Climatic adaptation is an example of a genotype-by-environment interaction (G×E) of fitness. Sele... more 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 ...
Switchgrass is a promising feedstock for biofuel production, with potential for leveraging its na... more Switchgrass is a promising feedstock for biofuel production, with potential for leveraging its native microbial community to increase productivity and resilience to environmental stress. Here, we characterized the bacterial, archaeal and fungal diversity of the leaf microbial community associated with four switchgrass (Panicum virgatum) genotypes, subjected to two harvest treatments (annual harvest and unharvested control), and two fertilization levels (fertilized and unfertilized control), based on 16S rRNA gene and internal transcribed spacer (ITS) region amplicon sequencing. Leaf surface and leaf endosphere bacterial communities were significantly different with Alphaproteobacteria enriched in the leaf surface and Gammaproteobacteria and Bacilli enriched in the leaf endosphere. Harvest treatment significantly shifted presence/absence and abundances of bacterial and fungal leaf surface community members: Gammaproteobacteria were significantly enriched in harvested and Alphaproteob...
Telomere length has been implicated in the organismal response to stress, but the underlying mech... more Telomere length has been implicated in the organismal response to stress, but the underlying mechanisms are unknown. Here we examine the impact of telomere length changes on Arabidopsis thaliana responses to three contrasting abiotic environments, and measure 31 fitness, development, physiology and leaf-level anatomy traits. We report that telomere length in wild type and short telomere mutants is resistant to abiotic stress, while elongated telomeres in ku70 mutants are more plastic. We also detect significant pleiotropic effects of telomere length on flowering time and key leaf physiology and anatomical traits. Furthermore, our data reveal a significant genotype by environment (GxE) interaction for reproductive fitness, with the benefits and costs to performance depending on the growth conditions. These results imply that life-history tradeoffs between flowering time and reproductive fitness are impacted by telomere length variation. We postulate that telomere length in plants is subject to natural selection imposed by different environments.
RNA sequencing (RNA-seq) has proven invaluable for exploring gene expression variation under comp... more RNA sequencing (RNA-seq) has proven invaluable for exploring gene expression variation under complex environmental cues. However, the cost of standard RNA-seq (e.g., Illumina TruSeq or NEBNext) remains a barrier for high-throughput applications. 3'-Tag RNA-seq (3'-TagSeq) is a cost-effective solution that permits large-scale experiments. Unlike standard RNA-seq, which generates sequencing libraries for full-length mRNAs, 3'-TagSeq only generates a single fragment from the 3' end of each transcript (a tag read) and quantifies gene expression by tag abundance. Consequently, 3'-TagSeq requires lower sequencing depth (~5 million reads per sample) than standard RNA-seq (~30 million reads per sample), which reduces costs and allows increased technical and biological replication in experiments. Because 3'-TagSeq is considerably cheaper than standard RNA-seq while exhibiting comparable accuracy and reproducibility, researchers focusing on gene expression levels in large or extensive time-series experiments might find 3'-TagSeq to be superior to standard RNA-seq. In this chapter, we describe 3'-TagSeq sequencing library preparation and provide example bioinformatics and statistical analyses of gene expression data.
Ionomics measures elemental concentrations in biological organisms and provides a snapshot of phy... more Ionomics measures elemental concentrations in biological organisms and provides a snapshot of physiology under different conditions. In this study, we evaluate genetic variation of the ionome in outbred, perennial switchgrass in three environments across the species’ native range, and explore patterns of genotype-by-environment interactions. We grew 725 clonally replicated genotypes of a large full sib family from a four-way linkage mapping population, created from deeply diverged upland and lowland switchgrass ecotypes, at three common gardens. Concentrations of 18 mineral elements were determined in whole post-anthesis tillers using ion coupled plasma mass spectrometry (ICP-MS). These measurements were used to identify quantitative trait loci (QTL) with and without QTL-by-environment interactions (QTLxE) using a multi-environment QTL mapping approach. We found that element concentrations varied significantly both within and between switchgrass ecotypes, and GxE was present at both...
Long-term climate change and periodic environmental extremes threaten food and fuel security1and ... more Long-term climate change and periodic environmental extremes threaten food and fuel security1and 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 nort...
1. Plant responses to major environmental drivers like precipitation can influence important aspe... more 1. Plant responses to major environmental drivers like precipitation can influence important aspects of carbon (C) cycling like soil CO2 efflux (JCO2). These responses may be predicted by two independent classes of drivers: plant size—larger plants respire more and produce a larger quantity of labile C, and plant economics—plants possessing more acquisitive plant economics strategies (i.e., high metabolic rate and tissue nutrient content) produce higher-quality tissue that respires rapidly and decomposes quickly. 2. At two sites in central Texas, USA with similar climates and differing soil characteristics, we examined the response of eight Panicum virgatum genotypes to three annual precipitation levels defined by the driest, average, and wettest years from each site's precipitation history. We evaluated the individual and joint influence of plant genotypes and precipitation on JCO2 and traits related to plant economics and plant size. We then used confirmatory path analysis to evaluate whether effects of precipitation on JCO2 were in part related to effects of precipitation on plant economics traits or size ('mediated' effects). 3. These genotypes exhibited variation in plant economics traits and aboveground net primary productivity (ANPP), an aboveground measure of plant size. Increasing precipitation increased JCO2 and ANPP more than plant economics traits. At both sites, ANPP was the single best predictor of JCO2. Moreover, the sites differed in the ways that plant size and plant economics traits combined with precipitation to influence JCO2. At the Austin site, the positive effect of precipitation on JCO2 was mediated primarily by ANPP, offset by a smaller effect of leaf nitrogen content; no direct precipitation effect was detected. At the Temple site, increasing precipitation had positive direct and ANPP-mediated effects on JCO2. This suggests that greater water limitation at Austin may strengthen the links between plant size and JCO2. 4. Synthesis Estimates of C cycling can be improved by accounting for me [...]
Environmental heterogeneity can drive patterns of functional trait variation and lead to the form... more Environmental heterogeneity can drive patterns of functional trait variation and lead to the formation of locally adapted ecotypes. Plant ecotypes are often differentiated by suites of correlated root and shoot traits that share common genetic, developmental, and physiological relationships. For instance, although plant water loss is largely governed by shoot systems, root systems determine water access and constrain shoot water status. To evaluate the genetic basis of root and shoot trait divergence, we developed a recombinant inbred population derived from mesic and xeric ecotypes of the perennial grass Panicum hallii. Our study sheds light on the genetic architecture underlying the relationships between root and shoot traits. We identified several genomic "hotspots" which control suites of correlated root and shoot traits, thus indicating genetic coordination between plant organ systems in the process of ecotypic divergence. Genomic regions of colocalized quantitative trait locus (QTL) for the majority of shoot and root growth related traits were independent of colocalized QTL for shoot and root resource acquisition traits. The allelic effects of individual QTL underscore ecological specialization for drought adaptation between ecotypes and reveal possible hybrid breakdown through epistatic interactions. These results have implications for understanding the factors constraining or facilitating local adaptation in plants.
Intraspecific trait variation is caused by genetic and plastic responses to environment. This int... more Intraspecific trait variation is caused by genetic and plastic responses to environment. This intraspecific diversity is captured in immense natural history collections, giving us a window into trait variation across continents and through centuries of environmental shifts. Here we tested if hypotheses based on life history and the leaf economics spectrum explain intraspecific trait changes across global spatiotemporal environmental gradients. We measured phenotypes on a 216-year time series of Arabidopsis thaliana accessions from across the native range and applied spatially varying coefficient models to quantify region-specific trends in trait coordination and trait responses to climate gradients. All traits exhibited significant change across space and/or through time. For example, δ15N decreased over time across much of the range and leaf C:N increased, consistent with predictions based on anthropogenic changes in land use and atmosphere. Plants were collected later in the growi...
The stress hormone abscisic acid (ABA) is critical for drought resistance; however, mechanisms co... more The stress hormone abscisic acid (ABA) is critical for drought resistance; however, mechanisms controlling ABA levels are unclear. At low water potential, ABA accumulation in the Arabidopsis (Arabidopsis thaliana) accession Shahdara (Sha) was less than that in Landsberg erecta (Ler) or Columbia. Analysis of a Ler 3 Sha recombinant inbred line population revealed a single major-effect quantitative trait locus for ABA accumulation, which included 9-cis-epoxycarotenoid dioxygenase3 (NCED3) as a candidate gene. NCED3 encodes a rate-limiting enzyme for stress-induced ABA synthesis. Complementation experiments indicated that Sha has a reduced-function NCED3 allele. Compared with Ler, Sha did not have reduced NCED3 gene expression or protein level but did have four amino acid substitutions within NCED3. Sha differed from Ler in the apparent molecular mass of NCED3, indicative of altered NCED3 proteolytic processing in the chloroplast. Site-directed mutagenesis demonstrated that substitution at amino acid 271 was critical for the altered NCED3 molecular mass pattern, while the other Sha NCED3 polymorphisms were also involved in the reduced ABA accumulation. Sha did not have a reduced level of thylakoidbound NCED3 but did differ from Ler in the apparent molecular mass of stromal NCED3. As Sha was not impaired in known factors critical for NCED3 function in ABA synthesis (expression, chloroplast import, and thylakoid binding), the differences between Ler and Sha NCED3 may affect NCED3 activity or other factors influencing NCED3 function. These results identify functionally important sites on NCED3 and indicate a complex pattern of NCED3 posttranslational regulation in the chloroplast. During periods of drought stress and reduced water potential (c w), plant endogenous abscisic acid (ABA) levels increase dramatically. Increased ABA controls
Switchgrass (Panicum virgatum) is a promising biofuel crop native to the United States with genot... more Switchgrass (Panicum virgatum) is a promising biofuel crop native to the United States with genotypes that are adapted to a wide range of distinct ecosystems. Various plants have been shown to undergo symbioses with plant growth-promoting bacteria and fungi, however, plant-associated microbial communities of switchgrass have not been extensively studied to date. We present 16S ribosomal RNA gene and internal transcribed spacer (ITS) data of rhizosphere and root endosphere compartments of four switchgrass genotypes to test the hypothesis that host selection of its root microbiota prevails after transfer to non-native soil. We show that differences in bacterial, archaeal and fungal community composition and diversity are strongly driven by plant compartment and switchgrass genotypes and ecotypes. Plant-associated microbiota show an enrichment in Alphaproteobacteria and Actinobacteria as well as Sordariales and Pleosporales compared with the surrounding soil. Root associated compartments display low-complexity communities dominated and enriched in Actinobacteria, in particular Streptomyces, in the lowland genotypes, and in Alphaproteobacteria, specifically Sphingobium, in the upland genotypes. Our comprehensive root analysis serves as a snapshot of host-specific bacterial and fungal associations of switchgrass in the field and confirms that hostselected microbiomes persist after transfer to nonnative soil.
Environmental stress is a major driver of ecological community dynamics and agricultural producti... more Environmental stress is a major driver of ecological community dynamics and agricultural productivity. This is especially true for soil water availability, because drought is the greatest abiotic inhibitor of worldwide crop yields. Here, we test the genetic basis of drought responses in the genetic model for C 4 perennial grasses, Panicum hallii, through population genomics, field-scale gene-expression (eQTL) analysis, and comparison of two complete genomes. While gene expression networks are dominated by local cis-regulatory elements, we observe three genomic hotspots of unlinked trans-regulatory loci. These regulatory hubs are four times more drought responsive than the genome-wide average. Additionally, cis-and trans-regulatory networks are more likely to have opposing effects than expected under neutral evolution, supporting a strong influence of compensatory evolution and stabilizing selection. These results implicate trans-regulatory evolution as a driver of drought responses and demonstrate the potential for crop improvement in drought-prone regions through modification of gene regulatory networks.
While prokaryotic pan-genomes have been shown to contain many more genes than any individual orga... more While prokaryotic pan-genomes have been shown to contain many more genes than any individual organism, the prevalence and functional significance of differentially present genes in eukaryotes remains poorly understood. Whole-genome de novo assembly and annotation of 54 lines of the grass Brachypodium distachyon yield a pan-genome containing nearly twice the number of genes found in any individual genome. Genes present in all lines are enriched for essential biological functions, while genes present in only some lines are enriched for conditionally beneficial functions (e.g., defense and development), display faster evolutionary rates, lie closer to transposable elements and are less likely to be syntenic with orthologous genes in other grasses. Our data suggest that differentially present genes contribute substantially to phenotypic variation within a eukaryote species, these genes have a major influence in population genetics, and transposable elements play a key role in pan-genome...
The evolution of locally adapted ecotypes is a common phenomenon that generates diversity within ... more 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 ...
In the framework of phenotypic plasticity, tolerance to browsing can be operationally de®ned as a... more In the framework of phenotypic plasticity, tolerance to browsing can be operationally de®ned as a norm of reaction comparing plant performance in undamaged and damaged conditions. Genetic variation in tolerance is then indicated by heterogeneity in the slopes of norms of reaction from a population. We investigated ®eld gentian (Gentianella campestris) tolerance to damage in the framework of phenotypic plasticity using a sample of maternal lines from natural populations grown under common garden conditions and randomly split into either a control or an arti®cial clipping treatment. We found a diversity of tolerance norms of reaction at both the population and family level: the impacts of clipping ranged from poor tolerance (negative slope) to overcompensation (positive slope). We detected heterogeneity in tolerance norms of reaction in four populations. Similarly, we found a variety of plastic architectural responses to clipping and genetic variation in these responses in several populations. Overall, we found that the most tolerant populations were late ¯owering and also exhibit the greatest plastic increases in node (meristem) production in response to damage. We studied damage-imposed natural selection on plasticity in plant architecture in 10 of the sampled populations. In general, there was strong positive direct selection on ®nal number of nodes for both control and clipped plants. However, the total selection on nodes (direct + indirect selection) within each treatment category depended heavily on the frequency of damage and cross-treatment genetic correlations in node production. In some cases, strong correlated responses to selection across the damage treatment led to total selection against nodes in the more rare environment. This could ultimately lead to the evolution of maladaptive phenotypes in one or both of the treatment categories. These results suggest that tolerance and a variety of architectural responses to damage may evolve by both direct and indirect responses to natural selection. While the present study demonstrates the potential importance of cross-treatment genetic correlations in directing the evolution of tolerance traits, such as branch or node production, we did not ®nd any strong evidence of genetic trade-os in candidate tolerance traits between undamaged and damaged conditions.
Plant-pollinator interactions are thought to be major drivers of floral trait diversity. However,... more 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 Accepted Article This article is protected by copyright. All rights reserved. alone. Non-neutral divergence for multivariate quantitative traits suggests that selection by pollinators is maintaining a correlation between display and reward traits.
The presence of substantial genetic variation for water-use efficiency (WUE) suggests that natura... more 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 × 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 sugge...
Improving environmental adaptation in crops is essential for food security under global change, b... more 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 germplas...
Many crop plants are polyploids, hybrid or both, and these changes can lead to increased vigour a... more Many crop plants are polyploids, hybrid or both, and these changes can lead to increased vigour and transgressive phenotypes. However, their combined (and relative) impacts on plant reproduction remain enigmatic. To investigate the reproductive effects of polyploidy and hybridisation in a model species, we generated pairs of F1 hybrid triploids of Arabidopsis thaliana by reciprocally crossing inbred diploid accessions to a tetraploid tester line to generate triploid seed with additional copies of the genome inherited from the male and female parental gametes. The F1 hybrid triploids generated from different genotypes differed in their reproductive capacity when grown to maturity and selfed, and trade-offs were observed between different characters. Remarkably, we also observed differences in reproductive success between the pairs of genetically identical triploids indicating that Arabidopsis experiences long-lasting effects of inter-ploidy cross direction. By genomewide association ...
Background/Question/Methods Growing energy demands and concerns for climate change have pushed fo... more Background/Question/Methods Growing energy demands and concerns for climate change have pushed forward the time line for biofuel production. However, the effect of large-scale biofuel production in the U.S. on the agricultural industry, that is primarily responsible for food production and livestock feed, and on species diversity of many taxa (amphibians, birds, mammals, and reptiles) remains unclear. This study presents the first quantitative analysis of these trade-offs in the face of climate change. Switchgrass (Panicum virgatum L.) is a promising candidate for cellulosic feedstock production. Current and future (2080-2090) switchgrass productivity was estimated across the central and eastern U.S. using ALMANAC, a mechanistic model that simulates plant growth over time. Locations that minimize the impact on species diversity of all four taxa groups and minimize the proportion of agricultural and forested areas converted, while maximizing biomass production, were identified using ...
Climatic adaptation is an example of a genotype-by-environment interaction (G×E) of fitness. Sele... more 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 ...
Switchgrass is a promising feedstock for biofuel production, with potential for leveraging its na... more Switchgrass is a promising feedstock for biofuel production, with potential for leveraging its native microbial community to increase productivity and resilience to environmental stress. Here, we characterized the bacterial, archaeal and fungal diversity of the leaf microbial community associated with four switchgrass (Panicum virgatum) genotypes, subjected to two harvest treatments (annual harvest and unharvested control), and two fertilization levels (fertilized and unfertilized control), based on 16S rRNA gene and internal transcribed spacer (ITS) region amplicon sequencing. Leaf surface and leaf endosphere bacterial communities were significantly different with Alphaproteobacteria enriched in the leaf surface and Gammaproteobacteria and Bacilli enriched in the leaf endosphere. Harvest treatment significantly shifted presence/absence and abundances of bacterial and fungal leaf surface community members: Gammaproteobacteria were significantly enriched in harvested and Alphaproteob...
Telomere length has been implicated in the organismal response to stress, but the underlying mech... more Telomere length has been implicated in the organismal response to stress, but the underlying mechanisms are unknown. Here we examine the impact of telomere length changes on Arabidopsis thaliana responses to three contrasting abiotic environments, and measure 31 fitness, development, physiology and leaf-level anatomy traits. We report that telomere length in wild type and short telomere mutants is resistant to abiotic stress, while elongated telomeres in ku70 mutants are more plastic. We also detect significant pleiotropic effects of telomere length on flowering time and key leaf physiology and anatomical traits. Furthermore, our data reveal a significant genotype by environment (GxE) interaction for reproductive fitness, with the benefits and costs to performance depending on the growth conditions. These results imply that life-history tradeoffs between flowering time and reproductive fitness are impacted by telomere length variation. We postulate that telomere length in plants is subject to natural selection imposed by different environments.
RNA sequencing (RNA-seq) has proven invaluable for exploring gene expression variation under comp... more RNA sequencing (RNA-seq) has proven invaluable for exploring gene expression variation under complex environmental cues. However, the cost of standard RNA-seq (e.g., Illumina TruSeq or NEBNext) remains a barrier for high-throughput applications. 3'-Tag RNA-seq (3'-TagSeq) is a cost-effective solution that permits large-scale experiments. Unlike standard RNA-seq, which generates sequencing libraries for full-length mRNAs, 3'-TagSeq only generates a single fragment from the 3' end of each transcript (a tag read) and quantifies gene expression by tag abundance. Consequently, 3'-TagSeq requires lower sequencing depth (~5 million reads per sample) than standard RNA-seq (~30 million reads per sample), which reduces costs and allows increased technical and biological replication in experiments. Because 3'-TagSeq is considerably cheaper than standard RNA-seq while exhibiting comparable accuracy and reproducibility, researchers focusing on gene expression levels in large or extensive time-series experiments might find 3'-TagSeq to be superior to standard RNA-seq. In this chapter, we describe 3'-TagSeq sequencing library preparation and provide example bioinformatics and statistical analyses of gene expression data.
Ionomics measures elemental concentrations in biological organisms and provides a snapshot of phy... more Ionomics measures elemental concentrations in biological organisms and provides a snapshot of physiology under different conditions. In this study, we evaluate genetic variation of the ionome in outbred, perennial switchgrass in three environments across the species’ native range, and explore patterns of genotype-by-environment interactions. We grew 725 clonally replicated genotypes of a large full sib family from a four-way linkage mapping population, created from deeply diverged upland and lowland switchgrass ecotypes, at three common gardens. Concentrations of 18 mineral elements were determined in whole post-anthesis tillers using ion coupled plasma mass spectrometry (ICP-MS). These measurements were used to identify quantitative trait loci (QTL) with and without QTL-by-environment interactions (QTLxE) using a multi-environment QTL mapping approach. We found that element concentrations varied significantly both within and between switchgrass ecotypes, and GxE was present at both...
Long-term climate change and periodic environmental extremes threaten food and fuel security1and ... more Long-term climate change and periodic environmental extremes threaten food and fuel security1and 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 nort...
1. Plant responses to major environmental drivers like precipitation can influence important aspe... more 1. Plant responses to major environmental drivers like precipitation can influence important aspects of carbon (C) cycling like soil CO2 efflux (JCO2). These responses may be predicted by two independent classes of drivers: plant size—larger plants respire more and produce a larger quantity of labile C, and plant economics—plants possessing more acquisitive plant economics strategies (i.e., high metabolic rate and tissue nutrient content) produce higher-quality tissue that respires rapidly and decomposes quickly. 2. At two sites in central Texas, USA with similar climates and differing soil characteristics, we examined the response of eight Panicum virgatum genotypes to three annual precipitation levels defined by the driest, average, and wettest years from each site's precipitation history. We evaluated the individual and joint influence of plant genotypes and precipitation on JCO2 and traits related to plant economics and plant size. We then used confirmatory path analysis to evaluate whether effects of precipitation on JCO2 were in part related to effects of precipitation on plant economics traits or size ('mediated' effects). 3. These genotypes exhibited variation in plant economics traits and aboveground net primary productivity (ANPP), an aboveground measure of plant size. Increasing precipitation increased JCO2 and ANPP more than plant economics traits. At both sites, ANPP was the single best predictor of JCO2. Moreover, the sites differed in the ways that plant size and plant economics traits combined with precipitation to influence JCO2. At the Austin site, the positive effect of precipitation on JCO2 was mediated primarily by ANPP, offset by a smaller effect of leaf nitrogen content; no direct precipitation effect was detected. At the Temple site, increasing precipitation had positive direct and ANPP-mediated effects on JCO2. This suggests that greater water limitation at Austin may strengthen the links between plant size and JCO2. 4. Synthesis Estimates of C cycling can be improved by accounting for me [...]
Environmental heterogeneity can drive patterns of functional trait variation and lead to the form... more Environmental heterogeneity can drive patterns of functional trait variation and lead to the formation of locally adapted ecotypes. Plant ecotypes are often differentiated by suites of correlated root and shoot traits that share common genetic, developmental, and physiological relationships. For instance, although plant water loss is largely governed by shoot systems, root systems determine water access and constrain shoot water status. To evaluate the genetic basis of root and shoot trait divergence, we developed a recombinant inbred population derived from mesic and xeric ecotypes of the perennial grass Panicum hallii. Our study sheds light on the genetic architecture underlying the relationships between root and shoot traits. We identified several genomic "hotspots" which control suites of correlated root and shoot traits, thus indicating genetic coordination between plant organ systems in the process of ecotypic divergence. Genomic regions of colocalized quantitative trait locus (QTL) for the majority of shoot and root growth related traits were independent of colocalized QTL for shoot and root resource acquisition traits. The allelic effects of individual QTL underscore ecological specialization for drought adaptation between ecotypes and reveal possible hybrid breakdown through epistatic interactions. These results have implications for understanding the factors constraining or facilitating local adaptation in plants.
Intraspecific trait variation is caused by genetic and plastic responses to environment. This int... more Intraspecific trait variation is caused by genetic and plastic responses to environment. This intraspecific diversity is captured in immense natural history collections, giving us a window into trait variation across continents and through centuries of environmental shifts. Here we tested if hypotheses based on life history and the leaf economics spectrum explain intraspecific trait changes across global spatiotemporal environmental gradients. We measured phenotypes on a 216-year time series of Arabidopsis thaliana accessions from across the native range and applied spatially varying coefficient models to quantify region-specific trends in trait coordination and trait responses to climate gradients. All traits exhibited significant change across space and/or through time. For example, δ15N decreased over time across much of the range and leaf C:N increased, consistent with predictions based on anthropogenic changes in land use and atmosphere. Plants were collected later in the growi...
The stress hormone abscisic acid (ABA) is critical for drought resistance; however, mechanisms co... more The stress hormone abscisic acid (ABA) is critical for drought resistance; however, mechanisms controlling ABA levels are unclear. At low water potential, ABA accumulation in the Arabidopsis (Arabidopsis thaliana) accession Shahdara (Sha) was less than that in Landsberg erecta (Ler) or Columbia. Analysis of a Ler 3 Sha recombinant inbred line population revealed a single major-effect quantitative trait locus for ABA accumulation, which included 9-cis-epoxycarotenoid dioxygenase3 (NCED3) as a candidate gene. NCED3 encodes a rate-limiting enzyme for stress-induced ABA synthesis. Complementation experiments indicated that Sha has a reduced-function NCED3 allele. Compared with Ler, Sha did not have reduced NCED3 gene expression or protein level but did have four amino acid substitutions within NCED3. Sha differed from Ler in the apparent molecular mass of NCED3, indicative of altered NCED3 proteolytic processing in the chloroplast. Site-directed mutagenesis demonstrated that substitution at amino acid 271 was critical for the altered NCED3 molecular mass pattern, while the other Sha NCED3 polymorphisms were also involved in the reduced ABA accumulation. Sha did not have a reduced level of thylakoidbound NCED3 but did differ from Ler in the apparent molecular mass of stromal NCED3. As Sha was not impaired in known factors critical for NCED3 function in ABA synthesis (expression, chloroplast import, and thylakoid binding), the differences between Ler and Sha NCED3 may affect NCED3 activity or other factors influencing NCED3 function. These results identify functionally important sites on NCED3 and indicate a complex pattern of NCED3 posttranslational regulation in the chloroplast. During periods of drought stress and reduced water potential (c w), plant endogenous abscisic acid (ABA) levels increase dramatically. Increased ABA controls
Switchgrass (Panicum virgatum) is a promising biofuel crop native to the United States with genot... more Switchgrass (Panicum virgatum) is a promising biofuel crop native to the United States with genotypes that are adapted to a wide range of distinct ecosystems. Various plants have been shown to undergo symbioses with plant growth-promoting bacteria and fungi, however, plant-associated microbial communities of switchgrass have not been extensively studied to date. We present 16S ribosomal RNA gene and internal transcribed spacer (ITS) data of rhizosphere and root endosphere compartments of four switchgrass genotypes to test the hypothesis that host selection of its root microbiota prevails after transfer to non-native soil. We show that differences in bacterial, archaeal and fungal community composition and diversity are strongly driven by plant compartment and switchgrass genotypes and ecotypes. Plant-associated microbiota show an enrichment in Alphaproteobacteria and Actinobacteria as well as Sordariales and Pleosporales compared with the surrounding soil. Root associated compartments display low-complexity communities dominated and enriched in Actinobacteria, in particular Streptomyces, in the lowland genotypes, and in Alphaproteobacteria, specifically Sphingobium, in the upland genotypes. Our comprehensive root analysis serves as a snapshot of host-specific bacterial and fungal associations of switchgrass in the field and confirms that hostselected microbiomes persist after transfer to nonnative soil.
Environmental stress is a major driver of ecological community dynamics and agricultural producti... more Environmental stress is a major driver of ecological community dynamics and agricultural productivity. This is especially true for soil water availability, because drought is the greatest abiotic inhibitor of worldwide crop yields. Here, we test the genetic basis of drought responses in the genetic model for C 4 perennial grasses, Panicum hallii, through population genomics, field-scale gene-expression (eQTL) analysis, and comparison of two complete genomes. While gene expression networks are dominated by local cis-regulatory elements, we observe three genomic hotspots of unlinked trans-regulatory loci. These regulatory hubs are four times more drought responsive than the genome-wide average. Additionally, cis-and trans-regulatory networks are more likely to have opposing effects than expected under neutral evolution, supporting a strong influence of compensatory evolution and stabilizing selection. These results implicate trans-regulatory evolution as a driver of drought responses and demonstrate the potential for crop improvement in drought-prone regions through modification of gene regulatory networks.
While prokaryotic pan-genomes have been shown to contain many more genes than any individual orga... more While prokaryotic pan-genomes have been shown to contain many more genes than any individual organism, the prevalence and functional significance of differentially present genes in eukaryotes remains poorly understood. Whole-genome de novo assembly and annotation of 54 lines of the grass Brachypodium distachyon yield a pan-genome containing nearly twice the number of genes found in any individual genome. Genes present in all lines are enriched for essential biological functions, while genes present in only some lines are enriched for conditionally beneficial functions (e.g., defense and development), display faster evolutionary rates, lie closer to transposable elements and are less likely to be syntenic with orthologous genes in other grasses. Our data suggest that differentially present genes contribute substantially to phenotypic variation within a eukaryote species, these genes have a major influence in population genetics, and transposable elements play a key role in pan-genome...
The evolution of locally adapted ecotypes is a common phenomenon that generates diversity within ... more 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 ...
In the framework of phenotypic plasticity, tolerance to browsing can be operationally de®ned as a... more In the framework of phenotypic plasticity, tolerance to browsing can be operationally de®ned as a norm of reaction comparing plant performance in undamaged and damaged conditions. Genetic variation in tolerance is then indicated by heterogeneity in the slopes of norms of reaction from a population. We investigated ®eld gentian (Gentianella campestris) tolerance to damage in the framework of phenotypic plasticity using a sample of maternal lines from natural populations grown under common garden conditions and randomly split into either a control or an arti®cial clipping treatment. We found a diversity of tolerance norms of reaction at both the population and family level: the impacts of clipping ranged from poor tolerance (negative slope) to overcompensation (positive slope). We detected heterogeneity in tolerance norms of reaction in four populations. Similarly, we found a variety of plastic architectural responses to clipping and genetic variation in these responses in several populations. Overall, we found that the most tolerant populations were late ¯owering and also exhibit the greatest plastic increases in node (meristem) production in response to damage. We studied damage-imposed natural selection on plasticity in plant architecture in 10 of the sampled populations. In general, there was strong positive direct selection on ®nal number of nodes for both control and clipped plants. However, the total selection on nodes (direct + indirect selection) within each treatment category depended heavily on the frequency of damage and cross-treatment genetic correlations in node production. In some cases, strong correlated responses to selection across the damage treatment led to total selection against nodes in the more rare environment. This could ultimately lead to the evolution of maladaptive phenotypes in one or both of the treatment categories. These results suggest that tolerance and a variety of architectural responses to damage may evolve by both direct and indirect responses to natural selection. While the present study demonstrates the potential importance of cross-treatment genetic correlations in directing the evolution of tolerance traits, such as branch or node production, we did not ®nd any strong evidence of genetic trade-os in candidate tolerance traits between undamaged and damaged conditions.
Plant-pollinator interactions are thought to be major drivers of floral trait diversity. However,... more 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 Accepted Article This article is protected by copyright. All rights reserved. alone. Non-neutral divergence for multivariate quantitative traits suggests that selection by pollinators is maintaining a correlation between display and reward traits.
The presence of substantial genetic variation for water-use efficiency (WUE) suggests that natura... more 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 × 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 sugge...
Improving environmental adaptation in crops is essential for food security under global change, b... more 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 germplas...
Many crop plants are polyploids, hybrid or both, and these changes can lead to increased vigour a... more Many crop plants are polyploids, hybrid or both, and these changes can lead to increased vigour and transgressive phenotypes. However, their combined (and relative) impacts on plant reproduction remain enigmatic. To investigate the reproductive effects of polyploidy and hybridisation in a model species, we generated pairs of F1 hybrid triploids of Arabidopsis thaliana by reciprocally crossing inbred diploid accessions to a tetraploid tester line to generate triploid seed with additional copies of the genome inherited from the male and female parental gametes. The F1 hybrid triploids generated from different genotypes differed in their reproductive capacity when grown to maturity and selfed, and trade-offs were observed between different characters. Remarkably, we also observed differences in reproductive success between the pairs of genetically identical triploids indicating that Arabidopsis experiences long-lasting effects of inter-ploidy cross direction. By genomewide association ...
Background/Question/Methods Growing energy demands and concerns for climate change have pushed fo... more Background/Question/Methods Growing energy demands and concerns for climate change have pushed forward the time line for biofuel production. However, the effect of large-scale biofuel production in the U.S. on the agricultural industry, that is primarily responsible for food production and livestock feed, and on species diversity of many taxa (amphibians, birds, mammals, and reptiles) remains unclear. This study presents the first quantitative analysis of these trade-offs in the face of climate change. Switchgrass (Panicum virgatum L.) is a promising candidate for cellulosic feedstock production. Current and future (2080-2090) switchgrass productivity was estimated across the central and eastern U.S. using ALMANAC, a mechanistic model that simulates plant growth over time. Locations that minimize the impact on species diversity of all four taxa groups and minimize the proportion of agricultural and forested areas converted, while maximizing biomass production, were identified using ...
Uploads
Papers by Thomas Juenger