Dai-Yin Chao

A rice quantitative trait locus for salt tolerance encodes a sodium transporter

Many important agronomic traits in crop plants, including stress tolerance, are complex traits controlled by quantitative trait loci (QTLs). Isolation of these QTLs holds great promise to improve world agriculture but is a challenging task. We previously mapped a rice QTL, SKC1, that maintained K+ homeostasis in the salt-tolerant variety under salt stress, consistent with the earlier finding that K+ homeostasis is important in salt tolerance. To understand the molecular basis of this QTL, we isolated the SKC1 gene by map-based cloning and found that it encoded a member of HKT-type transporters. SKC1 is preferentially expressed in the parenchyma cells surrounding the xylem vessels. Voltage-clamp analysis showed that SKC1 protein functions as a Na+-selective transporter. Physiological analysis suggested that SKC1 is involved in regulating K+/Na+ homeostasis under salt stress, providing a potential tool for improving salt tolerance in crops.

QTLs for Na+ and K+ uptake of the shoots and roots controlling rice salt tolerance

An F2 and an equivalent F3 population derived from a cross between a high salt-tolerance indica variety, Nona Bokra, and a susceptible elite japonica variety, Koshihikari, were produced. We performed QTL mapping for physiological traits related to rice salt-tolerance. Three QTLs for survival days of seedlings (SDSs) under salt stress were detected on chromosomes 1, 6 and 7, respectively, and explained 13.9% to 18.0% of the total phenotypic variance. Based on the correlations between SDSs and other physiological traits, it was considered that damage of leaves was attributed to accumulation of Na+ in the shoot by transport of Na+ from the root to the shoot in external high concentration. We found eight QTLs including three for three traits of the shoots, and five for four traits of the roots at five chromosomal regions, controlled complex physiological traits related to rice salt-tolerance under salt stress. Of these QTLs, the two major QTLs with the very large effect, qSNC-7 for shoot Na+ concentration and qSKC-1 for shoot K+ concentration, explained 48.5% and 40.1% of the total phenotypic variance, respectively. The QTLs detected between the shoots and the roots almost did not share the same map locations, suggesting that the genes controlling the transport of Na+ and K+ between the shoots and the roots may be different.

A previously unknown zinc finger protein, DST, regulates drought and salt tolerance in rice via stomatal aperture control

Abiotic stresses, such as drought and salinity, lead to crop growth damage and a decrease in crop yields. Stomata control CO(2) uptake and optimize water use efficiency, thereby playing crucial roles in abiotic stress tolerance. Hydrogen peroxide (H(2)O(2)) is an important signal molecule that induces stomatal closure. However, the molecular pathway that regulates the H(2)O(2) level in guard cells remains largely unknown. Here, we clone and characterize DST (drought and salt tolerance)-a previously unknown zinc finger transcription factor that negatively regulates stomatal closure by direct modulation of genes related to H(2)O(2) homeostasis-and identify a novel pathway for the signal transduction of DST-mediated H(2)O(2)-induced stomatal closure. Loss of DST function increases stomatal closure and reduces stomatal density, consequently resulting in enhanced drought and salt tolerance in rice. These findings provide an interesting insight into the mechanism of stomata-regulated abiotic stress tolerance, and an important genetic engineering approach for improving abiotic stress tolerance in crops.

Overexpression of the trehalose-6-phosphate phosphatase gene OsTPP1 confers stress tolerance in rice and results in the activation of stress responsive genes.

Trehalose plays a protective role in yeast and microorganisms under abiotic stresses. However, little is known about its role in higher plants when subjected to environmental challenges. A systematic search of rice databases discovered a large TPS/TPP gene family in the rice genome, which is similar to that found in Arabidopsis thaliana, especially in the gene family structure. Expression analysis demonstrated that OsTPP1 was initially and transiently up-regulated after salt, osmotic and abscisic acid (ABA) treatments but slowly up-regulated under cold stress. OsTPP1 overexpression in rice enhanced tolerance to salt and cold stress. Analysis of the overexpression lines revealed that OsTPP1 triggered abiotic stress response genes, which suggests a possible transcriptional regulation pathway in stress induced reprogramming initiated by OsTPP1. The current study revealed the mechanism of an OsTPP gene involved in stress tolerance in rice and also suggested the use of OsTPP1 in abiotic stress engineering of crops.

Polyploids Exhibit Higher Potassium Uptake and Salinity Tolerance in Arabidopsis

Double Is Not Trouble The doubling of the genome to create polyploidy is common among land plants, and most major flowering plant lineages exhibit some history of genome duplication. However, the physiological advantages of a doubled genome are not well understood. Chao et al. (p. 658, published online 25 July) identified accessions of the model plant Arabidopsis thaliana with naturally doubled genomes and found that the cytotype of the root, but not shoot, in these natural, as well as in artificially induced, polyploid plants appears to confer increased salt tolerance by regulating leaf potassium levels. Certain thale cress plants collected in the wild contain a duplicated genome and can cope with salty soil. Genome duplication (or polyploidization) has occurred throughout plant evolutionary history and is thought to have driven the adaptive radiation of plants. We found that the cytotype of the root, and not the genotype, determined the majority of heritable natural variation in leaf potassium (K) concentration in Arabidopsis thaliana. Autopolyploidy also provided resistance to salinity and may represent an adaptive outcome of the enhanced K accumulation of plants with higher ploidy.

Salt-responsive genes in rice revealed by cDNA microarray analysis

ABSTRACTWe used cDNA microarrays containing ∼9,000 unigenes to identify 486 salt responsive expressed sequence tags (ESTs) (representing ∼450 unigenes) in shoots of the highly salt-tolerant rice variety, Nona Bokra (Oryza sativa L. ssp. Indica pv. Nona). Some of the genes identified in this study had previously been associated with salt stress. However the majority were novel, indicating that there is a great number of genes that are induced by salt exposure. Analysis of the salt stress expression profile data of Nona provided clues regarding some putative cellular and molecular processes that are undertaken by this tolerant rice variety in response to salt stress. Namely, we found that multiple transcription factors were induced during the initial salt response of shoots. Many genes whose encoded proteins are implicated in detoxification, protectant and transport were rapidly induced. Genes supporting photosynthesis were repressed and those supporting carbohydrate metabolism were altered. Commonality among the genes induced by salt exposure with those induced during senescence and biotic stress responses suggests that there are shared signaling pathways among these processes. We further compared the transcriptome changes of the salt-sensitive cultivar, IR28, with that of Nona rice. Many genes that are salt responsive in Nona were found to be differentially regulated in IR28. This study identified a large number of candidate functional genes that appear to be involved in salt tolerance and further examination of these genes may enable the molecular basis of salt tolerance to be elucidated.

Genome-Wide Association Studies Identify Heavy Metal ATPase3 as the Primary Determinant of Natural Variation in Leaf Cadmium in Arabidopsis thaliana

Understanding the mechanism of cadmium (Cd) accumulation in plants is important to help reduce its potential toxicity to both plants and humans through dietary and environmental exposure. Here, we report on a study to uncover the genetic basis underlying natural variation in Cd accumulation in a world-wide collection of 349 wild collected Arabidopsis thaliana accessions. We identified a 4-fold variation (0.5–2 µg Cd g−1 dry weight) in leaf Cd accumulation when these accessions were grown in a controlled common garden. By combining genome-wide association mapping, linkage mapping in an experimental F2 population, and transgenic complementation, we reveal that HMA3 is the sole major locus responsible for the variation in leaf Cd accumulation we observe in this diverse population of A. thaliana accessions. Analysis of the predicted amino acid sequence of HMA3 from 149 A. thaliana accessions reveals the existence of 10 major natural protein haplotypes. Association of these haplotypes with leaf Cd accumulation and genetics complementation experiments indicate that 5 of these haplotypes are active and 5 are inactive, and that elevated leaf Cd accumulation is associated with the reduced function of HMA3 caused by a nonsense mutation and polymorphisms that change two specific amino acids.

Genome-wide Association Mapping Identifies a New Arsenate Reductase Enzyme Critical for Limiting Arsenic Accumulation in Plants

A genome-wide association study identifies the enzyme in plants that transforms arsenate into arsenite, allowing its extrusion into the soil and thereby controlling arsenic accumulation.

Sphingolipids in the Root Play an Important Role in Regulating the Leaf Ionome in Arabidopsis thaliana

Sphingolipids are a diverse group of essential membrane lipids thought to play important roles in both membrane function and cellular signaling. By identifying an Arabidopsis thaliana mutant lacking 3-ketodihydrosphinganine reductase, a critical enzyme in sphingolipid biosynthesis, this work uncovers a connection between sphingolipid metabolism in roots and whole-plant mineral ion homeostasis. Sphingolipid synthesis is initiated by condensation of Ser with palmitoyl-CoA producing 3-ketodihydrosphinganine (3-KDS), which is reduced by a 3-KDS reductase to dihydrosphinganine. Ser palmitoyltransferase is essential for plant viability. Arabidopsis thaliana contains two genes (At3g06060/TSC10A and At5g19200/TSC10B) encoding proteins with significant similarity to the yeast 3-KDS reductase, Tsc10p. Heterologous expression in yeast of either Arabidopsis gene restored 3-KDS reductase activity to the yeast tsc10Δ mutant, confirming both as bona fide 3-KDS reductase genes. Consistent with sphingolipids having essential functions in plants, double mutant progeny lacking both genes were not recovered from crosses of single tsc10A and tsc10B mutants. Although the 3-KDS reductase genes are functionally redundant and ubiquitously expressed in Arabidopsis, 3-KDS reductase activity was reduced to 10% of wild-type levels in the loss-of-function tsc10a mutant, leading to an altered sphingolipid profile. This perturbation of sphingolipid biosynthesis in the Arabidopsis tsc10a mutant leads an altered leaf ionome, including increases in Na, K, and Rb and decreases in Mg, Ca, Fe, and Mo. Reciprocal grafting revealed that these changes in the leaf ionome are driven by the root and are associated with increases in root suberin and alterations in Fe homeostasis.

Biodiversity of Mineral Nutrient and Trace Element Accumulation in Arabidopsis thaliana

In order to grow on soils that vary widely in chemical composition, plants have evolved mechanisms for regulating the elemental composition of their tissues to balance the mineral nutrient and trace element bioavailability in the soil with the requirements of the plant for growth and development. The biodiversity that exists within a species can be utilized to investigate how regulatory mechanisms of individual elements interact and to identify genes important for these processes. We analyzed the elemental composition (ionome) of a set of 96 wild accessions of the genetic model plant Arabidopsis thaliana grown in hydroponic culture and soil using inductively coupled plasma mass spectrometry (ICP-MS). The concentrations of 17–19 elements were analyzed in roots and leaves from plants grown hydroponically, and leaves and seeds from plants grown in artificial soil. Significant genetic effects were detected for almost every element analyzed. We observed very few correlations between the elemental composition of the leaves and either the roots or seeds. There were many pairs of elements that were significantly correlated with each other within a tissue, but almost none of these pairs were consistently correlated across tissues and growth conditions, a phenomenon observed in several previous studies. These results suggest that the ionome of a plant tissue is variable, yet tightly controlled by genes and gene×environment interactions. The dataset provides a valuable resource for mapping studies to identify genes regulating elemental accumulation. All of the ionomic data is available at www.ionomicshub.org.