Genetic variation, environment and demography intersect to shape Arabidopsis defense metabolite variation across Europe

Genome-wide association studies meta-analysis uncovers NOJO and SGS3 novel genes involved in Arabidopsis thaliana primary root development and plasticity

BACKGROUND

Arabidopsis thaliana primary root growth has become a model for evo-devo studies due to its simplicity and facility to record cell proliferation and differentiation. To identify new genetic components relevant to primary root growth, we used a Genome-Wide Association Studies (GWAS) meta-analysis approach using data published in the last decade. In this work, we performed intra and inter-studies analyses to discover new genetic components that could participate in primary root growth.

METHODS AND RESULTS

We used 639 accessions from nine different studies under control conditions and performed different GWAS tests. We found that primary root growth changes were associated with 41 genes, of which six (14.6%) have been previously described as inhibitors or promoters of primary root growth. The knockdown lines of two genes, Suppressor of Gene Silencing (SGS3), involved in tasiRNA processing, and a gene with a Sterile Alpha Motif (SAM) motif named NOJOCH MOOTS (NOJO), confirmed their role as repressors of primary root growth, none has been shown to participate in this developmental process before.

CONCLUSIONS

In summary, our GWAS analysis of different available studies identified new genes that participate in primary root growth; two of them were identified as repressors of primary root growth.

Quality Appraisal of Research Reporting for Aromatherapy and Essential Oil Studies in Humans: Proposed Checklist for "Transparent Reporting for Essential oil and Aroma Therapeutic Studies"

Introduction: Reporting of aromatherapy-focused research often lacks sufficient quality and detail for replication and subsequent application of results. To our knowledge currently, no quality appraisal tool exists for aromatherapy research reporting. To address this gap, the Aromatic Research Quality Appraisal Taskforce (ARQAT) composed of aromatherapy professionals with varied expert backgrounds came together. Presented here is the Transparent Reporting for Essential oil and Aroma Therapeutic Studies (TREATS) checklist, which is a result of this collaborative effort. Methods: Creation of TREATS followed a three-stage process, including determination of interest/need, development, and dissemination. The shortcomings of existing aromatherapy research reporting quality were evaluated and responses to address these shortcomings were used to create checklist items that were then grouped into sections. Items for each section were brain-stormed with reference to the aromatherapy literature and ARQAT's expert knowledge, and the development of each section followed an iterative process until agreement was reached. An explanatory document was also created to assist more accurate use of the tool; it and the checklist were reviewed by a group of aromatherapy experts. Results: The TREATS checklist with 38 items in four sections was developed along with the explanatory document. The ARQAT and a global group of aromatherapy experts reviewed the TREATS. Their results and comments assisted development of the current version. The TREATS identifies key components of research involving essential oils, their application, and olfactory considerations that ARQAT considers the minimum necessary for high-quality aromatherapy research. Conclusion: The TREATS, explanatory document, and associated website (www.arqat.org) contribute to thorough aromatherapy research critique. The TREATS checklist aids appraisal of quality and can be used with any study design. It lays the foundation for the future development of aromatic research reporting guidelines.

Genome-wide association studies identify loci controlling specialized seed metabolites in Arabidopsis

Plants synthesize specialized metabolites to facilitate environmental and ecological interactions. During evolution, plants diversified in their potential to synthesize these metabolites. Quantitative differences in metabolite levels of natural Arabidopsis (Arabidopsis thaliana) accessions can be employed to unravel the genetic basis for metabolic traits using genome-wide association studies (GWAS). Here, we performed metabolic GWAS on seeds of a panel of 315 A. thaliana natural accessions, including the reference genotypes C24 and Col-0, for polar and semi-polar seed metabolites using untargeted ultra-performance liquid chromatography-mass spectrometry. As a complementary approach, we performed quantitative trait locus (QTL) mapping of near-isogenic introgression lines between C24 and Col-0 for specific seed specialized metabolites. Besides common QTL between seeds and leaves, GWAS revealed seed-specific QTL for specialized metabolites, indicating differences in the genetic architecture of seeds and leaves. In seeds, aliphatic methylsulfinylalkyl and methylthioalkyl glucosinolates associated with the ALKENYL HYDROXYALKYL PRODUCING loci (GS-ALK and GS-OHP) on chromosome 4 containing alkenyl hydroxyalkyl producing 2 (AOP2) and 3 (AOP3) or with the GS-ELONG locus on chromosome 5 containing methylthioalkyl malate synthase (MAM1) and MAM3. We detected two unknown sulfur-containing compounds that were also mapped to these loci. In GWAS, some of the annotated flavonoids (kaempferol 3-O-rhamnoside-7-O-rhamnoside, quercetin 3-O-rhamnoside-7-O-rhamnoside) were mapped to transparent testa 7 (AT5G07990), encoding a cytochrome P450 75B1 monooxygenase. Three additional mass signals corresponding to quercetin-containing flavonols were mapped to UGT78D2 (AT5G17050). The association of the loci and associating metabolic features were functionally verified in knockdown mutant lines. By performing GWAS and QTL mapping, we were able to leverage variation of natural populations and parental lines to study seed specialized metabolism. The GWAS data set generated here is a high-quality resource that can be investigated in further studies.

Traits linked to natural variation of sulfur content in Arabidopsis thaliana

Sulfur (S) is an essential mineral nutrient for plant growth and development; it is important for primary and specialized plant metabolites that are crucial for biotic and abiotic interactions. Foliar S content varies up to 6-fold under a controlled environment, suggesting an adaptive value under certain natural environmental conditions. However, a major quantitative regulator of S content in Arabidopsis thaliana has not been identified yet, pointing to the existence of either additional genetic factors controlling sulfate/S content or of many minor quantitative regulators. Here, we use overlapping information of two separate ionomics studies to select groups of accessions with low, mid, and high foliar S content. We quantify series of metabolites, including anions (sulfate, phosphate, and nitrate), thiols (cysteine and glutathione), and seven glucosinolates, gene expression of 20 genes, sulfate uptake, and three biotic traits. Our results suggest that S content is tightly connected with sulfate uptake, the concentration of sulfate and phosphate anions, and glucosinolate and glutathione synthesis. Additionally, our results indicate that the growth of pathogenic bacteria is enhanced in the A. thaliana accessions containing higher S in their leaves, suggesting a complex regulation between S homeostasis, primary and secondary metabolism, and biotic pressures.

Species-specific 'specialized' genomic region provides the new insights into the functional genomics characterizing metabolic polymorphisms in plants

Functional genomics approaches with comparative omics analyses of wild-accessions and cultivars/wild species, as well as comparative genomic analyses in plant species focusing on gene clusters, have successfully detected key metabolic polymorphisms in plant specialized metabolism. In recent decades, (i) intra-species specific metabolic polymorphisms, (ii) new functionalization of tandem duplicated genes, and (iii) metabolic gene clusters were found as the main factors creating metabolic diversity of specialized metabolites in plants. However, given findings aware us that the identification of genes in plant specialized metabolism requires strategic approaches depending on the target metabolic pathways. The increasing availability of plant genome sequences and transcriptome data has facilitated inter-specific comparative analyses, including genomic analysis and gene co-expression network analysis. Here, we introduce functional genomics approaches with the integration of inter-/intra-species comparative metabolomics, their key roles in providing genomic signatures of metabolic evolution, and discuss future prospects of functional genomics on plant specialized metabolism.

Laminarin-triggered defence responses are geographically dependent in natural populations of Solanum chilense

Natural plant populations are polymorphic and show intraspecific variation in resistance properties against pathogens. The activation of the underlying defence responses can depend on variation in perception of pathogen-associated molecular patterns or elicitors. To dissect such variation, we evaluated the responses induced by laminarin (a glucan, representing an elicitor from oomycetes) in the wild tomato species Solanum chilense and correlated this to observed infection frequencies of Phytophthora infestans. We measured reactive oxygen species burst and levels of diverse phytohormones upon elicitation in 83 plants originating from nine populations. We found high diversity in basal and elicitor-induced levels of each component. Further we generated linear models to explain the observed infection frequency of P. infestans. The effect of individual components differed dependent on the geographical origin of the plants. We found that the resistance in the southern coastal region, but not in the other regions, was directly correlated to ethylene responses and confirmed this positive correlation using ethylene inhibition assays. Our findings reveal high diversity in the strength of defence responses within a species and the involvement of different components with a quantitatively different contribution of individual components to resistance in geographically separated populations of a wild plant species.

Responses of Aroma Related Metabolic Attributes of Opisthopappus longilobus Flowers to Environmental Changes

Opisthopappus longilobus (Opisthopappus) and its descendant species, Opisthopappus taihangensis, commonly thrive on the Taihang Mountains of China. Being typical cliff plants, both O. longilobus and O. taihangensis release unique aromatics. To determine the potential differentiation and environmental response patterns, comparative metabolic analysis was performed on O. longilobus wild flower (CLW), O. longilobus transplant flower (CLT), and O. taihangensis wild flower (TH) groups. Significant differences in the metabolic profiles were found, not within O. longilobus, but between O. longilobus and O. taihangensis flowers. Within these metabolites, twenty-eight substances related to the scents were obtained (one alkene, two aldehydes, three esters, eight phenols, three acids, three ketones, three alcohols, and five flavonoids), of which eugenol and chlorogenic were the primary aromatic molecules and enriched in the phenylpropane pathway. Network analysis showed that close relationships occurred among identified aromatic substances. The variation coefficient (CV) of aromatic metabolites in O. longilobus was lower than O. taihangensis. The aromatic related compounds were significantly correlated with the lowest temperatures in October and in December of the sampled sites. The results indicated that phenylpropane, particularly eugenol and chlorogenic, played important roles in the responses of O. longilobus species to environmental changes.

Genetic architecture of seed glycerolipids in Asian cultivated rice

Glycerolipids are essential for rice development and grain quality but its genetic regulation remains unknown. Here we report its genetic base using metabolite-based genome-wide association study and metabolite-based quantitative traits locus (QTL) analyses based on lipidomic profiles of seeds from 587 Asian cultivated rice accessions and 103 chromosomal segment substitution lines, respectively. We found that two genes encoding phosphatidylcholine (PC):diacylglycerol cholinephosphotransferase (OsLP1) and granule-bound starch synthase I (Waxy) contribute to variations in saturated triacylglycerol (TAG) and lyso-PC contents, respectively. We demonstrated that allelic variation in OsLP1 sequence between indica and japonica results in different enzymatic preference for substrate PC-16:0/16:0 and different saturated TAG levels. Further evidence demonstrated that OsLP1 also affects heading date, and that co-selection of OsLP1 and a flooding-tolerant QTL in Aus results in the abundance of saturated TAGs associated with flooding tolerance. Moreover, we revealed that the sequence polymorphisms in Waxy has pleiotropic effects on lyso-PC and amylose content. We proposed that rice seed glycerolipids have been unintentionally shaped during natural and artificial selection for adaptive or import seed quality traits. Collectively, our findings provide valuable genetic resources for rice improvement and evolutionary insights into seed glycerolipid variations in rice.

Predicting Gene Regulatory Interactions Using Natural Genetic Variation

Genome-wide association studies (GWAS) are a powerful tool to elucidate the genotype-phenotype map. Although GWAS are usually used to assess simple univariate associations between genetic markers and traits of interest, it is also possible to infer the underlying genetic architecture and to predict gene regulatory interactions. In this chapter, we describe the latest methods and tools to perform GWAS by calculating permutation-based significance thresholds. For this purpose, we first provide guidelines on univariate GWAS analyses that are extended in the second part of this chapter to more complex models that enable the inference of gene regulatory networks and how these networks vary.

Genetic variation underlying differential ammonium and nitrate responses in Arabidopsis thaliana

Nitrogen is an essential element required for plant growth and productivity. Understanding the mechanisms and natural genetic variation underlying nitrogen use in plants will facilitate the engineering of plant nitrogen use to maximize crop productivity while minimizing environmental costs. To understand the scope of natural variation that may influence nitrogen use, we grew 1,135 Arabidopsis thaliana natural genotypes on two nitrogen sources, nitrate and ammonium, and measured both developmental and defense metabolite traits. By using different environments and focusing on multiple traits, we identified a wide array of different nitrogen responses. These responses are associated with numerous genes, most of which were not previously associated with nitrogen responses. Only a small portion of these genes appear to be shared between environments or traits, while most are predominantly specific to a developmental or defense trait under a specific nitrogen source. Finally, by using a large population, we were able to identify unique nitrogen responses, such as preferring ammonium or nitrate, which appear to be generated by combinations of loci rather than a few large-effect loci. This suggests that it may be possible to obtain novel phenotypes in complex nitrogen responses by manipulating sets of genes with small effects rather than solely focusing on large-effect single gene manipulations.

The Boechera model system for evolutionary ecology

Model systems in biology expand the research capacity of individuals and the community. Closely related to Arabidopsis, the genus Boechera has emerged as an important ecological model owing to the ability to integrate across molecular, functional, and eco-evolutionary approaches. Boechera species are broadly distributed in relatively undisturbed habitats predominantly in western North America and provide one of the few experimental systems for identification of ecologically important genes through genome-wide association studies and investigations of selection with plants in their native habitats. The ecologically, evolutionarily, and agriculturally important trait of apomixis (asexual reproduction via seeds) is common in the genus, and field experiments suggest that abiotic and biotic environments shape the evolution of sex. To date, population genetic studies have focused on the widespread species B. stricta, detailing population divergence and demographic history. Molecular and ecological studies show that balancing selection maintains genetic variation in ~10% of the genome, and ecological trade-offs contribute to complex trait variation for herbivore resistance, flowering phenology, and drought tolerance. Microbiome analyses have shown that host genotypes influence leaf and root microbiome composition, and the soil microbiome influences flowering phenology and natural selection. Furthermore, Boechera offers numerous opportunities for investigating biological responses to global change. In B. stricta, climate change has induced a shift of >2 weeks in the timing of first flowering since the 1970s, altered patterns of natural selection, generated maladaptation in previously locally-adapted populations, and disrupted life history trade-offs. Here we review resources and results for this eco-evolutionary model system and discuss future research directions.

Genome-wide association mapping within a local Arabidopsis thaliana population more fully reveals the genetic architecture for defensive metabolite diversity

A paradoxical finding from genome-wide association studies (GWAS) in plants is that variation in metabolite profiles typically maps to a small number of loci, despite the complexity of underlying biosynthetic pathways. This discrepancy may partially arise from limitations presented by geographically diverse mapping panels. Properties of metabolic pathways that impede GWAS by diluting the additive effect of a causal variant, such as allelic and genetic heterogeneity and epistasis, would be expected to increase in severity with the geographical range of the mapping panel. We hypothesized that a population from a single locality would reveal an expanded set of associated loci. We tested this in a French Arabidopsis thaliana population (less than 1 km transect) by profiling and conducting GWAS for glucosinolates, a suite of defensive metabolites that have been studied in depth through functional and genetic mapping approaches. For two distinct classes of glucosinolates, we discovered more associations at biosynthetic loci than the previous GWAS with continental-scale mapping panels. Candidate genes underlying novel associations were supported by concordance between their observed effects in the TOU-A population and previous functional genetic and biochemical characterization. Local populations complement geographically diverse mapping panels to reveal a more complete genetic architecture for metabolic traits. This article is part of the theme issue 'Genetic basis of adaptation and speciation: from loci to causative mutations'.

Evolutionary footprint of plant immunity

There are pieces of evidence from genomic footprints and fossil records indicating that plants have co-evolved with microbes after terrestrialization for more than 407 million years. Therefore, to truly comprehend plant evolution, we need to understand the co-evolutionary process and history between plants and microbes. Recent developments in genomes and transcriptomes of a vast number of plant species as well as microbes have greatly expanded our knowledge of the evolution of the plant immune system. In this review, we summarize recent advances in the co-evolution between plants and microbes with emphasis on the plant side and point out future research needed for understanding plant-microbial co-evolution. Knowledge of the evolution and variation of the plant immune system will better equip us on designing crops with boosted performance in agricultural fields.

Chemical phenotype as important and dynamic niche dimension of plants

Niche theory considering the traits of species and individuals provides a powerful tool to integrate ecology and evolution of species. In plant ecology, morphological and physiological traits are commonly considered as niche dimensions, whereas phytochemical traits are mostly neglected in this context despite their pivotal functions in plant responses to their environment and in mediating interactions. The diversity of plant phytochemicals can thus mediate three key processes: niche choice, conformance and construction. Here, we integrate frameworks from niche theory with chemical ecology and argue that plants use their individual-specific diversity in phytochemicals (chemodiversity) for different niche realization processes. Our concept has important implications for ecosystem processes and stability and increases the predictive ability of chemical ecology.

Identification and Quantification of Glucosinolates and Phenolics in a Large Panel of Brassica napus Highlight Valuable Genetic Resources for Chemical Ecology and Breeding

Glucosinolate (GLS) and phenolic contents in Brassicaceae contribute to biotic and abiotic stress responses. Breeding crop accessions harboring agroecologically relevant metabolic profiles require a characterization of the chemical diversity in Brassica germplasm. This work investigates the diversity of specialized metabolites in 281 accessions of B. napus. First, an LC-HRMS2-based approach allowed the annotation of 32 phenolics and 36 GLSs, revealing 13 branched and linear alkyl-GLSs and 4 isomers of hydroxyphenylalkyl-GLSs, many of which have been rarely reported in Brassica. Then, quantitative UPLC-UV-MS-based profiling was performed in leaves and roots for the whole panel. This revealed striking variations in the content of 1-methylpropyl-GLS (glucocochlearin) and a large variation of tetra- and penta-glucosyl kaempferol derivatives among accessions. It also highlighted two main chemotypes related to sinapoyl-O-hexoside and kaempferol-O-trihexoside contents. By offering an unprecedented overview of the phytochemical diversity in B. napus, this work provides a useful resource for chemical ecology and breeding.

Evolutionary Ecology of Plant-Arthropod Interactions in Light of the "Omics" Sciences: A Broad Guide

Aboveground plant-arthropod interactions are typically complex, involving herbivores, predators, pollinators, and various other guilds that can strongly affect plant fitness, directly or indirectly, and individually, synergistically, or antagonistically. However, little is known about how ongoing natural selection by these interacting guilds shapes the evolution of plants, i.e., how they affect the differential survival and reproduction of genotypes due to differences in phenotypes in an environment. Recent technological advances, including next-generation sequencing, metabolomics, and gene-editing technologies along with traditional experimental approaches (e.g., quantitative genetics experiments), have enabled far more comprehensive exploration of the genes and traits involved in complex ecological interactions. Connecting different levels of biological organization (genes to communities) will enhance the understanding of evolutionary interactions in complex communities, but this requires a multidisciplinary approach. Here, we review traditional and modern methods and concepts, then highlight future avenues for studying the evolution of plant-arthropod interactions (e.g., plant-herbivore-pollinator interactions). Besides promoting a fundamental understanding of plant-associated arthropod communities' genetic background and evolution, such knowledge can also help address many current global environmental challenges.

Experimental demonstration and pan-structurome prediction of climate-associated riboSNitches in Arabidopsis

Background

Genome-wide association studies (GWAS) aim to correlate phenotypic changes with genotypic variation. Upon transcription, single nucleotide variants (SNVs) may alter mRNA structure, with potential impacts on transcript stability, macromolecular interactions, and translation. However, plant genomes have not been assessed for the presence of these structure-altering polymorphisms or “riboSNitches.”

Results

We experimentally demonstrate the presence of riboSNitches in transcripts of two Arabidopsis genes, ZINC RIBBON 3 (ZR3) and COTTON GOLGI-RELATED 3 (CGR3), which are associated with continentality and temperature variation in the natural environment. These riboSNitches are also associated with differences in the abundance of their respective transcripts, implying a role in regulating the gene's expression in adaptation to local climate conditions. We then computationally predict riboSNitches transcriptome-wide in mRNAs of 879 naturally inbred Arabidopsis accessions. We characterize correlations between SNPs/riboSNitches in these accessions and 434 climate descriptors of their local environments, suggesting a role of these variants in local adaptation. We integrate this information in CLIMtools V2.0 and provide a new web resource, T-CLIM, that reveals associations between transcript abundance variation and local environmental variation.

Conclusion

We functionally validate two plant riboSNitches and, for the first time, demonstrate riboSNitch conditionality dependent on temperature, coining the term “conditional riboSNitch.” We provide the first pan-genome-wide prediction of riboSNitches in plants. We expand our previous CLIMtools web resource with riboSNitch information and with 1868 additional Arabidopsis genomes and 269 additional climate conditions, which will greatly facilitate in silico studies of natural genetic variation, its phenotypic consequences, and its role in local adaptation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13059-022-02656-4.

A keystone gene underlies the persistence of an experimental food web

Genes encode information that determines an organism's fitness. Yet we know little about whether genes of one species influence the persistence of interacting species in an ecological community. Here, we experimentally tested the effect of three plant defense genes on the persistence of an insect food web and found that a single allele at a single gene promoted coexistence by increasing plant growth rate, which in turn increased the intrinsic growth rates of species across multiple trophic levels. Our discovery of a "keystone gene" illustrates the need to bridge between biological scales, from genes to ecosystems, to understand community persistence.

Revisiting a GWAS peak in Arabidopsis thaliana reveals possible confounding by genetic heterogeneity

Genome-wide association studies (GWAS) have become a standard approach for exploring the genetic basis of phenotypic variation. However, correlation is not causation, and only a tiny fraction of all associations have been experimentally confirmed. One practical problem is that a peak of association does not always pinpoint a causal gene, but may instead be tagging multiple causal variants. In this study, we reanalyze a previously reported peak associated with flowering time traits in Swedish Arabidopsis thaliana population. The peak appeared to pinpoint the AOP2/AOP3 cluster of glucosinolate biosynthesis genes, which is known to be responsible for natural variation in herbivore resistance. Here we propose an alternative hypothesis, by demonstrating that the AOP2/AOP3 flowering association can be wholly accounted for by allelic variation in two flanking genes with clear roles in regulating flowering: NDX1, a regulator of the main flowering time controller FLC, and GA1, which plays a central role in gibberellin synthesis and is required for flowering under some conditions. In other words, we propose that the AOP2/AOP3 flowering-time association may be yet another example of a spurious, "synthetic" association, arising from trying to fit a single-locus model in the presence of two statistically associated causative loci. We conclude that caution is needed when using GWAS for fine-mapping.

Getting the metabolites right

A study of almost 800 Arabidopsis thaliana plants from across Europe reveals how the environment and evolutionary pressures shape their metabolites.