Identification and characterisation of cold stress-related proteins in Oryza rufipogon at the seedling stage using label-free quantitative proteomic analysis.

In this study, label-free quantitative proteomics were used to study cold stress-related proteins in Dongxiang wild rice (Oryza rufipogon Griff., DWR) and cold sensitive cultivated rice 'Xieqingzao B'(Oryza sativa L. ssp. indica cv., XB). The results demonstrated the presence of 101 and 216 differentially expressed proteins (DEPs) were detected in DWR and XB, respectively, after cold stress. Bioinformatics analysis showed that DWR and XB differed significantly in their ability to scavenge reactive oxygen species (ROS) and regulate energy metabolism. Of the 101 DEPs of DWR, 46 DEPs related to differential expressed genes were also detected by transcriptome analysis. And 13 out of 101 DEPs were located in previous cold related quantitative trait loci (QTL). Quantitative real-time PCR analysis indicated that protein expression and transcription patterns were not similar in XB and DWR. Protein-protein interaction (PPI) network was constituted using the DEPs of DWR and XB, and the following three centre proteins were identified: Q8H3I3, Q9LDN2, and Q2QXR8. Next, we selected a centre protein and two of the 37 DEPs with high levels of differential expression (fold change ≥ 2) were used for cloning and prokaryotic expression. We found that Q5Z9Q8 could significantly improve the cold tolerance of Escherichia coli.

Unlocking the potential antioxidant and anti-inflammatory activities of Rhododendron molle G. Don.

Rhododendron molle G. Don is an important traditional Chinese medicinal plant, which has been applied to treat some inflammatory diseases. In the present study, ethanol extracts of R. molle flower (RFE) and leaf (RLE) were used for phytochemical, antioxidant and anti-inflammatory analysis. The antioxidant activity was investigated using the free radicals of 1,1-diphenyl-2-picrylhydrazyl (DPPH), hydroxyl radical (OH-)-scavenging activity, super oxide anion radical (O2.-)-scavenging activity and iron reducing power (FRAP). Production of nitric oxide (NO) was an indicator to evaluate the anti-inflammatory activity. The results showed that compared with RFE, RLE was more active against DPPH (56.66%), FRAP (51.29%) and hydroxyl radical (OH-) (69.66%) at 100µg/mL. In the same time, RLE and RFE had significant anti-inflammatory activity which could reduce nitrite production from 8.76µM to 5.08µM and 6.01µM, respectively. In addition, GC-MS analysis showed that 43 compounds were identified in R. molle. Among them, 11 compounds had antioxidant and 5 compounds had anti-inflammatory effect. Results showed that ethanol extracts of R. molle have significant antioxidant and anti-inflammatory activity. These results would be helpful for further investigation on the anti-inflammatory mechanism of R. molle.

Transcriptome analysis of phosphorus stress responsiveness in the seedlings of Dongxiang wild rice (Oryza rufipogon Griff.).

BACKGROUND: Low phosphorus availability is a major factor restricting rice growth. Dongxiang wild rice (Oryza rufipogon Griff.) has many useful genes lacking in cultivated rice, including stress resistance to phosphorus deficiency, cold, salt and drought, which is considered to be a precious germplasm resource for rice breeding. However, the molecular mechanism of regulation of phosphorus deficiency tolerance is not clear. RESULTS: In this study, cDNA libraries were constructed from the leaf and root tissues of phosphorus stressed and untreated Dongxiang wild rice seedlings, and transcriptome sequencing was performed with the goal of elucidating the molecular mechanisms involved in phosphorus stress response. The results indicated that 1184 transcripts were differentially expressed in the leaves (323 up-regulated and 861 down-regulated) and 986 transcripts were differentially expressed in the roots (756 up-regulated and 230 down-regulated). 43 genes were up-regulated both in leaves and roots, 38 genes were up-regulated in roots but down-regulated in leaves, and only 2 genes were down-regulated in roots but up-regulated in leaves. Among these differentially expressed genes, the detection of many transcription factors and functional genes demonstrated that multiple regulatory pathways were involved in phosphorus deficiency tolerance. Meanwhile, the differentially expressed genes were also annotated with gene ontology terms and key pathways via functional classification and Kyoto Encyclopedia of Gene and Genomes pathway mapping, respectively. A set of the most important candidate genes was then identified by combining the differentially expressed genes found in the present study with previously identified phosphorus deficiency tolerance quantitative trait loci. CONCLUSION: The present work provides abundant genomic information for functional dissection of the phosphorus deficiency resistance of Dongxiang wild rice, which will be help to understand the biological regulatory mechanisms of phosphorus deficiency tolerance in Dongxiang wild rice.

Transcriptome analysis of phosphorus stress responsiveness in the seedlings of Dongxiang wild rice (Oryza rufipogon Griff.)

Abstract Background: Low phosphorus availability is a major factor restricting rice growth. Dongxiang wild rice (Oryza rufipogon Griff.) has many useful genes lacking in cultivated rice, including stress resistance to phosphorus deficiency, cold, salt and drought, which is considered to be a precious germplasm resource for rice breeding. However, the molecular mechanism of regulation of phosphorus deficiency tolerance is not clear. Results: In this study, cDNA libraries were constructed from the leaf and root tissues of phosphorus stressed and untreated Dongxiang wild rice seedlings, and transcriptome sequencing was performed with the goal of elucidating the molecular mechanisms involved in phosphorus stress response. The results indicated that 1184 transcripts were differentially expressed in the leaves (323 up-regulated and 861 down-regulated) and 986 transcripts were differentially expressed in the roots (756 up-regulated and 230 down-regulated). 43 genes were up-regulated both in leaves and roots, 38 genes were up-regulated in roots but down-regulated in leaves, and only 2 genes were down-regulated in roots but up-regulated in leaves. Among these differentially expressed genes, the detection of many transcription factors and functional genes demonstrated that multiple regulatory pathways were involved in phosphorus deficiency tolerance. Meanwhile, the differentially expressed genes were also annotated with gene ontology terms and key pathways via functional classification and Kyoto Encyclopedia of Gene and Genomes pathway mapping, respectively. A set of the most important candidate genes was then identified by combining the differentially expressed genes found in the present study with previously identified phosphorus deficiency tolerance quantitative trait loci. Conclusion: The present work provides abundant genomic information for functional dissection of the phosphorus deficiency resistance of Dongxiang wild rice, which will be help to understand the biological regulatory mechanisms of phosphorus deficiency tolerance in Dongxiang wild rice.

Mapping QTLs for Fertility Restoration of Different Cytoplasmic Male Sterility Types in Rice Using Two Oryza sativa ×O. rufipogon Backcross Inbred Line Populations.

Hybrid rice breeding using cytoplasmic male sterility/fertility restoration (CMS/Rf) systems plays an important role in ensuring global food security. Two backcross inbred line (BIL) populations derived from either Xieqingzao B (XB)//XB/Dongxiang wild rice (DWR) (XXD) or XB//DWR/XB (XDX) were used to detect quantitative trait loci (QTLs) for fertility restoration of Dwarf wild abortive- (DA-), Indonesia Paddy- (ID-), and DWR-type CMS in rice. Lines with ID- and DA-type CMS were testcrossed with both the XXD- and XDX-BILs, while the line with DWR-type CMS was testcrossed with the XDX-BILs only. A total of 16 QTLs for fertility restoration of CMS systems were identified, including three for DWR-type CMS, six for DA-type CMS, and seven for ID-type CMS. All of the additive alleles in the QTLs were derived from Oryza rufipogon. Eleven QTLs were clustered in five chromosomal regions, indicating that common Rf loci restored different CMS systems, and the favorable O. rufipogon alleles could be used to develop restorer lines for various CMS types by marker-assisted selection.

[Index screening and comprehensive evaluation of phenotypic traits of low nitrogen tolerance using BILs population derived from Dongxiang wild rice (Oryza rufipogon Griff)].

To identify the low nitrogen tolerance of Dongxiang wild rice (DXWR) and its progenies, ten phenotypic traits including plant height (PH), heading day (HD), panicle length (PL), number of effective tillers per plant (NETP), number of filled grains per panicle (NFGP), number of grains per panicle (NGP), grain density (GD), spikelet fertility (SF), 1000-grain mass (TGM) and grain yield per plant (GYP) were studied under normal and low nitrogen treatments, using backcross inbred lines (BILs) of Xieqingzao B//DXWR/Xieqingzao B in BC1 F12. Comprehensive evaluation on the low nitrogen tolerance of the BILs population was conducted using principal component analysis and the subordinate function. The evaluation results indicated that the low nitrogen tolerance of the line 116, 143 and 157 was the strongest, which could be served as the intermediate materials for genetic studies on the low nitrogen tolerance of DXWR and breeding for the low nitrogen tolerance in rice. The optimal regression equation of the low nitrogen tolerance in rice was established using stepwise regression analysis. The relative values of five traits including PH, NGP, SF, TGM and GYP were screened out and could be used as comprehensive evaluation indices for the low nitrogen tolerance in the whole growth stage. Therefore, more attention should be paid to the relative values of these five traits, especially for NGP and GYP, in the genetic improvement of the low nitrogen tolerance in rice.

[Drought resistance evaluation system for backcross lines of Dongxiang common wild rice (Oryza rufipogon Griff.)].

A total of 79 rice materials containing Dongxiang wild rice (Oryza rufipogon Griff. ) backcross lines (Dwr)/Xie-qingzao B (Xqz B)//Xqz B and their parents were chosen as the test objects to study the relationships between the drought resistance of these materials and the 31 drought resistance indices at germinating stage, seedling stage, booting stage, and mature stage. The results showed that the drought resistance index or the drought resistance coefficient of these materials were significantly correlated to the relative germination energy (RGE) under 15% PEG-6000 drought stress, the germination drought resistance index (GDRI) and relative germination energy (RGE) under 20% PEG-6000 drought stress, and the relative value of maximum root length (MRL), seeding height (SH), fresh root mass (FRM), dry root mass (DRM), root relative water content (RRWC), wilting rate (WR), leaf soluble sugar content (LSSC), leaf proline content (LPC), leaf MDA content (LMDAC), leaf relative water content (LRWC), level of rolling leaf (RL), plant height (PH), tiller number per plant (TNP), productive tiller number per plant (PTNP), filled spikelets per panicle (FSP), panicle density (PD), seed setting rate (SR), and 1000-grain mass (TGM) under water stress. Through stepwise regression analysis, nine drought resistance indices including the RGE under 20% PEG-6000 drought stress and the relative values of DRM, RRWC, LSSC, LPC, LMDAC, ETNP, SR, and TGM under water stress were selected. Base on these indices and their partial correlation coefficients, the drought resistance evaluation equation (D value) and evaluation system were established, which could well assess the drought resistance of the Dongxiang common wild rice backcross lines at different growth stages.

[Characterisation of a rice dwarf and twist leaf 1 (dtl1) mutant and fine mapping of DTL1 gene].

Plant height is one of the most important agronomic traits, which determines grain yield. By a largescale screening of our mutant population, we identified a dwarf with twisty leaf mutant (dwarf and twist leaf 1, dtl1). Besides dwarf with twisty leaf, dtl1 also showed reduced tiller number and sterile phenotypes. Based on the internode length of dtl1, this mutant belongs to the nl type of dwarfing phenotype. Physiological assay with two phytohormones, gibberellin (GA), and brassinosteroid (BR), suggested that dtl1 was neither deficient nor insensitive to GA and BR. Genetic analysis showed that the phenotype of dtl1 was controlled by a single recessive gene. Using F2 population derived from a cross between dtl1 and an indica cultivar Taichung Native 1, the DTL1 gene was narrowed down to a 70.4 kb between two SSR markers, RM25923 and RM6673, on the long arm of chromosome 10, and co-segregated with InDel marker Z10-29, where thirteen open reading frames were predicted without known gene involved in controlling plant height. Thus, the DTL1 gene might be a novel gene which is related to plant height in rice.

Mapping of quantitative trait loci for fiber and lignin contents from an interspecific cross Oryza sativa×Oryza rufipogon.

Rice straw is always regarded as a by-product of rice production, but it could be a significant energy source for ruminant animals. Knowledge of the genetic variation and genetic architecture of cell wall traits will facilitate rice breeders by improving relevant traits through selective breeding and genetic engineering. The common wild rice, Oryza rufipogon Griff., which is considered to be the progenitor of Oryza sativa, has been widely utilized for the identification of genes of agronomic importance for rice genetic improvement. In the present study, the mapping of quantitative trait loci (QTLs) for acid detergent fiber (ADF), neutral detergent fiber (NDF), acid detergent lignin (ADL), and ADL/NDF ratio was carried out in two environments using a backcrossed inbred line (BIL) population derived from a cross between the recurrent parent Xieqingzao B (XB) and an accession of Dongxiang wild rice (DWR). The results indicated that all four traits tested were continuously distributed among the BILs, but many BILs showed transgressive segregation. A total of 16 QTLs were identified for the four traits, but no QTLs were in common in two environments, suggesting that environment has dramatic effects on fiber and lignin syntheses. Compared to the QTL positions for grain yield-related traits, there were no unfavorable correlations between grain yield components and cell wall traits in this population. The QTLs identified in this study are useful for the development of dual-purpose rice varieties that are high in grain yield and are also high in straw quality.

[Effect of physico-chemical characteristics of activated carbon on the adsorption of organic pollutants in natural water].

In this paper, the adsorption characteristics of two synthetic organic compounds (SOCs), i. e., methyl parathion(MP) and trichloroethylene (TCE), and natural organic matter (NOM) on powdered activated carbons (PAC) in natural water were studied. On the basis of fully characterizing the physical and chemical characteristics of PAC, the effect of physical and chemical properties of PAC on the adsorption of low molecular weight SOCs in natural water was studied by correlation analysis. The effect of molecular weight fractionation on the adsorption of NOM on PAC was investigated using high performance size exclusion chromatography (HPSEC). It was found that, compared to the surface chemistry, the physical property (pore properties) of PAC was the critical factor to determine its adsorption capacity of MP and TCE in natural water. The adsorption of the low molecular weight SOC and NOM with apparent molecular weight (AMW) < 500 on PAC was primarily impacted by the micropore surface area, and that of NOM with 500 < AMW < 3 000 was affected by the mesopore surface area combined with the mesopore size distribution.

[Recent advances in molecular mapping and cloning of useful genes from wild rice and their application in breeding].

Wild rice has adapted to weather and unfavorable environments under natural selection. It has been well recognized as a natural gene bank that conserves a lot of specific genes presently not available for extinct in the cultivated rice. There is an urgent need to explore these specific genes. The present paper summarized current researches in molecular mapping and cloning of useful genes from wild rice,and their potential application in breeding.

[Mapping of fertility-restoring genes with main effects and epistatic effects for CMS-DA in rice].

A test-cross population was established for mapping genes conditioning fertility restoration for dwarf-wild-abortive cytoplasmic male sterility(CMS-DA) in rice. A recombinant inbred line(RIL) population consisting of 210 lines was derived from the cross Xieqingzao B/Miyang 46, in which Xieqingzao B is the maintainer line of CMS-DA Xieqingzao A, and Miyang 46 is the restorer line. Each of the RILs was crossed to Xieqingzao A, and the resulting F1s were used for phenotyping of the spikelet fertility in 1999 and 2000. A linkage map consisting of 129 RFLP and SSLP markers was constructed. QTLs having significant main effects and/or epistatic effects for spikelet fertility were determined with QTLMAPPER 1.0 of mixed linear model. Background genetic variation due to main and epistatic effects of important markers was controlled. Four QTLs having significant main effects for fertility restoration were detected. A major gene qRf-10-2 was located in interval RM258-RZ811 on the long arm of chromosome 10, and QTL qRf-1 displaying a moderate main effect was located in a position close to RG532 on chromosome 1. Two other QTLs were located on chromosome 5 (qRF-5) and the short arm of chromosome 10 (qRf-10-1), in which the main effect of qRf-5 bacame significant only in the absence of qRf-10-2. A significant digenic interaction was detected, which occurred between QTLs qRf-1 and qRf-5. No significant QTL by environmental interactions and epistasis by environmental interactions were detected. Analyses on the gene effects based on markers closest to the Rf genes were made, and multi-locus interactions were implied. The present results were also compared to a previous study on mapping fertility restoration genes in Milyang 46 for wild-abortive CMS Zhenshan 97A, and to other published reports. It was indicated that differences on the genetic control of fertility restoration among different rice populations were mainly attributed to variations on genes with minor main effects and epistatic effects.