Leonard Wade

Proteomic analysis of rice leaves during drought stress and recovery

Three‐week old plants of rice (Oryza sativa L. cv CT9993 and cv IR62266) developed gradual water stress over 23 days of transpiration without watering, during which period the mid‐day leaf water potential declined to ∼–2.4 MPa, compared with ∼–1.0 MPa in well‐watered controls. More than 1000 protein spots that were detected in leaf extracts by proteomic analysis showed reproducible abundance within replications. Of these proteins, 42 spots showed a significant change in abundance under stress, with 27 of them exhibiting a different response pattern in the two cultivars. However, only one protein (chloroplast Cu‐Zn superoxide dismutase) changed significantly in opposite directions in the two cultivars in response to drought. The most common difference was for proteins to be up‐regulated by drought in CT9993 and unaffected in IR62266; or down‐regulated by drought in IR62266 and unaffected in CT9993. By 10 days after rewatering, all proteins had returned completely or largely to the abundance of the well‐watered control. Mass spectrometry helped to identify 16 of the drought‐responsive proteins, including an actin depolymerizing factor, which was one of three proteins detectable under stress in both cultivars but undetectable in well‐watered plants or in plants 10 days after rewatering. The most abundant protein up‐regulated by drought in CT9993 and IR62266 was identified only after cloning of the corresponding cDNA. It was found to be an S‐like RNase homologue but it lacked the two active site histidines required for RNase activity. Four novel drought‐responsive mechanisms were revealed by this work: up‐regulation of S‐like RNase homologue, actin depolymerizing factor and rubisco activase, and down‐regulation of isoflavone reductase‐like protein.

A proteomic approach to analyzing drought- and salt-responsiveness in rice

The analysis of stress-responsiveness in plants is an important route to the discovery of genes conferring stress tolerance and their use in breeding programs. Proteomic analysis provides a broad view of plant responses to stress at the level of proteins. In recent years this approach has increased in sensitivity and power as a result of improvements in two-dimensional polyacrylamide gel electrophoresis (2DE), protein detection and quantification, fingerprinting and partial sequencing of proteins by mass spectrometry (MS), bioinformatics, and methods for gene isolation. 2DE provides information on changes in abundance and electrophoretic mobility of proteins, the latter reflecting post-translational modifications such as phosphorylation and free-radical cleavage. Here we review the technical aspects of proteomics and demonstrate its use in analyzing the response of rice plants to drought and salinity. More than 2000 proteins were detected reproducibly in drought-stressed and well-watered leaves. Out of >1000 proteins that were reliably quantified, 42 proteins changed significantly in abundance and/or position. We identified several leaf proteins whose abundance increased significantly during drought and declined on re-watering. The three most marked changes were seen with actin depolymerizing factor, a homologue of the S-like ribonucleases and the chloroplastic glutathione-dependent dehydroascorbate reductase. Proteomic comparisons of salt stress-tolerant and stress-sensitive genotypes revealed numerous constitutive and stress-induced differences in root proteins. Among them was caffeoyl-CoA O-methyltransferase, an enzyme of lignin biosynthesis. The abundance of ascorbate peroxidase was much higher in salt-tolerant Pokkali than in salt-sensitive IR29 in the absence of stress.

Increased food and ecosystem security via perennial grains

Perennial grains hold promise, especially for marginal landscapes or with limited resources where annual versions struggle. Despite doubling of yields of major grain crops since the 1950s, more than one in seven people suffer from malnutrition (1). Global population is growing; demand for food, especially meat, is increasing; much land most suitable for annual crops is already in use; and production of nonfood goods (e.g., biofuels) increasingly competes with food production for land (2). The best lands have soils at low or moderate risk of degradation under annual grain production but make up only 12.6% of global land area (16.5 million km2) (3). Supporting more than 50% of world population is another 43.7 million km2 of marginal lands (33.5% of global land area), at high risk of degradation under annual grain production but otherwise capable of producing crops (3). Global food security depends on annual grains—cereals, oilseeds, and legumes—planted on almost 70% of croplands, which combined supply a similar portion of human calories (4, 5). Annual grain production, though, often compromises essential ecosystem services, pushing some beyond sustainable boundaries (5). To ensure food and ecosystem security, farmers need more options to produce grains under different, generally less favorable circumstances than those under which increases in food security were achieved this past century. Development of perennial versions of important grain crops could expand options.

Mapping QTLs for root morphology of a rice population adapted to rainfed lowland conditions

Abstract.In the rainfed lowlands, rice (Oryza sativa L.) develops roots under anaerobic soil conditions with ponded water, prior to exposure to water stress and aerobic soil conditions that arise later in the season. Constitutive root system development in anaerobic soil conditions has been reported to have a positive effect on subsequent expression of adaptive root traits and water extraction during progressive water stress in aerobic soil conditions. We examined quantitative trait loci (QTLs) for constitutive root morphology traits using a mapping population derived from a cross between two rice lines which were well-adapted to rainfed lowland conditions. The effects of phenotyping environment and genetic background on QTLs identification were examined by comparing the experimental data with published results from four other populations. One hundred and eighty-four recombinant inbred lines (RILs) from a lowland indica cross (IR58821/IR52561) were grown under anaerobic conditions in two experiments. Seven traits, categorized into three groups (shoot biomass, deep root morphology, root thickness) were measured during the tillering stage. Though parental lines showed consistent differences in shoot biomass and root morphology traits across the two seasons, genotype-by-environment interaction (G×E) and QTL-by-environment interaction were significant among the progeny. Two, twelve, and eight QTLs for shoot biomass, deep root morphology, and root thickness, respectively, were identified, with LOD scores ranging from 2.0 to 12.8. Phenotypic variation explained by a single QTL ranged from 6% to 30%. Only two QTLs for deep root morphology, in RG256-RG151 in chromosome 2 and in PC75M3-PC11M4 in chromosome 4, were identified in both experiments. Comparison of positions of QTLs across five mapping populations (the current population plus populations from four other studies) revealed that these two QTLs for deep root morphology were only identified in populations that were phenotyped under anaerobic conditions. Fourteen and nine chromosome regions overlapped across different populations as putative QTLs for deep root morphology and root thickness, respectively. PC41M2-PC173M5 in chromosome 2 was identified as an interval that had QTLs for deep root morphology in four mapping populations. The PC75M3-PC11M4 interval in chromosome 4 was identified as a QTL for root thickness in three mapping populations with phenotypic variation explained by a single QTL consistently as large as 20–30%. Three QTLs for deep root morphology were found only in japonica/indica populations but not in IR58821/IR52561. The results identifying chromosome regions that had putative QTLs for deep root morphology and root thickness over different mapping populations indicate potential for marker-assisted selection for these traits.

Submergence tolerance in rainfed lowland rice: physiological basis and prospects for cultivar improvement through marker-aided breeding

Two important factors influencing rice plant survival during submergence are limitations to gas diffusion under water, and reduced irradiance that impair photosynthesis and efficient utilization of carbohydrates. Thus, survival during submergence may largely depend on accumulation of high carbohydrate concentrations prior to submergence and a capacity for maintaining energy production through rapid alcoholic fermentation under oxygen shortage. During flash flooding, a third factor thought to affect survival is the aerobic shock during the post-submergence period when floodwaters recede. Changes in the level of antioxidants and enzymes such as superoxide dismutase (SOD) suggest that tolerant rice cultivars develop protective systems to air after exposure to hypoxic or anoxic environments. These responses are similar to other wetland plants. The capacity to survive submergence depends not only on specific environmental factors, but also on the strategy that plants have evolved for adoption to particular flood-prone environments. In rice the two main strategies are to elongate and escape, or not to elongate and conserve resources. For rainfed lowland rice exposed to flash flooding, elongation growth during complete submergence has major adverse effects on survival, presumably since this competes with maintenance processes which require carbohydrates and energy. Selection for minimal elongation during submergence is currently being exploited as a trait for submergence tolerance by rainfed lowland rice breeders in south and southeast Asia. Gene mapping for submergence tolerance has been useful in identifying one prominent locus for submergence tolerance. Fine scale gene mapping and sequencing may facilitate further progress in the physiology and genetics of submergence tolerance. Recently published data demonstrate that improving submergence tolerance may be possible through up-regulation of genes for particular traits such as pyruvate decarboxylase (PDC) for alcoholic fermentation. Validation of appropriate mechanisms in other cultivars for target environments, and development and utilization of molecular markers to follow these traits in breeding programs, will therefore be high priorities for future work on submergence tolerance of rice.

Genotypic Variation in Response of Rainfed Lowland Rice to Drought and Rewatering : II.Root growth

Abstract Genotypic variation in the root system is a potential source for improving drought tolerance of rainfed lowland rice (Oryza sativa L.). Our work aimed at characterizing both constitutive root traits (those present under well -watered conditions) and adaptive root traits (those developed in response to drought and rewatering) among eight diverse rice genotypes in three sets of greenhouse experiments (experiments 1, 2, and 3). Under well–watered conditions, genotypic variation was observed in root to shoot ratio, root growth rate, specific root length, deep root ratio, root mass per tiller, and root thickness. CT9993 and IR58821 had a high root to shoot ratio, deep and thick root system, and high root mass per tiller. However, CT9993 had a slow root growth rate and short specific root length. In response to drought in experiments 2 and 3, the total amount of assimilate distributed to roots was reduced and roots became thinner, but the proportion of total assimilate supply assigned to deeper layers increased, thereby maintaining deep root mass and increasing specific root length. On rewatering, root to shoot ratio increased, surface roots increased, and roots became thicker. During drought, NSG19, KDML105, Mahsuri, and IR58821 partitioned a larger proportion of assimilate to deep roots and had more deep root branching.

OPPORTUNITIES TO MANIPULATE NUTRIENT-BY-WATER INTERACTIONS IN RAINFED LOWLAND RICE SYSTEMS

Water stress, accompanied by changes in soil aeration, severely limits rice productivity in rainfed systems. These factors affect nutrient availability. Nitrate (NO3) that accumulates in aerobic soil is rapidly lost through leaching or denitrification in flooded soil. Green manures can act as NO3 catch crops and legumes may gain additional N from biological N fixation. Direct seeding permits additional crops to be grown. Roots are commonly shallow in rainfed lowlands. It is not clear to what extent rice yields in rainfed lowlands are Limited by water, nutrients, and the interactions between them, over diverse soil types, cultural practices and seasonal conditions. Research must determine what really Limits root growth, water extraction and nutrient uptake. Some evidence suggests that manipulation of controlled-release fertilizer and root system development may be the key to optimizing nutrient release and capture in fluctuating environments. The potential for using strategic application of nutrients Co buffer water Limitation and stabilize yields must be examined. Models such as QUEFTS (Quantitative Evaluation of the Fertility of Tropical Soils) provide a potential framework for analyzing the effects of soil fertility and water availability on growth and yield of rice

Radiation-use efficiency response to vapor pressure deficit for maize and sorghum

Variability within a crop species in the amount of dry mass produced per unit intercepted solar radiation, or radiation-use efficiency (RUE), is important for the quantification of plant productivity. RUE has been used to integrate (1) leaf area, (2) solar radiation interception, and (3) productivity per unit leaf area into crop productivity. Responsiveness of RUE to vapor pressure deficit (VPD) should relate closely to responsiveness of CO2 exchange rate (CER) to VPD. The objective of this study was to compare independent RUE measurements to published response functions relating VPD with RUE of maize (Zea mays L.) and grain sorghum [Sorghum bicolor L. (Moench)]. Data sets from five locations covering a wide range of mean VPD values were compared to published response functions. Predicted RUE values were nearly always within the 95% confidence intervals of measurements. Measured RUE of maize decreased as VPD increased from 0.9 to 1.7 kPa. For sorghum, measured values of RUE agreed closely with predictions. RUE of sorghum decreased as VPD increased from 1.1 to 2.2 kPa. The relative RUE:VPD responses for these two species were similar to CER:VPD responses reported in the literature. Thus, these RUE:VPD responses may be general and appear to be related to carbon exchange rates. We calculated the expected impacts of VPD on RUE at three USA locations during maize and sorghum growing seasons. The RUE:VPD equations offer hope in describing location effects and time-of-year effects on RUE.

Root penetration of strong soil in rainfed lowland rice: comparison of laboratory screens with field performance

Rice cvs with better hardpan penetration would be expected to be more drought resistant in the rainfed lowlands. Although laboratory methods to facilitate the identification or breeding of cvs with good root-penetration ability have been described, there is a need to validate such screens against field performance. Here, we compare previous field measurements with laboratory screening measurements in eight cvs (IR20, CT9993, KDML 105, IR58821, NSG 19, IR62266, Mahsuri and IR52561). These were screened (together with Moroberekan, SG329 and IR36 for comparative purposes) using a flooded wax-layer screen. Of the eight cvs, IR58821 gave the best penetration of a 60% wax layer, with a mean penetration of 5.8 root axes per plant. The worst performer was IR52561, with a mean of 0.6 axes per plant. The cvs IR20, CT9993, KDML 105, IR58821 were also screened (together with Azucena, Bala, Moroberekan, Kinandang Patong and IR36 for comparative purposes) using a (non-flooded) sand-core screen. The sand-core screen allowed mechanical impedance of the whole sand core to be varied independently of aeration and water status. High impedance treatments were obtained by placing weights on the sand cores, which greatly decreased root growth, although differences between cvs in response to impedance in the sand-core screen were small. The ability of rice roots to penetrate wax layers did not appear to be related to their elongation through strong sand, but rather to their ability to resist buckling on encountering the wax layer. Comparison with field measurements showed that cvs with good performance in the wax-layer screen did not necessarily have good hardpan penetration in the field, although IR58821 was the best performer in the field. It is concluded that further work is required to compare root penetration in the field with root penetration in laboratory screens.

Genotypic Variation in Response of Rainfed Lowland Rice to Prolonged Drought and Rewatering

Abstract Duration of the drought period is important for plant response during drought and after rewatering. We hypothesized that, if drought duration is extended, (1) high seedling vigor and rapid development of a deep root system will not be advantageous, and (2) osmotic adjustment will be more important. Six diverse rice (Oryza sativa L.) genotypes were selected from rainfed lowland germplasms to examine the development of a deep root system and osmotic adjustment, and their relationship with biomass production during drought and after rewatering, under two different drought durations (shorter and prolonged) in the greenhouse. NSG19 and KDML105 had greater seedling vigor (larger seedling biomass), developed a deep root system earlier in response to drought, extracted soil water more quickly, and their pre-dawn leaf water potential declined more rapidly during the prolonged drought period. These two genotypes showed superior drought recovery even after a prolonged drought period in which they suffered a greater reduction in transpiration, water use efficiency, and biomass production. The superior recovery ability was associated with larger plant size by the end of the drought period rather than with plant water status during drought, such as osmotic adjustment or leaf water potential. Osmotic adjustment was greater during prolonged drought periods (ca. 0.7 MPa) than during shorter drought periods (ca. 0.5 MPa), and lower osmotic adjustment was mostly associated with a higher leaf water potential. Genotypic variation in osmotic adjustment was observed, but there was no clear relationship between osmotic adjustment and biomass production during drought periods. These patterns of response of rice seedlings to drought and rewatering in the greenhouse should help to explain the patterns of adaptation of rainfed lowland rice in the field. Selection for drought recovery ability should be an advantageous strategy for early season drought.