Comparative proteomic study reveals dynamic proteome changes between superhybrid rice LYP9 and its parents at different developmental stages

Heterosis is a common phenomenon in which the hybrids exhibit superior agronomic performance than either inbred parental lines. Although hybrid rice is one of the most successful apotheoses in crops utilizing heterosis, the molecular mechanisms underlying rice heterosis remain elusive. To gain a better understanding of the molecular mechanisms of rice heterosis, comparative leaf proteomic analysis between a superhybrid rice LYP9 and its parental cultivars 9311 and PA64s at tillering, flowering and grain-filling stages were carried out. A total of 384 differentially expressed proteins (DP) were detected and 297 DP were identified, corresponding to 222 unique proteins. As DP were divided into those between the parents (DP_PP) and between the hybrid and its parents (DP_HP), the comparative results demonstrate that proteins in the categories of photosynthesis, glycolysis, and disease/defense were mainly enriched in DP. Moreover, the number of identified DP_HP involved in photosynthesis, glycolysis, and disease/defense increased at flowering and grain-filling stages as compared to that at the tillering stage. Most of the up-regulated DP_HP involved in the three categories showed greater expression in LYP9 at flowering and grain-filling stages than at the tillering stage. In addition, CO₂ assimilation rate and apparent quantum yield of photosynthesis also showed a greater increase in LYP9 at flowering and grain-filling stages than at the tillering stage. These results suggest that the proteins involved in photosynthesis, glycolysis, and disease/defense as well as their dynamic regulation at different developmental stages may be responsible for heterosis in rice.     

Fine mapping of qHd1, a minor heading date QTL with pleiotropism for yield traits in rice (Oryza sativa L.)

Key message

A minor QTL for heading date located on the long arm of rice chromosome 1 was delimitated to a 95.0-kb region using near isogenic lines with sequential segregating regions.

Abstract

Heading date and grain yield are two key factors determining the commercial potential of a rice variety. In this study, rice populations with sequential segregating regions were developed and used for mapping a minor QTL for heading date, qHd1. A total of 18 populations in six advanced generations through BC₂F₆ to BC₂F₁₁ were derived from a single BC₂F₃ plant of the indica rice cross Zhenshan 97 (ZS97)///ZS97//ZS97/Milyang 46. The QTL was delimitated to a 95.0-kb region flanked by RM12102 and RM12108 in the terminal region of the long arm of chromosome 1. Results also showed that qHd1 was not involved in the photoperiodic response, having an additive effect ranging from 2.4 d to 2.9 d observed in near isogenic lines grown in the paddy field and under the controlled conditions of either short day or long day. The QTL had pleiotropic effects on yield traits, with the ZS97 allele delaying heading and increasing the number of spikelets per panicle, the number of grains per panicle and grain yield per plant. The candidate region contains ten annotated genes including two genes with functional information related to the control of heading date. These results lay a foundation for the cloning of qHd1. In addition, this kind of minor QTLs could be of great significance in rice breeding for allowing minor adjustment of heading date and yield traits.     

The plasticity of the growth and proliferation of wheat root system under elevated CO2

Background and Aims

Understanding crop responses to increasing atmospheric CO₂ requires knowledge of how their root systems grow, proliferate and function. The effect of elevated CO₂ on the growth and proliferation of wheat root system (Triticum aestivum L.), was examined.

Methods

Two pairs of sister lines of wheat contrasting in vigour (CV97 and CV207) and tillering (7750N and 7750PF) were grown in rhizo-boxes under ambient (380 μl L^?1) and elevated CO₂ (700 μl L^?1), and the root growth and proliferation mapped.

Results

Elevated CO₂ effects on shoot and root biomass were observed in the lines contrasting for vigour, but not in the lines contrasting for tillering. Root biomass was reduced by 67 % in the high vigour line CV97, reducing total plant biomass by 26 % compared to the low vigour line, CV207. This was due to a reduction in root length down the 1 m soil profile and root proliferation in the top 0.2 m layer. The reduction in root biomass was not compensated by an increase in shoot biomass.

Conclusions

The reduction in root biomass under elevated CO₂ in the vigour line CV97 can be explained through its inability to increase the sink strength due to the failure to increase tiller number to which the plant presumably responded by increasing losses of the newly assimilated carbon by respiration.     

N- and P-mediated seminal root elongation response in rice seedlings

Aims

In rice, seminal root elongation plays an important role in acquisition of nutrients such as N and P, but the extent to which different N forms and P concentrations affect root growth is poorly understood. This study aimed to examine N- and P-mediated seminal root elongation response and to identify putative QTLs associated with seminal root elongation.

Methods

Seminal root elongation was evaluated in 15 diverse wild and cultivated accessions of rice, along with 48 chromosome segment substitution lines (CSSLs) derived from a cross between the rice variety ‘Curinga’ and Oryza rufipogon (IRGC 105491). Root elongation in response to different forms of N (NH₄ ⁺, NO₃ ^? and NH₄NO₃) and concentrations of P was evaluated under hydroponic conditions, and associated putative QTL regions were identified.

Results

The CSSL parents had contrasting root responses to N and P. Root elongation in O. rufipogon was insensitive to N source and concentration, whereas Curinga was responsive. In contrast to N, seminal root elongation and P concentration was positively correlated. Three putative QTLs for seminal root elongation in response to N were detected on chromosome 1, and one QTL on chromosome 3 was associated with low P concentration.

Conclusions

Genetic variation in seminal root elongation and plasticity of nutrient response may be appropriate targets for marker-assisted selection to improve rice nutrient acquisition efficiency.     

The contribution of entrapped gas bubbles to the soil methane pool and their role in methane emission from rice paddy soil in free-air [CO2] enrichment and soil warming experiments

Purpose

We attempted to determine the contribution of entrapped gas bubbles to the soil methane (CH₄) pool and their role in CH₄ emissions in rice paddies open to the atmosphere.

Methods

We buried pots with soil and rice in four treatments comprising two atmospheric CO₂ concentrations (ambient and ambient +200 μmol mol^?1) and two soil temperatures (ambient and ambient +2 °C). Pots were retrieved for destructive measurements of rice growth and the gaseous CH₄ pool in the soil at three stages of crop development: panicle formation, heading, and grain filling. Methane flux was measured before pot retrieval.

Results

Bubbles that contained CH₄ accounted for a substantial fraction of the total CH₄ pool in the soil: 26–45 % at panicle formation and 60–68 % at the heading and grain filling stages. At panicle formation, a higher CH₄ mixing ratio in the bubbles was accompanied by a greater volume of bubbles, but at heading and grain filling, the volume of bubbles plateaued and contained ~35 % CH₄. The bubble-borne CH₄ pool was closely related to the putative rice-mediated CH₄ emissions measured at each stage across the CO₂ concentration and temperature treatments. However, much unexplained variation remained between the different growth stages, presumably because the CH₄ transport capacity of rice plants also affected the emission rate.

Conclusions

The gas phase needs to be considered for accurate quantification of the soil CH₄ pool. Not only ebullition but also plant-mediated emission depends on the gaseous-CH₄ pool and the transport capacity of the rice plants.     

Nitrogen use efficiency (NUE) in rice links to NH4 + toxicity and futile NH4 + cycling in roots

Aims

Rice is known as an ammonium (NH₄ ⁺)-tolerant species. Nevertheless, rice can suffer NH₄ ⁺ toxicity, and excessive use of nitrogen (N) fertilizer has raised NH₄ ⁺ in many paddy soils to levels that reduce vegetative biomass and yield. Examining whether thresholds of NH₄ ⁺ toxicity in rice are related to nitrogen-use efficiency (NUE) is the aim of this study.

Methods

A high-NUE (Wuyunjing 23, W23) and a low-NUE (Guidan 4, GD) rice cultivar were cultivated hydroponically, and growth, root morphology, total N and NH₄ ⁺ concentration, root oxygen consumption, and transmembrane NH₄ ⁺ fluxes in the root meristem and elongation zones were determined.

Results

We show that W23 possesses greater capacity to resist NH₄ ⁺ toxicity, while GD is more susceptible. We furthermore show that tissue NH₄ ⁺ accumulation and futile NH₄ ⁺ cycling across the root-cell plasma membrane, previously linked to inhibited plant development under elevated NH₄ ⁺, are more pronounced in GD. NH₄ ⁺ efflux in the root elongation zone, measured by SIET, was nearly sevenfold greater in GD than in W23, and this was coupled to strongly stimulated root respiration. In both cultivars, root growth was affected more severely by high NH₄ ⁺ than shoot growth. High NH₄ ⁺ mainly inhibited the development of total root length and root area, while the formation of lateral roots was unaffected.

Conclusions

It is concluded that the larger degree of seedling growth inhibition in low- vs. high-NUE rice genotypes is associated with significantly enhanced NH₄ ⁺ cycling and tissue accumulation in the elongation zone of the root.     

Does radial oxygen loss and iron plaque formation on roots alter Cd and Pb uptake and distribution in rice plant tissues?

Background and Aims

Metal (e.g. Cd and Pb) pollution in agricultural soils and crops have aroused considerable attention in recent years. This study aimed to evaluate the effects of ROL and Fe plaque on Cd and Pb accumulation and distribution in the rice plant.

Methods

A rhizobag experiment was employed to investigate the correlations among radial oxygen loss (ROL), Fe plaque formation and uptake and distribution of Cd and Pb in 25 rice cultivars.

Results

Large differences between the cultivars were found in rates of ROL (1.55 to 6.88 mmol O₂ kg^?1 root d.w. h^?1), Fe plaque formation (Fe: 6,117–48,167 mg kg^?1; Mn: 127–1,089 mg kg^?1), heavy metals in shoot (Cd: 0.13–0.35 mg kg^?1; Pb: 4.8–8.1 mg kg^?1) and root tissues (Cd: 1.1–3.5 mg kg^?1; Pb: 45–199 mg kg^?1), and in Fe plaque (Cd: 0.54–2.6 mg kg^?1; Pb: 102–708 mg kg^?1). Rates of ROL were positively correlated with Fe plaque formation and metal deposition on root surfaces, but negatively correlated with metal transfer factors of root/plaque and distributions in shoot and root tissues.

Conclusions

ROL-induced Fe plaque promotes metal deposition on to root surfaces, leading to a limitation of Cd and Pb transfer and distribution in rice plant tissues.     

Selection of mixed inoculants exhibiting growth-promoting activity in rice plants from undefined consortia obtained by continuous enrichment

Aims

The main objective of this study was to test the hypothesis that isolating and characterizing bacterial suspensions (undefined consortia) from the root/rhizosphere of rice will contribute to the selection of mixtures of rhizobacteria with better growth-promoting activity of rice plants.

Methods

Bacterial consortia were obtained from roots/rhizosphere soil samples of rice plants grown under upland and irrigated production systems. Those undefined consortia were subjected to five consecutive passes every 7 days in NFb (N-free broth) semisolid medium. Thereafter, strains of each growth-promoting consortia were isolated by plating on three different culture media. Then, undefined consortia, as well as mix and single bacterial strains, were characterized in terms of indoleacetic acid production, nitrogen fixation capacity, and growth promotion of rice plants.

Results

Of the 72 consortia analyzed, 41.7 % and 50.0 % increased nitrogenase activity and the production of indolic compounds, respectively, after 5 continuous passes in NFB medium. Three undefined consortia, 11 single strains and 5 strain mixtures, exhibited plant growth promotion in rice plants under greenhouse conditions.

Conclusions

Continuous enrichment in Nfb medium of undefined consortia from root/rhizosphere soil is a good strategy for the selection of plant growth-promoting bacteria for rice plants.     

The chemical-mediated allelopathic interaction between rice and barnyard grass

Aims

The possible involvement of the chemical-mediated interaction in allelopathy between rice and barnyard grass was investigated.

Methods

Effcts of rice seedlings and rice root exudate on the alleloapthic activity of barnyard grass were determined and a key compound invovled in the allelopathic interaction between rice and barnyard grass was isolated.

Results

Allelopathic activity of barnyard grass was increased by the presence of rice seedlings. Rice root exudates also elevated the allelopahtic activity of barnyard grass. A key compound, which increased the allelopathic activity of barnyard grass, in the rice root exudates was isolated and determined as momilactone B. Momilactone B increased the allelopathic activity of barnyard grass at concentrations greater than 3 μM, and increasing the momilactone B concentration increased the activity.

Conclusions

Momilactone B is known to act as a potent rice allelochemical and to possess strong growth inhibitory activity against barnyard grass. The present research suggests that barnyard grass may response to the presence of neighboring rice by sensing momilactone B in rice root exudates and increase allelopathic activity. Thus, momilactone B may not only act as a rice allelochemical but also play an important role in rice-induced allelopathy of barnyard grass. The induced-allelopathy may provide a competitive advantage for barnyard grass through the growth inhibition of competing plant species including rice. Barnyard grass allelopathy may be one of the inducible defense mechanisms by chemical-mediated plant interaction between rice and barnyard grass. Rice allelopathy was also reported to be increased by the presence of barnyard grass through increasing production and secretion of momilactone B into surrounding environments. During the evolutional process, rice and barnyard grass may have developed the chemical cross talk to activate the defense mechanisms against some biotic stress conditions by detection of certain key compounds.     

Root-induced changes in radial oxygen loss, rhizosphere oxygen profile, and nitrification of two rice cultivars in Chinese red soil regions

Aims

To evaluate the external and internal morphological differences of roots that might influence rice root radial oxygen loss (ROL) and the corresponding rhizosphere nitrification activity, growth characteristics and nitrogen nutrition of rice.

Methods

The root ROL and rhizosphere oxygen profile were determined using a miniaturised Clark-type oxygen microelectrode system, and the rhizosphere nitrification activity was studied with a short-term nitrification activity assay.

Results

The rice biomass, nitrogen accumulation and nitrogen use efficiency (NUE) of ZH (high yield) were significantly higher than those of HS (low yield). The root biomass, number, diameter and porosity of ZH were also much greater than those of HS. The inner and surface oxygen concentrations of the root of ZH were significantly higher than those of HS. The order of paddy soil oxygen penetration depth was ZH?>?HS?>?CK, and the order of the oxygen concentrations detected in the water layer and rhizosphere soil was the same. The rhizosphere nitrification activity and nitrate concentration of ZH were significantly higher than those of HS.

Conclusions

More porous and thicker roots improved the individual root ROL, and more adventitious root numbers enhanced the entire plant ROL and correspondingly improved the rhizosphere nitrification activity, which might influence the growth and nitrogen nutrition of rice.     

Determination of heterotic groups for tropical Indica hybrid rice germplasm

Key message

Two heterotic groups and four heterotic patterns were identified for IRRI hybrid rice germplasm to develop hybrid rice in the tropics based on SSR molecular data and field trials.

Abstract

Information on heterotic groups and patterns is a fundamental prerequisite for hybrid crop breeding; however, no such clear information is available for tropical hybrid rice breeding after more than 30 years of hybrid rice commercialization. Based on a study of genetic diversity using molecular markers, 18 parents representing hybrid rice populations historically developed at the International Rice Research Institute (IRRI) were selected to form diallel crosses of hybrids and were evaluated in tropical environments. Yield, yield heterosis and combining ability were investigated with the main objectives of (1) evaluating the magnitude of yield heterosis among marker-based parental groups, (2) examining the consistency between marker-based group and heterotic performance of hybrids, and (3) identifying foundational hybrid parents in discrete germplasm pools to provide a reference for tropical indica hybrid rice breeding. Significant differences in yield, yield heterosis and combining ability were detected among parents and among hybrids. On average, the hybrids yielded 14.8 % higher than the parents. Results revealed that inter-group hybrids yielded higher, with higher yield heterosis than intra-group hybrids. Four heterotic patterns within two heterotic groups based on current IRRI B- and R-line germplasm were identified. Parents in two marker-based groups were identified with limited breeding value among current IRRI hybrid rice germplasm because of their lowest contribution to heterotic hybrids. Heterotic hybrids are significantly correlated with high-yielding parents. The efficiency of breeding heterotic hybrids could be enhanced using selected parents within identified marker-based heterotic groups. This information is useful for exploiting those widely distributed IRRI hybrid rice parents.     

Net root growth and nutrient acquisition in response to predicted climate change in two contrasting heathland species

Background and aims

Accurate predictions of nutrient acquisition by plant roots and mycorrhizas are critical in modelling plant responses to climate change.

Methods

We conducted a field experiment with the aim to investigate root nutrient uptake in a future climate and studied root production by ingrowth cores, mycorrhizal colonization, and fine root N and P uptake by root assay of Deschampsia flexuosa and Calluna vulgaris.

Results

Net root growth increased under elevated CO₂, warming and drought, with additive effects among the factors. Arbuscular mycorrhizal colonization increased in response to elevated CO₂, while ericoid mycorrhizal colonization was unchanged. The uptake of N and P was not increased proportionally with root growth after 5 years of treatment.

Conclusions

While aboveground biomass was unchanged, the root growth was increased under elevated CO₂. The results suggest that plant production may be limited by N (but not P) when exposed to elevated CO₂. The species-specific response to the treatments suggests different sensitivity to global change factors, which could result in changed plant competitive interactions and belowground nutrient pool sizes in response to future climate change.     

Root growth response of rainfed lowland rice to aerobic conditions in northeastern Thailand

Background and aims

Rice plants alternately experience anaerobic and aerobic conditions during their life cycle in rainfed lowlands. Each condition affects root growth differently. Our objective was to clarify the specific rice root response to aerobic conditions in rainfed lowlands.

Methods

At the Ubon Ratchathani Rice Research Center in northeastern Thailand, we obtained root samples from 17 ‘Surin1’ (Thai variety) BC₃-derived lines and 7 CT9993-5-10-1-M × IR62266-42-6-2 doubled-haploid lines from flooded and non-flooded paddy fields at the reproductive stage in 2010 and 2011.

Results

In the non-flooded trial, rice was grown aerobically by draining the perched water; soil moisture at a depth of 20 cm fluctuated between ?10 and ?30 kPa. Deep rooting was likely promoted under aerobic conditions, but slightly drier soils under longer dry spells seemed to restrict root penetration, as the topsoil rapidly hardened during dry spells of only a few days. Fine-root development in the topsoil was inhibited under aerobic conditions.

Conclusions

Even without drought stress, rice roots respond significantly to the disappearance of standing water in rainfed lowlands via deep rooting and root branching. We identified one promising ‘Surin1’ BC₃-derived line showing an adaptive response of deep rooting under aerobic conditions, which can be used as a breeding material for rainfed lowland rice in Thailand.     

Genetic variation in plant below-ground response to elevated CO2 and two herbivore species

Aims

It is unclear how changing atmospheric conditions, including rising carbon dioxide concentration, influence interactions between above and below-ground systems and if intraspecific variation exists in this response.

Methods

We assessed interactive effects of atmospheric CO₂ concentration, above-ground herbivory, and plant genotype on root traits and mycorrhizal associations. Plants from five families of Asclepias syriaca, a perennial forb, were grown under ambient and elevated atmospheric CO₂ concentrations. Foliar herbivory by either lepidopteran caterpillars or phloem-feeding aphids was imposed. Mycorrhizal colonization, below-ground biomass, root biomass, and secondary defensive chemistry in roots were quantified.

Results

We observed substantial genetic variation among A. syriaca families in their mycorrhizal colonization levels in response to elevated CO₂ and herbivory treatments. Elevated CO₂ treatment increased root biomass in all genetic families, whereas foliar herbivory tended to decrease root biomass. Root cardenolide concentration and composition varied greatly among plant families, and elevated CO₂ treatment increased root cardenolides in two of the five plant families. Moreover, herbivores differentially affected the composition of cardenolides expressed below ground.

Conclusions

Increased atmospheric CO₂ has the potential to influence interactions among plants, herbivores and mycorrhizal fungi and intraspecific variation suggests that such interactions can evolve.