The evolution of locally adapted ecotypes is a common phenomenon that generates diversity within plant species. However, we know surprisingly little about the genetic mechanisms underlying the locally adapted traits involved in ecotype formation. The genetic architecture underlying locally adapted traits dictates how an organism will respond to environmental selection pressures and has major implications for evolutionary ecology, conservation, and crop breeding. To understand the genetic architecture underlying the divergence of switchgrass (Panicum virgatum) ecotypes, we constructed a genetic mapping population through a four-way outbred cross between two northern upland and two southern lowland accessions. Trait segregation in this mapping population was largely consistent with multiple independent loci controlling the suite of traits that characterizes ecotype divergence. We assembled a joint linkage map using ddRADseq and mapped quantitative trait loci (QTL) for traits that are divergent between ecotypes, including flowering time, plant size, physiological processes, and disease resistance. Overall, we found that most QTL had small to intermediate effects. While we identified colocalizing QTLs for multiple traits, we did not find any large-effect QTLs that clearly controlled multiple traits through pleiotropy or tight physical linkage. These results indicate that ecologically important traits in switchgrass have a complex genetic basis and that similar loci may underlie divergence across the geographic range of the ecotypes.

Switchgrass is a key component of plans to develop sustainable cellulosic ethanol production for bioenergy in the USA.We sought quantitative trait loci (QTL) for leaf structure and function, using the Albany full-sib mapping population, an F1 derived from lowland tetraploid parents. We also assessed both genotype × environment interactions (G×E) in response to drought and spatial trends within experimental plots, using the mapping population and check clones drawn from the parent cultivars. Phenotypes for leaf structure and
physiological performance were determined under wellwatered conditions in two consecutive years, and we applied drought to one of two replicates to test for G×E. Phenotypes for check clones varied with location in our plot and were impacted by drought, but there was limited evidence of G×E except in quantum yield (ΦPSII). Phenotypes of Albany were also influenced by plant location within our plot, and after correcting for experimental design factors and spatial effects,
we detected QTL for leaf size, tissue density (LMA), and stomatal conductance (gs). Clear evidence of G×E was detected at a QTL for intrinsic water use efficiency (iWUE) that was expressed only under drought. Loci influencing physiological traits had small additive effects, showed complex patterns of heritability, and did not co-localize with QTL for morphological traits. These insights into the genetic architecture of leaf structure and function set the stage for consideration of leaf physiological phenotypes as a component of switchgrass improvement for bioenergy purposes.

Plant-pollinator interactions are thought to be major drivers of floral trait diversity. However, the relative importance of divergent pollinator-mediated selection versus neutral processes in floral character evolution has rarely been explored. We tested for adaptive floral trait evolution by comparing differentiation at neutral genetic loci to differentiation at quantitative floral traits in a putative Ipomopsis aggregata hybrid zone. Typical I. aggregata subsp. candida displays slender white tubular flowers that are typical of flowers pollinated by hawkmoths and subsp. collina displays robust red tubular flowers typical of flowers pollinated by hummingbirds; yet hybrid flower morphs are abundant across the East Slope of the Colorado Rockies. We estimated genetic differentiation (F_ST ) for nuclear and chloroplast microsatellite loci and used a half-sib design to calculate quantitative trait divergence (Q_ST ) from collection sites across the morphological hybrid zone. We found little evidence for population structure and estimated mean F_ST to be 0.032. Q_ST values for several floral traits including corolla tube length and width, color, and nectar volume were large and significantly greater than mean F_ST . We performed multivariate comparisons of neutral loci to genetic correlations within and between populations and found a strong signal for divergent selection, suggesting that specific combinations of floral display and reward traits may be the targets of selection. Our results show little support for historical subspecies categories, yet floral traits are more diverged than expected due to drift alone. Non-neutral divergence for multivariate quantitative traits suggests that selection by pollinators is maintaining a correlation between display and reward traits.

Climatic adaptation is an example of a genotype-by-environment interaction (G×E) of fitness. Selection upon gene expression regulatory variation can contribute to adaptive phenotypic diversity; however, surprisingly few studies have examined how genome-wide patterns of gene expression G×E are manifested in response to environmental stress and other selective agents that cause climatic adaptation. Here, we characterize drought-responsive expression divergence between upland (drought-adapted) and lowland (mesic) ecotypes of the perennial C4 grass, Panicum hallii, in natural field conditions. Overall, we find that cis-regulatory elements contributed to gene expression divergence across 47% of genes, 7.2% of which exhibit drought-responsive G×E. While less well-represented, we observe 1294 genes (7.8%) with trans effects. Trans-by-environment
interactions are weaker and much less common than cis G×E, occurring in only 0.7% of trans-regulated genes. Finally, gene expression heterosis is highly enriched in expression phenotypes with significant G×E. As such, modes of inheritance that drive heterosis, such as dominance or overdominance, may be common among G×E genes. Interestingly, motifs specific to drought-responsive transcription factors are highly enriched in the promoters of genes exhibiting G×E and trans regulation, indicating that expression G×E and heterosis may result from the evolution of transcription factors or their binding sites. P. hallii serves as the genomic model for its close relative and emerging biofuel crop, switchgrass (Panicum virgatum). Accordingly, the results here not only aid in the discovery of the genetic mechanisms that underlie local adaptation but also provide a foundation to improve switchgrass yield under water-limited conditions.

The presence of substantial genetic variation for water-use efficiency (WUE) suggests that natural selection plays a role in maintaining alleles that affect WUE. Soil water deficit can reduce plant survival, and is likely to impose selection to increase WUE, whereas competition for resources may select for decreased WUE to ensure water acquisition. We tested the fitness consequences of natural allelic variation in a single gene (MPK12) that influences WUE in Arabidopsis, using transgenic lines contrasting in MPK12 alleles, under four treatments; drought/competition, drought/no competition, well-watered/competition, well-watered/no competition. Results revealed an allele 9 environment interaction: Low WUE plants performed better in competition, resulting from increased resource consumption. Contrastingly, high WUE individuals performed better in no competition, irrespective of water availability, presumably from enhanced water conservation and nitrogen acquisition. Our findings suggest that selection can influence MPK12 evolution, and represents the first assessment of plant fitness resulting from natural allelic variation at a single locus affecting WUE.

Aims
Variation in precipitation strongly influences plant growth, species distributions and genetic diversity. Intraspecific variation in phenotypic plasticity, the ability of a genotype to alter its growth, morphology or physiology in response to the environment, could influence species responses to changing precipitation and climate change. Despite this, the patterns and mechanisms of intraspecific variation in plasticity to variable precipitation, and the degree to which genotype responses to precipitation are influenced by variation in edaphic conditions, remain poorly understood. Thus, we determined whether genotypes of a widespread C4 grass (Panicum virgatum L., switchgrass) varied in aboveground productivity in response to changes in precipitation, and if site edaphic conditions modified genotype aboveground productivity responses to precipitation. We also determined if genotype productivity responses to precipitation are related to plasticity in underlying growth and phenological traits.
Methods
Nine P. virgatum genotypes originating from an aridity gradient were grown under four treatments spanning the 10th to the 90th percentiles of annual precipitation at two sites in central Texas: one site with deep, fine-textured soils and another site with shallow, coarse-textured soils. We measured volumetric soil water content (VWC), aboveground net primary productivity (ANPP), tiller production (tiller number), average tiller mass, canopy height, leaf area index (LAI) and flowering time on all plants at both sites and examined genotype responses to changes in precipitation.
Important Findings
Across precipitation treatments, VWC was 39% lower and more variable at the site with shallow, coarse-textured soils compared to the site with deep, fine-textured soils. ANPP averaged across genotypes and precipitation treatments was also 103% higher at the site with deep, fine-textured soils relative to the site with shallow, coarse-textured soils, indicating substantial differences in site water limitation. Where site water limitation was higher, ANPP of most genotypes increased with increasing precipitation. Where site water limitation was less, genotypes expressed variable plasticity in response to precipitation, from no change to almost a 5-fold increase in ANPP with increasing precipitation. Genotype ANPP increased with greater tiller mass, LAI and later flowering time at both sites, but not with tiller number at either site. Genotype ANPP plasticity increased with genotype tiller mass and LAI plasticity at the site with deep, fine-textured soils, and only with genotype tiller mass plasticity at the site with shallow, coarse-textured soils. Thus, variation in genotype ANPP plasticity was explained primarily by variation in tiller and leaf growth. Genotype ANPP plasticity was not associated with temperature or aridity at the genotype’s origin. Edaphic factors such as soil depth and texture may alter genotype ANPP responses to precipitation, and the underlying growth traits contributing to the ANPP response. Thus, edaphic factors may contribute to spatial variation in genotype performance and success under altered precipitation.

Chromosomal inversions can provide windows onto the cytogenetic, molecular, evolutionary and demographic histories of a species. Here we investigate a paracentric 1.17 Mb inversion on chromosome 4 of Arabidopsis thaliana with nucleotide precision of its borders. The inversion is created by Vandal transposon activity, splitting an F-box and relocating a pericentric heterochromatin segment in juxtaposition with euchromatin without affecting the epigenetic landscape. Examination of the RegMap panel and the 1001 Arabidopsis genomes revealed more than 170 inversion accessions in Europe and North America. The SNP patterns revealed historical recombinations from which we infer diverse haplotype patterns, ancient introgression events and phylogenetic relationships. We find a robust association between the inversion and fecundity under drought. We also find linkage disequilibrium (LD) between the inverted region and the early flowering Col-FRIGIDA allele. Finally, SNP analysis elucidates the origin of the inversion to South-Eastern Europe ~5,000 years ago and the FRI-Col allele to North-West Europe, and reveals the spreading of a single haplotype to North America during the 17th to 19th century. The “American haplotype” was identified from several European localities, potentially due to return migration.

Identifying the physiological and genetic basis of stress tolerance in plants has proven to be critical to understanding adaptation in both agricultural and natural systems. However, many discoveries were initially made in the controlled conditions of greenhouses or laboratories, not in the field. To test the comparability of drought responses across field and greenhouse environments, we undertook three independent experiments using the switchgrass reference genotype Alamo AP13. We analyzed physiological and gene-expression variation across four locations, two sampling times and three years. Relatively similar physiological responses and expression coefficients of variation across experiments masked highly dissimilar gene expression responses to drought. Critically, a drought experiment utilizing small pots in the greenhouse elicited nearly identical physiological changes as an experiment conducted in the field, but an order of magnitude more differentially expressed genes. However, we were able to define a suite of several hundred genes that were differentially expressed across all experiments. This list was strongly enriched in photosynthesis, water status and reactive oxygen species responsive genes. The strong across-experiment correlations between physiological plasticity—but not differential gene expression—highlight the complex and diverse genetic mechanisms that can produce phenotypically similar responses to various soil water deficits.

All plants must optimize their growth with finite resources. Water use efficiency (WUE) measures the relationship between biomass acquisition and transpired water. In the present study, we performed two experiments to understand the genetic basis of WUE and other parameters of plant-water interaction under control and water-limited conditions. Our study used two inbred natural accessions of Brachy-podium distachyon, a model grass species with close phylogenetic affinity to temperate forage and cereal crops. First, we identify the soil water content which causes a reduction in leaf relative water content and an increase in WUE. Second, we present results from a large phenotyping experiment utilizing a recombinant inbred line mapping population derived from these same two natural accessions. We identify QTLs associated with environmentally-insensitive genetic variation in WUE, including a pair of epistatically interacting loci. We also identify QTLs associated with constitutive differences in biomass and a QTL describing an environmentally-sensitive difference in leaf carbon content. Finally, we present a new link-age map for this mapping population based on new SNP markers as well as updated genomic positions for previously described markers. Our studies provide an initial characterization of plant-water relations in B. distachyon and identify candidate genomic regions involved in WUE.

Heterosis has been widely used in agriculture, but the molecular mechanism for this remains largely elusive. In Arabidopsis hybrids and allopolyploids, increased photosynthetic and metabolic activities are linked to altered expression of circadian clock regulators, including CIRCADIAN CLOCK ASSOCIATED1 (CCA1). It is unknown whether a similar mechanism mediates heterosis in maize hybrids. Here we report that higher levels of carbon fixation and starch accumulation in the maize hybrids are associated with altered temporal gene expression. Two maize CCA1 homologs, ZmCCA1a and ZmCCA1b, are diurnally up-regulated in the hybrids. Expressing ZmCCA1 complements the cca1 mutant phenotype in Arabidopsis, and overexpressing ZmCCA1b disrupts circadian rhythms and biomass heterosis. Furthermore, overexpressing ZmCCA1b in maize reduced chlorophyll content and plant height. Reduced height stems from reduced node elongation but not total node number in both greenhouse and field conditions. Phenotypes are less severe in the field than in the greenhouse, suggesting that enhanced light and/or metabolic activities in the field can compensate for altered circadian regulation in growth vigor. Chromatin immunoprecipitation-sequencing (ChIP-seq) analysis reveals a temporal shift of ZmCCA1-binding targets to the early morning in the hybrids, suggesting that activation of morning-phased genes in the hybrids promotes photosynthesis and growth vigor. This temporal shift of ZmCCA1-binding targets correlated with nonadditive and additive gene expression in early and late stages of seedling development. These results could guide breeding better hybrid crops to meet the growing demand in food and bioenergy.

Brachypodium distachyon and its congeners are found in diverse
environments throughout the temperate regions of the world. Brachypodium species also show considerable variation in life history strategy, with species representing short-season annual habits and other species persisting for multiple years. This variation in ecological setting and life history suggests the existence of considerable genetic diversity in adaptation to the abiotic environment, both in constitutive tolerance to local conditions and in the capacity of single genotypes to acclimate to changing or unpredictable conditions. We review the limited but growing empirical literature on the physiology, development, and molecular biology of the interaction of Brachypodium with the abiotic environment. We highlight how these findings inform studies of ecologically and agriculturally-important plant species, and identify areas of future research that will extend the utility of Brachypodium as a model genetic system for understanding plant-environment interactions.

Soil water availability represents one of the most important selective agents for plants in nature and the single greatest abiotic determinant of agricultural productivity, yet the genetic bases of drought acclimation responses remain poorly understood. Here, we developed a systems-genetic approach to characterize quantitative trait loci (QTLs), physiological traits and genes that affect responses to soil moisture deficit in the TSUxKAS mapping population of Arabidopsis thaliana. To determine the effects of candidate genes underlying QTLs, we analyzed gene expression as a covariate within the QTL model in an effort to mechanistically link markers, RNA expression, and the phenotype. This strategy produced ranked lists of candidate genes for several drought-associated traits, including water use efficiency, growth, abscisic acid concentration (ABA), and proline concentration. As a proof of concept, we recovered known causal loci for several QTLs. For other traits, including ABA, we identified novel loci not previously associated with drought. Furthermore, we documented natural variation at two key steps in proline metabolism and demonstrated that the mitochondrial genome differentially affects genomic QTLs to influence proline accumulation. These findings demonstrate that linking genome, transcriptome, and phenotype data holds
great promise to extend the utility of genetic mapping, even when QTL effects are modest or complex.

The genetic distance between hybridizing parents affects heterosis; however, the mechanisms for this remain unclear. Here we report that this genetic distance correlates with natural variation and epigenetic regulation of circadian clock-mediated stress responses. In intraspecific hybrids of Arabidopsis thaliana, genome-wide expression of many biotic and abiotic stress-responsive genes is diurnally repressed and this correlates with biomass heterosis and biomass quantitative trait loci. Expression differences of selected stress-responsive genes among diverse ecotypes are predictive of heterosis in their hybrids. Stress-responsive genes are repressed in the hybrids under normal conditions but are induced to mid-parent or higher levels under stress at certain times of the day, potentially balancing the tradeoff between stress responses and growth. Consistent with this hypothesis, repression of two candidate stress-responsive genes increases growth vigour. Our findings may therefore provide new criteria for effectively selecting parents to produce high- or low-yield hybrids.

Genetic and genomic resources have recently been developed for the bioenergy crop switchgrass (Panicum virgatum). Despite these advances, little research has been focused on identifying genetic loci involved in natural variation of important bioenergy traits, including biomass. Quantitative trait locus (QTL) mapping is typically used to discover loci that contribute to trait variation. Once identified, QTLs can be used to improve agronomically important traits through marker-assisted selection. In this study, we conducted QTL mapping in Austin, TX, USA, with a full-sib mapping population derived from a cross between tetraploid clones of two major switchgrass cultivars (Alamo-A4 and Kanlow-K5). We observed significant among-genotype variation for the vast majority of growth, morphological, and phenological traits measured on the mapping population. Overall, we discovered 27 significant QTLs across 23 traits. QTLs for biomass production colocalized on linkage group 9b across years, as well as with a major biomass QTL discovered in another recent switchgrass QTL study. The experiment was conducted under a rainout shelter, which allowed us to examine the effects of differential irrigation on trait values. We found very minimal effects of the reduced watering treatment on traits, with no significant effect on biomass production. Overall, the results of our study set the stage for future crop improvement through marker-assisted selection breeding.

Context Expansion of bioenergy production is part of a global effort to reduce greenhouse gas emissions and mitigate climate change. Dedicated biomass crops will compete with other land uses as most high quality arable land is already used for agriculture, urban development, and biodiversity conservation. Objective First, we explore the trade-offs between converting land enrolled in the U.S. Conservation Reserve Program (CRP) to switchgrass for biofuel production or preserving it for biodiversity. Next, we examine the trade-offs between agriculture, biodiversity, and biofuel across the central and eastern U.S. Methods We compiled measures of biodiversity, agriculture, and biofuel from land cover classifications, species range maps, and mechanistic model output of switchgrass yield. We used a spatially explicit optimization algorithm to analyze the impacts of small-to-large scale biomass production by identifying locations that maximize biofuel produced from switchgrass and minimize negative impacts on biodiversity and agriculture. Results Using CRP land for switchgrass production increases the land area required to meet biomass goals and the species range area altered for birds, amphibians, mammals, and reptiles. When conversion is not limited to CRP, conversion scenarios including biodiversity and agriculture trade-offs require greater than 100 % more area for switchgrass to reach the same production goals. When land conversion scenarios do not include biodiversity, twice the range area for reptiles and amphibians could be altered. Conclusions Land-use trade-offs between biofuel production, agriculture, and biodiversity exist and alter optimum location of land conversion for low-to high
biofuel levels. This highlights the need for systematic land-use planning for the future.

Improving environmental adaptation in crops is essential for food security under global change, but phenotyping adaptive traits remains a major bottleneck. If associations between single-nucleotide polymorphism (SNP) alleles and environment of origin in crop landraces reflect adaptation, then these could be used to predict phenotypic variation for adaptive traits. We tested this proposition in the global food crop Sorghum bicolor, characterizing 1943 georeferenced landraces at 404,627 SNPs and quantifying allelic associations with bioclimatic and soil gradients. Environment explained a substantial portion of SNP variation, independent of geographical distance, and genic SNPs were enriched for environmental associations. Further, environment-associated SNPs predicted genotype-by-environment interactions under experimental drought stress and aluminum toxicity. Our results suggest that genomic signatures of environmental adaptation may be useful for crop improvement, enhancing germplasm identification and marker-assisted selection. Together, genome-environment associations and phenotypic analyses may reveal the basis of environmental adaptation.

Determining the patterns and mechanisms of natural selection in the wild is of fundamental importance to understanding the differentiation of populations and the evolution of new species. However, it is often unknown the extent to which adaptive genetic variation is distributed among ecotypes between distinct habitats versus along large-scale geographic environmental gradients, such as those that track latitude. Classic studies of selection in the wild in switchgrass, Panicum virgatum, tested for adaptation at both of these levels of natural variation. Here we review what these field experiments and modern agronomic field trials have taught us about natural variation and selection at both the ecotype and environmental gradient levels in P. virgatum. With recent genome sequencing efforts in P. virgatum, it is poised to become an excellent system for understanding the adaptation of grassland species across the eastern half of North America. The identification of genetic loci involved in different types of adaptations will help to understand the evolutionary mechanisms of diversification within P. virgatum and provide useful information for the breeding of highyielding cultivars for different ecoregions.