Construction of a genetic linkage map of Thlaspi caerulescens and quantitative trait loci analysis of zinc accumulation

Increasing resistance of lawn grasses to zinc and copper pollution

Coppe and zinc are priority pollutants in city soils. Copper and zinc are the limiting factors for lawn grasses. Cell selection can increase the resistance of lawn grasses to zinc and copper. The effect of zinc on the morphogenic ability of the callus was determined. The results of this study showed that zinc is less toxic to calli than copper. The method of obtaining lawn grass resistant to zinc has been developed. The results were used to develop the cell selection technology for obtaining plants resistant to the complex effect of zinc and copper. Concentrations of Copper (75 mg/l) and zinc (150 mg/L) were selected as selective. The author developed the cell selection scheme for obtaining plants resistant to the complex effect of Cu and Zn. The regenerants showed increased resistance to copper and zinc.

Enhancing the potential for cadmium phytoremediation by introducing Perilla frutescens genes in tobacco

To improve the potential of cadmium phytoremediation, distant hybridization between tobacco (Nicotiana tabacum L. var. 78-04), a high-biomass crop, and Perilla frutescens var. frutescens, a wild Cd-hyperaccumulator, was carried out, developing a new variety N. tabacum L. var. ZSY. Seedlings at the six-leaf stage were grown in hydroponics and treated with 0 (control), 10 µM, 180 µM, and 360 µM CdCl₂ for 7 days; then, the differences in Cd tolerance and accumulation and physiological and metabolic responses were evaluated among "ZSY" and its parents. At high Cd dose, the growth of "ZSY," such as fresh weight, plant height, and root length, was evidently better than "78-04." In contrast to P. frutescens and "78-04," "ZSY" could accumulate more Cd in shoots than roots. Under the same treatment, "ZSY" accumulated greater amounts of Cd in both shoots (195-1523 mg kg^-1) and roots (140-1281 mg kg^-1) than "78-04" (shoots: 35-89 mg kg^-1, roots: 39-252 mg kg^-1), followed by P. frutescens (shoots: 156-454 mg kg^-1, roots: 103-761 mg kg^-1). BCF and TF values of "ZSY" reached 38-195 and 1.2-1.4, which were far higher than those of "78-04" (BCF: 2.2-35.3, TF: 0.35-0.9). Perilla frutescens was found with BCF and TF of 11-156 and 0.5-1.5. Cd stress obviously promoted the production of ROS and MDA in seedlings but reduced chlorophyll contents, especially in "78-04." As a response to Cd stress, "ZSY" had higher SOD and CAT activities when compared to P. frutescens and "78-04," while "78-04" produced more POD and proline than those of P. frutescens and "ZSY." Cd stress could affect the production and accumulation of alkaloids and phenolic compounds in root (endodermis and cortex) and mesophyll. At high Cd doses, P. frutescens and "ZSY" had more alkaloids in tissues than "78-04." Phenolic compounds in "78-04" were more obviously inhibited compared with P. frutescens and "ZSY." These secondary metabolites may play an important role in eliminating oxidative damage and enhancing Cd tolerance and accumulation in "ZSY" and P. frutescens. Results indicated that distant hybridization could be one of effective methods for introducing excellent genes from metal-hyperaccumulators into high biomass species, creating plants with superior phytoremediation potential.

OUP accepted manuscript

The molecular biology and genetics of the Ni–Cd–Zn hyperaccumulator Noccaea caerulescens has been extensively studied, but no information is yet available on Ni and Zn redistribution and mobilization during seed germination. Due to the different physiological functions of these elements, and their associated transporter pathways, we expected differential tissue distribution and different modes of translocation of Ni and Zn during germination. This study used synchrotron X-ray fluorescence tomography techniques as well as planar elemental X-ray imaging to elucidate elemental (re)distribution at various stages of the germination process in contrasting accessions of N. caerulescens. The results show that Ni and Zn are both located primarily in the cotyledons of the emerging seedlings and Ni is highest in the ultramafic accessions (up to 0.15 wt%), whereas Zn is highest in the calamine accession (up to 600 μg g^–1). The distribution of Ni and Zn in seeds was very similar, and neither element was translocated during germination. The Fe maps were especially useful to obtain spatial reference within the seeds, as it clearly marked the vasculature. This study shows how a multimodal combination of synchrotron techniques can be used to obtain powerful insights about the metal distribution in physically intact seeds and seedlings.

Phytoremediation of Toxic Metals: A Sustainable Green Solution for Clean Environment

Contamination of aquatic ecosystems by various sources has become a major worry all over the world. Pollutants can enter the human body through the food chain from aquatic and soil habitats. These pollutants can cause various chronic diseases in humans and mortality if they collect in the body over an extended period. Although the phytoremediation technique cannot completely remove harmful materials, it is an environmentally benign, cost-effective, and natural process that has no negative effects on the environment. The main types of phytoremediation, their mechanisms, and strategies to raise the remediation rate and the use of genetically altered plants, phytoremediation plant prospects, economics, and usable plants are reviewed in this review. Several factors influence the phytoremediation process, including types of contaminants, pollutant characteristics, and plant species selection, climate considerations, flooding and aging, the effect of salt, soil parameters, and redox potential. Phytoremediation’s environmental and economic efficiency, use, and relevance are depicted in our work. Multiple recent breakthroughs in phytoremediation technologies are also mentioned in this review.

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.

Intraspecific Variation in Nickel Tolerance and Hyperaccumulation among Serpentine and Limestone Populations of Odontarrhena serpyllifolia (Brassicaceae: Alysseae) from the Iberian Peninsula

Odontarrhena serpyllifolia (Desf.) Jord. & Fourr. (=Alyssum serpyllifolium Desf.) occurs in the Iberian Peninsula and adjacent areas on a variety of soils including both limestone and serpentine (ultramafic) substrates. Populations endemic to serpentine are known to hyperaccumulate nickel, and on account of this remarkable phenotype have, at times, been proposed for recognition as taxonomically distinct subspecies or even species. It remains unclear, however, to what extent variation in nickel hyperaccumulation within this taxon merely reflects differences in the substrate, or whether the different populations show local adaptation to their particular habitats. To help clarify the physiological basis of variation in nickel hyperaccumulation among these populations, 3 serpentine accessions and 3 limestone accessions were cultivated hydroponically under common-garden conditions incorporating a range of Ni concentrations, along with 2 closely related non-accumulator species, Clypeola jonthlaspi L. and Alyssum montanum L. As a group, serpentine accessions of O. serpyllifolia were able to tolerate Ni concentrations approximately 10-fold higher than limestone accessions, but a continuous spectrum of Ni tolerance was observed among populations, with the least tolerant serpentine accession not being significantly different from the most tolerant limestone accession. Serpentine accessions maintained relatively constant tissue concentrations of Ca, Mg, K, and Fe across the whole range of Ni exposures, whereas in the limestone accessions, these elements fluctuated widely in response to Ni toxicity. Hyperaccumulation of Ni, defined here as foliar Ni concentrations exceeding 1g kg^-1 of dry biomass in plants not showing significant growth reduction, occurred in all accessions of O. serpyllifolia, but the higher Ni tolerance of serpentine accessions allowed them to hyperaccumulate more strongly. Of the reference species, C. jonthlaspi responded similarly to the limestone accessions of O. serpyllifolia, whereas A. montanum displayed by far the lowest degree of Ni tolerance and exhibited low foliar Ni concentrations, which only exceeded 1 g kg^-1 in plants showing severe Ni toxicity. The continuous spectrum of physiological responses among these accessions does not lend support to segregation of the serpentine populations of O. serpyllifolia as distinct species. However, the pronounced differences in degrees of Ni tolerance, hyperaccumulation, and elemental homeostasis observed among these accessions under common-garden conditions argues for the existence of population-level adaptation to their local substrates.

Imaging Zn and Ni distributions in leaves of different ages of the hyperaccumulator Noccaea caerulescens by synchrotron-based X-ray fluorescence

Mapping of leaves of hyperaccumulators can provide insights into the mechanisms these species utilize to accumulate high metal concentrations. We used synchrotron-based X-ray fluorescence (SXRF) to perform Zn and Ni imaging in leaves of different ages of Noccaea caerulescens. A mature leaf of the related non-hyperaccumulator Thlaspi arvense was also imaged. The concentrations of Zn, Ni, Co, and Cr in N. caerulescens grown on an ultramafic soil were 9-, 10-, 12-, and 3-fold higher than T. arvense. N. caerulescens showed an exceptional ability to accumulate Zn from the soil, posing a bioconcentration factor of 6.7. T. arvense had Zn and Ni distributed uniformly in the leaf blade with doubling fluorescence counts in the tip and margins, suggesting a strategy to excrete metals and avoid toxicity. On the other hand, N. caerulescens displayed distinctly different Zn and Ni accumulation patterns, regardless of the age or metal concentration in the leaves. Zinc was mainly distributed in the cells surrounding the central and secondary veins. Nickel accumulated in the margins and tips of the leaf blade. Given the time required to image large leaves in synchrotron facilities, small leaves can be used to represent the leaf distribution of Zn and Ni in N. caerulescens.

Spatially-resolved localization and chemical speciation of nickel and zinc in Noccaea tymphaea and Bornmuellera emarginata

Hyperaccumulator plants present the ideal model system for studying the physiological regulation of the essential (and potentially toxic) transition elements nickel and zinc. This study used synchrotron X-ray Fluorescence Microscopy (XFM) elemental imaging and spatially resolved X-ray Absorption Spectroscopy (XAS) to elucidate elemental localization and chemical speciation of nickel and zinc in the hyperaccumulators Noccaea tymphaea and Bornmuellera emarginata (synonym Leptoplax emarginata). The results show that in the leaves of N. tymphaea nickel and zinc have contrasting localization, and whereas nickel is present in vacuoles of epidermal cells, zinc occurs mainly in the mesophyll cells. In the seeds Ni and Zn are similarly localized and strongly enriched in the cotyledons in N. tymphaea. Nickel is strongly enriched in the tip of the radicle of B. emarginata. Noccaea tymphaea has an Fe-rich provascular strand network in the cotyledons of the seed. The chemical speciation of Ni in the seeds of N. tymphaea is unequivocally associated with carboxylic acids, whereas Zn is present as the phytate complex. The spatially resolved spectroscopy did not reveal any spatial variation in chemical speciation of Ni and Zn within the N. tymphaea seed. The dissimilar ecophysiological behaviour of Ni and Zn in N. tymphaea and B. emarginata raises questions about the evolution of hyperaccumulation in these species.

Biomolecular approaches to understanding metal tolerance and hyperaccumulation in plants

Trace metal elements are essential for plant growth but become toxic at high concentrations, while some non-essential elements, such as Cd and As, show toxicity even in traces.

Can zinc pollution promote adaptive evolution in plants? Insights from a one-generation selection experiment

Human activities generate environmental stresses that can lead plant populations to become extinct. Population survival would require the evolution of adaptive responses that increase tolerance to these stresses. Thus, in pseudometallophyte species that have colonized anthropogenic metalliferous habitats, the evolution of increased metal tolerance is expected in metallicolous populations. However, the mechanisms by which metal tolerance evolves remain unclear. In this study, parent populations were created from non-metallicolous families of Noccaea caerulescens. They were cultivated for one generation in mesocosms and under various levels of zinc (Zn) contamination to assess whether Zn in soil represents a selective pressure. Individual plant fitness estimates were used to create descendant populations, which were cultivated in controlled conditions with moderate Zn contamination to test for adaptive evolution in functional traits. The number of families showing high fitness estimates in mesocosms was progressively reduced with increasing Zn levels in soil, suggesting increasing selection for metal tolerance. In the next generation, adaptive evolution was suggested for some physiological and ecological traits in descendants of the most exposed populations, together with a significant decrease of Zn hyperaccumulation. Our results confirm experimentally that Zn alone can be a significant evolutionary pressure promoting adaptive divergence among populations.

Transcriptome Comparison Reveals the Adaptive Evolution of Two Contrasting Ecotypes of Zn/Cd Hyperaccumulator Sedum alfredii Hance

Hyperaccumulating ecotype (HE) and non-hyperaccumulating ecotype (NHE) of Sedum alfredii Hance belong to the same species but exhibit contrasting characteristics regarding hyperaccumulation and hypertolerance to cadmium and zinc. The Illumina Hiseq 2500 platform was employed to sequence HE and NHE to study the genetic evolution of this contrasting trait. Greater than 90 million clean reads were obtained and 118,479/228,051 unigenes of HE/NHE were annotated based on seven existing databases. We identified 149,668/319,830 single nucleotide polymorphisms (SNPs) and 12,691/14,428 simple sequence repeats (SSRs) of HE/NHE. We used a branch-site model to identify 18 divergent orthologous genes and 57 conserved orthologous genes of S. alfredii Hance. The divergent orthologous genes were mainly involved in the transcription and translation processes, protein metabolism process, calcium (Ca²⁺) pathway, stress response process and signal transduction process. To the best of our knowledge, this is the first study to use RNA-seq to compare the genetic evolution of hyperaccumulating and non-hyperaccumulating plants from the same species. In addition, this study made the sole concrete for further studies on molecular markers and divergent orthologous genes to depict the evolution process and formation of the hyperaccumulation and hypertolerance traits in S. alfredii Hance.

Responses and acclimation of Chinese cork oak (Quercus variabilis Bl.) to metal stress: the inducible antimony tolerance in oak trees

Antimony (Sb) pollution has become a pressing environmental problem in recent years. Trees have been proven to have great potential for the feasible phytomanagement; however, little is known about Sb retention and tolerance in trees. The Chinese cork oak (Quercus variabilis Bl.) is known to be capable of growth in soils containing high concentrations of Sb. This study explored in detail the retention and acclimation of Q. variabilis under moderate and high external Sb levels. Results revealed that Q. variabilis could tolerate and accumulate high Sb (1623.39 mg kg(-1) DW) in roots. Dynamics of Sb retention in leaves, stems, and roots of Q. variabilis were different. Leaf Sb remained at a certain level for several weeks, while in roots and stems, Sb concentrations continued to increase. Sb damaged tree's PSII reaction cores but elicited defense mechanism at the donor side of PSII. It affected the electron transport flow after QA (-) more strongly than the oxygen-evolving complex and light-harvesting pigment-protein complex II. Sb also decreased leaf chlorophyll concentrations and therefore inhibited plant growth. During acclimation to Sb toxicity, Sb concentrations in leaves, stems, and roots decreased, with photosynthetic activity and pigments recovering to normal levels by the end of the experiment. These findings suggest that Sb tolerance in Q. variabilis is inducible. Acclimation seems to be related to homeostasis of Sb in plants. Results of this study can provide useful information for trees breeding and selection of Sb phytomanagement strategies, exploiting the established ability of Q. variabilis to transport, delocalize in the leaves, and tolerate Sb pollutions.

Towards the identification of the loci of adaptive evolution

1. Establishing the genetic and molecular basis underlying adaptive traits is one of the major goals of evolutionary geneticists in order to understand the connection between genotype and phenotype and elucidate the mechanisms of evolutionary change. Despite considerable effort to address this question, there remain relatively few systems in which the genes shaping adaptations have been identified. 2. Here, we review the experimental tools that have been applied to document the molecular basis underlying evolution in several natural systems, in order to highlight their benefits, limitations and suitability. In most cases, a combination of DNA, RNA and functional methodologies with field experiments will be needed to uncover the genes and mechanisms shaping adaptation in nature.

Enhancement of cadmium tolerance and accumulation by introducing Perilla frutescens (L.) Britt var. frutescens genes in Nicotiana tabacum L. plants

The tobacco has the genetic potential to remove toxic metals from the soil. To develop hyperaccumulating tobacco plants, distant hybridization between tobacco (Nicotiana tabacum L.), a high-biomass crop, and Perilla frutescens (L.) Britt var. frutescens, a newfound Cd-hyperaccumulator species, was carried out using a novel method viz. pollination following grafting. Their hybrid nature was preliminarily confirmed by phenotype, isozyme pattern, random amplified polymorphic DNA (RAPD) and metabolites analysis. About 120 putative F2 hybrids derived from the cross-combination [(N. sylvestris Speg. & Comes rootstock + N. tabacum L. var. 78-04 scion) × P. frutescens (L.) Britt var. frutescens] were then subjected to up to 300 μM CdCl2 in hydroponic conditions for 10 days. Results showed five seedlings were more resistant to Cd than female parent and accumulated 314.6 ± 99.9 mg kg(-1) Cd in their aerial biomass, which was 5.7 times greater than that in "78-04" tobacco (47.2 ± 3.56 mg kg(-1)) (P ≤ 0.05). Two of these seedlings exceeded male parent P. frutescens in the Cd concentration of shoots and reached 424 and 396 mg kg(-1), which was 13% and 6% greater for that of perilla (374.2 ± 10.38 mg kg(-1)), respectively. Compared with parents, two other F2 hybrids tended to accumulate more Cd in the root with bioconcentration factor (BCF) 7.05 and 5.17, respectively. Only one hybrid showed lower Cd concentration but transferred Cd more effectively from the root to the shoot than parents and other F2 hybrids, with the maximum translocation factor (TF) value 1.37. These indicated that the introduction of P. frutescens genes could obviously enhance the cadmium tolerance and accumulation of superior individuals.

A comprehensive set of transcript sequences of the heavy metal hyperaccumulator Noccaea caerulescens

Noccaea caerulescens is an extremophile plant species belonging to the Brassicaceae family. It has adapted to grow on soils containing high, normally toxic, concentrations of metals such as nickel, zinc, and cadmium. Next to being extremely tolerant to these metals, it is one of the few species known to hyperaccumulate these metals to extremely high concentrations in their aboveground biomass. In order to provide additional molecular resources for this model metal hyperaccumulator species to study and understand the mechanism of adaptation to heavy metal exposure, we aimed to provide a comprehensive database of transcript sequences for N. caerulescens. In this study, 23,830 transcript sequences (isotigs) with an average length of 1025 bp were determined for roots, shoots and inflorescences of N. caerulescens accession "Ganges" by Roche GS-FLEX 454 pyrosequencing. These isotigs were grouped into 20,378 isogroups, representing potential genes. This is a large expansion of the existing N. caerulescens transcriptome set consisting of 3705 unigenes. When translated and compared to a Brassicaceae proteome set, 22,232 (93.2%) of the N. caerulescens isotigs (corresponding to 19,191 isogroups) had a significant match and could be annotated accordingly. Of the remaining sequences, 98 isotigs resembled non-plant sequences and 1386 had no significant similarity to any sequence in the GenBank database. Among the annotated set there were many isotigs with similarity to metal homeostasis genes or genes for glucosinolate biosynthesis. Only for transcripts similar to Metallothionein3 (MT3), clear evidence for an additional copy was found. This comprehensive set of transcripts is expected to further contribute to the discovery of mechanisms used by N. caerulescens to adapt to heavy metal exposure.

Comparative transcriptome analysis of the metal hyperaccumulator Noccaea caerulescens

The metal hyperaccumulator Noccaea caerulescens is an established model to study the adaptation of plants to metalliferous soils. Various comparators have been used in these studies. The choice of suitable comparators is important and depends on the hypothesis to be tested and methods to be used. In high-throughput analyses such as microarray, N. caerulescens has been compared to non-tolerant, non-accumulator plants like Arabidopsis thaliana or Thlaspi arvense rather than to the related hypertolerant or hyperaccumulator plants. An underutilized source is N. caerulescens populations with considerable variation in their capacity to accumulate and tolerate metals. Whole transcriptome sequencing (RNA-Seq) is revealing interesting variation in their gene expression profiles. Combining physiological characteristics of N. caerulescens accessions with their RNA-Seq has a great potential to provide detailed insight into the underlying molecular mechanisms, including entirely new gene products. In this review we will critically consider comparative transcriptome analyses carried out to explore metal hyperaccumulation and hypertolerance of N. caerulescens, and demonstrate the potential of RNA-Seq analysis as a tool in evolutionary genomics.

The evaluation of heavy metal accumulation and application of a comprehensive bio-concentration index for woody species on contaminated sites in Hunan, China

Fast-growing metal-accumulating woody plants are considered potential candidates for phytoextraction of metals. Shuikoushan mining, one of the biggest Pb and Zn production bases in China, presents an important source of the pollution of environment during the last 100 years. Over 150 km(2) of fertile soil have been contaminated by the dust, slag, and tailings from this mining. The goal of the present work has been to determine the content of Pb, Zn, Cd, and Cu in wild woody plants (18 species) naturally growing in this area. Two hundred five plant and soil samples from 11 contaminated sites were collected and analyzed. In addition, to assess the ability of multi-metal accumulation of these trees, we proposed a predictive comprehensive bio-concentration index (CBCI) based on fuzzy synthetic assessment. Our data suggest some adult trees could also accumulate a large amount of metals. Pb concentrations in leaves of Paulownia fortunei (Seem.) Hemsl. (1,179 mg/kg) exceeded the hyperaccumulation threshold (1,000 mg/kg). Elevated Pb concentrations (973.38 mg/kg) were also found in the leaves of Broussonetia papyrifera (L.) Vent., with a Pb bio-concentration factor of up to 0.701. Endemic species, Zenia insignis Chun exhibited huge potential for Zn and Cd phytoextraction, with the highest concentrations of Zn (1,968 mg/kg) and Cd (44.40 mg/kg), characteristic root nodules, and fast growth rates in poor soils. As for multi-metal accumulation ability, native species B. papyrifera was calculated to have the most exceptional ability to accumulate various metals simultaneously (CBCI 2.93), followed by Amorpha fruticosa L. (CBCI 2.72) and Lagerstroemia indica L. (CBCI 2.53). A trend of increasing metal from trunks to leaves (trunks < branches < leaves) and towards fine roots has been shown by metal partitioning between tissues. The proposed CBCI would allow for the selection of suitable trees for phytoremediation in the future.

Facultative hyperaccumulation of heavy metals and metalloids

Approximately 500 species of plants are known to hyperaccumulate heavy metals and metalloids. The majority are obligate metallophytes, species that are restricted to metalliferous soils. However, a smaller but increasing list of plants are "facultative hyperaccumulators" that hyperaccumulate heavy metals when occurring on metalliferous soils, yet also occur commonly on normal, non-metalliferous soils. This paper reviews the biology of facultative hyperaccumulators and the opportunities they provide for ecological and evolutionary research. The existence of facultative hyperaccumulator populations across a wide edaphic range allows intraspecific comparisons of tolerance and uptake physiology. This approach has been used to study zinc and cadmium hyperaccumulation by Noccaea (Thlaspi) caerulescens and Arabidopsis halleri, and it will be instructive to make similar comparisons on species that are distributed even more abundantly on normal soil. Over 90% of known hyperaccumulators occur on serpentine (ultramafic) soil and accumulate nickel, yet there have paradoxically been few experimental studies of facultative nickel hyperaccumulation. Several hypotheses suggested to explain the evolution of hyperaccumulation seem unlikely when most populations of a species occur on normal soil, where plants cannot hyperaccumulate due to low metal availability. In such species, it may be that hyperaccumulation is an ancestral phylogenetic trait or an anomalous manifestation of physiological mechanisms evolved on normal soils, and may or may not have direct adaptive benefits.

Identification of a novel pathway involving a GATA transcription factor in yeast and possibly in plant Zn uptake and homeostasis

To gain a better understanding of the regulation of Zn homeostasis in plants and the degree of conservation of Zn homeostasis between plants and yeast, a cDNA library from the Zn/Cd hyperaccumulating plant species, Noccaea caerulescens, was screened for its ability to restore growth under Zn limiting conditions in the yeast mutant zap1Δ. ZAP1 is a transcription factor that activates the Zn dependent transcription of yeast genes involved in Zn uptake, including ZRT1, the yeast high affinity Zn transporter. From this screen two members of the E2F family of transcription factors were found to activate ZRT1 expression in a Zn independent manner. The activation of ZRT1 by the plant E2F proteins involves E2F-mediated activation of a yeast GATA transcription factor which in turn activates ZRT1 expression. A ZRT1 promoter region necessary for activation by E2F and GATA proteins is upstream of two zinc responsive elements previously shown to bind ZAP1 in ZRT1. This activation may not involve direct binding of E2F to the ZRT1 promoter. The expression of E2F genes in yeast does not replace function of ZAP1; instead it appears to activate a novel GATA regulatory pathway involved in Zn uptake and homeostasis that is not Zn responsive.

Histidine promotes the loading of nickel and zinc, but not of cadmium, into the xylem in Noccaea caerulescens

Histidine is known to be involved in Ni hyperaccumulation. Recently, histidine-dependent xylem loading of Ni and Zn has been demonstrated in the Zn/Ni/Cd hyperaccumulator, Noccaea caerulescens. Here we tested the hypothesis whether Cd xylem loading is histidine-dependent, too. In contrast to that of Ni and Zn, the xylem loading of Cd was not affected by exogenous histidine. Histidine accumulation in root cells appears to facilitate the radial transport of Ni and Zn, but not Cd, across the roots. This may be due to the relatively high preference of Cd for coordination with sulfur over coordination with nitrogen, in comparison with Ni and Zn.

The proteomics of heavy metal hyperaccumulation by plants

Hyperaccumulators are distinguished from non-hyperaccumulators on the basis of their capacity to extract heavy metal ions from the soil, their more efficient root-to-shoot translocation of these ions and their greater ability to detoxify and sequester heavy metals in the shoot. The understanding of the mechanisms underlying metal ion accumulation has progressed beyond the relevant biochemistry and physiology to encompass the genetic and molecular regulatory systems which differentiate hyperaccumulators from non-hyperaccumulators. This paper reviews the literature surrounding the application of proteomics technology to plant metal hyperaccumulation, in particular involving the elements As, Cd, Cu, Ni, Pb and Zn. The hyperaccumulation process across a number of unrelated plant species appears to be associated with proteins involved in energy metabolism, the oxidative stress response and abiotic and biotic stress. The relevance of transducers of the metal stress response to the phenomenon of hyperaccumulation is summarized. Proteomic data complement the more voluminous genomic and transcriptomic data sets in providing a more nuanced picture of the process, and should therefore help in the identification of the major genetic determinants of the hyperaccumulation phenomenon.

Genetic analyses of nickel tolerance in a North American serpentine endemic plant, Caulanthus amplexicaulis var. barbarae (Brassicaceae)

PREMISE OF THE STUDY

The evolution of metal tolerance in plants is an important model for studies of adaptation to environment, population genetics, and speciation. Here, we investigated nickel tolerance in the North American serpentine endemic Caulanthus amplexicaulis var. barbarae in comparison with its nonserpentine sister taxon C. amplexicaulis var. amplexicaulis. We hypothesized that the serpentine endemic would have a heritable growth advantage on nickel-containing substrates.

METHODS

We employed an artificial growth assay to quantify biomass accumulation. Study plants were crossed to create an F(2:3) population that was used to determine the heritability of nickel tolerance and to map quantitative trait loci (QTL). Nickel accumulation in both laboratory populations and native specimens was examined using energy-dispersive x-ray fluorescence (EDXRF).

KEY RESULTS

The serpentine endemic had a dramatic growth advantage at concentrations of nickel >30 µmol/L. Caulanthus amplexicaulis var. barbarae and its nonserpentine sister taxon both accumulated nickel to substantial levels. Nickel tolerance was highly heritable (h(2) = 0.59) and not associated with accumulation. The QTL analyses identified two major loci for nickel tolerance, on linkage group 2 (LG2) and linkage group 9 (LG9).

CONCLUSIONS

In our study, nickel tolerance was determined by two major loci with large effects. At both loci, alleles from the serpentine parent conferred positive effects on nickel tolerance, suggesting that they are adaptive in the natural serpentine environment. The mechanism of nickel tolerance in the serpentine plant was not exclusion of nickel. Nickel tolerance may have an inducible component in C. amplexicaulis var. barbarae.

QTLs for resistance to the false brome rust Puccinia brachypodii in the model grass Brachypodium distachyon L

The potential of the model grass Brachypodium distachyon L. (Brachypodium) for studying grass-pathogen interactions is still underexploited. We aimed to identify genomic regions in Brachypodium associated with quantitative resistance to the false brome rust fungus Puccinia brachypodii . The inbred lines Bd3-1 and Bd1-1, differing in their level of resistance to P. brachypodii, were crossed to develop an F(2) population. This was evaluated for reaction to a virulent isolate of P. brachypodii at both the seedling and advanced growth stages. To validate the results obtained on the F(2), resistance was quantified in F(2)-derived F(3) families in two experiments. Disease evaluations showed quantitative and transgressive segregation for resistance. A new AFLP-based Brachypodium linkage map consisting of 203 loci and spanning 812 cM was developed and anchored to the genome sequence with SSR and SNP markers. Three false brome rust resistance QTLs were identified on chromosomes 2, 3, and 4, and they were detected across experiments. This study is the first quantitative trait analysis in Brachypodium. Resistance to P. brachypodii was governed by a few QTLs: two acting at the seedling stage and one acting at both seedling and advanced growth stages. The results obtained offer perspectives to elucidate the molecular basis of quantitative resistance to rust fungi.

Diversity analysis of the response to Zn within the Arabidopsis thaliana species revealed a low contribution of Zn translocation to Zn tolerance and a new role for Zn in lateral root development

This work reports the first characterization of the natural variation of Zn tolerance and accumulation in Arabidopsis thaliana. Root and shoot growth as well as Zn content were determined for 27 A. thaliana accessions grown in vitro in presence of Zn concentrations ranging from 1 to 250 µm. All traits varied by at least twofold and their broad sense heritability varied from 0.36 to 0.91. Primary and lateral root developments were differently affected by Zn in the different accessions. Remarkably, Zn was for the first time shown to be essential for the development of lateral roots. As a general rule, the different traits showed uncorrelated variations. In particular, variation in Zn tolerance was not linked to either root or shoot Zn contents. The only detectable relationship between different traits linked Zn sensitivity of roots to root-to-shoot Zn translocation but the correlation between variation of these traits was pretty low. This suggests that Zn translocation from root to shoots explains only a part of Zn tolerance. Our analysis opens the way to the characterization of genetic determinants controlling different Zn-related traits through the identification of particular accessions displaying contrasted phenotypes and representing excellent starting material to develop quantitative trait locus (QTL) studies.

Metal hyperaccumulation and hypertolerance: a model for plant evolutionary genomics

In the course of evolution, plants adapted to widely differing metal availabilities in soils and therefore represent an important source of natural variation of metal homeostasis networks. Research on plant metal homeostasis can thus provide insights into the functioning, regulation and adaptation of biological networks. Here, we describe major recent breakthroughs in the understanding of the genetic and molecular basis of metal hyperaccumulation and associated hypertolerance, a naturally selected complex trait which represents an extreme adaptation of the metal homeostasis network. Investigations in this field reveal further the molecular alterations underlying the evolution of natural phenotypic diversity and provide a highly relevant framework for comparative genomics.

Generation of nonvernal-obligate, faster-cycling Noccaea caerulescens lines through fast neutron mutagenesis

Noccaea caerulescens (formerly Thlaspi caerulescens) is a widely studied metal hyperaccumulator. However, molecular genetic studies are challenging in this species because of its vernal-obligate biennial life cycle of 7-9months. Here, we describe the development of genetically stable, faster cycling lines of N. caerulescens which are nonvernal-obligate. A total of 5500 M(0) seeds from Saint Laurent Le Minier (France) were subjected to fast neutron mutagenesis. Following vernalization of young plants, 79% of plants survived to maturity. In all, 80,000 M(2) lines were screened for flowering in the absence of vernalization. Floral initials were observed in 35 lines, with nine flowering in <12wk. Two lines (A2 and A7) were selfed to the M(4) generation. Floral initials were observed 66 and 87d after sowing (DAS) in A2 and A7, respectively. Silicle development occurred for all A2 and for most A7 at 92 and 123 DAS, respectively. Floral or silicle development was not observed in wild-type (WT) plants. Leaf zinc (Zn) concentration was similar in WT, A2 and A7 lines. These lines should facilitate future genetic studies of this remarkable species. Seed is publicly available through the European Arabidopsis Stock Centre (NASC).

Differentiation of metallicolous and non-metallicolous Salix caprea populations based on phenotypic characteristics and nuclear microsatellite (SSR) markers

The Salicaceae family comprises a large number of high-biomass species with remarkable genetic variability and adaptation to ecological niches. Salix caprea survives in heavy metal contaminated areas, translocates and accumulates Zn/Cd in leaves. To reveal potential selective effects of long-term heavy metal contaminations on the genetic structure and Zn/Cd accumulation capacity, 170 S. caprea isolates of four metal-contaminated and three non-contaminated middle European sites were analysed with microsatellite markers using Wright's F statistics. The differentiation of populations North of the Alps are more pronounced compared to the Southern ones. By grouping the isolates based on their contamination status, a weak but significant differentiation was calculated between Northern metallicolous and non-metallicolous populations. To quantify if the contamination and genetic status of the populations correlate with Zn/Cd tolerance and the accumulation capacity, the S. caprea isolates were exposed to elevated Cd/Zn concentrations in perlite-based cultures. Consistent with the genetic data nested anova analyses for the physiological traits find a significant difference in the Cd accumulation capacity between the Northern and Southern populations. Our data suggest that natural populations are a profitable source to uncover genetic mechanisms of heavy metal accumulation and biomass production, traits that are essential for improving phytoextraction strategies.

Proteomics of Thlaspi caerulescens accessions and an inter-accession cross segregating for zinc accumulation

Metal hyperaccumulator plants have previously been characterized by transcriptomics, but reports on other profiling techniques are scarce. Protein profiles of Thlaspi caerulescens accessions La Calamine (LC) and Lellingen (LE) and lines derived from an LCxLE cross were examined here to determine the co-segregation of protein expression with the level of zinc (Zn) hyperaccumulation. Although hydrophobic proteins such as membrane transporters are not disclosed, this approach has the potential to reveal other proteins important for the Zn hyperaccumulation trait. Plants were exposed to metals. Proteins were separated using two-dimensional electrophoresis and those showing differences among accessions, lines or metal exposures were subjected to mass-spectrometric analysis for identification. Crossing decreased the number of different proteins in the lines compared with the parents, more so in the shoots than in the roots, but the frequencies of Zn-responsive proteins were about the same in the accessions and the selection lines. This supports the finding that the Zn accumulation traits are mainly determined by the root and that Zn accumulation itself is not the reason for the co-segregation. This study demonstrates that crossing accessions with contrasting Zn accumulation traits is a potent tool to investigate the mechanisms behind metal hyperaccumulation. Four tentatively identified root proteins showed co-segregation with high or low Zn accumulation: manganese superoxide dismutase, glutathione S-transferase, S-formyl glutathione hydrolase, and translation elongation factor 5A-2. However, these proteins may not be the direct determinants of Zn accumulation. The role of these and other tentatively identified proteins in Zn accumulation and tolerance is discussed.

Metal hyperaccumulation in plants

During the history of life on Earth, tectonic and climatic change repeatedly generated large territories that were virtually devoid of life and exhibited harsh environmental conditions. The ability of a few specialist pioneer plants to colonize such hostile environments was thus of paramount ecological importance for the continuous maintenance of primary production over time. Yet, we know very little about how extreme traits evolve and function in plants. Recent breakthroughs have given first insights into the molecular basis underlying the complex extreme model trait of metal hyperaccumulation and associated metal hypertolerance. This review gives an introduction into the hyperaccumulator research field and its history; provides an overview of hyperaccumulator germplasm; describes the state of the art of our understanding of the physiological, molecular, and genetic basis underlying metal hyperaccumulation and its evolution; and highlights future research needs and opportunities.

Molecular mechanisms of metal hyperaccumulation in plants

Metal hyperaccumulator plants accumulate and detoxify extraordinarily high concentrations of metal ions in their shoots. Metal hyperaccumulation is a fascinating phenomenon, which has interested scientists for over a century. Hyperaccumulators constitute an exceptional biological material for understanding mechanisms regulating plant metal homeostasis as well as plant adaptation to extreme metallic environments.Our understanding of metal hyperaccumulation physiology has recently increased as a result of the development of molecular tools. This review presents key aspects of our current understanding of plant metal – in particular cadmium (Cd),nickel (Ni) and zinc (Zn) – hyperaccumulation.

MTP1-dependent Zn sequestration into shoot vacuoles suggests dual roles in Zn tolerance and accumulation in Zn-hyperaccumulating plants

The integral membrane protein Thlaspi goesingense metal tolerance protein 1 (TgMTP1) has been suggested to play an important role in Zn hyperaccumulation in T. goesingense. Here, we show that the TgMTP1 protein is accumulated to high levels at the vacuolar membrane in shoot tissue of T. goesingense. TgMTP1 is likely to act in the transport of Zn into the vacuole, enhancing both Zn accumulation and tolerance. By specifically expressing TgMTP1 in Arabidopsis thaliana shoots, we show that TgMTP1, localized at the vacuolar membrane, can drive the enhanced shoot accumulation of Zn by initiating a systemic Zn deficiency response. The systematic response includes increased expression of Zn transporters (ZIP3, ZIP4, ZIP5 and ZIP9) in both shoot and root tissue. Furthermore, shoot-specific accumulation of TgMTP1 at the vacuolar membrane also leads to increased resistance to Zn in A. thaliana, probably through enhanced Zn compartmentalization in the vacuole. Such evidence leads to the conclusion that the high levels of TgMTP1 at the vacuolar membrane in shoot tissue of the Zn hyperaccumulator T. goesingense play a role in both Zn tolerance and enhanced Zn uptake and accumulation, via the activation of a systemic Zn deficiency response.

Thlaspi caerulescens (Brassicaceae) population genetics in western Switzerland: is the genetic structure affected by natural variation of soil heavy metal concentrations?

Thlaspi caerulescens (Brassicaceae) is a promising plant model with which to study heavy metal hyperaccumulation. Population genetics studies are necessary for a better understanding of its history, which will be useful for further genomic studies on the evolution of heavy metal hyperaccumulation.The genetic structure of 24 natural Swiss locations was investigated using nuclear and plastid loci. Population genetics parameters were estimated and genetic pools were identified using Bayesian inference on eight putatively neutral nuclear loci.Finally, the effect of cadmium (Cd) and zinc (Zn) soil concentrations on genetic differentiation at loci located in genes putatively involved in heavy metal responses was examined using partial Mantel tests in Jura, western Switzerland.Four main genetic clusters were recognized based on nuclear and plastid loci,which gave mostly congruent signals. In Jura, genetic differentiation linked to heavy metal concentrations in soil was shown at some candidate loci, particularly for genes encoding metal transporters. This suggests that natural selection limits gene flow between metalliferous and non metalliferous locations at such loci.Strong historical factors explain the present genetic structure of Swiss T. caerulescens populations, which has to be considered in studies testing for relationships between environmental and genetic variations. Linking of genetic differentiation at candidate genes with soil characteristics offers new perspectives in the study of heavy metal hyperaccumulation.

Investigating heavy-metal hyperaccumulation using Thlaspi caerulescens as a model system

BACKGROUND

Metal-hyperaccumulating plant species are plants that are endemic to metalliferous soils and are able to tolerate and accumulate metals in their above-ground tissues to very high concentrations. One such hyperaccumulator, Thlaspi caerulescens, has been widely studied for its remarkable properties to tolerate toxic levels of zinc (Zn), cadmium (Cd) and sometimes nickel (Ni) in the soil, and accumulate these metals to very high levels in the shoot. The increased awareness regarding metal-hyperaccumulating plants by the plant biology community has helped spur interest in the possible use of plants to remove heavy metals from contaminated soils, a process known as phytoremediation. Hence, there has been a focus on understanding the mechanisms that metal-hyperaccumulator plant species such as Thlaspi caerulescens employ to absorb, detoxify and store metals in order to use this information to develop plants better suited for the phytoremediation of metal-contaminated soils.

SCOPE

In this review, an overview of the findings from recent research aimed at better understanding the physiological mechanisms of Thlaspi caerulescens heavy-metal hyperaccumulation as well as the underlying molecular and genetic determinants for this trait will be discussed. Progress has been made in understanding some of the fundamental Zn and Cd transport physiology in T. caerulescens. Furthermore, some interesting metal-related genes have been identified and characterized in this plant species, and regulation of the expression of some of these genes may be important for hyperaccumulation.

CONCLUSIONS

Thlaspi caerulescens is a fascinating and useful model system not only for studying metal hyperaccumulation, but also for better understanding micronutrient homeostasis and nutrition. Considerable future research is still needed to elucidate the molecular, genetic and physiological bases for the extreme metal tolerance and hyperaccumulation exhibited by plant species such as T. caerulescens.

Using Arabidopsis to explore zinc tolerance and hyperaccumulation

Identifying the particular gene or genes underlying a specific adaptation is a major challenge in modern biology. Currently, the study of naturally occurring variation in Arabidopsis thaliana provides a bridge between functional genetics and evolutionary analyses. Nevertheless, the use of A. thaliana to study adaptation is limited to those traits that have undergone selection. Therefore, to understand fully the genetics of adaptation, the vast arsenal of genetic resources developed in A. thaliana must be extended to other species that display traits absent in this model species. Here, we discuss how A. thaliana resources can significantly enhance the study of heavy-metal tolerance and hyperaccumulation in the wild species Arabidopsis halleri.

Variation in root-to-shoot translocation of cadmium and zinc among different accessions of the hyperaccumulators Thlaspi caerulescens and Thlaspi praecox

Efficient root-to-shoot translocation is a key trait of the zinc/cadmium hyperaccumulators Thlaspi caerulescens and Thlaspi praecox, but the extent of variation among different accessions and the underlying mechanisms remain unclear. Root-to-shoot translocation of Cd and Zn and apoplastic bypass flow were determined in 10 accessions of T. caerulescens and one of T. praecox, using radiolabels (109)Cd and (65)Zn. Two contrasting accessions (Pr and Ga) of T. caerulescens were further characterized for TcHMA4 expression and metal compartmentation in roots. Root-to-shoot translocation of (109)Cd and (65)Zn after 1 d exposure varied 4.4 to 5-fold among the 11 accessions, with a significant correlation between the two metals, but no significant correlation with uptake or the apoplastic bypass flow. The F(2) progeny from a cross between accessions from Prayon, Belgium (Pr) and Ganges, France (Ga) showed a continuous phenotype pattern and transgression. There was no significant difference in the TcHMA4 expression in roots between Pr and Ga. Compartmentation analysis showed a higher percentage of (109)Cd sequestered in the root vacuoles of Ga than Pr, the former being less efficient in translocation than the latter. Substantial natural variation exists in the root-to-shoot translocation of Cd and Zn, and root vacuolar sequestration may be an important factor related to this variation.

Statistical analysis of amplified fragment length polymorphism data: a toolbox for molecular ecologists and evolutionists

Recently, the amplified fragment length polymorphism (AFLP) technique has gained a lot of popularity, and is now frequently applied to a wide variety of organisms. Technical specificities of the AFLP procedure have been well documented over the years, but there is on the contrary little or scattered information about the statistical analysis of AFLPs. In this review, we describe the various methods available to handle AFLP data, focusing on four research topics at the population or individual level of analysis: (i) assessment of genetic diversity; (ii) identification of population structure; (iii) identification of hybrid individuals; and (iv) detection of markers associated with phenotypes. Two kinds of analysis methods can be distinguished, depending on whether they are based on the direct study of band presences or absences in AFLP profiles ('band-based' methods), or on allelic frequencies estimated at each locus from these profiles ('allele frequency-based' methods). We investigate the characteristics and limitations of these statistical tools; finally, we appeal for a wider adoption of methodologies borrowed from other research fields, like for example those especially designed to deal with binary data.

Improved understanding of hyperaccumulation yields commercial phytoextraction and phytomining technologies

This paper reviews progress in phytoextraction of soil elements and illustrates the key role of hyperaccumulator plant species in useful phytoextraction technologies. Much research has focused on elements which are not practically phytoextracted (Pb); on addition of chelating agents which cause unacceptable contaminant leaching and are cost prohibitive; and on plant species which offer no useful phytoextraction capability (e.g., Brassica juncea Czern). Nickel phytoextraction by Alyssum hyperaccumulator species, which have been developed into a commercial phytomining technology, is discussed in more detail. Nickel is ultimately accumulated in vacuoles of leaf epidermal cells which prevents metal toxicity and provides defense against some insect predators and plant diseases. Constitutive up-regulation of trans-membrane element transporters appears to be the key process that allows these plants to achieve hyperaccumulation. Cadmium phytoextraction is needed for rice soils contaminated by mine wastes and smelter emissions with 100-fold more soil Zn than Cd. Although many plant species can accumulate high levels of Cd in the absence of Zn, when Cd/Zn>100, only Thlaspi caerulescens from southern France has demonstrated the ability to phytoextract useful amounts of Cd. Production of element-enriched biomass with value as ore or fertilizer or improved food (Se) or feed supplement may offset costs of phytoextraction crop production. Transgenic phytoextraction plants have been achieved for Hg, but not for other elements. Although several researchers have been attempting to clone all genes required for effective hyperaccumulation of several elements, success appears years away; such demonstrations will be needed to prove we have identified all necessary processes in hyperaccumulation.

Almost forgotten or latest practice? AFLP applications, analyses and advances

Amplified fragment length polymorphism (AFLP) DNA fingerprinting is a firmly established molecular marker technique, with broad applications in population genetics, shallow phylogenetics, linkage mapping, parentage analyses, and single-locus PCR marker development. Technical advances have presented new opportunities for data analysis, and recent studies have addressed specific areas of the AFLP technique, including comparison to other genotyping methods, assessment of errors, homoplasy, phylogenetic signal and appropriate analysis techniques. Here we provide a synthesis of these areas and explore new directions for the AFLP technique in the genomic era, with the aim of providing a review that will be applicable to all AFLP-based studies.

Isolation of Zn-responsive genes from two accessions of the hyperaccumulator plant Thlaspi caerulescens

Several populations with different metal tolerance, uptake and root-to-shoot transport are known for the metal hyperaccumulator plant Thlaspi caerulescens. In this study, genes differentially expressed under various Zn exposures were identified from the shoots of two T. caerulescens accessions (calaminous and non-calaminous) using fluorescent differential display RT-PCR. cDNA fragments from 16 Zn-responsive genes, including those encoding metallothionein (MT) type 2 and type 3, MRP-like transporter, pectin methylesterase (PME) and Ole e 1-like gene as well as several unknown genes, were eventually isolated. The full-length MT2 and MT3 sequences differ from those previously isolated from other Thlaspi accessions, possibly representing new alleles or isoforms. Besides the differential expression in Zn exposures, the gene expression was dependent on the accession. Thlaspi homologues of ClpP protease and MRP transporter were induced at high Zn concentrations. MT2 and PME were expressed at higher levels in the calaminous accession. The MTs and MRP transporter expressed in transgenic yeasts were capable of conferring Cu and Cd tolerance, whereas the Ole e 1-like gene enhanced toxicity to these metals. The MTs increased yeast intracellular Cd content. As no significant differences were found between Arabidopsis and Thlaspi MTs, they apparently do not differ in their capacity to bind metals. However, the higher levels of MT2 in the calaminous accession may contribute to the Zn-adapted phenotype.

Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits

A central challenge in evolutionary biology is to identify genes underlying ecologically important traits and describe the fitness consequences of naturally occurring variation at these loci. To address this goal, several novel approaches have been developed, including 'population genomics,' where a large number of molecular markers are scored in individuals from different environments with the goal of identifying markers showing unusual patterns of variation, potentially due to selection at linked sites. Such approaches are appealing because of (1) the increasing ease of generating large numbers of genetic markers, (2) the ability to scan the genome without measuring phenotypes and (3) the simplicity of sampling individuals without knowledge of their breeding history. Although such approaches are inherently applicable to non-model systems, to date these studies have been limited in their ability to uncover functionally relevant genes. By contrast, quantitative genetics has a rich history, and more recently, quantitative trait locus (QTL) mapping has had some success in identifying genes underlying ecologically relevant variation even in novel systems. QTL mapping, however, requires (1) genetic markers that specifically differentiate parental forms, (2) a focus on a particular measurable phenotype and (3) controlled breeding and maintenance of large numbers of progeny. Here we present current advances and suggest future directions that take advantage of population genomics and quantitative genetic approaches - in both model and non-model systems. Specifically, we discuss advantages and limitations of each method and argue that a combination of the two provides a powerful approach to uncovering the molecular mechanisms responsible for adaptation.

Zinc in plants

Zinc (Zn) is an essential component of thousands of proteins in plants, although it is toxic in excess. In this review, the dominant fluxes of Zn in the soil-root-shoot continuum are described, including Zn inputs to soils, the plant availability of soluble Zn(2+) at the root surface, and plant uptake and accumulation of Zn. Knowledge of these fluxes can inform agronomic and genetic strategies to address the widespread problem of Zn-limited crop growth. Substantial within-species genetic variation in Zn composition is being used to alleviate human dietary Zn deficiencies through biofortification. Intriguingly, a meta-analysis of data from an extensive literature survey indicates that a small proportion of the genetic variation in shoot Zn concentration can be attributed to evolutionary processes whose effects manifest above the family level. Remarkable insights into the evolutionary potential of plants to respond to elevated soil Zn have recently been made through detailed anatomical, physiological, chemical, genetic and molecular characterizations of the brassicaceous Zn hyperaccumulators Thlaspi caerulescens and Arabidopsis halleri.

A quantitative trait loci analysis of zinc hyperaccumulation in Arabidopsis halleri

The mechanisms of metal hyperaccumulation are still not understood, so we conducted a quantitative trait locus (QTL) analysis of zinc (Zn) hyperaccumulation in Arabidopsis halleri, in a cross between this and its sister species, A. petraea, in order to determine the number and approximate location of the genomic regions significantly contributing to this adaptation. An F2 cross between the two species was made, and the leaf Zn concentration of 92 individuals was measured at both low (10 microm) and high (100 microm) Zn concentrations. Twenty-five markers were established that were distributed on all of the eight chromosomes. Mapping of the markers established that they were essentially collinear with previous studies. QTLs exceeding a logarithm to the base 10 of the odds (LOD) value of 3 were found on chromosomes 4 (low Zn), 6 (high Zn) and 7 (both high and low Zn). Evidence for a QTL on chromosome 3 (low Zn) was also found. This analysis validates a previously used method of QTL analysis, based on microarray analysis of segregating families. Genes that have altered during the evolution of this character should also be QTL: this analysis calls into question a number of candidate genes from consideration as such primary genes because they do not appear to be associated with QTLs.

QTL analysis of cadmium and zinc accumulation in the heavy metal hyperaccumulator Thlaspi caerulescens

Thlaspi caerulescens (Tc; 2n = 14) is a natural Zn, Cd and Ni hyperaccumulator species belonging to the Brassicaceae family. It shares 88% DNA identity in the coding regions with Arabidopsis thaliana (At) (Rigola et al. 2006). Although the physiology of heavy metal (hyper)accumulation has been intensively studied, the molecular genetics are still largely unexplored. We address this topic by constructing a genetic map based on AFLP markers and expressed sequence tags (ESTs). To establish a genetic map, an F(2) population of 129 individuals was generated from a cross between a plant from a Pb/Cd/Zn-contaminated site near La Calamine, Belgium, and a plant from a comparable site near Ganges (GA), France. These two accessions show different degrees of Zn and, particularly, Cd accumulation. We analyzed 181 AFLP markers (of which 4 co-dominant) and 13 co-dominant EST sequences-based markers and mapped them to seven linkage groups (LGs), presumably corresponding to the seven chromosomes of T. caerulescens. The total length of the genetic map is 496 cM with an average density of one marker every 2.5 cM. This map was used for Quantitative Trait Locus (QTL) mapping in the F(2). For Zn as well as Cd concentration in root we mapped two QTLs. Three QTLs and one QTL were mapped for Zn and Cd concentration in shoot, respectively. These QTLs explain 23.8-60.4% of the total variance of the traits measured. We found only one common locus (LG6) for Zn and Cd (concentration in root) and one common locus for shoot and root concentrations of Zn (LG1) and of Cd (LG3). For all QTLs, the GA allele increased the trait value except for two QTLs for Zn accumulation in shoot (LG1 and LG4) and one for Zn concentration in root (LG1).

Gene polymorphisms for elucidating the genetic structure of the heavy-metal hyperaccumulating trait in Thlaspi caerulescens and their cross-genera amplification in Brassicaceae

Genetic polymorphism was investigated in Thlaspi caerulescens J. & C. Presl at 15 gene regions, of which seven have been identified to putatively play a role in heavy-metal tolerance or hyperaccumulation. Single nucleotide and length polymorphisms were assessed at four cleaved amplified polymorphic sequences (CAPS) and 11 simple sequence repeat (microsatellite) loci, respectively. The utility of these loci for genetic studies in T. caerulescens was measured among seven natural populations (135 individuals). Fourteen loci rendered polymorphism, and the number of alleles per locus varied from 2 to 5 and 1 to 27 for CAPS and microsatellites, respectively. Up to 12 alleles per locus were detected in a population. The global observed heterozygosity per population varied between 0.01 and 0.31. Additionally, cross-species/genera amplification of loci was investigated on eight other Brassicaceae (five individuals per population). Overall, 70% of the cross-species/genera amplifications were successful, and among them, more than 40% provided intraspecific polymorphisms within a single population. This indicates that such markers may, as well, allow comparative population genetic or mapping studies between and within several Brassicaceae, particularly for genes involved in traits such as heavy-metal tolerance and/or hyperaccumulation.