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Deterioration of rice (Oryza sativa L.) affects grain quality and seed viability during storage. Lipoxygenase (LOX), a key enzyme in lipid metabolism, directly affects the rate of ageing. Here, we found that knock-out of lipoxygenase gene OsLOX1 by CRISPR/Cas9 delayed loss of seed viability and quality. Transcriptome analysis showed that during storage, OsLOX1 affected transcription of multiple genes, including genes related to lipid metabolism and antioxidant pathways such as phosphatase and acetaldehyde dehydrogenase, which may regulate the seed storability. The genes significantly down- and up-regulated only in Ningjing 4 after NA for 13 months and 3 days of AA suggesting that OsLOX1 likely promoted seed viability in rice by balancing ageing and storage related genes, and regulated the seed storability through the amino acid synthesis and metabolic pathways. Moreover, knock-out of OsLOX1 without CRISPR/Cas9 not only improved the seed viability, but also had little impact on agronomic traits. More importantly, the OsLOX1 knock-out lines were approved in 2019 (Agricultural Foundation of China Report No. 770). Collectively, our study showed that knock-out of OsLOX1 is beneficial for prolongation of seed viability and can be directly applied to agricultural production. [ABSTRACT FROM AUTHOR]

The properties of different organic fertilizers and their potential for stabilizing toxic metals(loids) in soil have not been fully investigated. This study characterized and evaluated three organic fertilizers from different raw materials. The mushroom residue organic fertilizer (MO) had higher C, H, and O contents and more functional groups (-OH, C-H, and C = O). Its application significantly increased pH (1.00 ~ 1.32 units), organic matter (OM) content (26.58 ~ 69.11%), and cation exchange capacity (CEC) (31.52 ~ 39.91%) of soil. MO treatments can simultaneously reduce the bioavailable TCLP-Cd and TCLP-As in soil, solving the difficulties of remediating the combined Cd and As pollution. MO treatments inhibited the migration of Cd and As from soil to plant, promoting plant growth. Redundancy analysis (RDA) revealed that metal(loid) variations in plants were related to soil properties (40.09%) and TCLP-Cd/As (44.74%). Furthermore, the toxic metals(loids) risk assessment for all organic fertilizers was at safe levels. This study provided a valuable reference for choosing organic fertilizers and presented a novel option for the "producing while remediating" of farmlands with low pollution. [ABSTRACT FROM AUTHOR]

Rice quality has a major impact on its economic value, necessitating the breeding of high-quality grain varieties. In addition, varieties with superior germination and growth at low temperatures are required for direct sowing, which enables the low-cost production of rice. We developed Akikei770, a near-isogenic line from the high-quality, good-tasting cultivar Akitakomachi, carrying the qLTG3-1 gene from the Maratelli cultivar, which enhances low-temperature germinability. Although Akikei770 exhibited improved low-temperature germinability, it was inferior to Akitakomachi in appearance quality of brown rice and in eating quality of cooked rice. In Akikei770, a short arm region of up to 222 kb on chromosome 3 from Maratelli was introgressed, and only the qLTG3-1 gene exhibited polymorphisms within the coding region compared to Akitakomachi. The qLTG3-1 genotype was significantly associated with brown rice quality in the F2 population, which indicates that the qLTG3-1 gene was involved in this trait with no involvement of other chromosomal regions of Akikei770. The functional qLTG3-1 allele in Akikei770, encoding a hybrid glycine-rich protein (HyGRP) that is localized on the cell wall or membrane, enhanced the low-temperature germinability. Because a loss-of-function allele of qLTG3-1 increased the appearance quality of brown rice in a recessive manner, it was concluded that HyGRP, which enhances low-temperature germinability, has a pleiotropic effect that reduces the appearance quality of brown rice. [ABSTRACT FROM AUTHOR]

Key message: Serendipita indica induced metabolic reprogramming in colonized plants complements phosphorus-management in improving their tolerance to arsenic stress on multifaceted biological fronts. Restoration of the anthropic damage done to our environment is inextricably linked to devising strategies that are not only economically sound but are self-renewing and ecologically conscious. The dilemma of heavy metal (HM) dietary ingestion, especially arsenic (As), faced by humans and animals alike, necessitates the exploitation of such technologies and the cultivation of healthy and abundant crops. The remarkable symbiotic alliance between plants and ‘mycorrhizas’ has evolved across eons, benefiting growth/yield aspects as well as imparting abiotic/biotic stress tolerance. The intricate interdependence of Serendipita indica (S. indica) and rice plant reportedly reduce As accumulation, accentuating the interest of microbiologists, agriculturists, and ecotoxicological scientists apropos of the remediation mechanisms of As in the soil–AMF–rice system. Nutrient management, particularly of phosphorus (P), is also praised for mitigating As phytotoxicity by deterring the uptake of As molecules due to the rhizospheric cationic competition. Taking into consideration the reasonable prospects of success in minimizing As acquisition by rice plants, this review focuses on the physiological, metabolic, and transcriptional alterations underlying S. indica symbiosis, recuperation of As stress together with nutritional management of P by gathering case studies and presenting successful paradigms. Weaving together a volume of literature, we assess the chemical forms of As and related transport pathways, discuss As–P–rice interaction and the significance of fungi in As toxicity mitigation, predominantly the role of mycorrhiza, as well as survey of the multifaceted impacts of S. indica on plants. A potential strategy for simultaneous S. indica + P administration in paddy fields is proposed, followed by future research orientation to expand theoretic comprehension and encourage field-based implementation. [ABSTRACT FROM AUTHOR]

Bacterial leaf blight, sometimes known as BLB, is one of the most damaging diseases that may jeopardize the world’s supply of rice. It is caused by the bacterium Xanthomonas oryzae pv. oryzae (Xoo). It has caused sharp decline in production in regions of the globe that produce rice. More than 40 previously characterized resistance (R) genes enable host tolerance for diverse Xoo strains. In this study, three BLB resistant genes, including xa5, xa13, and Xa21, which have been crucial in disease prevention in Bangladesh, were introgressed into populations. These populations were created by crossing IRRI 154, a popular rice variety with a modern genetic background, with IRBB66 (resistant to BLB). Fifteen virulent bacterial isolates were used for BLB infection, and promising recombinants from the F5 and BC2F4 generations were found to be resistant. Using marker assisted selection (MAS) with gene-specific primers on generations F5 and BC2F4, we were able to find that 60 recombinant introgressed lines (RILs) had a pyramiding of BLB resistance genes. In terms of agronomic performance, the RILs outperformed both their donor and recipient parents, demonstrating that the RILs had pyramided three resistance genes, therefore conferring broad-spectrum BLB resistance. The produced BLB-resistant RILs offer substantial future development potential, either as cultivable crops or as BLB resistance donor material for use in boosting the yields of other rice lines. [ABSTRACT FROM AUTHOR]

As the source of isoprenoid precursors, the plastidial methylerythritol phosphate (MEP) pathway plays an essential role in plant development. Here, we report a novel rice (Oryza sativa L.) mutant ygl3 (yellow-green leaf3) that exhibits yellow-green leaves and lower photosynthetic efficiency compared to the wild type due to abnormal chloroplast ultrastructure and reduced chlorophyll content. Map-based cloning showed that YGL3, one of the major genes involved in the MEP pathway, encodes 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, which is localized in the thylakoid membrane. A single base substitution in ygl3 plants resulted in lower 4-hydroxy-3-methylbut-2-enyl diphosphate reductase activity and lower contents of isopentenyl diphosphate (IPP) compared to the wild type. The transcript levels of genes involved in the syntheses of chlorophyll and thylakoid membrane proteins were significantly reduced in the ygl3 mutant compared to the wild type. The phytochrome interacting factor-like gene OsPIL11 regulated chlorophyll synthesis during the de-etiolation process by directly binding to the promoter of YGL3 to activate its expression. The findings provides a theoretical basis for understanding the molecular mechanisms by which the MEP pathway regulate chloroplast development in rice. [ABSTRACT FROM AUTHOR]

Rice grain quality is a multifarious attribute mainly governed by multiple nutritional factors. Grain protein is the central component of rice grain nutrition dominantly affecting eating–cooking qualities. Grain protein content is quantitatively influenced by its protein fractions. Genetic quantification of five protein fractions—albumins, globulins, prolamins, glutelin, and grain protein content—were evaluated by exploiting two BC3F2 mapping populations, derived from Kongyu131/TKM9 (population-I) and Kongyu131/Bg94-1 (population-II), which were grown in a single environment. Correlation studies among protein fractions and grain protein content were thoroughly investigated. A genetic linkage map was developed by using 146 single sequence repeat (SSR) markers in population-I and 167 markers in population-II. In total, 40 QTLs were delineated for five traits in both populations. Approximately 22 QTLs were dissected in population-I, derived from Kongyu131/TKM9, seven QTLs for albumin content, four QTLs for globulin content, three QTLs for prolamin content, four QTLs for glutelin content, and four QTLs for grain protein content. In total, 18 QTLs were detected in population-II, derived from Kongyu131/Bg94-1, five QTLs for albumin content, three QTLs for globulin content, four QTLs for prolamin content, two QTLs for glutelin content, and four QTLs for grain protein content. Three QTLs, qAlb7.1, Alb7.2, and qGPC7.2, derived from population-II (Kongyu131/Bg94-1) for albumin and grain protein content were successfully validated in the near isogenic line (NIL) populations. The localized chromosomal locus of the validated QTLs could be helpful for fine mapping via map-based cloning to discover underlying candidate genes. The functional insights of the underlying candidate gene would furnish novel perceptivity for the foundation of rice grain protein content and trigger the development of nutritionally important rice cultivars by combining marker-assisted selection (MAS) breeding. [ABSTRACT FROM AUTHOR]

The re-occurrence of weedy rice in the imidazolinone (IMI) herbicide-tolerant (HT) rice fields in Malaysia suggested that the weed has evaded the IMI herbicide application. This study aimed to evaluate the seed morphological traits as potential escape mechanisms of weedy rice in response to IMI-herbicide (imazapic+imazapyr) treatment. A total of 96 weedy rice samples collected from IMI-HT rice fields were characterized according to seed characteristics. The samples were evaluated for seed dormancy and susceptibility against IMI-herbicide using a standard germination test. Herbicide-induced germination test recorded a high germination (61.99–74.43%) despite strong initial dormancy (9.09–13.14%), indicating potential dormancy breaking by the herbicide. A total of 64.7% of weedy rice morphotypes displayed high seedlings survival (>10%) after herbicide treatment suggesting variation in potential IMI-resistance of weedy rice. Correlation analysis demonstrated the herbicide responses were associated with various seed adaptive traits, especially on pericarp colour (r = 0.3701), hull colour (r = −0.2457), seed dormancy (r = 0.4351), and shattering capability (r = −0.3110). This study demonstrated that seed morphological and physiological characteristics have a significant correlation with resistance towards IMI-herbicide. Resistant genes might be linked with these weedy traits as part of the adaptive mechanism for weedy rice through consequential conferment of the genes from HT-rice into weedy rice. [ABSTRACT FROM AUTHOR]

Main conclusion: The zqdm1identified from a rice mutant is a novel allele of BRD2 and is responsible for regulating rice plant height, grain size and appearance, which has possibilities on improving rice quality. Plant height is an important agronomic trait related to rice yield, and grain size directly determines grain yield in rice (Oryza sativa L.). With the development of molecular biotechnology and genome sequencing technology, more and more key genes associated with plant height and grain size have been cloned and identified in recent years. This study identified the zqdm1 gene from a mutant with reduced plant height and grain size. The zqdm1 gene was revealed to be a new allele of BRASSINOSTEROID DEFICIENT DWARF 2 (BRD2), encoding a FAD-linked oxidoreductase protein involved in the brassinosteroid (BR) biosynthesis pathway, and regulates plant height by reducing cell number of longitudinal sections of the internode and regulates grain size by altering cell expansion. A 369-bp DNA fragment was found inserted at the first exon, resulting in protein-coding termination. This mutation has not been discovered in previous studies. Complementation tests have confirmed that 369-bp insertion in BRD2 was responsible for the plant height and grain size changing in the zqdm1 mutant. Over-expression of BRD2 driven by different promoters into indica rice variety Jiafuzhan (JFZ) results in slender grains, suggesting its function on regulating grain shape. In summary, the current study has identified a new BRD2 allele, which facilitated the further research on the molecular mechanism of this gene on regulating growth and development. [ABSTRACT FROM AUTHOR]

Oryza sativa, king of cereals, is staple food for almost one third of global population. Water deficit is one of the main abiotic factors mitigating its yield potential. Among possible controlling practices, application of Silicon and Selenium are known to affect various physiological and biochemical mechanisms to curtail water deficiency stress. The purpose of the present research was to observe the effects of Silicon (Si) and Selenium (Se) to minimize the harmful effects of water deficient condition. Treatments included control (CK), water stress (40 % water holding capacity, WHC), water stress + Silicon (40 % WHC + 1.5 mM Silicon), water stress + Selenium (40 % WHC + 0.5 mM Se) and water stress + Silicon + Selenium (40 % WHC + 1.5 mM Si and 0.5mM Se solutions). Data of root and shoot length, plant height, root and shoot dry and fresh weight, relative water contents, chlorophyll contents, protein contents, grain length, grain width and grain yield were collected. Application of Si and Se promoted plant growth and development, yield and quality traits under drought stress but maximum performance was observed with co-application of both micronutrients. It is concluded that combine application of Silicon and Selenium alleviates the effect of drought stress on growth and yield of rice by reducing the water loss and improving the chlorophyll contents. [ABSTRACT FROM AUTHOR]

A greenhouse pot experiment was conducted to investigate the effects of organic fertilizer application on Cd activity in soil and Cd accumulation in rice in paddy soils with different levels of contamination from varying Cd sources in Guizhou Province (the soil types are NJ, which is a soil with a high geological background of Cd; and QX and JZ, which are anthropogenic Cd-polluted soils). The application of organic fertilizer increased the content of organic matter in the soil and reduced the concentration of acetic acid-extractable Cd in QX and JZ paddy soils. Organic fertilizer increased rice yields and significantly decreased the Cd concentration in brown rice. In the QX and JZ soils, however, the concentration of Cd in brown rice exceeded the allowable maximum levels (MLs) of Cd in China. In contrast, the concentration of Cd in brown rice in NJ soil met the MLs of Cd. Additionally, the average daily dose and the health risk index of Cd in NJ soil were much lower than those in QX and JZ soils. The results indicate that organic fertilizer application is a promising and economic means to control Cd pollution in paddy soil. Moreover, risk assessment shows that the risk of exposure to Cd in the high geological background soil (NJ) was much lower than that in anthropogenically polluted soils (QX and JZ). [ABSTRACT FROM AUTHOR]

Neodymium (Nd) potentially threatens ecological equilibrium for its wide usage in industries. In this study, the accumulation and effect of Nd on roots were investigated in the rice seedlings (Oryza sativa L.) exposed to different concentrations of Nd (0, 1, 10, 100, and 1000 μM). The toxic effect of Nd on rice growth was observed at the higher concentration, but the positive effects were found at the lower concentration. The accumulation of Nd was present in six different chemical forms, and the insoluble phosphate and oxalate Nd were the major forms of Nd in the roots. In addition, Nd was accumulated in the soluble fractions, organelles, and cell walls of rice seedlings, and the root cell wall was a major Nd sink site. The result of Fourier transform infrared spectrometer spectral analysis indicated that the functional groups of -OH and C-OH were the major binding sites of Nd in the cell wall of roots. Moreover, the level of reactive oxygen species (ROS) and the activity of catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD) were significantly increased with the increase of Nd concentration. The enhanced antioxidant capacity also played an important role in Nd detoxification of rice seedlings. In all, the results indicated that forming of inactive oxalate or phosphate and efficient sequestration into the root cell wall was a key process in Nd accumulation and detoxification of rice seedlings. [ABSTRACT FROM AUTHOR]

Salinity tolerance plays an important role in direct seeding cultivation since tolerance to salinity at the bud burst stage of rice directly affects seedling formation and yield. However, information on the quantitative trait loci (QTL) associated with salinity tolerance at the bud burst stage is limited. Here, a recombinant inbred line (RIL) population, derived from a cross between Kongyu131 (salinity-sensitive) and Xiaobaijingzi (salinity-tolerant), was used to identify QTLs for salinity tolerance at the bud burst stage using a high-density genetic map. Four QTLs were identified. The threshold LOD score for QTL identification was 3.0. Among the four QTLs detected, two QTLs namely qRSL3 (PVE, 22.59%) and qRRL3 (PVE, 21.21%) were considered to be one QTL, named qST3, which was the major QTL related to salinity tolerance on chromosome 3. This major QTL was located within an interval of 2.55 Mb and contained 253 candidate genes. Using RNA-seq data, 51 differentially expressed genes (DEGs) were detected among the candidate region. According to Rice Annotation Project and quantitative real-time PCR (qRT-PCR) analysis, Os03g0664800 was accepted as the most likely candidate gene for qST3. These results will be useful for improving salinity tolerance of rice and for developing rice cultivars suitable for direct seeding in salinized soil. [ABSTRACT FROM AUTHOR]

Manganese (Mn) is an essential element for plant growth but it becomes phytotoxic at higher concentrations. The effect of Mn-excess in hydroponics medium was examined on growth, oxidative stress, and ultrastructural changes in chloroplasts and mitochondria as well proteomic alterations in rice (Oryza sativa L.) seedlings. Seedlings grown with 1 mM and 2 mM Mn in nutrient medium for 8 days showed decline in length and fresh biomass, and decline in net photosynthetic rate, transpiration rate, and stomatal conductance. Shoots of the seedlings had higher Mn content than roots. Mn-treated seedlings showed increased production of O2·−, H2O2, and .OH, increased lipid peroxidation, increased carbonylation of proteins, and increased proteolytic activity compared to untreated seedlings. Mn-treated seedlings showed disorganization and swelling of chloroplasts with appearance of plastoglobuli in TEM images and deformity in shape of mitochondria. Using confocal microscopy depolarization of mitochondrial membrane was observed marked by green fluorescence of JC-1 dye monomers in Mn-treated roots. Proteomics studies from leaves of Mn-treated seedlings involving 2DE and PDQuest analysis showed differential expression of 23 proteins, among which MALDI-TOF/TOF mass spectrometry analysis revealed Mn-led downregulation of photosynthesis-related proteins, namely oxygen-evolving complex protein associated with PSII, PAP-3, enzyme involved in protein folding peptidyl-prolyl cis-trans isomerase (PPIase) and carbohydrate metabolizing enzymes hydrolase, fructose-bisphosphate aldolase, transketolase, and isocitrate dehydrogenase, whereas ATP-dependent Clp protease, peroxidase, and nucleic acid–binding proteins were downregulated due to Mn treatment. Results indicate that Mn-excess inhibits growth of rice plants with induction of oxidative stress, causing structural alterations in chloroplasts, mitochondria, inhibiting photosynthesis, and downregulating many photosynthesis and carbohydrate metabolism–related proteins. [ABSTRACT FROM AUTHOR]

Background: Salt stress is one of the main abiotic stresses that limits rice production worldwide. Rice salt tolerance at the bud burst stage directly affects the seedling survival rate and the final yield in the direct seeding cultivation model. However, the reports on quantitative trait locus (QTL) mapping and map-based cloning for salt tolerance at the bud burst stage are limited. Results: Here, an F2:3 population derived from a cross between IR36 (salt-sensitive) and Weiguo (salt-tolerant) was used to identify salt-tolerant QTL interval at the bud burst stage using a whole-genome sequencing-based QTL-seq containing 40 extreme salt-tolerant and 40 extreme salt-sensitive individuals. A major QTL, qRSL7, related to relative shoot length (RSL) was detected on chromosome 7 using ΔSNP index algorithms and Euclidean Distance (ED) algorithms. According to single nucleotide polymorphisms (SNPs) between the parents, 25 Kompetitive allele-specific PCR (KASP) markers were developed near qRSL7, and regional QTL mapping was performed using 199 individuals from the F2:3 population. We then confirmed and narrowed down qRSL7 to a 222 kb genome interval. Additionally, RNA sequencing (RNA-seq) was performed for IR36 and Weiguo at 36 h after salt stress and control condition at the bud burst stage, and 5 differentially expressed genes (DEGs) were detected in the candidate region. The qRT-PCR results showed the same expression patterns as the RNA-seq data. Furthermore, sequence analysis revealed a 1 bp Indel difference in Os07g0569700 (OsSAP16) between IR36 and Weiguo. OsSAP16 encodes a stress-associated protein whose expression is increased under drought stress. Conclusion: These results indicate that OsSAP16 was the candidate gene of qRSL7. The results is useful for gene cloning of qRSL7 and for improving the salt tolerance of rice varieties by marker assisted selection (MAS). [ABSTRACT FROM AUTHOR]

As one of the important traits, hull color is the morphological marker of rice, which plays an important role in the mechanized color selection of hybrid rice seed production but lacks good application. Here, we obtained a reddish-brown hull 1 (rbh1) mutant from an Indica maintainer material H9808 by aerospace mutagenesi. In the rbh1 mutant, the hull color was reddish brown, and the grain width and 1000-grain weight decreased significantly, but the other agronomic traits did not change significantly. Furthermore, the total flavonoids and anthocyanin content in the rbh1 hulls deposition was remarkably higher than WT, and the lignin level in the rbh1 hull was reduced. Genetic analysis indicated that the reddish-brown hull trait was controlled by a pair of recessive nuclear genes. Map-based cloning indicated that RBH1 was located within the physical distance of 48 kb on the short arm of chromosome 2. The comparative analysis of genome DNA sequence between rbh1 and WT found that a substitution from T to C (+ 1001) occurred in the fourth exon of LOC_Os02g09490 in rbh1 mutant. Genetic complementation experiments indicate that RBH1 is an allele of the previously reported GH2, which encoding a cinnamyl alcohol dehydrogenase protein involving in lignin biosynthesis. qRT-PCR showed that the relative expression of lignin and flavonoid-related genes in the hulls of rbh1 mutant was significantly upregulated, confirming that GH2/RBH1 is an important gene in the metabolism of lignin and flavonoids; and provides material basis for further studying the mechanism of GH2/RBH1 regulating the rice hull color.. In addition, the hybrid F1 combination analysis indicated that the rbh1 mutation site did not affect the agronomic traits and yield of the hybrid rice, which was to cultivate the rbh1 locus into a new sterile line or restorer line with reddish-brown hulls and rice breeding application of rbh1 locus on mechanized seed production of hybrid rice provides a theoretical basis. [ABSTRACT FROM AUTHOR]

Cadmium (Cd) stress is a serious concern in agricultural soils worldwide, and increasing accumulation and subsequent transfer to humans via the food chain can have potentially harmful effects. In this study, field experiments were conducted to examine the uptake and translocation of Cd in rice, changes in the soil Cd speciation, and the subsequent effect on Cd accumulation in rice under combined organic (farmyard manure and crop straw) and inorganic (sepiolite, lime, and calcium-magnesium phosphate) soil amendments. The results showed that farmyard manure combined with sepiolite or lime and straw combined with lime or calcium-magnesium phosphate reduced the Cd translocation from the rice roots to the straw and the grains, significantly decreasing the Cd accumulation in brown rice. In addition, straw combined with sepiolite, lime, or calcium-magnesium phosphate reduced the Cd accumulation in brown rice but increased the Cd translocation from the roots to the straw by 37.8–279.3% compared with the control. Organic-inorganic amendments also decreased the soil exchangeable Cd and increased the organic-bound Cd by more than 40%. Fe-Mn oxide-bound Cd also increased but varied with growth. Cd accumulation in brown rice showed a significant positive relationship with soil exchangeable Cd at 90 days after transplantation, while at 30 days, the increase in Fe-Mn oxide- and organic-bound Cd was found to be the key factor in reducing the Cd accumulation in rice. These findings suggest that straw (under rice-rape rotation) and farmyard manure (under rice-wheat rotation) combined with sepiolite or lime are widely applicable as agronomic control techniques aimed at lowering Cd pollution. [ABSTRACT FROM AUTHOR]

Grain shape is an important agronomic trait in rice, which influences the yield and quality. In order to dissect the genetic basis of the large grain shape in 'Nanyangzhan', a recombinant inbred line (RIL) population derived from Nanyangzhan (NYZ) and Zhenshan 97B (ZS97) was used to map quantitative trait loci (QTLs) for grain length (GL), width (GW), thickness (GT), length-to-width ratio (LWR) and kilo-grain weight (KGW). A total of 53 QTLs were detected and distributed on 11 chromosomes in 2 years. Among those, QTLs for GW and GL showed a concentrated distribution on chromosome 2 and chromosome 3, respectively. NYZ, the parent with large grain shape, carried 44 alleles showing positive effects on the studied traits. In addition, the near-isogenic lines (NILs) of two novel QTLs, qGT3.1 and qGL3.4, were constructed with the background of ZS97. Results showed that NIL- qGT3.1 , the NIL carrying homozygous qGT3.1 regions from NYZ, showed an increased value of 0.12 mm in grain thickness on average as compared to NIL- qGT3.1 . Similarly, NIL- qGL3.4 increased the length of each grain by 0.47 mm on average as compared to NIL- qGL3.4 . Taken together, these results would be of great use in breeding rice cultivars with desirable grain shape. [ABSTRACT FROM AUTHOR]

Abiotic stresses such as salinity, iron toxicity, and low temperatures are the main limiting factors of rice ( Oryza sativa L.) yield. The elucidation of the genes involved in responses to these stresses is extremely important to understand the mechanisms that confer tolerance, as well as for the development of cultivars adapted to these conditions. In this study, the RNA-seq technique was used to compare the transcriptional profile of rice leaves (cv. BRS Querência) in stage V3, exposed to cold, iron, and salt stresses for 24 h. A range of 41 to 51 million reads was aligned, in which a total range of 88.47 to 89.21 % was mapped in the reference genome. For cold stress, 7905 differentially expressed genes (DEGs) were observed, 2092 for salt and 681 for iron stress; 370 of these were common to the three DEG stresses. Functional annotation by software MapMan demonstrated that cold stress usually promoted the greatest changes in the overall metabolism, and an enrichment analysis of overrepresented gene ontology (GO) terms showed that most of them are contained in plastids, ribosome, and chloroplasts. Saline stress induced a more complex interaction network of upregulated overrepresented GO terms with a relatively low number of genes compared with cold stress. Our study demonstrated a high number of differentially expressed genes under cold stress and a greater relationship between salt and iron stress levels. The physiological process most affected at the molecular level by the three stresses seems to be photosynthesis. [ABSTRACT FROM AUTHOR]

Soil contamination with toxic heavy metals (such as Cd or Zn) is becoming a serious problem worldwide because of the rapid development of social economy. Silicon plays a substantial role in alleviating heavy metal toxicity in crop plants. In this study, two rice varieties, Feng-Hua-Zhan and Hua-Hang-Si-Miao, were chosen to determine the effects of Si application on root morphological traits, cell structure and exudates of rice roots under Cd and/or Zn stress. Single or combined applications of Cd and Zn resulted in significant reduction of total root length, root surface area, root volume, average root diameter and root activity. However, 1.5 mM Si addition reversed these negative effects. Transmission electron microscopy observations showed that rice root cortex cells were heavily damaged under Cd and/or Zn stress for both two varieties, whereas Si addition resulted in improved cell structure integrity. In addition, lower levels of oxalic, acetic, tartaric, maleic and fumaric acids in root exudates were observed for Feng-Hua-Zhan under Cd and/or Zn stress, but addition of Si increased the acid levels. For Hua-Hang-Si-Miao, heavy metal treatments significantly reduced oxalic and fumaric acid levels and increased acetic, tartaric and maleic acid levels, whereas Si treatment showed opposite results. The above results indicated that Si could ameliorate the toxicity of heavy metals (Cd and Zn) for rice which resulted in improving root traits, cell structure and influencing root exudates. [ABSTRACT FROM AUTHOR]

In rice ( Oryza sativa L.), damage from diseases such as brown spot, caused by Bipolaris oryzae, and bacterial seedling rot and bacterial grain rot, caused by Burkholderia glumae, has increased under global warming because the optimal temperature ranges for growth of these pathogens are relatively high (around 30 °C). Therefore, the need for cultivars carrying genes for resistance to these diseases is increasing to ensure sustainable rice production. In contrast to the situation for other important rice diseases such as blast and bacterial blight, no genes for complete resistance to brown spot, bacterial seedling rot or bacterial grain rot have yet been discovered. Thus, rice breeders have to use partial resistance, which is largely influenced by environmental conditions. Recent progress in molecular genetics and improvement of evaluation methods for disease resistance have facilitated detection of quantitative trait loci (QTLs) associated with resistance. In this review, we summarize the results of worldwide screening for cultivars with resistance to brown spot, bacterial seedling rot and bacterial grain rot and we discuss the identification of QTLs conferring resistance to these diseases in order to provide useful information for rice breeding programs. [ABSTRACT FROM AUTHOR]

Purpose: Previous studies showed that rapeseed cake increased rice grain yields and significantly lowered the heavy metal concentrations in the brown rice. The pH, dissolved organic carbon (DOC), and their dynamic changes in the soil solution have been seldom considered at different crop growth stages after organic amendments. Thus, the aim of the present study was to investigate the dynamic changes of soil solution and the mechanisms by which rapeseed cake (RSC) immobilized Cd and Cu in the soil-rice system. Materials and methods: A glasshouse pot experiment lasting 5 months during the rice ( Oryza sativa L.) growth season was carried out to ascertain the effects of three organic amendments (organic carbon material (OCM), RSC, and pig manure PM) on the growth and heavy metals uptake of rice at heavy metals mixed contaminated paddy soil. Several items were determined including pH, organic matter content, available P and K in soil, and total N, P, K, Cd, Cu, and Zn in the contaminated soil and amendments. Total and CaCl-extractable Cd, Cu, and Zn in different parts of rice crop in addition to pH, dissoluble organic carbon, and total Cd, Cu, Zn, and N in the soil solution were determined. Results and discussion: After application of RSC and PM to this contaminated soil, the DOC concentration in the soil solution from pre-tillering to booting stage increased, and then soil soluble heavy metal concentrations declined; thus, bioavailability declined result in the decreasing of Cd and Cu concentrations in the brown rice. RSC contains higher amounts of nitrogen compounds than OCM and PM, and the decomposition products of RSC increase dissolved organic nitrogen (DON) in the soil solution at tillering stages. The application of RSC reduced soil solution heavy metal concentrations at pre-tillering and tillering stages when rice crop was sensitive to heavy metal stress and resulted in higher grain yield and lower Cd and Cu concentrations in brown rice. The decline of heavy metal concentration in soil solution resulted from the adsorption, complexation, and precipitation reactions by the decomposition products. Conclusions: In summary, the application of RSC resulted in a rise of DOC and DON concentration in the soil solution of rice crop which reduced heavy metal concentrations in soil solution and lowered the heavy metals bioavailability. Our results suggest that RSC was effective in immobilizing metals in soil and alleviation of their toxicity to rice crop, and thus can be used to amend the Cd- and Cu-contaminated soils. [ABSTRACT FROM AUTHOR]

Aluminum (Al) is a major constraint to crop productivity in acid soils, whereas water deficit severely limits crop production in arid and semi-arid regions of the world. The objective of the present study was to examine the effects of both stresses, Al excess and water deficit, individually and in combination on the production of the reactive oxygen species (ROS) superoxide anion (O˙), hydrogen peroxide (HO), hydroxyl radical, and lipid peroxidation and the activity of antioxidant enzymes superoxide dismutase (SOD), catalase (CAT), and guaiacol peroxidase (GPX) in the seedlings of two rice ( Oryza sativa L.) cvs. Malviya-36 (sensitive to water deficit and Al) and Vandana (tolerant to water deficit and Al). When 15-day grown seedlings were exposed to water deficit (created with 15 % polyethylene glycol, PEG-6000) or Al (1 mM AlCl) treatment or both treatments together for 24-72 h, the lengths and fresh weights of root/shoot declined in the seedlings of the sensitive cultivar, whereas in the tolerant seedlings, either little or insignificant decline in these parameters was observed due to the treatments. Biochemical determinations and histochemical studies revealed that under a similar level of water deficit, Al, or combined treatment, seedlings of sensitive cultivar showed a higher level of production of O˙, HO, hydroxyl radical, and lipid peroxides compared to the tolerant seedlings. Seedlings of tolerant cultivars, both in roots and shoots, had constitutively higher activity levels of antioxidative enzymes SOD, CAT, and GPX and showed a greater increase in activity under water deficit or Al treatment alone or in combination compared to the similarly treated seedlings of sensitive cultivar. Our results suggest that a lower constitutive level of ROS and a high antioxidative enzyme capacity are associated with tolerance to both water deficit and Al excess in rice seedlings. [ABSTRACT FROM AUTHOR]

Zinc (Zn) is an important micronutrient for the physiology of plants. It is poorly available to the plants in soil solution. A pot experiment was conducted to evaluate effectiveness of various Zn application methods on key enzyme activities and protein content of two contrasting rice genotypes viz., PD16 (Zn efficient) and NDR359 (Zn inefficient). The treatments were, control (0 mg Zn kg soil), soil application (5 mg Zn kg soil), foliar application (0.5 % ZnSO + 0.25 % lime at 30, 60 and 90 days after transplanting), soil (5 mg Zn kg soil) + foliar application of 0.5 % ZnSO + 0.25 % lime at 30, 60 and 90 days after transplanting. Among all the methods tested soil+foliar application of Zn fertilizers was found most effective in increasing superoxide dismutase (SOD) and carbonic anhydrase (CA) activities as well as chlorophyll and protein content in both the rice varieties. NDR359, showed higher enzyme activities and more chlorophyll content in leaves than PD16, when Zn was applied either through foliar spray alone or in soil along with foliar application. Regarding the protein content in grains, PD16 showed higher protein content than NDR359, thus showed better translocation of Zn from leaves to grains. [ABSTRACT FROM AUTHOR]

Background and aims: Rice contaminated by mercury [Hg, especially methylmercury (MeHg)] has given rise to great concern in recent years. This study investigated variations in ecophysiological features (anatomy, organic acid secretions, Fe plaque formation) of rice roots and their effects on the uptake and accumulation of total mercury (THg) and MeHg by rice plants. Methods: The development of apoplastic barriers in roots of four rice cultivars was observed by a hydroponic experiment while the concentrations of five organic acids, Fe and THg in Fe plaque were determined using a rhizobag trial with different Hg treatments. Results: Cultivars with low Hg accumulation tended to develop strong apoplastic barriers in endodermis, secrete less organic acids and form more Fe plaque on root surfaces and in rhizosphere. Fe concentrations were positively correlated with THg concentrations in rhizosphere's Fe plaque (R = 0.60, P < 0.01), whereas the latter was negatively correlated with bioavailable Hg concentrations in rhizosphere (R = 0.40, P < 0.01). Conclusions: Organic acids and Fe plaque formation of rice roots play important roles in Hg uptake and accumulation. The development of apoplastic barriers in root restricts Hg uptake but the significance of suberin deposition on Hg uptake needs further investigations. [ABSTRACT FROM AUTHOR]

The goal of this work was to establish a transformation pipeline for upland Curinga rice ( Oryza sativa L. ssp. japonica) with bar gene selection employing bialaphos and phosphinothricin as selection agents. The following genes of interest: AtNCED3, Lsi1, GLU2, LEW2, PLD- alpha, DA1, TOR, AVP1, and Rubisco were cloned into the binary vector p7i2x-Ubi and were transferred into Agrobacterium strain EHA 105. Embryogenic calli derived from the mature embryos were transformed, and transgenic cells and shoots were selected on the medium supplemented with bialaphos or phosphinothricin (PPT) using a stepwise selection scheme. Molecular analyses were established using polymerase chain reaction and Southern blot for the bar gene and the NOS terminator. Overall, 273 putative transgenic plants were analyzed by Southern blot with 134 events identified. In total, 77 events had a single copy of the transgene integrated in the plant genome while 29 events had two copies. We tested backbone integration in 101 transgenic plants from all constructs and found 60 transgenic plants having no additional sequence integrated in the plant genome. The bar gene activity was evaluated by the chlorophenol red test and the leaf painting test using phosphinothricin with several transgenic plants. The majority of T0 plants carrying the single copy of transgene produced T1 seeds in the screen house. [ABSTRACT FROM AUTHOR]

Aims: Induction of lignin biosynthesis is an adaptive response of plants subjected to many abiotic stresses. In this study, we examined the response of lignin biosynthesis to copper (Cu) stress, with a particular focus on the regulatory mechanism. Methods: We performed a transcriptomic analysis of rice ( Oryza sativa L.) roots, and the microarray data on lignin biosynthesis pathway genes were corroborated by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis. Physiological analyses of rice seedlings treated with Cu(II) sulfate (CuSO) were used to confirm the relationship between excess Cu and lignin biosynthesis. In addition, we examined the role of hydrogen peroxide (HO) in Cu-induced lignin biosynthesis through pretreatments with an NADPH oxidase inhibitor (diphenyleneiodonium, DPI) and a HO scavenger (dimethylthiourea, DMTU). Results: Lignin biosynthesis pathway genes were upregulated under Cu stress. The lignin content of rice roots increased significantly with increasing concentrations and durations of Cu treatment; elevations in root lignin content were correlated with marked inhibitions in root growth. Pretreatments with DPI and DMTU inhibited the activities of Cu-induced lignin polymerization enzymes (peroxidase, POD and laccase, LAC) and lignin accumulation in rice roots. Conversely, exogenous HO increased the root lignin content. Conclusions: Rice roots under Cu stress accumulate lignin through enhanced polymerization of lignin monolignol, a mechanism that requires Cu stress induced HO. [ABSTRACT FROM AUTHOR]

Background and Aims: Mercury (Hg) pollution in paddy fields and rice has aroused great concern in recent years. This study investigated the dynamic changes of radial oxygen loss (ROL) and Fe plaque formation on roots, and their effects on Hg accumulation in rice plants. Methods: A rhizobag experiment was conducted to study temporal variations and correlations between ROL (amounts and rates), Fe plaque formation, total Hg (THg) and methylmercury (MeHg) in plant tissues and in plaque of four rice cultivars during six growth stages. Results: ROL amounts and Fe plaque formation increased from tillering to reproductive stages, then ROL amounts gradually decreased until maturation stage, whereas Fe plaque remained relatively stable. ROL rates continued to decline during the entire growth period. Both ROL amounts and Fe concentrations in plaque were positively correlated with THg concentrations in the plaque, whereas negatively correlated with THg in straw and brown rice. However, there were no significant relationships between ROL, Fe in plaque and MeHg in plaque and in plant tissues. Conclusions: ROL has great effects on THg but not MeHg accumulation in rice plants. Rice cultivars with higher ROLs tend to have a greater ability to reduce THg accumulation in brown rice. [ABSTRACT FROM AUTHOR]

To produce agronomically competitive rice with nutritionally superior, environmentally safe phytic acid (PA) levels, hairpin RNA (hpRNA)- and artificial microRNA (amiRNA)-mediated gene silencing approaches were explored to reduce both myo-inositol kinase gene ( OsMIK) expression and PA accumulation in rice seeds. hpRNA and amiRNA sequences targeted to OsMIK (hpMIK and amiMIK), under the control of a rice Ole18 promoter, were transformed into the rice cultivar Nipponbare. Fourteen and 21 independent transgenic events were identified containing the hpMIK and amiMIK constructs, respectively, from which five stable homozygous transgenic lines of each were developed together with their null siblings. Southern blotting demonstrated transgene integration into the genome and quantitative real-time PCR showed that gene silencing was restricted to seeds. OsMIK transcripts were significantly reduced in both transgenic amiMIK and hpMIK seeds, which had PA levels reduced by 14.9-50.2 and 38.1-50.7 %, respectively, compared with their respective null siblings. There were no systematic significant differences in agronomic traits between the transgenic lines and their non-transgenic siblings, and no correlation between seed PA contents and decreased rates of seed germination and seedling emergence. The results of the present study suggest that Ole 18-driven OsMIK silencing via hpRNA and amiRNA could be an effective way to develop agronomically competitive low phytic acid rice. [ABSTRACT FROM AUTHOR]

The present investigation was carried out to evaluate 33 rice landrace genotypes for assessment of their salt tolerance at seedling stage. Growth parameters like root length, shoot length and plant biomass were measured after 12 days of exposure to six different levels of saline solution (with electrical conductivity of 4, 6, 8, 10, 12 or 14 dS m ). Genotypes showing significant interaction and differential response towards salinity were assessed at molecular level using 11 simple sequence repeats (SSR) markers, linked with salt tolerance quantitative trait loci. Shoot length, root length and plant biomass at seedling stage decreased with increasing salinity. However, relative salt tolerance in terms of these three parameters varied among genotypes. Out of the 11 SSR markers RM8094, RM336 and RM8046, the most competent descriptors to screen the salt tolerant genotypes with higher polymorphic information content coupled with higher marker index value, significantly distinguished the salt tolerant genotypes. Combining morphological and molecular assessment, four lanraces viz. Gheus, Ghunsi, Kuthiahara and Sholerpona were considered as true salt tolerant genotypes which may contribute in greater way in the development of salt tolerant genotypes in rice. [ABSTRACT FROM AUTHOR]

Interactive effects of two heavy metal pollutants Cd and Pb in the growth medium were examined on their uptake, production of reactive oxygen species (ROS), induction of oxidative stress and antioxidative defence responses in Indica rice ( Oryza sativa L.) seedlings. When rice seedlings in sand culture were exposed to 150 μM Cd (NO) or 600 μM Pb (CHCOO) individually or in combination for 8-16 days, a significant reduction in root/shoot length, fresh weight, relative water content, photosynthetic pigments and increased production of ROS (O˙ and HO) was observed. Both Cd and Pb were readily taken up by rice roots and localisation of absorbed metals was greater in roots than in shoots. When present together in the growth medium, uptake of both the metals Cd and Pb declined by 25-40 %. Scanning electron microscope (SEM) imaging of leaf stomata revealed that Pb caused more distortion in the shape of guard cells than Cd. Dithizone staining of roots showed localisation of absorbed Cd on root hairs and epidermal cells. Both Cd and Pb caused increased lipid peroxidation, protein carbonylation, decline in protein thiol and increase in non-protein thiol. The level of reduced forms of non-enzymic antioxidants glutathione (GSH) and ascorbate (AsA) and their redox ratios (GSH/AsA) declined, whereas the activities of antioxidative enzymes superoxide dismutase (SOD) and guaiacol peroxidase (GPX) increased in metal treated seedlings compared to controls. In-gel activity staining also revealed increased intensities of SOD and GPX isoforms with metal treatments. Catalase (CAT) activity increased during early days (8 days) of metal exposure and declined by 16 days. Results suggest that oxidative stress is an important component in expression of Cd and Pb toxicities in rice, though uptake of both metals gets reduced considerably when present together in the medium. [ABSTRACT FROM AUTHOR]

Effects of perchlorate stress on the growth and physiological characteristics of rice ( Oryza sativa L.) were studied in controlled water culture experiments. Perchlorate stress resulted in varied patterns of biomass allocation to O. sativa organs (roots, stems, and leaves). When stressed with higher perchlorate concentrations, the proportion of root biomass was higher, stem biomass was invariant, while leaf biomass was lower. Coefficients of variation in biomass of different organs followed the order leaf > stem > root, indicating that leaf growth has a higher sensitivity to perchlorate. Compared to the control, the chlorophyll and protein content of leaves and root vigor were lower, whereas malondialdehyde (MDA) content and catalase (CAT) activity were higher and related to perchlorate concentration and duration of stress. Superoxide dismutase (SOD) activity was initially high and then decreased markedly during the experiment, while peroxidase (POX) activity in perchlorate-treated rice was always higher than the POX activity of the control. POX was the most sensitive antioxidant enzyme to perchlorate stress. Correlation analysis showed a positive correlation between SOD activity and the fresh weight of the whole plant, and negative correlation with MDA content. The results suggest that perchlorate could induce oxidative stress and oxidative damage may be the main cause of physiological damage and growth inhibition in rice plants under perchlorate stress. [ABSTRACT FROM AUTHOR]

CEBiP, a plasma membrane-localized glycoprotein of rice, directly binds with chitin elicitors (CE), and has been identified as a receptor for CE by using CEBiP-RNAi rice cells. To further clarify the function of CEBiP, we produced CEBiP-disrupted rice plants by applying an efficient Agrobacterium-mediated gene-targeting system based on homologous recombination, which has recently been developed for rice. Homologous recombination occurred at the CEBiP locus in ~0.5 % of the positive/negative selected calli. In the self-pollinated next generation, it was confirmed that the first exon of CEBiP was replaced with the hygromycin selection cassette as designed, and that the expression of CEBiP was completely deficient in homozygous cebip lines. Affinity-labeling analysis using biotinylated N-acetylchitooctaose demonstrated that CEBiP is the major CE-binding protein in rice cultured cells and leaves, which was consistent with the result that the response to CE in cebip cells was greatly diminished. Nevertheless, we observed a significant decrease in disease resistance against Magnaporthe oryzae, the causal agent of rice blast disease, only when the cebip leaf sheaths were inoculated with a weakly virulent strain, suggesting that CE perception during the infection process of M. oryzae is limited. The response to peptidoglycan and lipopolysaccharides in cebip cells was not affected, strongly suggesting that CEBiP is a CE-specific receptor. [ABSTRACT FROM AUTHOR]

Plant growth and productivity are greatly affected due to changes in the environmental conditions. In the present investigation, the interactive effects of two important abiotic stresses, i.e., water deficit and Al toxicity, were examined in the seedlings of two rice ( Oryza sativa L.) cvs. Malviya-36 (water deficit/Al sensitive) and Vandana (water deficit/Al tolerant). When 15 days grown seedlings were exposed to water deficit (created with 15 % polyethylene glycol 6000) or Al (1 mM AlCl) treatment or both the treatments together for 48 h, the lengths of root/shoot, relative water content, and chlorophyll greatly declined in the seedlings of the sensitive cultivar, whereas in the tolerant seedlings, either little or insignificant decline in these parameters was observed due to the treatments. Seedlings subjected to water deficit or Al treatment alone or in combination showed increased intensity of the isoenzyme activity bands of superoxide dismutase (SOD), guaiacol peroxidase (GPX), and ascorbate peroxidase (APX) in in-gel activity staining studies. Water deficit caused decrease in intensity of catalase (CAT) activity bands; however, when seedlings were exposed to AlCl alone or in combination with water deficit, the intensity of the CAT isoforms increased in both the rice cultivars. The level of expression of the activity bands of SOD, CAT, GPX, and APX was always higher in the seedlings of tolerant cv. Vandana compared to the sensitive cv. Malviya-36 under both controls as well as stress treatments. Higher intensity of isozymes representing higher activity levels of antioxidative enzymes in the rice seedlings and their further increase under water deficit, Al exposure, or in combination of both the stresses appears to serve as useful marker for specifying a combination of water deficit and Al tolerance in rice. [ABSTRACT FROM AUTHOR]

This study quantified Cd, Pb, and Cu content, and the soil-plant transfer factors of these elements in rice paddies within Cam Pha, Quang Ninh province, northeastern Vietnam. The rice paddies are located at a distance of 2 km from the large Coc Sau open-pit coal mine. Electron microprobe analysis combined with backscattered electron imaging and energy-dispersive spectroscopy revealed a relatively high proportion of carbon particles rimmed by an iron sulfide mineral (probably pyrite) in the quartz-clay matrix of rice paddy soils at 20-30 cm depth. Bulk chemical analysis of these soils revealed the presence of Cd, Cu, and Pb at concentrations of 0.146 ± 0.004, 23.3 ± 0.1, and 23.5 ± 0.1 mg/kg which exceeded calculated background concentrations of 0.006 ± 0.004, 1.9 ± 0.5, and 2.4 ± 1.5 mg/kg respectively at one of the sites. Metals and metalloids in Cam Pha rice paddy soils, including As, Cd, Cr, Cu, Hg, Mn, Ni, Pb, and Zn, were found in concentrations ranging from 0.2 ± 0.1 to 140 ± 3 mg/kg, which were in close agreement with toxic metal contents in mine tailings and Coc Sau coal samples, suggesting mining operations as a major cause of paddy soil contamination. Native and model Oryza sativa L. rice plants were grown in the laboratory in a growth medium to which up to 1.5 mg/kg of paddy soil from Cam Pha was added to investigate the effects on plant growth. A decrease in growth by up to 60 % with respect to a control sample was found for model plants, whereas a decrease of only 10 % was observed for native (Nep cai hoa vang variety) rice plants. This result suggests an adaptation of native Cam Pha rice plants to toxic metals in the agricultural lands. The Cd, Cu, and Pb contents of the native rice plants from Cam Pha paddies exceeded permitted levels in foods. Cadmium and Pb were highest in the rice plant roots with concentrations of 0.84 ± 0.02 and 7.7 ± 0.3 mg/kg, suggesting an intake of these metals into the rice plant as shown, for example, by Cd and Pb concentrations of 0.09 ± 0.01 and 0.10 ± 0.04 mg/kg respectively in the rice grain endosperm. The adaptation of native rice plants, combined with bioaccumulation ratios of 1 ± 0.6 to 1.4 ± 0.7 calculated for Cd transfer to the rice grain endosperm, and maximum Cd transfer factors of 4.3 ± 2.1 to the plant roots, strongly suggest a continuous input of some toxic metals from coal-mining operations to agricultural lands in the region of Cam Pha. In addition, our results imply a sustained absorption of metals by native rice plant varieties, which may lead to metal accumulation (e.g., Cd) in human organs and in turn to severe disease. [ABSTRACT FROM AUTHOR]

In both yeast and mammals, the major constituent of the endosomal sorting complex required for transport-II (ESCRT-II) is the VPS22/EAP30 protein, which plays an important role in ubiquitin-mediated degradation of membrane proteins through the multivesicular body pathway. However, the functions of ESCRT-II subunits in plants are largely unknown. In this work, we report the genetic analysis and phenotypic characterization of mutants in OsVPS22 gene, which encodes a functional VPS22 homolog in rice. On the basis of a collection of T-DNA lines, we identified a T-DNA insertion mutant, which showed abnormal segregation ratios; we then found that the T-DNA insertion is located within the sixth intron of the OsVPS22 gene. Compared with the wild type, this vps22 mutant exhibited seedling lethality and severe reduction in shoot and root growth. In addition, the vps22 mutant had a chalky endosperm in the grain. In summary, our data suggest that OsVPS22 may be required for seedling viability and grain filling in rice, thus providing a valuable resource for further exploration of the functions of the ESCRTing machinery in plants. [ABSTRACT FROM AUTHOR]

Lemma and palea are unique floral structures found only in Poaceae, and are responsible for protecting the inner floral organs and kernels from environmental stresses. However, the mechanism underlying specification of their morphology remains unclear. In this study, we characterized a rice mutant, beak like spikelet1 ( bls1), which specifically affects development of the lemma and palea. In bls1 mutant, floral-organ identity and floral-organ patterning are normal, and the defects occur at the stage of the lemma and palea expansion, whereas the other aspects of floral architecture and form are not affected. We isolated BLS1 by positional cloning and found that it encodes a protein with a conserved domain of unknown function. BLS1 is expressed strongly in young inflorescence, specifically the young lemmas and paleas of spikelets. Subcellular localization analysis showed that BLS1 is localized in the nucleus. Expression of the AP1-like and SEP-like floral homeotic genes were not changed in the bls1 mutant. Our study suggested that BLS1 is required for lateral development of the lemma and palea and does not function at stages of floral-organ initiation and patterning. [ABSTRACT FROM AUTHOR]

Grain weight, one of the three major components of rice yield, is largely determined by grain size, which is controlled by quantitative trait loci (QTLs). In a previous study, we identified qGS5 as a major QTL for grain width. Here, we report our identification of two more major grain-size QTLs ( qGL3 and qGW2a) by using a recombinant inbred line (RIL) population from a cross of two indica varieties, 'Zhenshan 97' and 'SLG'. To investigate the contribution of the three grain-size QTLs to final grain weight, we developed near-isogenic lines (NILs) NIL- qGL3, NIL- qGW2a, and NIL- qGS5 and used these to build the combined QTLs-NIL in the genetic background of 'Zhenshan 97' by marker-assisted selection and conventional backcrossing, respectively. A BCF population of 957 individuals was developed from the combined QTLs-NIL for further study of the genetic control of grain size. The QTL analysis revealed that qGW2a and qGL3 played more important roles in grain weight gain than qGS5. All three QTLs showed additive effects with respect to grain weight, with no interaction. These results clearly indicate that pyramiding of major grain-size QTLs is a useful approach for improving rice yield. [ABSTRACT FROM AUTHOR]

Rice blast is one of the most serious diseases in rice ( Oryza sativa L.) worldwide. Jin 23B is the maintainer line, a parent for a number of hybrid rice varieties used widely in China. However, Jin 23B is highly susceptible to rice blast. In this study, Pi1, Pi2, and D12 were introgressed to improve the blast resistance of Jin 23B and its derived hybrids, Jinyou 402 and Jinyou 207, by marker-assisted selection (MAS). The improved Jin 23B, which carried single, two, and three genes, were evaluated for their resistance to rice blast using natural inoculation methods in disease nursery of Xianfeng, Hubei, China. The results showed that, the greater the number of genes contained in the improved Jin 23B and hybrids, the higher the resistance to rice blast. Pi1, Pi2, and D12 showed a strong dosage effect on the resistance to blast in the hybrid background during the entire growth duration in the field condition, being very useful for breeding blast-resistant hybrids. The result of examining agronomic traits showed that the improved Jin 23B and its derived hybrid rice were taller than or similar to controls, when there was no disease stress. [ABSTRACT FROM AUTHOR]

The production of secondary metabolites and biomass of plants may be altered by coexistence and competition. Rice has coexisted with barnyardgrass in paddy systems for centuries and represents a model system for understanding plant-plant interactions. Despite increasing knowledge of allelochemicals produced and released by rice involved in coexistence of these two species, relatively little is known about the role and production of beneficial chemicals of rice in response to competing barnyardgrass. The purpose of this study was to quantify the growth-stimulating allantoin (5-ureidohydantoin) and its effect on barnyardgrass growth in a rice-barnyardgrass system. In this system, rice produced and released allantoin but barnyardgrass did not. The production of allantoin by rice responded to competition from barnyardgrass, and its concentration varied among rice cultivars tested. At 1:1 barnyardgrass and rice mixture proportion, allantoin concentration in allelopathic cultivars was obviously lowered by competing barnyardgrass, while no significant variation of allantoin concentration was observed in non-allelopathic cultivars. Barnyardgrass biomass was reduced in mixed-culture with rice cultivars, in particular, allelopathic cultivars. There was a positive relationship between allantoin concentration in rice cultivars and barnyardgrass biomass. Furthermore, allantoin stimulated the growth of barnyardgrass once released from rice or added to soil. The results suggest that rice plants of allelopathic cultivars appear to be able to detect the presence of competing barnyardgrass and respond by decreasing production of growth-stimulating allantoin, regulating the growth of barnyardgrass. In this manner, given rice cultivars may alleviate the competition of barnyardgrass and provide greater benefit to their own growth. [ABSTRACT FROM AUTHOR]

A hydroponic experiment was conducted to determine the possible effect of exogenous glutathione (GSH) in alleviating chromium (Cr) stress through examining plant growth, chlorophyll contents, antioxidant enzyme activity, and lipid peroxidation in rice seedlings exposed to Cr toxicity. The results showed that plant growth and chlorophyll content were dramatically reduced when rice plants were exposed to 100 μM Cr. Addition of GSH in the culture solution obviously alleviated the reduction of plant growth and chlorophyll content. The activities of some antioxidant enzymes, including superoxide dismutase, catalase (CAT) and glutathione reductase in leaves, and CAT and glutathione peroxidase in roots showed obvious increase under Cr stress. Addition of GSH reduced malondialdehyde accumulation and increased the activities of these antioxidant enzymes in both leaves and roots, suggesting that GSH may enhance antioxidant capacity in Cr-stressed plants. Furthermore, exogenous GSH caused significant decrease of Cr uptake and root-to-shoot transport in the Cr-stressed rice plants. It can be assumed that GSH is involved in Cr compartmentalization in root cells. [ABSTRACT FROM AUTHOR]

Root border cells (RBCs), which are generated during plant growth and surround the root cap, and iron plaque (IP), ubiquitously formed on the root surfaces of rice, are known to alleviate aluminum (Al) toxicity. To verify the interactive effects of IP and RBCs on ameliorating Al toxicity, two rice cultivars differing in Al resistance were used to compare Al tolerance between cultivars. Additionally, root elongation, Al uptake and RBCs viability were measured as indicators of the effects of Al. The amounts of DCB-extractable Fe and Al on the root surfaces were much higher in the presence of IP than the absence. IP presence significantly decreased Al-induced inhibition of root elongation and Al contents in roots and root tips. The removal of RBCs from the root tips caused a more severe inhibition of root elongation and a higher Al accumulation in rice roots and root tips. Furthermore, root growth inhibition and Al contents in roots and root tips were significantly lower in roots with a combination of IP and RBCs than in roots with IP or RBCs only. The formation of IP on the root surface maintained higher RBCs viability and depressed mucilage exudation in an Al-tolerant rice cultivar. The results suggest that both IP and RBCs ameliorate Al toxicity, and IP has a greater capacity for Al resistance. The combination of IP and RBCs exhibited a synergistic effect associated with Al resistance. [ABSTRACT FROM AUTHOR]

The brown planthopper (BPH) is the most devastating insect pest in rice-producing areas. Shanyou 63 has become a widely cultivated hybrid in China over the last two decades; however, this line has become increasingly susceptible to bacterial blight (BB), blast, and BPH, resulting in a rapid decline in its use in rice production. In this study, a molecular marker-assisted selection (MAS) introgression of Bph14 and Bph15 was performed to improve the BPH resistance of Minghui 63 and its derived hybrids such as Shanyou 63. The effect of pyramiding genes was then comprehensively evaluated using three tests that comprised seedbox screening, feeding rate, and antixenosis for settling in the field. The results showed that the improved hybrids containing a single BPH resistance gene showed enhanced resistance (lower resistance score, honeydew weight and number of BPH settling) compared to conventional hybrids, while pyramiding two genes provided even higher resistance. Moreover, both Bph14 and Bph15 are partial dominance genes, and have a strong dosage effect on the resistance to BPH in the hybrid background, which is useful for breeding BPH-resistant hybrids. Field trial data demonstrated that yields of improved hybrid rice were higher than or similar to the control (Shanyou 63) under natural field conditions. These improved versions could be used in breeding programs for 'green super rice.' [ABSTRACT FROM AUTHOR]

Transgressive segregation is a common phenomenon in plant species. In this study, transgressive segregation for kilo-grain weight (KGW) was observed in a recombinant inbred line (RIL) population derived from the cross between an indica variety, Teqing, and a wide compatible japonica variety, 02428, in three environments. A genetic linkage map with 154 single sequence repeat markers (SSR) was developed. Effects on KGW of quantitative trait loci (QTLs), digenetic epistasis, and their environmental interaction (QE) were determined using a mixed linear model approach. 13 QTLs with additive effects and 8 digenetic interactions involving 16 loci were identified. Eight QTLs were involved in interactions. Two QTLs and one epistasis showed QE. 30.0 and 14.0% of variation was explained by the additive effects and epistasis, respectively, which were much greater than the 4.4% of variation explained by QE. According to the model used, predicted KGW values of extreme phenotypes in the RIL population were very close to their observed values. This indicated that complementary action of additive QTLs and epistasis can adequately account for the important genetic bases of transgressive segregation for KGW in the rice RIL population. [ABSTRACT FROM AUTHOR]

The effects of arsenite treatment on generation of reactive oxygen species, induction of oxidative stress, response of antioxidative system, and synthesis of phytochelatins were investigated in two indica rice ( Oryza sativa L.) cvs. Malviya-36 and Pant-12 grown in sand cultures for a period of 5-20 days. Arsenite (AsO; 25 and 50 μM) treatment resulted in increased formation of superoxide anion (O), elevated levels of HO and thiobarbituric acid reactive substances, showing enhanced lipid peroxidation. An enhanced level of ascorbate (AA) and glutathione (GSH) was observed irrespective of the variation in the level of dehydroascorbate (DHA) and oxidized glutathione (GSSG) which in turn influenced redox ratios AA/DHA and GSH/GSSG. With progressive arsenite treatment, synthesis of total acid soluble thiols and phytochelatins (PC) increased in the seedlings. Among antioxidative enzymes, the activities of superoxide dismutase (EC 1.15.1.1), catalase (EC 1.11.1.6), total ascorbate peroxidase (APX, EC 1.11.1.11), chloroplastic ascorbate peroxidase, guaiacol peroxidase (EC 1.11.1.7), monodehydroascorbate reductase (EC 1.6.5.4), and glutathione reductase (EC 1.6.4.2) increased in arsenite treated seedlings, while dehyroascorbate reductase (EC 1.8.5.1) activity declined initially during 5-10 days and increased thereafter. Results suggest that arsenite treatment causes oxidative stress in rice seedlings, increases the levels of many enzymatic and non-enzymatic antioxidants, and induces synthesis of thiols and PCs, which may serve as important components in mitigating arsenite-induced oxidative damage. [ABSTRACT FROM AUTHOR]

In this study, a F population derived from the cross between deep-rooted variety 'Moroberekan' with shallow-rooted variety 'IR20' were used to identify and validate of SSR markers associated with root morphological traits. The F lines were divided into two groups. In the first group, 152 seedling having minimum of four tillers were chosen and separated into four plantlets to plant them in polyvinyl chloride pipes for root study under well-watered (WW) condition at maturity stage. The lines were genotyped using SSR markers. QTLs for maximum root length (MRL) and root dry weight showed co-segregation with RM472, RM7 and RM201. The same material was forwarded to next generation (F) to validate the linked markers under both WW and low-moisture stress (LMS) conditions. These three markers were associated consistently with MRL across generations. In the second group, 1240 F plants were forwarded to F using SSD breeding method to test the effectiveness of the marker-assisted selection (MAS) method for drought resistant. The high performing genotypic group was significantly superior to low performing genotypic group for MRL, grain yield, root volume, root dry weight and root number, indicating the efficiency of MAS for root-related traits under LMS. Comparing MAS with farmer selection in F, the results showed that MAS group means were significantly different from farmer group means for MRL, root volume, root dry weight and root number. Thus, MAS was combined with participatory selection to select five high-yielding and deep rooted promising lines. Identification of stable QTL for root morphological traits under WW and LMS conditions can aid in MAS and to introduce them into varieties with good yield potential and accepted by farmer. [ABSTRACT FROM AUTHOR]

The effects of Al2(SO4)3·18H2O on growth of root and apical root cells were studied in seedlings of rice cultivars differing in Al resistance including I Kong Pao and Aiwu (Al-sensitive) and IRAT 112 and IR6023-10-1-1 (Al-resistant). Inhibition of root growth was a typical effect of Al, and the extent of the inhibition depended on both cultivar and Al concentration. Al impaired the activity of the root meristem as indicated by reductions in its size, mitotic activity and the diameter of the meristematic cell nucleoli. Cell size in the elongation zone of the root was also reduced by Al. The reliability of the haematoxylin staining method to classify rice cultivars according to their Al-sensitivity failed to discriminate the Al-resistant IR6023-10-1-1 cultivar from the two sensitive cultivars. The results are discussed in relation to the Al resistance mechanisms operating in rice. [ABSTRACT FROM AUTHOR]

Segmental duplication is particularly frequent within plant genomes and the ability of the original single-copy gene to gain a new function for the change of regulatory elements is one of the prominent consequences of duplication. Thus, it is important to study the pattern of conserved non-coding sequence (CNS) between paralogous genes. We report the result of a survey of CNSs among paralogous regions in rice ( Oryza sativa L.), as well as the comparison of CNS dataset between rice and Arabidopsis thaliana. Some common properties, such as the change of A + T content near the CNS boundaries and CNS are enriched in regulatory genes, were observed. However, the content of CNSs differs between rice and Arabidopsis, and it is interesting that the rice metabolic network includes both CNS-poor and CNS-rich genes, which indicated a fine-tuned metabolic network presents in rice. [ABSTRACT FROM AUTHOR]

Mutation techniques have been used for generating genetic variation and breeding new varieties during the past decades. However, the skepticism has also persisted during the course on the sole mutational origin of genetic variation in mutated populations. We addressed this issue using three unique rice genetic lines in this study. First, we confirmed that gamma rays had significant effect on the growth of M1 plants, leading to significant reduction of fertility, seed set and plant height at doses 200 Gy and above. Second, we proved that out-crossing derived genetic variants existed in M2 population (0.8%) and among selected putative mutants (0–33.3%), in addition to induced mutants. Third, we demonstrated that true induced mutant lines had identical microsatellite haplotypes to their parents. We proposed microsatellite assay as a method to exclude any genetic contaminants from induced mutants, with appropriate numbers for different levels of power based on reported microsatellite mutation rate and microsatellite polymorphic index. [ABSTRACT FROM AUTHOR]