Mapping of ionomic traits in Mimulus guttatus reveals Mo and Cd QTLs that colocalize with MOT1 homologues

Genetic architecture of root and shoot ionomes in rice (Oryza sativa L.)

KEY MESSAGE

Association analysis for ionomic concentrations of 20 elements identified independent genetic factors underlying the root and shoot ionomes of rice, providing a platform for selecting and dissecting causal genetic variants. Understanding the genetic basis of mineral nutrient acquisition is key to fully describing how terrestrial organisms interact with the non-living environment. Rice (Oryza sativa L.) serves both as a model organism for genetic studies and as an important component of the global food system. Studies in rice ionomics have primarily focused on above ground tissues evaluated from field-grown plants. Here, we describe a comprehensive study of the genetic basis of the rice ionome in both roots and shoots of 6-week-old rice plants for 20 elements using a controlled hydroponics growth system. Building on the wealth of publicly available rice genomic resources, including a panel of 373 diverse rice lines, 4.8 M genome-wide single-nucleotide polymorphisms, single- and multi-marker analysis pipelines, an extensive tome of 321 candidate genes and legacy QTLs from across 15 years of rice genetics literature, we used genome-wide association analysis and biparental QTL analysis to identify 114 genomic regions associated with ionomic variation. The genetic basis for root and shoot ionomes was highly distinct; 78 loci were associated with roots and 36 loci with shoots, with no overlapping genomic regions for the same element across tissues. We further describe the distribution of phenotypic variation across haplotypes and identify candidate genes within highly significant regions associated with sulfur, manganese, cadmium, and molybdenum. Our analysis provides critical insight into the genetic basis of natural phenotypic variation for both root and shoot ionomes in rice and provides a comprehensive resource for dissecting and testing causal genetic variants.

Ionomic Approaches for Discovery of Novel Stress-Resilient Genes in Plants

Plants, being sessile, face an array of biotic and abiotic stresses in their lifespan that endanger their survival. Hence, optimized uptake of mineral nutrients creates potential new routes for enhancing plant health and stress resilience. Recently, minerals (both essential and non-essential) have been identified as key players in plant stress biology, owing to their multifaceted functions. However, a realistic understanding of the relationship between different ions and stresses is lacking. In this context, ionomics will provide new platforms for not only understanding the function of the plant ionome during stresses but also identifying the genes and regulatory pathways related to mineral accumulation, transportation, and involvement in different molecular mechanisms under normal or stress conditions. This article provides a general overview of ionomics and the integration of high-throughput ionomic approaches with other "omics" tools. Integrated omics analysis is highly suitable for identification of the genes for various traits that confer biotic and abiotic stress tolerance. Moreover, ionomics advances being used to identify loci using qualitative trait loci and genome-wide association analysis of element uptake and transport within plant tissues, as well as genetic variation within species, are discussed. Furthermore, recent developments in ionomics for the discovery of stress-tolerant genes in plants have also been addressed; these can be used to produce more robust crops with a high nutritional value for sustainable agriculture.

QTL x environment interactions underlie ionome divergence in switchgrass

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 the trait and QTL level. Concentrations of 14 of the 18 elements were under some genetic control, and 77 QTL were detected for these elements. 74% of QTL colocalized multiple elements, half of QTL exhibited significant QTLxE, and roughly equal numbers of QTL had significant differences in magnitude and sign of their effects across environments. The switchgrass ionome is under moderate genetic control and by loci with highly variable effects across environments.

Beyond cadmium accumulation: Distribution of other trace elements in soils and cacao beans in Ecuador

Since cacao beans accumulate Cd in high levels and restrictions have been imposed on safe levels of chocolate consumption, concern about whether or not cacao trees store other toxic elements seems to be inevitable. Following a previous study in Ecuador examining Cd content in five cacao varieties collected in pristine areas and in places impacted by oil activities, we present here the concentrations of 11 trace elements (TEs) (As, Ba, Co, Cu, Cr, Mo, Mn, Ni, Pb, V and Zn) in soils, cacao tissues (leaves, pod husks, beans) and cocoa liquor (CL). Several TEs showed concentrations in topsoils above the Ecuadorian limits, and may have a mixed natural and anthropogenic origin. Ba and Mo concentrations in cacao tissues are slightly higher than those reported in other surveys, but this was not the case for toxic elements (As and Pb). TE contents are lower in CL, than in beans, except for Pb and Co, but no risk was identified for human health. Compared with control areas, Enrichment Factors were below 2 in impacted areas, except for Ba. Transfer factors (from soils to cacao) indicated that cacao does not accumulate TEs. A positive correlation was found between Cd and Zn in topsoils and cacao tissues for the CCN-51 variety, and between Cd and Ni for the Nacional variety. Identifying patterns of TE distribution and potential interactions in order to explain plant internal mechanisms, which is also dependent on the cacao variety, is a difficult task and needs further research.

Relationships between soil and leaf mineral composition are element-specific, environment-dependent and geographically structured in the emerging model Arabidopsis halleri

Leaf mineral composition, the leaf ionome, reflects the complex interaction between a plant and its environment including local soil composition, an influential factor that can limit species distribution and plant productivity. Here we addressed within-species variation in plant-soil interactions and edaphic adaptation using Arabidopsis halleri, a well-suited model species as a facultative metallophyte and metal hyperaccumulator. We conducted multi-element analysis of 1972 paired leaf and soil samples from 165 European populations of A. halleri, at individual resolution to accommodate soil heterogeneity. Results were further confirmed under standardized conditions upon cultivation of 105 field-collected genotypes on an artificially metal-contaminated soil in growth chamber experiments. Soil-independent between- and within-population variation set apart leaf accumulation of zinc, cadmium and lead from all other nutrient and nonessential elements, concurring with differential hypothesized ecological roles in either biotic interaction or nutrition. For these metals, soil-leaf relationships were element-specific, differed between metalliferous and nonmetalliferous soils and were geographically structured both in the field and under standardized growth conditions, implicating complex scenarios of recent ecological adaptation. Our study provides an example and a reference for future related work and will serve as a basis for the molecular-genetic dissection and ecological analysis of the observed phenotypic variation.

Plant Ionomics: From Elemental Profiling to Environmental Adaptation

Ionomics is a high-throughput elemental profiling approach to study the molecular mechanistic basis underlying mineral nutrient and trace element composition (also known as the ionome) of living organisms. Since the concept of ionomics was first introduced more than 10 years ago, significant progress has been made in the identification of genes and gene networks that control the ionome. In this update, we summarize the progress made in using the ionomics approach over the last decade, including the identification of genes by forward genetics and the study of natural ionomic variation. We further discuss the potential application of ionomics to the investigation of the ecological functions of ionomic alleles in adaptation to the environment.

In silico ionomics segregates parasitic from free-living eukaryotes

Ion transporters are fundamental to life. Due to their ancient origin and conservation in sequence, ion transporters are also particularly well suited for comparative genomics of distantly related species. Here, we perform genome-wide ion transporter profiling as a basis for comparative genomics of eukaryotes. From a given predicted proteome, we identify all bona fide ion channels, ion porters, and ion pumps. Concentrating on unicellular eukaryotes (n = 37), we demonstrate that clustering of species according to their repertoire of ion transporters segregates obligate endoparasites (n = 23) on the one hand, from free-living species and facultative parasites (n = 14) on the other hand. This surprising finding indicates strong convergent evolution of the parasites regarding the acquisition and homeostasis of inorganic ions. Random forest classification identifies transporters of ammonia, plus transporters of iron and other transition metals, as the most informative for distinguishing the obligate parasites. Thus, in silico ionomics further underscores the importance of iron in infection biology and suggests access to host sources of nitrogen and transition metals to be selective forces in the evolution of parasitism. This finding is in agreement with the phenomenon of iron withholding as a primordial antimicrobial strategy of infected mammals.

Challenges and prospects in genome-wide quantitative trait loci mapping of standing genetic variation in natural populations

A considerable challenge in evolutionary genetics is to understand the genetic mechanisms that facilitate or impede evolutionary adaptation in natural populations. For this, we must understand the genetic loci contributing to trait variation and the selective forces acting on them. The decreased costs and increased feasibility of obtaining genotypic data on a large number of individuals have greatly facilitated gene mapping in natural populations, particularly because organisms whose genetics have been historically difficult to study are now within reach. Here we review the methods available to evolutionary ecologists interested in dissecting the genetic basis of traits in natural populations. Our focus lies on standing genetic variation in outbred populations. We present an overview of the current state of research in the field, covering studies on both plants and animals. We also draw attention to particular challenges associated with the discovery of quantitative trait loci and discuss parallels to studies on crops, livestock, and humans. Finally, we point to some likely future developments in genetic mapping studies.

Genetic architecture of naturally occurring quantitative traits in plants: an updated synthesis

Deciphering the genetic and molecular bases of quantitative variation is a long-standing challenge in plant biology because it is essential for understanding evolution and for accelerating plant breeding. Recent multi-trait analyses at different phenotypic levels are uncovering the pleiotropy and the genetic regulation underlying high-level complex traits. Thus, the number of known causal loci, genes and nucleotide polymorphisms is expanding. Current plant causal catalogs contain ∼400 genes and natural polymorphisms revealing several dysfunctional allelic series that involve multiple mutations. In addition, repeated evolution of quantitative traits mediated by large effect alleles is found across plant phylogeny. Finally, systematic analyses of genetic and environmental interactions are beginning to elucidate the molecular mechanisms of relevant interactions.