Genetic analysis and fine mapping of the pubescence gene GL6 in rice (Oryza sativa L.)

The pubescence of the leaf blade surface is an important agronomic characteristic for rice morphology and significantly influences rice growth as well as physiological characteristics. This characteristic was analyzed in F1 and F2 plants derived by crossing cultivar 75-1-127 with the indica cultivar Minghui 63, as well as the glabrous cultivar Lemont and indica cultivar 9311. Results indicated that the pubescence of the leaf blade surface was a dominant trait and controlled by a single gene. The GL6 gene was primarily mapped on rice chromosome 6 with recessive F2 population derived from 75-1-127/Minghui 63 by combining bulked segregation analysis and recessive class analysis using the Mapmaker3.0/MapDraw software. The genetic distances between the simple sequence repeat markers RM20491 and RM20547 were 7.2 and 2.2 cM, respectively. The GL6 gene was fine mapped in the interval between InDel-106 and InDel-115 at genetic distances of 0.3 and 0.1 cM, respectively. The large, recessive F2 population was derived from 75-1-127/Minghui 63. A high-resolution genetic and physical map of GL6 was constructed. Derived from the map-based sequences published by the International Rice Genome Sequencing Project, the GL6 gene was localized at an interval of 79 (japonica) and 116.82 kb (9311) bracketed by InDel-106 and InDel-115 within the BAC accession numbers AP008403 and AP005760. Seven annotated genes (japonica) and eight annotated genes (9311) were present. The basis was further set for GL6 cloning and function analysis.     

Genetic structure and eco-geographical differentiation of cultivated Hsien rice (Oryza sativa L. subsp. indica) in China revealed by microsatellites

Indica is not only an important rice subspecies widely planted in Asia and the rest of the world,but it is also the genetic background of the majority of hybrid varieties in China.Studies on genetic structure and genetic diversity in indica germplasm resources are important for the classification and utilization of cultivated rice in China.Using a genetically representative core collection comprising 1482 Chinese indica landraces,we analysed the genetic structure,geographic differentiation and diversity.Model-based structure analysis of varieties within three ecotypes revealed nine eco-geographical types partially accordant with certain ecological zones in China.Differentiation of eco-geographical types was attributed to local ecological adaption and physical isolation.These groups may be useful for developing heterotic groups of indica.To facilitate the identification of different ecotypes and eco-geographical types,we identified characteristic SSR alleles of each ecotype and eco-geographical type and a rapid index of discrimination based on characteristic alleles.The characteristic alleles and rapid discrimination index may guide development of heterotic groups,and selection of hybrid parents.     

Molecular evolution of rice S 5 n and functional comparison among different sequences

The wide compatibility gene, S ₅ ⁿ , can overcome embryo sac sterility between indica and japonica subspecies of rice. Therefore, it is very important to characterize the features of the S ₅ ⁿ sequence to reveal the origin and evolution of S ₅ ⁿ . In this paper, 26 cultivated rice haplotypes and 22 wild rice accessions harboring S ₅ ⁿ were used to sequence S ₅ ⁿ . The results showed that 15 genotypes among the 48 materials were fully consistent with control cultivar 02428 (CK). The other 33 accessions had different degrees of variation in the S ₅ ⁿ sequence. Variations in the coding region mainly occurred in the second exon and eight materials showed a 10-bp deletion at 1710?C1719 bp, including wild (O. nivara) and cultivated rice, such as IRW501 and Yuetai B. S ₅ ⁿ sequences were not biased and evolved neutrally. The 48 materials could be divided into 4 categories using a phylogenetic tree of the amino acid sequences. Most of the wild rice clustered together, and the cultivated rice clustered into another group. Eight cultivated rice and O. nivara (wild rice) clustered in another group, which were found to lack 10 consecutive bases in exon 2. Eight rice varieties with high numbers of differences in their S ₅ ⁿ coding regions were crossed with testers (typically indica and japonica) to produced test cross F₁ populations. The F₁s were examined for their ability to overcome indica-japonica hybrid sterility. The result showed that the embryo sac fertility of S ₅ ⁿ -containing hybrids increased significantly compared with control hybrids, but there were no differences among the materials with divergent sequences, indirectly proving that S ₅ ⁿ is a non-functional gene.     

Effect of CO2 enrichment on the glucosinolate contents under different nitrogen levels in bolting stem of Chinese kale (Brassica alboglabra L.)

The effects of CO₂ enrichment on the growth and glucosinolate (GS) concentrations in the bolting stem of Chinese kale (Brassica alboglabra L.) treated with three nitrogen (N) concentrations (5, 10, and 20 mmol/L) were investigated. Height, stem thickness, and dry weights of the total aerial parts, bolting stems, and roots, as well as the root to shoot ratio, significantly increased as CO₂ concentration was elevated from 350 to 800 μl/L at each N concentration. In the edible part of the bolting stem, 11 individual GSs were identified, including 7 aliphatic and 4 indolyl GSs. GS concentration was affected by the elevated CO₂ concentration, N concentration, and CO₂×N interaction. At 5 and 10 mmol N/L, the concentrations of aliphatic GSs and total GSs significantly increased, whereas those of indolyl GSs were not affected, by elevated atmospheric CO₂. However, at 20 mmol N/L, elevated CO₂ had no significant effects on the concentrations of total GSs and total indolyl GSs, but the concentrations of total aliphatic GSs significantly increased. Moreover, the bolting stem carbon (C) content increased, whereas the N and sulfur (S) contents decreased under elevated CO₂ concentration in the three N treatments, resulting in changes in the C/N and N/S ratios. Also the C/N ratio is not a reliable predictor of change of GS concentration, while the changes in N and S contents and the N/S ratio at the elevated CO₂ concentration may influence the GS concentration in Chinese kale bolting stems. The results demonstrate that high nitrogen supply is beneficial for the growth of Chinese kale, but not for the GS concentration in bolting stems, under elevated CO₂ condition.     

Fractal analysis for root growth of plant seedlings under doubled CO2 concentration

Fractal geometry was applied and box dimension was used as an indicator to analyze the effects of doubled CO₂ concentration on the root growth of plant seedlings. Results showed that doubled CO₂ concentration displayed different effects on root branching characteristics of C₃ and C₄ plants. There was an obvious increase of root branches in spring wheat while there were no significant effects on roots of sweet sorghum. In different soil layers, root branching of spring wheat was stimulated and this promotion was most significant in the second layer (10–20 cm), which denoted that elevated CO₂ altered the root branching pattern. That means higher CO₂ concentration influences not only root growth but also its differentiation and development.     

Effect of elevated CO2 on CH4 emission

Global CH₄ emission may increase under CO₂ enrichment condition, which is projected for the future. CO₂ enrichment could affect CH₄ emission in two ways: (i) Photosynthesis of plants that also include plants in rice paddies and natural wetlands will be stimulated under CO₂ enrichment condition. CH₄ emission rate may be increased due to the accumulation of more plant biomass, root exudes and soil organic matters. (ii) Combined with other global warming forces, CO₂ enrichment may bring a change of atmospheric temperature and precipitation around the world. CH₄ emission will also be changed with the variation of the area and distribution of rice paddies and natural wetlands.     

A meta-analysis of responses of wheat yield formation to elevated ozone concentration

The meta-analysis method was applied to quantitatively investigate effects of the elevated ozone concentration ([O₃]) on chlorophyll concentration, gas exchange and yield components of wheat. There were 39 effective references through Web of Science (ISI, USA) and Chinese journal full-text database (CNKI, China). The results of meta-analysis indicated that elevated [O₃] decreased grain yield, grain weight, grain number per ear, ear number per plant and harvest index by 26%, 18%, 11%, 5% and 11%, respectively, relative to ambient air. The decrease in leaf physiological characters was much greater than that in yield when wheat was expose to elevated [O₃], while light-saturated photosynthetic rate (Asat), stomatal conductance (Gs) and chlorophyll content (Chl) decreased by 40%, 31%, and 46%, respectively. The responses to elevated [O₃] between spring wheat and winter wheat were similar. Most of the variables showed a linear decrease trend with an increase of [O₃]. The most significant decrease for Asat, Gs and Chl was found in grain filling stage. Elevated [CO₂] could significantly ameliorated or offset the detrimental effects caused by elevated [O₃]. Supported by National Natural Science Foundation of China (Grant No. 30670387), Eco-Frontier Fellowship of the Ministry of Environment, Japan (Grant No. 07-C062-03) and Ministry of Science and Technology of People’s Republic China with 973 Project (Grant No. 2002CB410803)     

亚高山红桦根及根际土壤生化特性对升高温度和CO2的响应

通过川西亚高山野外大型控制实验,研究了红桦不同密度下的根系生物量、根际土壤微生物数量和根际土壤酶活性对短期升高温度（ET,相对室外平均升温2.4±0.4 ℃）、升高大气CO2浓度（EC,平均增加15.5±1.0 μmol·L^-1）及交互作用（ETC,生长室相对室外平均升温2.2±0.5　℃并CO₂浓度平均增加15.8±1.2　μmol·L^-1）的响应.初步结果表明：升高大气温度或CO₂浓度均能够显著促进红桦低密度和高密度下单株根系生物量;升高温度和CO₂浓度及二者共同升高对微生物类群和数量影响不同,升高温度细菌、真菌数量以及低密度下放线菌数量显著增加,而高密度下放线菌数量显著下降;升高CO₂浓度下高密度时细菌和真菌数量增加而低密度下均显著下降;升高温度（ET）显著抑制高、低密度下红桦根际土壤多酚氧化酶活性,升高CO₂（EC）根际土壤过氧化氢酶活性在2种密度条件下均不同程度升高,土壤脲酶和多酚氧化酶活性则降低;ETC条件下,根际土壤多酚氧化酶和过氧化氢酶在2种密度下均表现出不同程度的降低,但脲酶活性在高、低密度条件下对ETC表现出不同的响应结果.     

Responses of rice growth to copper stress under free-air CO2 enrichment （FACE）

The responses of rice to the second degree contamination of copper were studied by pot experiments under free-air CO2 enrichment （FACE） with 570 μmol ·mol^-1 of CO2. The results showed that the content of copper in rice leaves was reduced with the CO2 concentration reaching 570 μmol· mol^-1 and this happened more significantly under the second degree contamination of copper. Under FACE, activities of superoxide dismutase （SOD） enzyme in rice leaves treated by copper contamination were induced, whereas the contents of glutathione （GSH） and glutathione disulfide （GSSG） had no significant difference from the control. In the presence of ambient CO2, activities of SOD enzyme treated by copper pollution were suppressed during the whole rice growth, however, the contents of GSH and GSSG were induced at tillering and jointing stages, and then restored to the control levels in later growth under the second degree contamination of copper. With the rice growing, the content of malondialdehyde （MDA） rises continuously, but there had been no significant difference between the treatments at the same growth stage. Further studies are needed on the response mechanism of rice to Cu stress under elevated CO2.     

Static opaque chamber-based technique for determination of net exchange of CO<Subscript>2</Subscript> between terrestrial ecosystem and atmosphere

Terrestrial carbon cycling is one of the hotspots in global change issues. In this paper, we presented the rationale for determination of net exchange of CO₂ between terrestrial and the atmosphere (NEE) and the methods for measuring several relevant components. Three key processes for determination of NEE were addressed, including the separation of shoot autotrophic respiration from total CO₂ emissions of the ecosystem, the partition of root respiration from soil CO₂ efflux, and the quantification of rhizodeposition C from NPP. With an understanding of the processes involved in the CO₂ exchange between terrestrial and the atmosphere, we estimated NEE of rice ecosystem in Nanjing based on field measurements of CO₂ emissions and several relevant biotic components as well as abiotic factors. The field measurements of CO₂ emissions were made over the rice-growing seasons in 2001 and 2002 with the static opaque chamber method. Calculations indicated that the seasonal pattern of NEE is comparable for two seasons. Either net carbon emission or fractional carbon fixation occurred during 3 weeks after rice transplanting and thereafter net carbon fixation appeared with an increasing trend as rice growing. Higher net carbon fixation occurred in the rice developmental period from elongating to heading. A decline trend in the fixation was documented after rice heading. The mean daily NEE was -6.06 gC·m⁻² in 2001 season and -7.95 gC·m⁻² in 2002 season, respectively. These values were comparable to the results obtained by Campbell et al. who made field measurements with the Bowen ratio-energy balance technique in irrigated rice, Texas USA. Moreover, the mean daily NEE in this study was also comparable to the values obtained from a Japanese rice paddy with the eddy covariance method under the similar water regime, either drainage course or waterlogged. It is concluded that NEE determined by the static opaque chamber method is comparable and in agreement with those measured by Bowen ratioenergy balance and eddy covariance methods.     

Experimental validation of inter-subspecific genetic diversity in rice represented by the differences between the DNA sequences of ＇Nipponbare＇ and ＇93-11＇

The pedigrees of three sequenced rice cultivars were analyzed to show that a majority of the genetic composition of ＇Nipponbare＇ originates from japonica cultivars while the minority originates from indica cultivars. In contrast, ＇93-11＇ is derived mainly from indica cultivars with a smaller contribution from japonica cultivars. All ancestors of ＇Guang lu ai 4＇ appeared to be indica lines. A set of molecular markers （46 InDels and 53 SSRs） polymorphic between ＇Nipponbare＇ and ＇93-11＇ were examined in 46 typical indica and 47 typical japonica cultivars selected from 443 accessions according to Cheng＇s index. All cultivars were divided into indica and japonica groups without overlapping when clustered by Cheng＇s index, InDels and SSRs. Much higher InDel and SSR diversity between groups than within groups implies that the marker polymorphisms between ＇Nipponbare＇ and ＇93-11＇ represent a large proportion of inter-subspecific diversity. About 85% of indica cultivars and more than 90% of japonica cultivars were confirmed to have the same PCR banding patterns as ＇93-11＇ and ＇Nipponbare＇, respectively. Some polymorphic loci between ＇Nipponbare＇ and ＇93-11＇ cannot be validated in other indica and japonica cultivars, either as subspecies-specific but not predominant alleles, or alleles not specific between the two groups. It was concluded that molecular markers developed from sequence polymorphism between ＇Nipponbare＇ and ＇93-11＇ often represent inter-subspecific diversity, although some exceptions were sensitive to either particular marker loci or particular cultivars.     

Study on heterosis of intersubspecies between indica and japonica rice （Oryza sativa L.） using chromosome segment substitution lines

Great heterosis exists in the inter-subspecific crossesbetween indica and japonica rice cultivars[1,2] and the ex-ploitation of this heterosis has long been considered as apromising method to further increase rice yield potential[3].Previous studies indicated that there were large differencesbetween the two subspecies with respect to morphology,isozyme, polymorphism of molecular markers and DNAstructure due to long time genetic differentiation[4,5]. Thosedifferences were identified to be clos…     

Advances in the understanding of inter-subspecific hybrid sterility and wide-compatibility in rice

Hybrid sterility is a major form of postzygotic reproductive isolation and frequently occurs in hybrids between divergent populations, such as the indica and japonica subspecies of Asian cultivated rice （Oryza sativa L.）. It has been a major barrier for utilization of the strong heterosis expressed in hybrids between indica and japonica. A large number of loci for rice inter-subspecific hybrid sterility have been identified by genetic analysis. Cytological studies revealed that male and female gamete abortions and reduced affinity between the uniting gametes all occurred in indica-japonica hybrids, suggesting the complexity of the causes for inter-subspecific hybrid sterility. Two genes conditioning embryo-sac and pollen sterility respectively in indica-japonica hybrids have been cloned recently, providing opportunities for molecular characterization of the indica-japonica hybrid sterility and wide-compatibility. Future studies should aim at cloning more genes for indica-japonica hybrid sterility, characterizing the underlying molecular mechanism, and utilization of the findings for the development of inter-subspecific hybrids to increase rice productivity.     

Introduction of antisensewaxy gene into main parent lines ofindica hybrid rice

Amylose content in rice endosperm is one of the key determinants of rice eating and cooking quality, and the poor quality ofindica hybrid rice is closely related to the high amylose level in rice grains. In order to improve the grain quality of theindica hybrid rice by genetic engineering, an antisense fragment of ricewaxy gene, driven by the 5′-franking sequences of the ricewaxy gene, was successfully introduced into three major parent lines ofindica hybrid rice, all contain a high amylose level in the grains, viaAgrobacterium, and more than 100 hygromycinresistant plants were regenerated. The analysis of PCR amplification and Southern blots indicated that the T-DNA containing the antisensewaxy gene had been integrated into the genome of transgenic rice plants. Most of the primary transgenic rice plants grew normally, and the mature seeds from these transgenic plants were performed for analysis of the amylose content. The results showed that the amylose content in the endosperm of some grains was reduced and the lowest reached 7.02% in one homozygous transgenic line, 72.4% lower than that of the wild type. The influence of the altered amylose content on the gelatinization temperature and gel consistency was also observed in several homozygous transgenic rice plants. The two authors contributed equally to this work.     

Incorporating temporal variability to improve geostatistical analysis of satellite-observed CO2 in China

Observations of atmospheric carbon dioxide (CO2 ) from satellites offer new data sources to understand global carbon cycling. The correlation structure of satellite-observed CO2 can be analyzed and modeled by geostatistical methods, and CO2 values at unsampled locations can be predicted with a correlation model. Conventional geostatistical analysis only investigates the spatial correlation of CO2 , and does not consider temporal variation in the satellite-observed CO2 data. In this paper, a spatiotemporal geostatistical method that incorporates temporal variability is implemented and assessed for analyzing the spatiotemporal correlation structure and prediction of monthly CO2 in China. The spatiotemporal correlation is estimated and modeled by a product-sum variogram model with a global nugget component. The variogram result indicates a significant degree of temporal correlation within satellite-observed CO2 data sets in China. Prediction of monthly CO2 using the spatiotemporal variogram model and spacetime kriging procedure is implemented. The prediction is compared with a spatial-only geostatistical prediction approach using a cross-validation technique. The spatiotemporal approach gives better results, with higher correlation coefficient (r2 ), and less mean absolute prediction error and root mean square error. Moreover, the monthly mapping result generated from the spatiotemporal approach has less prediction uncertainty and more detailed spatial variation of CO2 than those from the spatial-only approach.     

Development of Fe(III)-containing ether-functionalized imidazolium ionic liquids for aryl Grignard cross-coupling of alkyl halides

A series of Fe(Ⅲ)-containing imidazolium-based ionic liquids containing ether substituents,including[C3OMim][FeCl4](1,[C3OMim]=1-(2-methoxyethyl)-3-methylimidazolium),[C3OiPim][FeCl4](2,[C3OiPim]=1-isopropyl-3-(2-methoxyethyl)imidazolium),[C3OBim][FeCl4](3,[C3OBim]=1-butyl-3-(2-methoxyethyl)imidazolium),[(C3O)2im][FeCl4](4,[(C3O)2im]=1,3-bis(2-methoxyethyl)imidazolium),[C3OMim][FeBr4](5)and[(C3O)2im][FeBr4](6),were prepared and characterized by elemental analysis,Raman spectroscopy and electrospray ionization mass spectrometry.The catalytic performances of 1–6 and related Fe(III)-based catalysts in the cross-coupling of aryl Grignard reagents with alkyl halides bearing-hydrogens were studied,revealing that mono(ether)functionality improves the catalytic activity and that bis(ether)functionality improves the reusability.After simply decanting the product contained in the ethereal layer,complex 4,which containing bis(ether)-functionalized imidazolium cation,could be successfully recycled seven times.     

Reactions of [FeL2(CH3CN)2](PF6)2 (L = N-pyrimid-2-ylimidazol-ylidene) with N-, P-, O-, and S-donors and its catalytic activity

Reactions of [FeL2(CH3CN)2]2+(L = N-pyrimid-2-ylimidazolylidene) with various N-,P-,O-,and S-donors were investigated.By replacing the labile acetonitrile,various iron-NHC complexes containing additional N-,P-,O-,and S-ligands were prepared.All the iron-NHC complexes were fully characterized by NMR spectroscopy and X-ray crystallography.[FeL2(CH3CN)2]2+ could efficiently catalyze the coupling reactions of various Grignard reagents with heteroaryl bromides or chlorides.     

分子标记鉴定红莲型细胞质雄性不育杂交水稻组合及其亲本

利用RAPD分子标记对红莲型细胞质雄性不育(HL—CMS)杂交水稻组合及其亲本进行了DNA多态性分析。从124个随机引物中筛选出具有非常明显的多态性，且只能扩增出1～5个片段的4个引物能有效地区分和鉴定红莲型(HL)2个杂交水稻组合(粤泰系列，从广系列)的杂种及其亲本。     

Efficient indica and japonica rice identification based on the InDel molecular method: Its implication in rice breeding and evolutionary research

An efficient molecular method for the accurate and efficient identification of indica and japonica rice was created based on the polymorphisms of insertion/deletion (InDel) DNA fragments obtained from the basic local alignment search tool (BLAST) to the entire genomic sequences of indica (93-11) and japonica rice (Nipponbare). The 45 InDel loci were validated experimentally by the polymerase chain reaction (PCR) and polyacrylamide gel electrophoresis (PAGE) in 44 typical indica and japonica rice varieties, including 93-11 and Nipponbare. A neutrality test of the data matrix generated from electrophoretic banding patterns of various InDel loci indicated that 34 InDel loci were strongly associated with the differentiation of indica and japonica rice. More extensive analyses involving cultivated rice varieties from 11 Asian countries, and 12 wild Oryza species with various origins confirmed that indica and japonica characteristics could accurately be determined via calculating the average frequency of indica- or japonica-specific alleles on different InDel loci across the rice genome. This method was named as the “InDel molecular index” that combines molecular and statistical methods in determining the indica and japonica characteristics of rice varieties. Compared with the traditional methods based essentially on morphology, the InDel molecular index provides a very accurate, rapid, simple, and efficient method for identifying indica and japonica rice. In addition, the InDel index can be used to determine indica or japonica characteristics of wild Oryza species, which largely extends the utility of this method. The InDel molecular index provides a new tool for the effective selection of appropriate indica or japonica rice germplasm in rice breeding. It also offers a novel model for the study of the origin, evolution, and genetic differentiation of indica and japonica rice adapted to various environmental changes.     

High-quality reference genes for quantifying the transcriptional responses of Oryza sativa L. (ssp. indica and japonica) to abiotic stress conditions

Rice (Oryza sativa L.) is important to food security and is also an excellent model plant for numerous cereal crops. A functional genomics study in rice includes characterization of the expression dynamics of genes by quantitative real-time PCR (qPCR) analysis; this is a significant key for developing rice varieties that perform well in the face of adverse climate change. The qPCR analysis requires the use of appropriate reference genes in order to make any quantitative interpretations meaningful. Here, the new potential reference genes were selected from a huge public database of rice microarray experiments. The expression stability of 14 candidates and 4 conventional reference genes was validated by geNorm PLUS and NormFinder software. Seven candidates are superior to the conventionally used reference genes in qPCR and three genes can be used reliably for quantitating the expression of genes involved in abiotic stress responses. These high-quality references EP (LOC_Os05g08980), HNR (LOC_Os01g71770), and TBC (LOC_Os09g34040) worked very well in three indica genotypes and one japonica genotype. One of indica genotypes including the Jasmine rice, KDML105 developed in Thailand for which no reference genes have been reported until now.