Insight into the genetic components of community genetics: QTL mapping of insect association in a fast-growing forest tree

Genetic underpinnings of arthropod community distributions in Populus trichocarpa

Community genetics seeks to understand the mechanisms by which natural genetic variation in heritable host phenotypes can encompass assemblages of organisms such as bacteria, fungi, and many animals including arthropods. Prior studies that focused on plant genotypes have been unable to identify genes controlling community composition, a necessary step to predict ecosystem structure and function as underlying genes shift within plant populations. We surveyed arthropods within an association population of Populus trichocarpa in three common gardens to discover plant genes that contributed to arthropod community composition. We analyzed our surveys with traditional single-trait genome-wide association analysis (GWAS), multitrait GWAS, and functional networks built from a diverse set of plant phenotypes. Plant genotype was influential in structuring arthropod community composition among several garden sites. Candidate genes important for higher level organization of arthropod communities had broadly applicable functions, such as terpenoid biosynthesis and production of dsRNA binding proteins and protein kinases, which may be capable of targeting multiple arthropod species. We have demonstrated the ability to detect, in an uncontrolled environment, individual genes that are associated with the community assemblage of arthropods on a host plant, further enhancing our understanding of genetic mechanisms that impact ecosystem structure.

Advanced Breeding for Biotic Stress Resistance in Poplar

Poplar is one of the most important forest trees because of its high economic value. Thanks to the fast-growing rate, easy vegetative propagation and transformation, and availability of genomic resources, poplar has been considered the model species for forest genetics, genomics, and breeding. Being a field-growing tree, poplar is exposed to environmental threats, including biotic stresses that are becoming more intense and diffused because of global warming. Current poplar farming is mainly based on monocultures of a few elite clones and the expensive and long-term conventional breeding programmes of perennial tree species cannot face current climate-change challenges. Consequently, new tools and methods are necessary to reduce the limits of traditional breeding related to the long generation time and to discover new sources of resistance. Recent advances in genomics, marker-assisted selection, genomic prediction, and genome editing offer powerful tools to efficiently exploit the Populus genetic diversity and allow enabling molecular breeding to support accurate early selection, increasing the efficiency, and reducing the time and costs of poplar breeding, that, in turn, will improve our capacity to face or prevent the emergence of new diseases or pests.

Growing up aspen: ontogeny and trade-offs shape growth, defence and reproduction in a foundation species

BACKGROUND AND AIMS

Intraspecific variation in foundation species of forest ecosystems can shape community and ecosystem properties, particularly when that variation has a genetic basis. Traits mediating interactions with other species are predicted by simple allocation models to follow ontogenetic patterns that are rarely studied in trees. The aim of this research was to identify the roles of genotype, ontogeny and genotypic trade-offs shaping growth, defence and reproduction in aspen.

METHODS

We established a common garden replicating >500 aspen genets in Wisconsin, USA. Trees were measured through the juvenile period into the onset of reproduction, for growth, defence chemistry (phenolic glycosides and condensed tannins), nitrogen, extrafloral nectaries, leaf morphology (specific leaf area), flower production and foliar herbivory and disease. We also assayed the TOZ19 sex marker and heterozygosity at ten microsatellite loci.

KEY RESULTS

We found high levels of genotypic variation for all traits, and high heritabilities for both the traits and their ontogenetic trajectories. Ontogeny strongly shaped intraspecific variation, and trade-offs among growth, defence and reproduction supported some predictions while contradicting others. Both direct resistance (chemical defence) and indirect defence (extrafloral nectaries) declined during the juvenile stage, prior to the onset of reproduction. Reproduction was higher in trees that were larger, male and had higher individual heterozygosity. Growth was diminished by genotypic allocation to both direct and indirect defence as well as to reproduction, but we found no evidence of trade-offs between defence and reproduction.

CONCLUSIONS

Key traits affecting the ecological communities of aspen have high levels of genotypic variation and heritability, strong patterns of ontogeny and clear trade-offs among growth, defence and reproduction. The architecture of aspen's community genetics - its ontogeny, trade-offs and especially its great variability - is shaped by both its broad range and the diverse community of associates, and in turn further fosters that diversity.

Consistent community genetic effects in the context of strong environmental and temporal variation in Eucalyptus

Provenance translocations of tree species are promoted in forestry, conservation, and restoration in response to global climate change. While this option is driven by adaptive considerations, less is known of the effects translocations can have on dependent communities. We investigated the relative importance and consistency of extended genetic effects in Eucalyptus using two species-E. globulus and E. pauciflora. In E. globulus, the dependent arthropod and pathogen canopy communities were quantified based on the abundance of 49 symptoms from 722 progeny from 13 geographic sub-races across 2 common gardens. For E. pauciflora, 6 symptoms were quantified over 2 years from 238 progeny from 16 provenances across 2 common gardens. Genetic effects significantly influenced communities in both species. However, site and year effects outweighed genetic effects with site explaining approximately 3 times the variation in community traits in E. globulus and site and year explaining approximately 6 times the variation in E. pauciflora. While the genetic effect interaction terms were significant in some community traits, broad trends in community traits associated with variation in home-site latitude for E. globulus and home-site altitude for E. pauciflora were evident. These broad-scale trends were consistent with patterns of adaptive differentiation within each species, suggesting there may be extended consequences of local adaptation. While small in comparison to site and year, the consistency of genetic effects highlights the importance of provenance choice in tree species, such as Eucalyptus, as adaptive divergence among provenances may have significant long-term effects on biotic communities.

Linking plant genes to insect communities: Identifying the genetic bases of plant traits and community composition

Community genetics aims to understand the effects of intraspecific genetic variation on community composition and diversity, thereby connecting community ecology with evolutionary biology. Thus far, research has shown that plant genetics can underlie variation in the composition of associated communities (e.g., insects, lichen and endophytes), and those communities can therefore be considered as extended phenotypes. This work, however, has been conducted primarily at the plant genotype level and has not identified the key underlying genes. To address this gap, we used genome-wide association mapping with a population of 445 aspen (Populus tremuloides) genets to identify the genes governing variation in plant traits (defence chemistry, bud phenology, leaf morphology, growth) and insect community composition. We found 49 significant SNP associations in 13 Populus genes that are correlated with chemical defence compounds and insect community traits. Most notably, we identified an early nodulin-like protein that was associated with insect community diversity and the abundance of interacting foundation species (ants and aphids). These findings support the concept that particular plant traits are the mechanistic link between plant genes and the composition of associated insect communities. In putting the "genes" into "genes to ecosystems ecology", this work enhances understanding of the molecular genetic mechanisms that underlie plant-insect associations and the consequences thereof for the structure of ecological communities.

Resistance to an eriophyid mite in an interspecific hybrid pedigree of Populus

Schizoempodium mesophyllincola is an eriophyid mite that feeds in leaves of Populus trichocarpa in the central part of this cottonwood tree’s range (i.e., coastal British Columbia, Washington and Oregon) in the Pacific Northwest (PNW) of North America, and on some interspecific hybrids planted in short-rotation, intensive forestry in the region. The mite, a leaf vagrant, sucks the contents of spongy mesophyll cells, causing leaf discoloration, or “bronzing.” Here, we investigate the inheritance pattern of resistance to leaf bronzing using a three-generation Populus trichocarpa x P. deltoides hybrid pedigree. We found that resistance to the mite is an exaptation in that its source in two related F₂ families of the TxD hybrid pedigree was the non-native host, P. deltoides. Two grandparental genotypes of the latter, ‘ILL-5’ and ‘ILL-129’, were completely free of the bronzing symptom and that phenotype was inherited in a Mendelian manner in the F₁ and F₂. Resistance to S. mesophyllincola is similar to resistance to many other regional pathogens of P. trichocarpa (e.g., Melampsora occidentalis, Venturia inopina, Sphaerulina populicola, and Taphrina sp.) in that it is inherited from the non-native grandparent (e.g., P. deltoides, P. nigra, or P. maximowiczii) in three-generation, hybrid pedigrees. In addition to finding evidence for Mendelian inheritance, we found two QTLs with LOD scores 5.03 and 3.12 mapped on linkage groups (LG) III and I, and they explained 6.7 and 4.2% of the phenotypic variance, respectively. The LG I QTL is close to, or synonymous with, one for resistance to sap-feeding arthropods and leaf developmental traits as expressed in a British study utilizing the same pedigree.

Genotypic variation in plant traits shapes herbivorous insect and ant communities on a foundation tree species

Community genetics aims to understand the effects of intraspecific genetic variation on community composition and diversity, thereby connecting community ecology with evolutionary biology. Multiple studies have shown that different plant genotypes harbor different communities of associated organisms, such as insects. Yet, the mechanistic links that tie insect community composition to plant genetics are still not well understood. To shed light on these relationships, we explored variation in both plant traits (e.g., growth, phenology, defense) and herbivorous insect and ant communities on 328 replicated aspen (Populus tremuloides) genets grown in a common garden. We measured traits and visually surveyed insect communities annually in 2014 and 2015. We found that insect communities overall exhibited low heritability and were shaped primarily by relationships among key insects (i.e., aphids, ants, and free-feeders). Several tree traits affected insect communities and the presence/absence of species and functional groups. Of these traits, tree size and foliar phenology were the most important. Larger trees had denser (i.e., number of insects per unit tree size) and more diverse insect communities, while timing of bud break and bud set differentially influenced particular species and insect groups, especially leaf modifying insects. These findings will inform future research directed toward identification of plant genes and genetic regions that underlie the structure of associated insect communities.

Large effect quantitative trait loci for salicinoid phenolic glycosides in Populus: Implications for gene discovery

Genomic studies have been used to identify genes underlying many important plant secondary metabolic pathways. However, genes for salicinoid phenolic glycosides (SPGs)—ecologically important compounds with significant commercial, cultural, and medicinal applications—remain largely undescribed. We used a linkage map derived from a full‐sib population of hybrid cottonwoods (Populus spp.) to search for quantitative trait loci (QTL) for the SPGs salicortin and HCH‐salicortin. SSR markers and primer sequences were used to anchor the map to the V3.0 P. trichocarpa genome. We discovered 21 QTL for the two traits, including a major QTL for HCH‐salicortin (R² = .52) that colocated with a QTL for salicortin on chr12. Using the V3.0 Populus genome sequence, we identified 2,983 annotated genes and 1,480 genes of unknown function within our QTL intervals. We note ten candidate genes of interest, including a BAHD‐type acyltransferase that has been potentially linked to PopulusSPGs. Our results complement other recent studies in Populus with implications for gene discovery and the evolution of defensive chemistry in a model genus. To our knowledge, this is the first study to use a full‐sib mapping population to identify QTL intervals and gene lists associated with SPGs.

The Extended Community-Level Effects of Genetic Variation in Foliar Wax Chemistry in the Forest Tree Eucalyptus globulus

Genetic variation in foundation trees can influence dependent communities, but little is known about the mechanisms driving these extended genetic effects. We studied the potential chemical drivers of genetic variation in the dependent foliar community of the focal tree Eucalyptus globulus. We focus on the role of cuticular waxes and compare the effects to that of the terpenes, a well-studied group of secondary compounds known to be bioactive in eucalypts. The canopy community was quantified based on the abundance of thirty-nine distinctive arthropod and fungal symptoms on foliar samples collected from canopies of 246 progeny from 13 E. globulus sub-races grown in a common garden trial. Cuticular waxes and foliar terpenes were quantified using gas chromatography - mass spectrometry (GC-MC). A total of 4 of the 13 quantified waxes and 7 of the 16 quantified terpenes were significantly associated with the dependent foliar community. Variation in waxes explained 22.9% of the community variation among sub-races, which was equivalent to that explained by terpenes. In combination, waxes and terpenes explained 35% of the genetic variation among sub-races. Only a small proportion of wax and terpene compounds showing statistically significant differences among sub-races were implicated in community level effects. The few significant waxes have previously shown evidence of divergent selection in E. globulus, which signals that adaptive variation in phenotypic traits may have extended effects. While highlighting the role of the understudied cuticular waxes, this study demonstrates the complexity of factors likely to lead to community genetic effects in foundation trees.

A community genetics perspective: opportunities for the coming decade

Community genetics was originally proposed as a novel approach to identifying links between genes and ecosystems, and merging ecological and evolutional perspectives. The dozen years since the birth of community genetics have seen many empirical studies and common garden experiments, as well as the rise of eco-evolutionary dynamics research and a general shift in ecology to incorporate intraspecific variation. So what have we learned from community genetics? Can individual genes affect entire ecosystems? Are there interesting questions left to be answered, or has community genetics run its course? This perspective makes a series of key points about the general patterns that have emerged and calls attention to gaps in our understanding to be addressed in the coming years.

Cryptic eco-evolutionary dynamics

Natural systems harbor complex interactions that are fundamental parts of ecology and evolution. These interactions challenge our inclinations and training to seek the simplest explanations of patterns in nature. Not least is the likelihood that some complex processes might be missed when their patterns look similar to predictions for simpler mechanisms. Along these lines, theory and empirical evidence increasingly suggest that environmental, ecological, phenotypic, and genetic processes can be tightly intertwined, resulting in complex and sometimes surprising eco-evolutionary dynamics. The goal of this review is to temper inclinations to unquestioningly seek the simplest explanations in ecology and evolution, by recognizing that some eco-evolutionary outcomes may appear very similar to purely ecological, purely evolutionary, or even null expectations, and thus be cryptic. We provide theoretical and empirical evidence for observational biases and mechanisms that might operate among the various links in eco-evolutionary feedbacks to produce cryptic patterns. Recognition that cryptic dynamics can be associated with outcomes like stability, resilience, recovery, or coexistence in a dynamically changing world provides added impetus for finding ways to study them.

Effects of hybridization and evolutionary constraints on secondary metabolites: the genetic architecture of phenylpropanoids in European populus species

The mechanisms responsible for the origin, maintenance and evolution of plant secondary metabolite diversity remain largely unknown. Decades of phenotypic studies suggest hybridization as a key player in generating chemical diversity in plants. Knowledge of the genetic architecture and selective constraints of phytochemical traits is key to understanding the effects of hybridization on plant chemical diversity and ecological interactions. Using the European Populus species P. alba (White poplar) and P. tremula (European aspen) and their hybrids as a model, we examined levels of inter- and intraspecific variation, heritabilities, phenotypic correlations, and the genetic architecture of 38 compounds of the phenylpropanoid pathway measured by liquid chromatography and mass spectrometry (UHPLC-MS). We detected 41 quantitative trait loci (QTL) for chlorogenic acids, salicinoids and flavonoids by genetic mapping in natural hybrid crosses. We show that these three branches of the phenylpropanoid pathway exhibit different geographic patterns of variation, heritabilities, and genetic architectures, and that they are affected differently by hybridization and evolutionary constraints. Flavonoid abundances present high species specificity, clear geographic structure, and strong genetic determination, contrary to salicinoids and chlorogenic acids. Salicinoids, which represent important defence compounds in Salicaceae, exhibited pronounced genetic correlations on the QTL map. Our results suggest that interspecific phytochemical differentiation is concentrated in downstream sections of the phenylpropanoid pathway. In particular, our data point to glycosyltransferase enzymes as likely targets of rapid evolution and interspecific differentiation in the 'model forest tree' Populus.

Foliar bacterial communities of trembling aspen in a common garden

Microbial associations with plants are widely distributed and are structured by a number of biotic and physical factors. Among biotic factors, the host plant genotype may be integral to these plant-microbe interactions. Trees in the genus Populus have become models for studies in scaling effects of host plant genetics and in plant-microbe interactions. Using 454 pyrosequencing of the 16S rRNA gene, we assessed the foliar bacterial community of 7 genotypes of mature trembling aspen trees (Populus tremuloides Michx.) grown in a common garden. Trees were selected based on prior analyses showing clonal variation in their concentration of chemicals conferring resistance against insect herbivores. At broad taxonomic designations, the bacterial community of trembling aspen was similar across all plant genotypes. At a finer taxonomic scale, the foliage of these trees varied in their community composition, but there was no distinct pattern to colonization or abundance related to plant genotype. The most abundant operational taxonomic units (OTUs) were classified as Ralstonia, Bradyrhizobium, Pseudomonas, and Brucella. These OTUs varied across the common garden, but there was no significant effect of host plant genotype or spatial position on the abundance of these members. Our results suggest that aspen genotype is less important in the structuring of its foliar bacterial communities than are other, poorly understood processes.