OsCOPT7 is a copper exporter at the tonoplast and endoplasmic reticulum and controls Cu translocation to the shoots and grain of rice.

Copper (Cu) is an essential micronutrient for all living organisms but is also highly toxic in excess. Cellular homoeostasis of Cu is maintained by various transporters and metallochaperones. Here, we investigated the biological function of OsCOPT7, a member of the copper transporters (COPT) family, in Cu homoeostasis in rice. OsCOPT7 was mainly expressed in the roots and the expression was upregulated by Cu deficiency. OsCOPT7 was localized at the tonoplast and the endoplasmic reticulum. Knockout of OsCOPT7 increased Cu accumulation in the roots but decreased Cu concentrations in the shoots and grain. The knockout mutants contained higher concentrations of Cu in the roots cell sap but markedly lower concentrations of Cu in the xylem sap than wild-type plants. Seed setting and grain yield were reduced significantly in the knockout mutants grown in a low Cu soil. Knockout mutants were more tolerant to Cu toxicity. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that OsCOPT7 interacts physically with the rice Cu chaperone antioxidant protein 1 (OsATX1). Taken together, our results indicate that OsCOPT7 is a specific Cu transporter functioning to export Cu from the vacuoles and the ER and plays an important role in controlling the root-to-shoot Cu translocation in rice.

The OsZIP2 transporter is involved in root-to-shoot translocation and intervascular transfer of cadmium in rice.

Cadmium (Cd) is a toxic metal that poses serious threats to human health. Rice is a major source of dietary Cd but how rice plants transport Cd to the grain is not fully understood. Here, we characterize the function of the ZIP (ZRT, IRT-like protein) family protein, OsZIP2, in the root-to-shoot translocation of Cd and intervascular transfer of Cd in nodes. OsZIP2 is localized at the plasma membrane and exhibited Cd2+ transport activity when heterologously expressed in yeast. OsZIP2 is strongly expressed in xylem parenchyma cells in roots and in enlarged vascular bundles in nodes. Knockout of OsZIP2 significantly enhanced root-to-shoot translocation of Cd and alleviated the inhibition of root elongation by excess Cd stress; whereas overexpression of OsZIP2 decreased Cd translocation to shoots and resulted in Cd sensitivity. Knockout of OsZIP2 increased Cd allocation to the flag leaf but decreased Cd allocation to the panicle and grain. We further reveal that the variation of OsZIP2 expression level contributes to grain Cd concentration among rice germplasms. Our results demonstrate that OsZIP2 functions in root-to-shoot translocation of Cd in roots and intervascular transfer of Cd in nodes, which can be used for breeding low Cd rice varieties.

IAR4 mutation enhances cadmium toxicity by disturbing auxin homeostasis in Arabidopsis thaliana.

Cadmium (Cd) is highly toxic to plants, but the targets and modes of toxicity remain unclear. We isolated a Cd-hypersensitive mutant of Arabidopsis thaliana, Cd-induced short root 2 (cdsr2), in the background of the phytochelatin synthase-defective mutant cad1-3. Both cdsr2 and cdsr2 cad1-3 displayed shorter roots and were more sensitive to Cd than their respective wild type. Using genomic resequencing and complementation, IAR4 was identified as the causal gene, which encodes a putative mitochondrial pyruvate dehydrogenase E1α subunit. cdsr2 showed decreased pyruvate dehydrogenase activity and NADH content, but markedly increased concentrations of pyruvate and alanine in roots. Both Cd stress and IAR4 mutation decreased auxin level in the root tips, and the effect was additive. A higher growth temperature rescued the phenotypes in cdsr2. Exogenous alanine inhibited root growth and decreased auxin level in the wild type. Cadmium stress suppressed the expression of genes involved in auxin biosynthesis, hydrolysis of auxin-conjugates and auxin polar transport. Our results suggest that auxin homeostasis is a key target of Cd toxicity, which is aggravated by IAR4 mutation due to decreased pyruvate dehydrogenase activity. Decreased auxin level in cdsr2 is likely caused by increased auxin-alanine conjugation and decreased energy status in roots.

Combined genomics to discover genes associated with tolerance to soil carbonate.

Carbonate-rich soils limit plant performance and crop production. Previously, local adaptation to carbonated soils was detected in wild Arabidopsis thaliana accessions, allowing the selection of two demes with contrasting phenotypes: A1 (carbonate tolerant, c+) and T6 (carbonate sensitive, c-). Here, A1(c+) and T6(c - ) seedlings were grown hydroponically under control (pH 5.9) and bicarbonate conditions (10 mM NaHCO3 , pH 8.3) to obtain ionomic profiles and conduct transcriptomic analysis. In parallel, A1(c+) and T6(c - ) parental lines and their progeny were cultivated on carbonated soil to evaluate fitness and segregation patterns. To understand the genetic architecture beyond the contrasted phenotypes, a bulk segregant analysis sequencing (BSA-Seq) was performed. Transcriptomics revealed 208 root and 2503 leaf differentially expressed genes in A1(c+) versus T6(c - ) comparison under bicarbonate stress, mainly involved in iron, nitrogen and carbon metabolism, hormones and glycosylates biosynthesis. Based on A1(c+) and T6(c - ) genome contrasts and BSA-Seq analysis, 69 genes were associated with carbonate tolerance. Comparative analysis of genomics and transcriptomics discovered a final set of 18 genes involved in bicarbonate stress responses that may have relevant roles in soil carbonate tolerance.

Sulfate-TOR signaling controls transcriptional reprogramming for shoot apex activation.

Plants play a primary role for the global sulfur cycle in the earth ecosystems by reduction of inorganic sulfate from the soil to organic sulfur-containing compounds. How plants sense and transduce the sulfate availability to mediate their growth remains largely unclear. The target of rapamycin (TOR) kinase is an evolutionarily conserved master regulator of nutrient sensing and metabolic signaling to control cell proliferation and growth in all eukaryotes. By tissue-specific Western blotting and RNA-sequencing analysis, we investigated sulfate-TOR signal pathway in regulating shoot apex development. Here, we report that inorganic sulfate exhibits high potency activating TOR and cell proliferation to promote true leaf development in Arabidopsis in a glucose-energy parallel pathway. Genetic and metabolite analyses suggest that this sulfate activation of TOR is independent from the sulfate-assimilation process and glucose-energy signaling. Significantly, tissue specific transcriptome analyses uncover previously unknown sulfate-orchestrating genes involved in DNA replication, cell proliferation and various secondary metabolism pathways, which largely depends on TOR signaling. Systematic comparison between the sulfate- and glucose-TOR controlled transcriptome further reveals that TOR kinase, as the central growth integrator, responds to different nutrient signals to control both shared and unique transcriptome networks, therefore, precisely modulates plant proliferation, growth and stress responses.

Molybdenum: More than an essential element.

Molybdenum (Mo) is an essential element for almost all living organisms. After being taken up into the cells as molybdate, it is incorporated into the molybdenum cofactor, which functions as the active site of several molybdenum-requiring enzymes and thus plays crucial roles in multiple biological processes. The uptake and transport of molybdate is mainly mediated by two types of molybdate transporters. The homeostasis of Mo in plant cells is tightly controlled, and such homeostasis likely plays vital roles in plant adaptation to local environments. Recent evidence suggests that Mo is more than an essential element required for plant growth and development; it is also involved in local adaptation to coastal salinity. In this review, we summarize recent research progress on molybdate uptake and transport, molybdenum homeostasis network in plants, and discuss the potential roles of the molybdate transporter in plant adaptation to their local environment.

Local and Systemic Response to Heterogeneous Sulfate Resupply after Sulfur Deficiency in Rice.

Sulfur (S) is an essential mineral nutrient required for plant growth and development. Plants usually face temporal and spatial variation in sulfur availability, including the heterogeneous sulfate content in soils. As sessile organisms, plants have evolved sophisticated mechanisms to modify their gene expression and physiological processes in order to optimize S acquisition and usage. Such plasticity relies on a complicated network to locally sense S availability and systemically respond to S status, which remains poorly understood. Here, we took advantage of a split-root system and performed transcriptome-wide gene expression analysis on rice plants in S deficiency followed by sulfate resupply. S deficiency altered the expressions of 6749 and 1589 genes in roots and shoots, respectively, accounting for 18.07% and 4.28% of total transcripts detected. Homogeneous sulfate resupply in both split-root halves recovered the expression of 27.06% of S-deficiency-responsive genes in shoots, while 20.76% of S-deficiency-responsive genes were recovered by heterogeneous sulfate resupply with only one split-root half being resupplied with sulfate. The local sulfate resupply response genes with expressions only recovered in the split-root half resupplied with sulfate but not in the other half remained in S deficiency were identified in roots, which were mainly enriched in cellular amino acid metabolic process and root growth and development. Several systemic response genes were also identified in roots, whose expressions remained unchanged in the split-root half resupplied with sulfate but were recovered in the other split-root half without sulfate resupply. The systemic response genes were mainly related to calcium signaling and auxin and ABA signaling. In addition, a large number of S-deficiency-responsive genes exhibited simultaneous local and systemic responses to sulfate resupply, such as the sulfate transporter gene OsSULTR1;1 and the O-acetylserine (thiol) lyase gene, highlighting the existence of a systemic regulation of sulfate uptake and assimilation in S deficiency plants followed by sulfate resupply. Our studies provided a comprehensive transcriptome-wide picture of a local and systemic response to heterogeneous sulfate resupply, which will facilitate an understanding of the systemic regulation of S homeostasis in rice.

Cadmium Inhibits Lateral Root Emergence in Rice by Disrupting OsPIN-Mediated Auxin Distribution and the Protective Effect of OsHMA3.

Cadmium (Cd) strongly inhibits root growth, especially the formation of lateral roots (LRs). The mechanism of Cd inhibition on LR formation in rice (Oryza sativa) remains unclear. In this study, we found that LR emergence in rice was inhibited significantly by 1 �M Cd and almost completely arrested by 5 �M Cd. Cd suppressed both the formation and subsequent development of the lateral root primordium (LRP). By using transgenic rice expressing the auxin response reporters DR5::GUS and DR5rev::VENUS, we found that Cd markedly reduced the auxin levels in the stele and LRP. Cd rapidly downregulated the expression of the auxin efflux transporter genes OsPIN1b, OsPIN1c and OsPIN9 in the stele and LRP. The emergence of LRs in a rice cultivar with a null allele of OsHMA3 (Heavy Metal ATPase 3) was more sensitive to Cd than cultivars with functional alleles. Overexpression of functional OsHMA3 in rice greatly alleviated the inhibitory effect of Cd, but the protective effect of OsHMA3 was abolished by the auxin polar transport inhibitor 1-N-naphthylphthalamic acid. The results suggest that Cd inhibits LR development in rice by disrupting OsPIN-mediated auxin distribution to LRP and OsHMA3 protects against Cd toxicity by sequestering Cd into the vacuoles.

Genome-Wide Association Studies Reveal the Genetic Basis of Ionomic Variation in Rice.

Rice (Oryza sativa) is an important dietary source of both essential micronutrients and toxic trace elements for humans. The genetic basis underlying the variations in the mineral composition, the ionome, in rice remains largely unknown. Here, we describe a comprehensive study of the genetic architecture of the variation in the rice ionome performed using genome-wide association studies (GWAS) of the concentrations of 17 mineral elements in rice grain from a diverse panel of 529 accessions, each genotyped at ∼6.4 million single nucleotide polymorphism loci. We identified 72 loci associated with natural ionomic variations, 32 that are common across locations and 40 that are common within a single location. We identified candidate genes for 42 loci and provide evidence for the causal nature of three genes, the sodium transporter gene Os-HKT1;5 for sodium, Os-MOLYBDATE TRANSPORTER1;1 for molybdenum, and Grain number, plant height, and heading date7 for nitrogen. Comparison of GWAS data from rice versus Arabidopsis (Arabidopsis thaliana) also identified well-known as well as new candidates with potential for further characterization. Our study provides crucial insights into the genetic basis of ionomic variations in rice and serves as an important foundation for further studies on the genetic and molecular mechanisms controlling the rice ionome.

High-Affinity Sulfate Transporter Sultr1;2 Is a Major Transporter for Cr(VI) Uptake in Plants.

Chromate (Cr[VI]) is a highly phytotoxic contaminant that is ubiquitous in soils. However, how Cr(VI) is taken up by plant roots remains largely unknown. Here, we show that the high-affinity sulfate transporter Sultr1;2 is responsible for Cr(VI) uptake by the roots of Arabidopsis thaliana. Sultr1;2 showed a much higher transport activity for Cr(VI) than Sultr1;1 when expressed in yeast cells. Knockdown of Sultr1;2 expression in Arabidopsis markedly reduced the Cr(VI) uptake rate, whereas knockout of Sultr1;1 had no or little effect. A double-knockout mutant (DKO) of the two genes lost the ability of Cr(VI) uptake almost completely. The Sultr1;2 knockdown mutant or DKO plants displayed higher resistance to Cr(VI) under normal sulfate conditions as a consequence of the lower tissue Cr accumulation. Overexpression of Sultr1;2 substantially increased Cr(VI) uptake with shoot Cr concentration being 1.6-2.0 times higher than that in the wild-type. These results indicate that Sultr1;2 is a major transporter responsible for Cr(VI) uptake in Arabidopsis, while Sultr1;1 plays a negligible role. Taken together, our study has identified a major transporter for Cr(VI) uptake in plants, providing potential strategies for engineering plants with low Cr accumulation and consequently enhanced Cr(VI) resistance and also plants with enhanced accumulation of Cr for the purpose of phytoremediation.

Fluctuating selection on migrant adaptive sodium transporter alleles in coastal Arabidopsis thaliana.

Stressors such as soil salinity and dehydration are major constraints on plant growth, causing worldwide crop losses. Compounding these insults, increasing climate volatility requires adaptation to fluctuating conditions. Salinity stress responses are relatively well understood in Arabidopsis thaliana, making this system suited for the rapid molecular dissection of evolutionary mechanisms. In a large-scale genomic analysis of Catalonian A. thaliana, we resequenced 77 individuals from multiple salinity gradients along the coast and integrated these data with 1,135 worldwide A. thaliana genomes for a detailed understanding of the demographic and evolutionary dynamics of naturally evolved salinity tolerance. This revealed that Catalonian varieties adapted to highly fluctuating soil salinity are not Iberian relicts but instead have immigrated to this region more recently. De novo genome assembly of three allelic variants of the high-affinity K+ transporter (HKT1;1) locus resolved structural variation between functionally distinct alleles undergoing fluctuating selection in response to seasonal changes in soil salinity. Plants harboring alleles responsible for low root expression of HKT1;1 and consequently high leaf sodium (HKT1;1HLS ) were migrants that have moved specifically into areas where soil sodium levels fluctuate widely due to geography and rainfall variation. We demonstrate that the proportion of plants harboring HKT1;1HLS alleles correlates with soil sodium level over time, HKT1;1HLS -harboring plants are better adapted to intermediate levels of salinity, and the HKT1;1HLS allele clusters with high-sodium accumulator accessions worldwide. Together, our evidence suggests that HKT1;1 is under fluctuating selection in response to climate volatility and is a worldwide determinant in adaptation to saline conditions.

Genetic mapping of ionomic quantitative trait loci in rice grain and straw reveals OsMOT1;1 as the putative causal gene for a molybdenum QTL qMo8.

Rice is a major dietary source of essential mineral nutrients and toxic elements (aka ionome) for humans. However, the genetic basis underlying the variation in ionome is still largely unknown. Here, we mapped 51 and 61 quantitative trait loci (QTLs) controlling the concentrations of 13 and 15 elements in rice (Oryza sativa L.) grain and straw, respectively, using a recombinant inbred lines (RILs) that were grown at three different field sites in 3 years. Several QTLs were repeatedly detected in both grain and straw or in multiple years; the resulting 87 unique QTLs with 17 of them (20%) were co-localized with previously reported corresponding QTLs and 70 were novel ionomic QTLs. At least, 14 genomic clusters that controlled the concentrations of multiple elements were identified. Furthermore, we identified a molybdate transporter gene OsMOT1;1 as the putative causal gene for a QTL controlling molybdenum concentration in both straw and grain. QTL analyses based on the concentrations of multiple elements in both grain and straw of RIL population grown in three field sites in 3 years allow us to identify tissue common QTLs and reproducible QTLs that were validated in multiple years. The identification of ionomic QTLs will be useful in revealing the molecular mechanisms underlying the accumulation of elements in rice and providing the opportunity to reduce the accumulation of toxic elements and enrich the accumulation of beneficial elements in rice grain.

Mutation in OsCADT1 enhances cadmium tolerance and enriches selenium in rice grain.

How cadmium (Cd) tolerance in rice is regulated remains poorly understood. We used a forward genetic approach to investigate Cd tolerance in rice. Using a root elongation assay, we isolated a rice mutant with enhanced Cd tolerance, cadt1, from an ethyl methanesulphonate (EMS)-mutagenized population of a widely grown Indica cultivar. The mutant accumulated more Cd in roots but not in shoots and grains. Using genomic resequencing and complementation, we identified OsCADT1 as the causal gene for the mutant phenotype, which encodes a putative serine hydroxymethyltransferase. OsCADT1 protein was localized to the nucleus and the OsCADT1 gene was expressed in both roots and shoots. OsCADT1 mutation resulted in higher sulphur and selenium accumulation in the shoots and grains. Selenate influx in cadt1 was 2.4 times that of the wild-type. The mutant showed higher expression of the sulphate/selenate transporter gene OsSULTR1;1 and the sulphur-deficiency-inducible gene OsSDI1. Thiol compounds including cysteine, glutathione and phytochelatins were significantly increased in the mutant, underlying its increased Cd tolerance. Growth and grain biomass were little affected. The results suggest that OsCADT1 acts as a negative regulator of sulphate/selenate uptake and assimilation. OsCADT1 mutation increases Cd tolerance and enriches selenium in rice grains, providing a novel solution for selenium biofortification.

OASTL-A1 functions as a cytosolic cysteine synthase and affects arsenic tolerance in rice.

Arsenic (As) contamination in paddy soil can cause phytotoxicity and elevated As accumulation in rice grains. Arsenic detoxification is closely linked to sulfur assimilation, but the genes involved have not been described in rice. In this study, we characterize the function of OASTL-A1, an O-acetylserine(thiol) lyase, in cysteine biosynthesis and detoxification of As in rice. Tissue expression analysis revealed that OsOASTL-A1 is mainly expressed in roots at the vegetative growth stage and in nodes at the reproductive stage. Furthermore, the expression of OsOASTL-A1 in roots was strongly induced by As exposure. Transgenic rice plants expressing pOsOASTL-A1::GUS (ß-glucuronidase) indicated that OsOASTL-A1 was strongly expressed in the outer cortex and the vascular cylinder in the root mature zone. Subcellular localization using OsOASTL-A1:eGFP (enhanced green fluorescent protein) fusion protein showed that OsOASTL-A1 was localized to the cytosol. In vivo and in vitro enzyme activity assays showed that OsOASTL-A1 possessed the O-acetylserine(thiol) lyase activity. Knockout of OsOASTL-A1 led to significantly lower levels of cysteine, glutathione, and phytochelatins in roots and increased sensitivity to arsenate stress. Furthermore, the osoastl-a1 knockout mutants reduced As accumulation in the roots, but increased As accumulation in shoots. We conclude that OsOASTL-A1 is the cytosolic O-acetylserine(thiol) lyase that plays an important role in non-protein thiol biosynthesis in roots for As detoxification.

Overexpression of the manganese/cadmium transporter OsNRAMP5 reduces cadmium accumulation in rice grain.

Rice is a major dietary source of the toxic metal cadmium (Cd), and reducing its accumulation in the grain is therefore important for food safety. We selected two cultivars with contrasting Cd accumulation and generated transgenic lines overexpressing OsNRAMP5, which encodes a major influx transporter for manganese (Mn) and Cd. We used two different promoters to control the expression, namely OsActin1 and maize Ubiquitin. Overexpression of OsNRAMP5 increased Cd and Mn uptake into the roots, but markedly decreased Cd accumulation in the shoots, whilst having a relatively small effect on Mn accumulation in the shoots. The overexpressed OsNRAMP5 protein was localized to the plasma membrane of all cell types in the root tips and lateral root primordia without polarity. Synchrotron X-ray fluorescence mapping showed that the overexpression lines accumulated more Cd in the root tips and lateral root primordia compared with the wild-type. When grown in three Cd-contaminated paddy soils, overexpression of OsNRAMP5 decreased concentration of Cd in the grain by 49-94% compared with the wild type. OsNRAMP5-overexpression plants had decreased Cd translocation from roots to shoots as a result of disruption of its radial transport into the stele for xylem loading, demonstrating the effect of transporter localization and polarity on ion homeostasis.

Overexpression of Rice OsHMA3 in Wheat Greatly Decreases Cadmium Accumulation in Wheat Grains.

Cereals are a major dietary source of the toxic metal cadmium (Cd). Reducing Cd accumulation in cereal crops such as wheat (Triticum aestivum) is important for food safety and human health. In this study, we show that three diverse cultivars of wheat had a high Cd translocation from roots to shoots, similar to a rice (Oryza sativa) cultivar possessing a nonfunctional tonoplast Cd transporter OsHMA3. We investigated the function of TaHMA3 genes in wheat. Three TaHMA3 genes were identified in wheat, all of which encode tonoplast-localized proteins. However, heterologous expression of TaHMA3 genes in yeast showed no transport activities for Cd, which likely explains the low Cd sequestration in wheat roots and subsequently the high Cd translocation to wheat shoots. To increase Cd sequestration in wheat roots, we overexpressed a rice functional OsHMA3 gene in wheat driven by a strong constitutive Ubiquitin promoter. Overexpression of the OsHMA3 gene decreased root-to-shoot Cd translocation in wheat by nearly 10-fold and Cd accumulation in wheat grain by 96%. The results suggest that high Cd translocation is a common trait in wheat caused by a loss of the Cd transport function of TaHMA3 proteins. Transgenic wheat overexpressing a functional OsHMA3 gene offers a highly effective solution to decrease Cd accumulation in wheat grain.

QTL pyramiding for producing nutritious and safe rice grains.

Breeding of rice varieties that are enriched with essential micronutrients and simultaneously have reduced levels of toxic elements in grains is largely unexplored in rice breeding practice. In this issue of JIPB, Liu et al. (2020) developed two rice lines with a low level of cadmium and simultaneously high levels of zinc or selenium accumulation in the grains, thus providing elite genetic materials for breeding rice varieties that are important for addressing mineral malnutrition and ensuring food safety.

Natural variation in a molybdate transporter controls grain molybdenum concentration in rice.

Molybdenum (Mo) is an essential micronutrient for most living organisms, including humans. Cereals such as rice (Oryza sativa) are the major dietary source of Mo. However, little is known about the genetic basis of the variation in Mo content in rice grain. We mapped a quantitative trait locus (QTL) qGMo8 that controls Mo accumulation in rice grain by using a recombinant inbred line population and a backcross introgression line population. We identified a molybdate transporter, OsMOT1;1, as the causal gene for this QTL. OsMOT1;1 exhibits transport activity for molybdate, but not sulfate, when heterogeneously expressed in yeast cells. OsMOT1;1 is mainly expressed in roots and is involved in the uptake and translocation of molybdate under molybdate-limited condition. Knockdown of OsMOT1;1 results in less Mo being translocated to shoots, lower Mo concentration in grains and higher sensitivity to Mo deficiency. We reveal that the natural variation of Mo concentration in rice grains is attributed to the variable expression of OsMOT1;1 due to sequence variation in its promoter. Identification of natural allelic variation in OsMOT1;1 may facilitate the development of rice varieties with Mo-enriched grain for dietary needs and improve Mo nutrition of rice on Mo-deficient soils.

Epigenetic regulation of sulfur homeostasis in plants.

Plants have evolved sophisticated mechanisms for adaptation to fluctuating availability of nutrients in soil. Such mechanisms are of importance for plants to maintain homeostasis of nutrient elements for their development and growth. The molecular mechanisms controlling the homeostasis of nutrient elements at the genetic level have been gradually revealed, including the identification of regulatory factors and transporters responding to nutrient stresses. Recent studies have suggested that such responses are controlled not only by genetic regulation but also by epigenetic regulation. In this review, we present recent studies on the involvement of DNA methylation, histone modifications, and non-coding RNA-mediated gene silencing in the regulation of sulfur homeostasis and the response to sulfur deficiency. We also discuss the potential effect of sulfur-containing metabolites such as S-adenosylmethionine on the maintenance of DNA and histone methylation.

Variation in the BrHMA3 coding region controls natural variation in cadmium accumulation in Brassica rapa vegetables.

Brassica rapa includes several important leafy vegetable crops with the potential for high cadmium (Cd) accumulation, posing a risk to human health. This study aims to understand the genetic basis underlying the variation in Cd accumulation among B. rapa vegetables. Cd uptake and translocation in 64 B. rapa accessions were compared. The role of the heavy metal ATPase gene BrHMA3 in the variation of Cd accumulation was investigated. BrHMA3 encodes a tonoplast-localized Cd transporter. Five full-length and four truncated haplotypes of the BrHMA3 coding sequence were identified, explaining >80% of the variation in the Cd root to shoot translocation among the 64 accessions and in F2 progeny. Truncated BrHMA3 haplotypes had a 2.3 and 9.3 times higher shoot Cd concentration and Cd translocation ratio, respectively, than full-length haplotypes. When expressed in yeast and Arabidopsis thaliana, full-length BrHMA3 showed activity consistent with a Cd transport function, whereas truncated BrHMA3 did not. Variation in the BrHMA3 promoter sequence had little effect on Cd translocation. Variation in the BrHMA3 coding sequence is a key determinant of Cd translocation to and accumulation in the leaves of B. rapa. Strong alleles of BrHMA3 can be used to breed for B. rapa vegetables that are low in Cd in their edible portions.