SNPs and the co‐localized SNPs by association analysis and linkage mapping, a total of 73 candidate genes were identified, regulating seed development. Additionally, seven miRNAs were found to situate within the linkage disequilibrium (LD) regions of the co‐localized SNPs, of which zma‐miR164e was demonstrated to cleave the mRNAs of Arabidopsis CUC1, CUC2 and NAC6 in vitro. Overexpression of zma‐miR164e resulted in the down‐regulation of these genes above and the failure of seed formation in Arabidopsis pods, with the increased branch number. These findings provide insights into the mechanism of seed development and the improvement of molecular marker‐assisted selection (MAS) for high‐yield breeding in maize.