Indica Rice Cultivars Research Articles

Increasing tolerance to bispyribac-sodium is able to allow glutathione homeostasis to recover in indica rice compared with japonica rice

The high activity and broad weed spectrum of BS has made it widely used in China. However, accidental crop injuries, particularly occurring in Jiangsu, Hunan, Hubei and Heilongjiang provinces in recent years, have resulted in limiting the application of BS in China. In this study, glutathione homeostasis was measured in the contrasting sensitivity of indica and japonica rice cultivar after bispyribac-sodium (BS) treatment. The results showed that japonica rice cultivar Nanjing 9108 was more sensitive to BS than indica rice Nanjing 11 and indica-hybrid cultivar Guangliangyou 6326. In response to the exposure of BS in all rice cultivars, especially Nanjing 9108, the perturbation of glutathione homeostasis occurred, including the decreased reduced glutathione (GSH) and increased oxidized glutathione (GSSG). These results were supported by increased activities of glutathione S-transferases (GSTs) in Nanjing 11 and Guangliangyou 6326. Further tests revealed that when Nanjing 11 was pretreated with the glutathione-depleting agents L-buthionine-sulfoximine (BSO) or diethylmaleate (DEM), the GSH levels, the activity of GSTs, and the gene expression levels of GR and GSTs decreased, finally increasing the phytotoxicity of BS. The aforementioned DEM inhibitory responses were further rescued by exogenously applied GSH. In contrast, the pretreatment of glutathione or N-acetyl-L-cysteine (NAC) not only increased the contents of GSH, the activities of GSTs, and the expression level of GR and GSTs gene, but also alleviated BS phytotoxicity in Nanjing 9108. In both cultivars, DEM increased phytotoxicity and GSH partially reversed this. This study suggests that increasing tolerance to BS was able to allow glutathione homeostasis to recover in indica rice cultivar compared with japonica rice cultivar.

Development of Novel Protocol to Al3+ Stress Tolerance at Germination Stage in Indica Rice through Statistical Approaches.

Rice production is decreasing by abiotic stresses like heavy metals. In such circumstances, producing food for growing human population is a challenge for plant breeders. Excess of Al3+ in soil has become threat for high yield of rice. Improvement of crop is one of potential solution for high production. The aim of this study was to develop the new method for optimization of Al3+ toxicity tolerance in indica rice at germination stag using two-way ANOVA and Duncan's multiple-range test (DMRT). Seeds of two indica rice cultivars (Pokkali and Pak Basmati) were exposed in different concentrations (control, 5 mM, 15 mM, and 20 mM) of Al3+ toxicity at pH 4 ±0.2 for two weeks. Germination traits such as final germination percentage (FG%), germination energy (GE), germination speed (GS), germination index (GI), mean time of germination (MGT), germination value (GV), germination velocity (GVe), peak value of germination (GPV), and germination capacity (GC) and growth traits such as root length (RL), shoot length (SL), total dry biomass (TDB), and germination vigour index (GVI) were measured. To obtain the maximum number of significance (≤ 0.01%) parameters in each concentration of Al3+ toxicity with control, two-way ANOVA was established and comparison of mean was done using DMRT. The results showed that 5 mM, 10 mM, and 15 mM have less significant effects on the above-mentioned parameters. However, 20 mM concentration of Al3+ produced significant effects (≤ 0.01%). Therefore, 20 mM of Al3+ is considered optimized limit for indica cultivars (Pokkali and Pak Basmati).

Effect of short-term heat exposure on physiological traits of indica rice at grain-filling stage

Heat stress impacts the quantity and quality of rice grains, particularly during grain-filling stage needed for grain development. In this study, the effect of short heat stress (42 °C, 30 min) on indica rice plants at the grain-filling stage (dough grain stage) was found by determining their physiological and growth traits Fv/Fm, ∆F/Fm′, chlorophyll content, leaf water potential (LWP), membrane stability, relative leaf area (RLA), relative plant height (RPH), total grain weight per panicle (TGW) and 1000 GW. Thai economic rice cvs. KDML105 and Pathumthani 1 (PTT1) were compared to the heat-tolerant rice cultivars N22 and Dular and to the heat-sensitive rice cultivar IR64. The results showed that short heat stress exhibited effects on physiology and growth greater than the control (35 °C, 30 min) by reducing of Fv/Fm, ∆F/Fm′, chlorophyll content, LWP, membrane stability and RLA. This result impacted the TGW and 1000 GW. A higher reduction of physiological traits was shown in IR64, followed by KDML105. In contrast, N22 and Dular were minimally affected by heat stress and were able to adapt and recover based on their grain weight that exhibited less of an effect. PTT1 was also impacted by heat stress similarly to Dular. Thus, short heat stress affected the physiological parameters of five rice cultivars at the dough grain stage. In addition, the five indica rice cultivars were classified into three groups: (1) the heat-tolerant group (N22, Dular and PTT1), (2) the moderately heat-tolerant group (KDML105), and (3) the heat-sensitive group (IR64) by PC-ORD program at 50% of similarity of the 13 physiological traits.

Identification and fine mapping of qWBPH11 conferring resistance to whitebacked planthopper (Sogatella furcifera Horvath) in rice (Oryza sativa L.)

The whitebacked planthopper (WBPH), Sogatella furcifera Horvath, is one of the most destructive pests in rice (Oryza sativa L.) production. Host-plant resistance has been considered as an efficient and eco-friendly strategy to reduce yield losses caused by WBPH. In this study, we found that an indica rice cultivar IR54751-2-44-15-24-2 (IR54751) displayed high resistance to WBPH at both seedling and tillering stages. The resistance of IR54751 was mainly contributed by antixenosis and tolerance rather than antibiosis. An F2 population derived from a cross between IR54751 and a susceptible japonica cultivar 02428 was constructed to detect the quantitative trait loci (QTLs) conferring the resistance to WBPH. In total, four QTLs including qWBPH3.1, qWBPH3.2, qWBPH11, and qWBPH12 were identified and distributed on three different chromosomes. The four QTLs had LOD scores of 3.8, 8.2, 5.8, and 3.9, accounting for 8.2, 21.5, 13.9, and 10.4% of the phenotypic variation, respectively. Except for qWBPH3.1, the resistance alleles of the other three QTLs were all from IR54751. Further, a secondary population harboring only single qWBPH11 locus was developed from the F2 population by marker-assisted selection. Finally, qWBPH11 was delimited in a 450-kb region between markers DJ53973 and SNP56. The identification of WBPH resistance QTLs and the fine mapping of qWBPH11 will be helpful for cloning resistance genes and breeding resistant rice cultivars.

Deployment of cold tolerance loci from Oryza sativa ssp. Japonica cv. ‘Nipponbare’ in a high‐yielding Indica rice cultivar ‘93‐11’

AbstractCold tolerance is a complex trait, and QTL pyramiding is required for rice breeding. In this study, a total of seven QTLs for cold tolerance in the Japonica rice variety ‘Nipponbare’ were identified in an F2:3 population. A stably inherited major QTL, called qCTS11, was detected in the region adjacent to the centromere of chromosome 11. In a near‐isogenic line population, the QTL was further dissected into two linked loci, qCTS11.1 and qCTS11.2. Both of the homozygous alleles of qCTS11.1 and qCTS11.2 from ‘Nipponbare’ showed major positive effects on cold tolerance. Through pyramiding the linked QTLs in the cold‐sensitive Indica rice cultivar ‘93‐11’, we have developed a new elite, high‐yielding Indica variety with cold tolerance.

Starch Synthase IIa-Deficient Mutant Rice Line Produces Endosperm Starch With Lower Gelatinization Temperature Than Japonica Rice Cultivars.

The gelatinization temperature of endosperm starch in most japonica rice cultivars is significantly lower than that in most indica rice cultivars. This is because three single nucleotide polymorphisms in the Starch synthase (SS) IIa gene in japonica rice cultivars (SSIIaJ) significantly reduce SSIIa activity, resulting in an increase in amylopectin short chains with degree of polymerization (DP) ≤ 12 compared to indica rice cultivars (SSIIaI). SSIIa forms a trimeric complex with SSI and starch branching enzyme (BE) IIb in maize and japonica rice, which is likely important for the biosynthesis of short and intermediate amylopectin chains (DP ≤ 24) within the amylopectin cluster. It was unknown whether the complete absence of SSIIa further increases amylopectin short chains and reduces gelatinization temperature and/or forms altered protein complexes due to the lack of a suitable mutant. Here, we identify the SSIIa-deficient mutant rice line EM204 (ss2a) from a screen of ca. 1,500 plants of the rice cultivar Kinmaze (japonica) that were subjected to N-methyl-N-nitrosourea mutagenesis. The SSIIa gene in EM204 was mutated at the boundary between intron 5 and exon 6, which generated a guanine to adenine mutation and resulted in deletion of exon 6 in the mRNA transcript. SSIIa activity and SSIIa protein in developing endosperm of EM204 were not detected by native-PAGE/SS activity staining and native-PAGE/immunoblotting, respectively. SSIIa protein was completely absent in mature seeds. Gel filtration chromatography of soluble protein extracted from developing seeds showed that the SSI elution pattern in EM204 was altered and more SSI was eluted around 300 kDa, which corresponds with the molecular weight of trimeric complexes in wild type. The apparent amylose content of EM204 rice grains was higher than that in its parent Kinmaze. EM204 also had higher content of amylopectin short chains (DP ≤ 12) than Kinmaze, which reduced the gelatinization temperature of EM204 starch by 5.6°C compared to Kinmaze. These results indicate that EM204 starch will be suitable for making foods and food additives that easily gelatinize and slowly retrograde.

Genome-wide analyses of late pollen-preferred genes conserved in various rice cultivars and functional identification of a gene involved in the key processes of late pollen development

BackgroundUnderstanding late pollen development, including the maturation and pollination process, is a key component in maintaining crop yields. Transcriptome data obtained through microarray or RNA-seq technologies can provide useful insight into those developmental processes. Six series of microarray data from a public transcriptome database, the Gene Expression Omnibus of the National Center for Biotechnology Information, are related to anther and pollen development.ResultsWe performed a systematic and functional study across the rice genome of genes that are preferentially expressed in the late stages of pollen development, including maturation and germination. By comparing the transcriptomes of sporophytes and male gametes over time, we identified 627 late pollen-preferred genes that are conserved among japonica and indica rice cultivars. Functional classification analysis with a MapMan tool kit revealed a significant association between cell wall organization/metabolism and mature pollen grains. Comparative analysis of rice and Arabidopsis demonstrated that genes involved in cell wall modifications and the metabolism of major carbohydrates are unique to rice. We used the GUS reporter system to monitor the expression of eight of those genes. In addition, we evaluated the significance of our candidate genes, using T-DNA insertional mutant population and the CRISPR/Cas9 system. Mutants from T-DNA insertion and CRISPR/Cas9 systems of a rice gene encoding glycerophosphoryl diester phosphodiesterase are defective in their male gamete transfer.ConclusionThrough the global analyses of the late pollen-preferred genes from rice, we found several biological features of these genes. First, biological process related to cell wall organization and modification is over-represented in these genes to support rapid tube growth. Second, comparative analysis of late pollen preferred genes between rice and Arabidopsis provide a significant insight on the evolutional disparateness in cell wall biogenesis and storage reserves of pollen. In addition, these candidates might be useful targets for future examinations of late pollen development, and will be a valuable resource for accelerating the understanding of molecular mechanisms for pollen maturation and germination processes in rice.

Evaluation and breeding application of six brown planthopper resistance genes in rice maintainer line Jin 23B

BackgroundThe brown planthopper (BPH), an insect species that feeds on rice plants (Oryza sativa L.), is one of the most destructive insect pests of rice. BPH can be controlled with chemical pesticides, but they are expensive in terms of the cost and environmental hazards. Hence, utilization of resistance genes in resistant varieties is considered as a more economical and eco-friendly effective method for control.ResultsIn this study, six dominant BPH-resistance genes (Bph3, Bph14, Bph15, Bph18, Bph20 and Bph21) were introduced into an elite indica rice cultivar Jin 23B using the marker-assisted selection (MAS) method of breeding. One line combining Bph14 and Bph15 and six single gene introgression lines were used to evaluate the gene effects based on three parameters: seedling and tillering resistance of the rice genotypes, honeydew weight, and BPH survival rate. Among all improved lines, combination of Bph14 and Bph15 had the largest effect in conferring resistance to BPH. Bioassays showed that the order of the gene effects was Bph14/Bph15 > Bph15 ≥ Bph14 ≥ Bph20 ≥ Bph21 ≥ Bph3 > Bph18 > none at the rice seedling stage. The pyramided or single-gene introgression lines showed enhanced resistance relative to the control. Furthermore, field trial data demonstrated that yields of improved Jin 23B lines were similar to the control under BPH-free field conditions.ConclusionsEach of the BPH resistance genes reduced BPH growth and development, and was effective at both the seedling and tillering growth stages. These lines can be used in rice hybrid and production in China.

Effect of degree of milling on physicochemical, structural, pasting and cooking properties of short and long grain Indica rice cultivars

The effects of degree of milling (DOM) between 0 and 8% on physico-chemical, structural, pasting and cooking properties of short and long grain Indica rice cultivars were studied. Ash, protein, lipids and minerals decreased while blue value and crystallinity increased with increase in DOM. The colour parameters (a∗, b∗) and cooking time (CT) decreased while L∗(lightness) increased with increase in DOM. Elongation ratio (ER), gruel solid loss (GSL), length/breadth (L/B) and paste viscosities during cooking increased with increase in DOM. Short grain rice contained lower ash, protein, lipids, Mn, K, Ca, CT and GSL than long grain while the later showed higher crystallinity, Mn, P, K, Ca and ER. Paste and dough characteristics measured using Rheometer and Mixolab, respectively correlated well and differed with cultivar and DOM. Short and long grain cultivars showed variation in loss of different chemical constituents during varied DOM causing variation in cooking characteristics.

Studies on growth dynamics of embryogenic cell suspension cultures of commercially important Indica rice cultivars ASD16 and Pusa basmati.

Significant efforts are being directed towards the improvement of rice using genetic manipulations. A good and reproducible system for recovering fertile Indica rice plants is imperative. The aim of this study was to study the influence of initial cell density on growth dynamics of suspension cultures. The cultures were initiated from 3-week-old embryogenic calli derived from mature seeds of Indica rice cultivars ASD16 and Pusa basmati. Growth kinetics of the rice cell suspensions were measured and the obtained data reveal that viable cells at 3% PCV using 20ml liquid (N6D) medium and sub-culturing at 7-day intervals resulted in rapid increase in fresh and dry weightsand the embryogenic competency of the cells were found to be high. The growth kinetics analysis revealed that ASD16 showed better efficiency for high frequency and viable somatic embryo formation as compared to Pusa basmati. The technique was found to be suitable for developing somatic embryos for both cultivars ASD16 and Pusa basmati, which can be used for many important applications including micropropagation and secondary metabolites production.

Minor-effect QTL for heading date detected in crosses between indica rice cultivar Teqing and near isogenic lines of IR24

Identification of quantitative trait loci (QTL) having small effects on heading date (HD) is important for fine-tuning flowering time in rice (Oryza sativa L.). In this study, minor-effect QTL for HD were identified using five segregating rice populations, including a recombinant inbred line population derived from crosses between indica cultivar Teqing and near isogenic lines of IR24, and four populations derived from residual heterozygotes identified in the original population. HD data from these populations were obtained in multiple years or at two locations with different photoperiods. A total of 11 QTL were detected; they had small additive effects ranging from 0.21 to 1.63days. The QTL were all detected in different populations, locations and/or years, having consistent allelic effects across experiments and a stable magnitude across years at the same location. These QTL, and other minor-effect QTL that have been cloned or fine-mapped, generally do not have strong photoperiod sensitivity, and thus can be used in a wide range of eco-geographical conditions. Seven of the 11 QTL were different from those that have been cloned or fine-mapped, providing new candidates for gene cloning and marker-assisted breeding. Allelic effects of QTL corresponding to those that had been cloned or fine-mapped, were much smaller in this study than previously reported. The results supported the assumption that qualitative and quantitative genes may be different alleles at the same loci, suggesting that it may be promising to identify minor-effect QTL from major heading date genes/QTL that have been cloned.

Estimates of rice lodging using indices derived from UAV visible and thermal infrared images

Rice lodging not only causes difficulty in harvest operations, but also drastically reduces yield. Rice lodging assessment contributes greatly to rice plantation and crop field management. In this study, we collected visible and thermal infrared images with an unmanned aerial vehicle. Then, based on hybrid image analysis and field investigation, we established a comprehensive rice lodging recognition model using a particle swarm optimization and support vector machine algorithm. The results showed that color and texture features were different between lodged and non-lodged rice plants. Moreover, the temperature was distinct between lodging and non-lodging areas, with lodged rice having higher canopy temperature. The developed model based on the visible and thermal infrared images was validated using different Indica and Japonica rice cultivars. The model had a false positives rate and false negatives rate of less than 10%, and estimated lodging rate with an R2 greater than 0.9. These results indicated that combination of visible and thermal infrared images feature significantly increased the rice lodging recognition accuracy. The developed model can be used to monitor rice lodging and estimate the lodging rate.

In vitro plant growth promotion by ZnO nanomaterials in indica rice seedlings (Oryza sativa L.)

This research focuses on zinc oxide nanomaterials (nano-ZnO) applied to agricultural fields. Plants were exposed to nanomaterials and responded differently in tolerance to the various concentrations and types of nanomaterials. Two cultivars (SP1 and SP90) of indica rice (Oryza sativa L.) seedlings were grown at 0-1,000 mg.L-1 nano-ZnO and their morphological and physiological response was determined. Rice seedlings were harvested 5, 7, 10 and 14 days after treatments. Results demonstrated a significant increase in biomass, growth tolerance index (GTI), chlorophyll contents and antioxidant enzyme activities of the treated plant at 100 mg.L-1 nano-ZnO but these parameters decreased with increasing nano-ZnO concentration in the treated plants at 300-1,000 mg.L-1 nano-ZnO when compared to control plants (0 mg.L-1 nano-ZnO). The high accumulations of biomass, GTI and chlorophyll contents were related to production of antioxidant enzyme activities (catalase and peroxidase) in plant cells when plants were exposed to a low dose of nano-ZnO. Further investigations will determine the effect of nano-ZnO on the plant productivity.

Marker-Assisted Selection of Xa21 Conferring Resistance to Bacterial Leaf Blight in indica Rice Cultivar LT2

Bacterial leaf blight of rice (BLB), caused by Xanthomonas oryzae pv. oryzae, is one of the most destructive diseases in Asian rice fields. A high-quality rice variety, LT2, was used as the recipient parent. IRBB21, which carries the Xa21 gene, was used as the donor parent. The resistance gene Xa21 was introduced into LT2 by marker-assisted backcrossing. Three Xoo races were used to inoculate the improved lines following the clipping method. Eleven BC3F3 lines carrying Xa21 were obtained based on molecular markers and agronomic performance. The 11 lines were then inoculated with the three Xoo races. All the 11 improved lines showed better resistance to BLB than the recipient parent LT2. Based on the level of resistance to BLB and their agronomic performance, five lines (BC3F3 5.1.5.1, BC3F3 5.1.5.12, BC3F3 8.5.6.44, BC3F3 9.5.4.1 and BC3F3 9.5.4.23) were selected as the most promising for commercial release. These improved lines could contribute to rice production in terms of food security.

Investigation of genetic loci controlling non-shattering behaviour in an Indica rice cultivar ‘IR36’

Investigation of genetic loci controlling non-shattering behaviour in an Indica rice cultivar ‘IR36’

In Planta transformation for conferring salt tolerance to a tissue-culture unresponsive indica rice (Oryza sativa L.) cultivar

Many farmer-popular indica rice (Oryza sativa L.) cultivars are recalcitrant to Agrobacterium-mediated transformation through tissue culture and regeneration. In planta transformation using Agrobacterium could therefore be a useful alternative for indica rice. A simple and reproducible in planta protocol with higher transformation efficiencies than earlier reports was established for a recalcitrant indica rice genotype. Agrobacterium tumefaciens containing the salt tolerance-enhancing Pea DNA Helicase45 (PDH45) gene, with the reporter and selectable marker genes, gus-INT (β-glucuronidase with intron) and hygromycin phosphotransferase (hpt), respectively, were used. Overnight-soaked mature embryos were infected and allowed to germinate, flower, and set T1 seeds. T0 plants were considered positive for the transgene if the spikelets of one or more of their panicles were positive for gus. Thereafter, selection at T1 was done by germination in hygromycin and transgenic status re-confirmation by subjecting plantlet DNA/RNA to gene-specific PCR, Southern and semi-quantitative RT-PCR. Additionally, physiological screening under saline stress was done at the T2 generation. Transformation efficiency was found to be 30–32% at the T0 generation. Two lines of the in planta transformed seedlings of the recalcitrant rice genotype were shown to be saline tolerant having lower electrolyte leakage, lower Na+/K+, minimal leaf damage, and higher chlorophyll content under stress, compared to the WT at the T2 generation.

The Effect of Season-Long Temperature Increases on Rice Cultivars Grown in the Central and Southern Regions of China.

Rice production is challenged by the asymmetric increases in day and night temperatures. Efforts are required to improve our understanding of the impact of climate change on rice production. To this end, 2-year experiment was conducted to evaluate the response of mid-season rice growth in the central and southern regions of China to elevated temperatures. Four replicates of four widely planted indica rice cultivars (Huanghuazhan: HHZ; Shanyou63: SY63; Yangliangyou6: YLY6; Liangyoupeijiu: LYPJ) were subjected to four elevated-temperature treatments (control: ambient temperature; NW: night-time warming; DW: daytime warming; AW: all-day warming) generated by an open-top hot-blast system under field conditions. This apparatus causes an ~2°C increase in the rice canopy temperature. Of all the elevated-temperature treatments, AW was the most devastating treatment for all rice cultivars, negatively affecting nearly all of investigated parameters, including grain yield and its components, dry matter accumulation, biomass, and harvest index (HI). The AW treatment decreased the grain yield by 11–35% and 43–78% in 2015 and 2016, respectively. No significant reduction in the grain yield was observed in the DW and NW treatments in 2015. However, the grain yield was decreased in DW and NW treatments by 20–52% and 18–55%, respectively, in 2016. Furthermore, the temperature-driven degradation of pollen viability, the number of pollen grains adhering to the stigma and pollen germination on the stigma caused spikelet sterility and thereby decreased the grain yield. The YLY6 and SY63 cultivars performed better than the HHZ and LYPJ cultivars with respect to grain yield and its components in all elevated-temperature treatments in both years. However, 42.97 and 61.01% reductions still occurred for the SY63 and YLY6 cultivars, respectively, in the AW treatment in 2016. The above results suggested that the elevated temperature may cause a noteworthy reduction in the productions of these widely planted genotypes in central and southern regions of China. To ensure the security of rice production in this region in an expected global warming environment, currently planted varieties will need to be replaced by heat-resistant varieties in the future.

Knockout of OsNramp5 using the CRISPR/Cas9 system produces low Cd-accumulating indica rice without compromising yield

Rice grain with excessive cadmium (Cd) is a major source of dietary Cd intake and a serious threat to health for people who consume rice as a staple food. The development of elite rice cultivars with consistently low Cd content is challenging for conventional breeding approaches, and new strategies urgently need to be developed. Here, we report the development of new indica rice lines with low Cd accumulation and no transgenes by knocking out the metal transporter gene OsNramp5 using CRISPR/Cas9 system. Hydroponic culture showed that Cd concentrations in shoots and roots of osnramp5 mutants were dramatically decreased, resulting in rescue of impaired growth in high Cd condition. Cd-contaminated paddy field trials demonstrated that Cd concentration in osnramp5 grains was consistently less than 0.05 mg/kg, in contrast to high Cd concentrations from 0.33 mg/kg to 2.90 mg/kg in grains of Huazhan (the wild-type indica rice). In particular, the plant yield was not significantly affected in osnramp5 mutants. Furthermore, we developed promising hybrid rice lines with extremely low Cd content in grains. Our work supplies a practical approach to developing Cd pollution-safe indica rice cultivars that minimizes Cd contamination risk in grains.

Meta-expression analysis of unannotated genes in rice and approaches for network construction to suggest the probable roles.

This work suggests 2020 potential candidates in rice for the functional annotation of unannotated genes using meta-analysis of anatomical samples derived from microarray and RNA-seq technologies and this information will be useful to identify novel morphological agronomic traits. Although the genome of rice (Oryza sativa) has been sequenced, 14,365 genes are considered unannotated because they lack putative annotation information. According to the Rice Genome Annotation Project Database ( http://rice.plantbiology.msu.edu/ ), the proportion of functionally characterized unannotated genes (0.35%) is quite limited when compared with the approximately 3.9% of annotated genes with assigned putative functions. Researchers require additional information to help them investigate the molecular mechanisms associated with those unannotated genes. To determine which of them might regulate morphological or physiological traits in the rice genome, we conducted a meta-analysis of expression data that covered a wide range of tissue/organ samples. Overall, 2020 genes showed cultivar-, tissue-, or organ-preferential patterns of expression. Representative candidates from featured groups were validated by RT-PCR, and the GUS reporter system was used to validate the expression of genes that were clustered according to their leaf or root preference. Taking a molecular and genetics approach, we examined meta-expression data and found that 127 genes were differentially expressed between japonica and indica rice cultivars. This is potentially significant for future agronomic applications. We also used a T-DNA insertional mutant and performed a co-expression network analysis of Sword shape dwarf1 (SSD1), a gene that regulates cell division. This network was refined via RT-PCR analysis. Our results suggested that SSD1 represses the expression of four genes related to the processes of DNA replication or cell division and provides insight into possible molecular mechanisms. Together, these strategies present a valuable tool for in-depth characterization of currently unannotated genes.

Tungsten (W) bioavailability in paddy rice soils and its accumulation in rice (Oryza sativa)

The aim of this study was to investigate the accumulation characteristics of tungsten (W) by different indica rice cultivars from the soil and to assess the potential risks to human health via dietary intake of W in rice consumption. A total of 153 rice (ear) samples of 15 cultivars and the corresponding surface soil samples were collected from 7 cities in Fujian Province of southeastern China. The available soil W were extracted using H2C2O4·2H2O-(NH4)2C2O4·H2O at pH 3.3). Results showed that the total soil W ranged from 2.03 mg kg−1 to 15.34 mg kg−1 and available soil W ranged from 0.03 mg kg−1 to 1.61 mg kg−1. The W concentration in brown rice varied from 7 μg kg−1 to 283 μg kg−1 and was significantly correlated with the available soil W. The highest mean TFavail (transfer factor based on available soil W) was 0.91 for Te-you 627 (hybrid, indica rice), whereas the lowest was 0.08 for Yi-you 673 (hybrid, indica rice). The TFavail decreased with the increase in available soil W, clay content, and cation exchange capacity. The consumption of the brown rice produced from the investigated areas in some cultivars by the present study may cause risks to human health.