Synthesis and Absolute Configuration of Natural Gregatin B

(S)-(+)-Gregatin B and racemic gregatin B were synthesized from tetrahydro-2-methyl-5-oxo-2-furancarboxylic acid and the absolute configuration of natural gregatin B was determined as (S).     

Synteny between Arabidopsis thaliana and rice at the genome level: a tool to identify conservation in the ongoing rice genome sequencing project

BLASTX alignment between 189.5 Mb of rice genomic sequence and translated Arabidopsis thaliana annotated coding sequences (CDS) identified 60 syntenic regions involving 4–22 rice orthologs covering ≤3.2 cM (centiMorgan). Most regions are <3 cM in length. A detailed and updated version of a table representing these regions is available on our web site. Thirty-five rice loci match two distinct A.thaliana loci, as expected from the duplicated nature of the A.thaliana genome. One A.thaliana locus matches two distinct rice regions, suggesting that rice chromosomal sequence duplications exist. A high level of rearrangement characterizing the 60 syntenic regions illustrates the ancient nature of the speciation between A.thaliana and rice. The apparent reduced level of microcollinearity implies the dispersion to new genomic locations, via transposon activity, of single or small clusters of genes in the rice genome, which represents a significant additional effector of plant genome evolution.     

Virus-Mediated Chemical Changes in Rice Plants Impact the Relationship between Non-Vector Planthopper Nilaparvata lugens St?l and Its Egg Parasitoid Anagrus nilaparvatae Pang et Wang

In order to clarify the impacts of southern rice black-streaked dwarf virus (SRBSDV) infection on rice plants, rice planthoppers and natural enemies, differences in nutrients and volatile secondary metabolites between infected and healthy rice plants were examined. Furthermore, the impacts of virus-mediated changes in plants on the population growth of non-vector brown planthopper (BPH), Nilaparvata lugens, and the selectivity and parasitic capability of planthopper egg parasitoid Anagrus nilaparvatae were studied. The results showed that rice plants had no significant changes in amino acid and soluble sugar contents after SRBSDV infection, and SRBSDV-infected plants had no significant effect on population growth of non-vector BPH. A. nilaparvatae preferred BPH eggs both in infected and healthy rice plants, and tended to parasitize eggs on infected plants, but it had no significant preference for infected plants or healthy plants. GC-MS analysis showed that tridecylic aldehyde occurred only in rice plants infected with SRBSDV, whereas octanal, undecane, methyl salicylate and hexadecane occurred only in healthy rice plants. However, in tests of behavioral responses to these five volatile substances using a Y-tube olfactometer, A. nilaparvatae did not show obvious selectivity between single volatile substances at different concentrations and liquid paraffin in the control group. The parasitic capability of A. nilaparvatae did not differ between SRBSDV-infected plants and healthy plant seedlings. The results suggested that SRBSDV-infected plants have no significant impacts on the non-vector planthopper and its egg parasitoid, A. nilaparvatae.     

Assessment of genetic diversity in salt-tolerant rice and its wild relatives for ten SSR loci and one allele mining primer of salT gene located on 1st chromosome

A heterogeneous collection of rice genotypes which included seven salt-tolerant rice lines, one salt-sensitive improved line, one wild rice (Oryza rufipogon) and one salt-tolerant wild rice relative (Porteresia coarctata) was screened with ten salt-tolerance-linked simple sequence repeat markers, of which nine were from the Saltol QTL mapped on rice 1st chromosome and the rest one from 8th chromosome, having high phenotypic variance for salt tolerance. Variation in molecular weight (in the form of base pairs) of the different amplified products using RM primers was used to find out the genetic relationship among the studied rice genotypes. Genomic DNA of the studied genotypes was also amplified with a reported allele mining primer for a salt-inducible gene (salT). The amplified products were sequenced and aligned to find out the closeness among the rice lines for the studied gene. Dendrogram derived from marker profiles showed partial similarity with salT gene-derived tree. Commonly, all the salt-tolerant lines were grouped into a single cluster, including IR36 (a salt-sensitive line) to which O. rufipogon (the wild rice) and P. coarctata (the wild rice relative) joined separately. The taxonomic identity and evolutionary relationship among the three groups (rice, wild rice and wild rice relative) were bioinformatically analysed using the nucleotide sequence of the studied salT gene.     

Residue of Kitazin P Metabolite in Rice Plants and Soil

Debutenoyl-aspertetronin A was synthesized from γ-valerolactone-γ-carboxylic acid (4) via 2, 5-dihydro-3-hydroxy-2-methyl-5-oxo-2-furanpropanoic acid. Starting from (?)-(S)-4, (+)-(S)-5-hexyl-4-hydroxy-5-methyl-2(5H)furanone (19) was synthesized, and by comparison of its optical rotation with that of an authentic sample it was proved that aspertetronin A had (R) configuration, and gregatin A had (S) configuration at their respective chiral carbon.     

Screening for strains of Aspergillus oryzae that degrade carbamide for use in sake brewing

We screened 65 strains of Aspergillus oryzae for ones that degraded carbamide, Two strains, IFO 5238 and IFO 30113, were selected and used to prepare rice koji. Sake made with the rice koji prepared with these strains had less than half (less than 15 ppm) of the carbamide in sake made with rice koji prepared with commercial spores of A. oryzae.     

Genome-Wide Association Study of Grain Appearance and Milling Quality in a Worldwide Collection of Indica Rice Germplasm

Grain appearance quality and milling quality are the main determinants of market value of rice. Breeding for improved grain quality is a major objective of rice breeding worldwide. Identification of genes/QTL controlling quality traits is the prerequisite for increasing breeding efficiency through marker-assisted selection. Here, we reported a genome-wide association study in indica rice to identify QTL associated with 10 appearance and milling quality related traits, including grain length, grain width, grain length to width ratio, grain thickness, thousand grain weight, degree of endosperm chalkiness, percentage of grains with chalkiness, brown rice rate, milled rice rate and head milled rice rate. A diversity panel consisting of 272 indica accessions collected worldwide was evaluated in four locations including Hangzhou, Jingzhou, Sanya and Shenzhen representing indica rice production environments in China and genotyped using genotyping-by-sequencing and Diversity Arrays Technology based on next-generation sequencing technique called DArTseq™. A wide range of variation was observed for all traits in all environments. A total of 16 different association analysis models were compared to determine the best model for each trait-environment combination. Association mapping based on 18,824 high quality markers yielded 38 QTL for the 10 traits. Five of the detected QTL corresponded to known genes or fine mapped QTL. Among the 33 novel QTL identified, qDEC1.1 (qGLWR1.1), qBRR2.2 (qGL2.1), qTGW2.1 (qGL2.2), qGW11.1 (qMRR11.1) and qGL7.1 affected multiple traits with relatively large effects and/or were detected in multiple environments. The research provided an insight of the genetic architecture of rice grain quality and important information for mining genes/QTL with large effects within indica accessions for rice breeding.     

Convergent or parallel molecular evolution of momilactone A and B: potent allelochemicals, momilactones have been found only in rice and the moss Hypnum plumaeforme

Plant second metabolites momilactone A and B, which act as potent phytoalexins and allelochemicals, have been found thus far only in rice and the moss Hypnum plumaeforme, although both plants are taxonomically quite distinct. The concentrations of momilactone A and B, respectively, in rice plants were 4.5-140 and 2.9-85 μg/g, and those in H. plumaeforme were 8.4-58.7 and 4.2-23.4 μg/g. Momilactone A and B concentrations in rice and H. plumaeforme plants were increased by UV irradiation, elicitor and jasmonic acid treatments. Rice and H. plumaeforme plants secrete momilactone A and B into the rhizosphere, and the secretion level was also increased by UV irradiation, elicitor and jasmonic acid treatments. In addition, although endogenous concentrations of momilactone A in rice and H. plumaeforme were greater than those of momilactone B, the secretion levels of momilactone B were greater than those of momilactone A in rice and H. plumaeforme, which suggests that momilactone B may be selectively secreted by both rice and H. plumaeforme. As momilactone A and B exert potent antifungal and growth inhibitory activities, momilactone A and B may play an important role in the defense responses in H. plumaeforme and rice against pathogen infections and in allelopathy. The secretion of momilactone A and B into the rhizosphere may also prevent bacterial and fungal infections and provide a competitive advantage for nutrients through the inhibition of invading root systems of neighboring plants as allelochemicals. Therefore, both plants, despite their evolutionary distance, may use same defense strategy with respect to the momilactone A and B production and secretion, which resulting from convergent or parallel evolutionary processes. In the case of parallel evolution, there may be plant species providing the missing link in molecular evolution of momilactones between H. plumaeforme and rice.     

Observations on the Foliar Nematode,Aphelenchoides besseyi,Infecting Tuberose and Rice in India

The foliar nematode Aphelenchoides besseyi causes white tip disease in rice (Oryza sativa L.) and floral malady in tuberose (Polianthes tuberosa L.). This nematode is widely distributed in the rice fields of many states of India, including West Bengal (WB), Andhra Pradesh (AP), Madhya Pradesh (MP) and Gujarat (GT). In order to generate information on intraspecific variations of A. besseyi as well as to confirm the identity of the nematode species infecting these important crops, morphological observation was undertaken of A. besseyi isolated from tuberose and rice from WB and rice from AP, MP and GT. The molecular study was only done for rice and tuberose populations from AP and WB. The variations were observed among the populations in the tail, esophageal and anterior regions, including the occurrence of four as well as six lateral lines in the lateral fields. The morphometrics of observed populations showed variations and those could be regarded as a consequence of host-induced or geographical variations. PCR amplification of the rDNA ITS 1 and 2 region of rice (AP) and tuberose (WB) populations of A. besseyi generated one fragment of approximately 830 bp, and the size of the ITS region was 788 bp and 791 bp for tuberose and rice population, respectively. Alignment of the two sequences showed almost 100% similarity. Blast analysis revealed a very high level of similarity of both the Indian strains to a Russian population. The Indian and Russian strains could be differentiated using restriction enzyme Bccl. Host tests revealed that rice (cv. IET 4094), oat (cv. OS-6) and teosinte (cv. TL-1) showed a typical distortion due to the infection of A. besseyi. Five germplasm lines of oat showed no infection of the nematode under field conditions. Local cultivars of onion, maize, chrysanthemum, gladiolus, and Sorghum halepense were also not infected by A. besseyi.     

Molecular Evolution of the TAC1 Gene from Rice （Oryza sativa L.）

Tiller angle is a key feature of the architecture of cultivated rice(Oryza sativa),since it determines planting density and influences rice yield.Our previous work identified Tiller Angle Control 1(TACl) as a major quantitative trait locus that controls rice tiller angle.To further clarify the evolutionary characterization of the TACl gene,we compared a TACl-containing 3164-bp genomic region among 113 cultivated varieties and 48 accessions of wild rice,including 43 accessions of O.rufipogon and five accessions of O.nivara.Only one single nucleotide polymorphism(SNP),a synonymous substitution,was detected in TACl coding regions of the cultivated rice varieties, whereas one synonymous and one nonsynonymous SNP were detected among the TACl coding regions of wild rice accessions.These data indicate that little natural mutation and modification in the TACl coding region occurred within the cultivated rice and its progenitor during evolution.Nucleotide diversities in the TACl gene regions of O.sativa and O.rufipogon of 0.00116 and 0.00112,respectively, further indicate that TACl has been highly conserved during the course of rice domestication.A functional nucleotide polymorphism (FNP) of TACl was only found in the japonica rice group.A neutrality test revealed strong selection,especially in the 3’-flanking region of the TACl coding region containing the FNP in the japonica rice group.However,no selection occurred in the indica and wild-rice groups.A phylogenetic tree derived from TACl sequence analysis suggests that the indica and japonica subspecies arose independently during the domestication of wild rice.     

Occurrence of Aphelenchoides besseyi in Louisiana Rice Seed and Its Interaction with Sclerotium oryzae in Selected Cultivars

Aphelenchoides besseyi, the nematode causal agent of white-tip disease of rice, was recovered from 5.5% of 474 seed samples obtained from rice seed warehouses in Louisiana. Laboratory tests in which A. besseyi-infested rice seed was treated with Phostoxin®, a compound used for control of insects in stored grain, indicate that it also has nematicidal properties. In 18-week-duration greenhouse tests, populations of A. besseyi increased 4-5-fold on the cultivars Saturn and Melrose and 3-fold on Nova ''76. Green weights of Nova ''76 plants inoculated with A. besseyi and Sclerotium oryzae, the causal agent of rice stem rot, were significantly reduced below those of plants inoculated with either organism alone or with distilled water. Weights of Melrose plants were reduced significantly by treatments with A. besseyi alone and A. besseyi plus S. oryzae, but not by S. oryzae alone. Saturn plant weights were not reduced significantly by either organism alone or by the two in combination.     

Resistance of transgenic rice events (rbcS:cry1Ac) against three lepidopteran rice pests

The transgenic rice expressing cry1Ac gene, which is linked to the rice rbcS promoter and its transit peptide sequence (tp), was highly resistant against all instars of Cnaphalocrocis medinalis (Guenetée) (Lepidoptera: Crambidae). In this study, we evaluated the larval mortality, behavior change, and field occurrence of three main rice pests, C. medinalis, Naranga aenescens (Moore) (Lepidoptera: Noctuidae), and Parnara guttata (Bremer & Grey) (Lepidoptera: Hesperiidae) in T4 generations of three Bt rice events (rbcS3:cry1Ac; 608102, 608104 and 608107) and non-Bt rice. All of the three Bt rice events were resistant to C. medinalis which showed significantly higher mortality for all instars compared to non-Bt rice. The resistance of Bt rice events against the larvae decreased gradually as the larvae developed. However, the survived larvae which ingested Bt rice events died eventually without further development. The resistance of three Bt rice events was investigated in the pot test, which was conducted with 3rd instars of C. medinalis, N. aenescens, and P. guttata, showed mortalities of over 70%. In behavioral assay, C. medinalis fed on the Bt rice events showed feeding avoidance and less leaf rolling behavior compared to that of the larvae fed on non-Bt rice. A 2-yr field survey conducted with larvae of C. medinalis and P. guttata also showed that the three Bt rice events significantly had lower damaged on leaves compared to that of non-Bt rice. Overall, the three Bt rice events were highly resistant to the larvae of lepidopteran target rice pests.     

Reciprocal adaptation of rice and Xanthomonas oryzae pv. oryzae: cross-species 2D GWAS reveals the underlying genetics

A 1D/2D genome-wide association study strategy was adopted to investigate the genetic systems underlying the reciprocal adaptation of rice (Oryza sativa) and its bacterial pathogen, Xanthomonas oryzae pv. oryzae (Xoo) using the whole-genome sequencing and large-scale phenotyping data of 701 rice accessions and 23 diverse Xoo strains. Forty-seven Xoo virulence-related genes and 318 rice quantitative resistance genes (QR-genes) mainly located in 41 genomic regions, and genome-wide interactions between the detected virulence-related genes and QR genes were identified, including well-known resistance genes/virulence genes plus many previously uncharacterized ones. The relationship between rice and Xoo was characterized by strong differentiation among Xoo races corresponding to the subspecific differentiation of rice, by strong shifts toward increased resistance/virulence of rice/Xoo populations and by rich genetic diversity at the detected rice QR-genes and Xoo virulence genes, and by genome-wide interactions between many rice QR-genes and Xoo virulence genes in a multiple-to-multiple manner, presumably resulting either from direct protein–protein interactions or from genetic epistasis. The observed complex genetic interaction system between rice and Xoo likely exists in other crop–pathogen systems that would maintain high levels of diversity at their QR-loci/virulence-loci, resulting in dynamic coevolutionary consequences during their reciprocal adaptation.

A complex system of genetic interactions leads to reciprocal adaptation between rice and its bacterial pathogen, Xanthomonas oryzae pv. oryzae.     

Protein-Protein Interactions of Tandem Affinity Purified Protein Kinases from Rice

Eighty-eight rice (Oryza sativa) cDNAs encoding rice leaf expressed protein kinases (PKs) were fused to a Tandem Affinity Purification tag (TAP-tag) and expressed in transgenic rice plants. The TAP-tagged PKs and interacting proteins were purified from the T1 progeny of the transgenic rice plants and identified by tandem mass spectrometry. Forty-five TAP-tagged PKs were recovered in this study and thirteen of these were found to interact with other rice proteins with a high probability score. In vivo phosphorylated sites were found for three of the PKs. A comparison of the TAP-tagged data from a combined analysis of 129 TAP-tagged rice protein kinases with a concurrent screen using yeast two hybrid methods identified an evolutionarily new rice protein that interacts with the well conserved cell division cycle 2 (CDC2) protein complex.     

Marker-assisted breeding of Xa4, Xa21 and Xa27 in the restorer lines of hybrid rice for broad-spectrum and enhanced disease resistance to bacterial blight

Hybrid rice based on heterosis can significantly increase rice yield compared to inbred rice. Bacterial blight (BB) of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most destructive bacterial diseases that affect hybrid rice production. To breed a broad-spectrum and high disease resistance to BB in hybrid rice, we introduced the Xa4, Xa21 and Xa27 genes into the restorer lines of Mianhui 725 or 9311 genetic backgrounds and pyramided the three R genes in the progeny derived from the cross between the two lines. A near-isogenic line of the Xa27 gene in the genetic background of 9311 [9311(Xa27)] and another line with the Xa4 and Xa21 genes in the genetic background of Mianhui 725 (WH421) were firstly developed through marker-assisted selection. A new restorer line carrying Xa4, Xa21 and Xa27, designated as XH2431, was selected from the F8 progeny of the cross between 9311(Xa27) and WH421 through marker-assisted breeding and pedigree selection. XH2431 and II You 2431, the hybrids derived from cytoplasmic male-sterile line II-32A and restorer line XH2431, conferred high resistance to all 23 Xoo strains collected from 10 countries. XH2431 restored the fertility of II-32A to the normal level in the F1 generation. In addition, II You 2431 showed good agronomic traits under greenhouse conditions. The development of XH2431, 9311(Xa27) and WH421 provides a set of restorer lines with broad-spectrum and enhanced resistance to BB for hybrid rice.     

Profiling of selected indigenous rice (Oryza sativa L.) landraces of Rarh Bengal in relation to osmotic stress tolerance

A total of ten rare indigenous rice landraces of West Bengal were screened for germination potential and seedling growth under varying concentrations of sodium chloride (NaCl) and polyethylene glycol (PEG) solutions as osmotic stress inducing agents. Among the studied rice landraces Kelas and Bhut Moori showed highest degree of tolerance to induced osmotic stresses. Proline content of the studied lines was also determined. Genetic relationship among the studied rice landraces was assessed with 22 previously reported osmotic stress tolerance linked Simple Sequence Repeat (SSR) markers. The identified allelic variants in form of amplified products size (molecular weight) for each SSR marker were documented to find out allele mining set for the linked markers of the studied genotypes in relation to osmotic stress tolerance. A Microsatellite Panel was constructed for the different allelic forms (size of amplified products) of each used marker. Among 22 SSR markers, ten showed unique alleles in form of single specific amplified product for the studied four genotypes which can be used for varietal identification. Genetic relationship among the studied rice lines was determined and a dendrogram was constructed to reveal their genetic inter-relationship. Polymorphism Information Content (PIC) for each used marker was also calculated for the studied rice lines.     

Functional conservation of the glycosyltransferase gene GT47A in the monocot rice

Glucuronoarabinoxylan is the major hemicellulose in grass cell walls, yet the mechanism of xylan synthesis in monocot plants is still unclear. Unraveling the genes involved in the biosynthesis of xylan in rice will be very important for the utilization of rice straw as a source of bioenergy in the future. In this report, we investigated the functional role of a rice gene homologous to Arabidopsis IRREGULAR XYLEM10 (IRX10), belonging to the glycosyl transferase (GT) gene family 47 (GT47), in the biosynthesis of xylan. The protein sequence of OsGT47A from rice exhibits a 93.49 % similarity to IRX10, which is involved in the biosynthesis of glucuronoxylan in Arabidopsis. Phylogenetic analysis of the GT47 glycosyl transferase family in the rice genome revealed that OsGT47A is a closely related homolog of IRX10 and IRX10L. Expression pattern analysis showed that the OsGT47A gene is highly expressed in the rice stem. Overexpression of OsGT47A in the irx10 irx10L double mutant rescued the plant growth phenotype and restored secondary wall thickness. Analysis of monosaccharides indicated that the rescued plants had levels of xylose identical to those of the wild type plants, and the fluorescence signals were restored in the complementation plants by xylan immunolocalization. The OsGT47A complementation under the native promoter of Arabidopsis IRX10L (ProIRX10L) partially rescued the double mutant, indicating that OsGT47A is functionally equivalent to IRX10L. Together, these results suggest that the IRX10 homolog OsGT47A exhibits functional conservation and is most likely involved in xylan synthesis in rice.     

Isolation and Characterization of a Chitinase and its cDNA Clone from Rice

A 35 kD chitinase has been purified to apparent homogeneity from extracts of rice bran of cv New Bonnet by ammonium sulfate fractionation, chitin affinity chromatography, cation exchange chromatography on carboxymethyl cellulose and gel filtration. The purified enzyme has an isoelectric point of 8.8. The enzyme inhibited the growth of Rhizoctonia solani (the sheath blight pathogen), Trichoderma viride, T. harzianum, Fusarium graminaerum and F. culmorum in vitro. A cDNA clone for chitinase was isolated from a developing rice seed cDNA library by probing with a barley chitinase cDNA probe. The nucleotide sequence of this 654 bp clone was determined, it contains an open reading frame of 519 nucleotides. The protein product encoded by this clone is homologous to chitinases from tobacco, bean and barley. Southern blot analysis of rice genomic DNA with this probe revealed that chitinases are encoded by a small multi-gene family in the rice genome.