论文信息 - Transgenic rice seed synthesizing diverse flavonoids at high levels: a new platform for flavonoid production with associated health benefits.

2004

MitoNuc : a database of nuclear genes encoding for mitochondrial proteins

Introduction Mitochondria are sub-cellular organelles, present in the majority of eukaryotic organisms, which play a central role in the energy metabolisms of cells. They are also involved in many other cellar processes such as apoptosis, aging and in a number of different human diseases, including Parkinson’s, diabetes mellitus and Alzheimer’s. Despite to their importance in the cell life maintenance, about the 95% of proteins, contributing to mitochondrial biogenesis and functional activities, are nuclear encoded, synthesized in the cytosol and targeted to mitochondria. The expression and assembling of these proteins are strictly dependent by the coordinated activities of the two genomes, mitochondrial and nuclear, but the molecular mechanisms and co-evolutionary processes of the cross-talk between these two genomes are still largely unknown. MitoNuc [1] is a specialized database of nuclear encoded mitochondrial proteins in Metazoa. It provides comprehensive data on genes and proteins consolidating information from external databases. These data include: gene sequence, structure and information from ENSEMBL [2], protein sequence and information from SWISSPROT [3], transcript sequence and structure from RefSeq [4] and UTRdb [5], disease information from OMIM [6]. Each database entry consists of a nuclear gene coding for a mitochondrial protein in a given species, and reports information on: species name and taxonomic classification; gene name, functional product, sub-cellular mitochondrial localization, protein tissue specificity, Enzyme Classification (EC) code for enzyme and disease data related to protein dysfunction. For each gene and gene product the Gene Ontology (GO) classification [7] with regard to molecular function, biological processes and cellular component is reported too. Links to external database resources are also provided. As far as the gene and transcript sequences data are concerned, in the previous MitoNuc releases they were extracted from the EMBL [8] related entries. Due to the high level of sequences redundancy in the primary database, the majority of MitoNuc entries contained more than one transcript and coding gene sequence for the same gene, thus introducing a remarkable redundancy level that affects the effectiveness of the database for sequence analysis aims. In order to remove redundancy we generated a MitoNuc section of gene and transcript sequences derived from those organisms whose genome sequence draft has been completed and annotated in ENSEMBL. These MitoNuc entries are available in the database section called “MitoNuc Genomics” that, at present, include the following species: Homo sapiens, Rattus Norvegicus and Mus Musculus. MitoNuc can be queried using the SRS Retrieval System [9] (http://www.ba.itb.cnr.it/srs/); the present release contains a total of 1344 entries among which 662 are collected in the MitoNuc Genomic section. The total number of species included in MitoNuc is about 64.

2020 - GM crops & food

Enhanced yield performance of transgenic cry1C* rice in saline-alkaline soil.

China has a large area of saline-alkaline land that can be utilized for the cultivation of transgenic rice. Therefore, the growth and reproductive behavior of transgenic rice are not only a problem for production that needs to be resolved, but also an important aspect of environmental risk assessment for saline alkali soil. In the present study, an insect-resistant transgenic cry1C* rice, T1C-19, was grown in farmland and saline-alkaline soils. The transcription and translation of the exogenous cry1C*, and vegetative and reproductive fitness, such as plant height, tiller number, biomass, filled grain number and weight per plant, were assessed. Our findings indicated that the transcription and translation of exogenous cry1C* gene in T1C-19 rice grown in saline-alkaline soil were lower than that grown in farmland; however, the correlation was not significant. The vegetative and reproductive growth abilities of T1C-19 were lower than that of the parental rice, Minghui63 (MH63), in farmland. In alkaline-saline soil, except for tiller number and biomass, there were no significant differences between T1C-19 and MH63 in other vegetative indices. In contrast, the reproductive indices of T1C-19 were significantly higher than those of MH63. The results suggested that T1C-19 had a strong reproductive capacity, and significantly reduced the loss of yield caused by insects, thereby leading to a higher yield than that of MH63 grown in saline-alkaline soils. This may promote the cultivation of saline-alkaline soil to permit farming of T1C-19 in China in the future, despite the possible increased ecological risks.

2017 - Journal of Wildlife Management

Seed density and waterfowl use of rice fields in Camargue, France

European rice fields provide potential nocturnal foraging habitat to waterfowl during winter. Agricultural practices may influence seed density and accessibility, thereby influencing the extent to which ducks use this managed habitat. To assess the potential influence of post-harvest stubble-management practices (i.e., flooding, burning, chopping, disking, plowing, and their combinations) on waste rice and weeds, and to evaluate the link of the latter 2 with nocturnal duck abundance, we conducted an experiment in rice fields of the Camargue, France. We assessed the density of available seeds 3 times across the winter, from harvest in late October to departure of the wintering ducks in early February, over 2 winters (2012–2013, 2013–2014). We monitored nocturnal duck use of the fields during the second year. Initial post-harvest rice and weed seed densities were positively correlated and highly variable. Mean seed density was not dependent on straw management procedure (i.e., burning, chopping, disking). Average rice density decreased by 89% and weed seed density by 69% between harvest and late winter. Seed depletion rate was dependent on initial seed density, and was greatest in plowed fields for rice. Winter flooding did not significantly affect seed depletion rate but was the main determinant of nocturnal duck use of the fields. Duck numbers were lower in burned fields than in chopped or disked fields. One hectare of rice field could support an average of 43 mallard (Anas platyrhynchos)-sized ducks/day for the entire wintering season (i.e., 5,202 duck-energy days/ha) given initial post-harvest seed densities. Harvested rice fields have a great potential as nocturnal foraging habitat for wintering ducks in the Camargue. Plowing should be avoided and flooding promoted to better allow ducks to use these fields. © 2016 The Wildlife Society.

2020 - Frontiers in Plant Science

Deployment of Genetic and Genomic Tools Toward Gaining a Better Understanding of Rice-Xanthomonas oryzae pv. oryzae Interactions for Development of Durable Bacterial Blight Resistant Rice

Rice is the most important food crop worldwide and sustainable rice production is important for ensuring global food security. Biotic stresses limit rice production significantly and among them, bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae (Xoo) is very important. BB reduces rice yields severely in the highly productive irrigated and rainfed lowland ecosystems and in recent years; the disease is spreading fast to other rice growing ecosystems as well. Being a vascular pathogen, Xoo interferes with a range of physiological and biochemical exchange processes in rice. The response of rice to Xoo involves specific interactions between resistance (R) genes of rice and avirulence (Avr) genes of Xoo, covering most of the resistance genes except the recessive ones. The genetic basis of resistance to BB in rice has been studied intensively, and at least 44 genes conferring resistance to BB have been identified, and many resistant rice cultivars and hybrids have been developed and released worldwide. However, the existence and emergence of new virulent isolates of Xoo in the realm of a rapidly changing climate necessitates identification of novel broad-spectrum resistance genes and intensification of gene-deployment strategies. This review discusses about the origin and occurrence of BB in rice, interactions between Xoo and rice, the important roles of resistance genes in plant’s defense response, the contribution of rice resistance genes toward development of disease resistance varieties, identification and characterization of novel, and broad-spectrum BB resistance genes from wild species of Oryza and also presents a perspective on potential strategies to achieve the goal of sustainable disease management.

2014 - BMC Genomics

Genome sequencing and comparative analysis of three Chlamydia pecorum strains associated with different pathogenic outcomes

BackgroundChlamydia pecorum is the causative agent of a number of acute diseases, but most often causes persistent, subclinical infection in ruminants, swine and birds. In this study, the genome sequences of three C. pecorum strains isolated from the faeces of a sheep with inapparent enteric infection (strain W73), from the synovial fluid of a sheep with polyarthritis (strain P787) and from a cervical swab taken from a cow with metritis (strain PV3056/3) were determined using Illumina/Solexa and Roche 454 genome sequencing.ResultsGene order and synteny was almost identical between C. pecorum strains and C. psittaci. Differences between C. pecorum and other chlamydiae occurred at a number of loci, including the plasticity zone, which contained a MAC/perforin domain protein, two copies of a >3400 amino acid putative cytotoxin gene and four (PV3056/3) or five (P787 and W73) genes encoding phospholipase D. Chlamydia pecorum contains an almost intact tryptophan biosynthesis operon encoding trpABCDFR and has the ability to sequester kynurenine from its host, however it lacks the genes folA, folKP and folB required for folate metabolism found in other chlamydiae. A total of 15 polymorphic membrane proteins were identified, belonging to six pmp families. Strains possess an intact type III secretion system composed of 18 structural genes and accessory proteins, however a number of putative inc effector proteins widely distributed in chlamydiae are absent from C. pecorum. Two genes encoding the hypothetical protein ORF663 and IncA contain variable numbers of repeat sequences that could be associated with persistence of infection.ConclusionsGenome sequencing of three C. pecorum strains, originating from animals with different disease manifestations, has identified differences in ORF663 and pseudogene content between strains and has identified genes and metabolic traits that may influence intracellular survival, pathogenicity and evasion of the host immune system.

2015 - Oncology letters

Expression changes of cell-cell adhesion-related genes in colorectal tumors.

Epithelial tissues achieve a highly organized structure due to cell-cell junction complexes. Carcinogenesis is accompanied by changes in cell interactions and tissue morphology, which appear in the early stages of benign tumors and progress along with invasive potential. The aim of the present study was to analyze the changes in expression levels of genes encoding intercellular junction proteins that have been previously identified to be differentially expressed in colorectal tumors compared with normal mucosa samples (fold change, >2.5) in genome-wide expression profiling. The expression of 20 selected genes was assessed using quantitative reverse transcription polymerase chain reaction in 26 colorectal cancer, 42 adenoma and 24 normal mucosa samples. Between these tissue types, differences were observed in the mRNA levels of genes encoding adherens junction proteins (upregulation of CDH3 and CDH11, and downregulation of CDH19 and PTPRF), tight junction proteins (upregulation of CLDN1 and CLDN2, and downregulation of CLDN5, CLDN8, CLDN23, CLDN15, JAM2 and CGN) and desmosomes (upregulation of DSC3 and DSG3, and downregulation of DSC2), in addition to a decrease in the expression of certain other genes involved in intercellular connections: PCDHB14, PCDH7, MUPCDH and NEO1. The differences between tissue types were statistically significant, and separate clustering of normal adenoma and carcinoma samples was observed in a hierarchical clustering analysis. These results indicate that the morphological changes in neoplastic colon tissue that occur during the 'adenoma-carcinoma sequence' are accompanied by specific changes in the expression of multiple genes encoding the majority of cell-cell junction complexes. The particular differential expression patterns appear to be consistent among patients with cancer and adenoma, in addition to normal mucosa samples.

2009 - Chinese Science Bulletin

Review and prospect of transgenic rice research

Rice is one of the most important crops as the staple food for more than half of the world’s population. Rice improvement has achieved remarkable success in the past half-century, with the yield doubled in most parts of the world and even tripled in certain regions, which has contributed greatly to food security globally. Rapid population growth and economic development pose a constantly increased food requirement. However, rice yield has been hovering in the past decade, which is mainly caused by the absence of novel breeding technologies, reduction of genetic diversity of rice cultivars, and serious yield loss due to increasingly severe occurrences of insects, diseases, and abiotic stresses. To address these challenges, Chinese scientists proposed a novel rice breeding goal of developing Green Super Rice to improve rice varieties and realize the sustainable development of agriculture, by focusing on the following 5 classes of traits: insect and disease resistance, drought-tolerance, nutrient-use efficiency, quality and yield potential. As a modern breeding approach, transgenic strategy will play an important role in realizing the goal of Green Super Rice. Presently, many transgenic studies of rice have been conducted, and most of target traits are consistent with the goal of Green Super Rice. In this paper, we firstly review technical advances of rice transformation, and then outline the main progress in transgenic rice research with respect to the most important traits: insect and disease-resistance, drought-tolerance, nutrient-use efficiency, quality, yield potential and herbicide-tolerance. The prospects of developing transgenic rice are also discussed.

2016

Inhibitory Effects of Organic Extracts against Aspergilus flavus and Their Comparative Efficacy upon Germination of Infested Rice Seeds

Aspergilus flavus is the most common seed born fungus that deteriorates the seed quality and minimizes the export value of rice all over the world. As the excessive use of chemicals worldwide has proved lethal environmentally so the present study was carried out to evaluate different organic extracts against fungal growth and their effects in improving the germination percentage of infested rice seeds. The experiment was carried out in-vitro using four different concentrations (2, 4, 6, 8%) of organic extracts as compared to control in a completely randomized design and all the data was subject to statistical analysis. Regarding mycelial growth, higher concentrations of plant extracts were significantly better as statistical results revealed that the organic extracts of Neem and Brassica were proved better and comparative to each other followed by activity of Diver (Mineral Oil), Onion and Garlic extracts. Similarly, the performance of Brassica and Neem extracts were recorded better regarding improvement in germination percentage of infested rice seeds as compared to Diver, Onion and garlic extracts. Hence we suggest avoiding the dangerous chemicals and use the organic extracts to manage the particular fungus efficiently and safely.

2006 - Developmental biology

RTK and TGF-beta signaling pathways genes in the sea urchin genome.

The Receptor Tyrosine kinase (RTK) and TGF-beta signaling pathways play essential roles during development in many organisms and regulate a plethora of cellular responses. From the genome sequence of Strongylocentrotus purpuratus, we have made an inventory of the genes encoding receptor tyrosine kinases and their ligands, and of the genes encoding cytokines of the TGF-beta superfamily and their downstream components. The sea urchin genome contains at least 20 genes coding for canonical receptor tyrosine kinases. Seventeen of the nineteen vertebrate RTK families are represented in the sea urchin. Fourteen of these RTK among which ALK, CCK4/PTK7, DDR, EGFR, EPH, LMR, MET/RON, MUSK, RET, ROR, ROS, RYK, TIE and TRK are present as single copy genes while pairs of related genes are present for VEGFR, FGFR and INSR. Similarly, nearly all the subfamilies of TGF-beta ligands identified in vertebrates are present in the sea urchin genome including the BMP, ADMP, GDF, Activin, Myostatin, Nodal and Lefty, as well as the TGF-beta sensu stricto that had not been characterized in invertebrates so far. Expression analysis indicates that the early expression of nodal, BMP2/4 and lefty is restricted to the oral ectoderm reflecting their role in providing positional information along the oral-aboral axis of the embryo. The coincidence between the emergence of TGF-beta-related factors such as Nodal and Lefty and the emergence of the deuterostome lineage strongly suggests that the ancestral function of Nodal could have been related to the secondary opening of the mouth which characterizes this clade, a hypothesis supported by functional data in the extant species. The sea urchin genome contains 6 genes encoding TGF-beta receptors and 4 genes encoding prototypical Smad proteins. Furthermore, most of the transcriptional activators and repressors shown to interact with Smads in vertebrates have orthologues in echinoderms. Finally, the sea urchin genome contains an almost complete repertoire of genes encoding extracellular modulators of BMP signaling including Chordin, Noggin, Sclerotin, SFRP, Gremlin, DAN and Twisted gastrulation. Taken together, these findings indicate that the sea urchin complement of genes of the RTK and TGF-beta signaling pathways is qualitatively very similar to the repertoire present in vertebrates, and that these genes are part of the common genetool kit for intercellular signaling of deuterostomes.

2011 - PLoS Neglected Tropical Diseases

Gene Expression Patterns in Larval Schistosoma mansoni Associated with Infection of the Mammalian Host

Background The infective schistosome cercaria develops within the intramolluscan daughter sporocyst from an undifferentiated germ ball, during which synthesis of proteins essential for infection occurs. When the aquatic cercaria locates the mammalian host it rapidly penetrates into the epidermis using glandular secretions. It then undergoes metamorphosis into the schistosomulum, including replacement of its tegument surface membranes, a process taking several days before it exits the skin. Patterns of gene expression underlying this transition have been characterised. Methods and Principal Findings All gene models from the S. mansoni genome (www.GeneDB.org) were incorporated into a high-density oligonucleotide array. Double-stranded cDNA from germ balls, cercariae, and day 3 schistosomula was hybridised to the array without amplification. Statistical analysis was performed using Bioconductor to reveal differentially transcribed loci. Genes were categorised on the basis of biological process, tissue association or molecular function to aid understanding of the complex processes occurring. Genes necessary for DNA replication were enriched only in the germ ball, while those involved in translation were up-regulated in the germ ball and/or day 3 schistosomulum. Different sets of developmental genes were up-regulated at each stage. A large number of genes encoding elastases and invadolysins, and some venom allergen-like proteins were up-regulated in the germ ball, those encoding cysteine and aspartic proteases in the cercaria and schistosomulum. Micro exon genes encoding variant secreted proteins were highly up-regulated in the schistosomulum along with tegument and gut-associated genes, coincident with remodelling of the parasite body. Genes encoding membrane proteins were prominently up-regulated in the cercaria and/or day 3 schistosomulum. Conclusions/Significance Our study highlights an expanded number of transcripts encoding proteins potentially involved in skin invasion. It illuminates the process of metamorphosis into the schistosomulum and highlights the very early activation of gut-associated genes whilst revealing little change in the parasite's energy metabolism or stress responses.

2011 - Pakistan Journal of Weed Science Research

Control of weedy rice in direct-seeded rice using the clearfield production system in Malaysia.

Weedy rice (Oryza sativa complex) is a serious threat to directseeded culture in Malaysia because of its taxonomic and physiological similarities to cultivated rice. This weedy rice problem was first observed in 1988 but later became widespread and prevalent in rice cultivation in the 2000’s. Farmers have considered weedy rice as of significant importance and a serious threat since no selective herbicide was available for controlling it prior to the advent of an imidazolinone tolerant variety (IMI-TR). The development of local IMI-TR rice, a collaborative project between MARDI and BASF (Malaysia) Sdn Bhd, started in 2003 at MARDI Station in Penang. IMI-TR Line No. 1770 from USA was crossed with a popular local rice cultivar MR 220 using conventional breeding techniques. The goal of the project is to offer farmers an effective and farmer friendly solution to the weedy rice problem with minimal changes to their normal practices. Two locally developed IMI-TR varieties namely MR 220CL1 and MR 220CL2 together with the technique known as Clearfield Production System (CPS) were officially launched on the 8 th July 2010 in FELCRA Seberang Perak rice granary. This CPS for rice was the first launch in Malaysia as well as in the Asia Pacific Region. This system is justified by the need to offer an innovative alternative method to manage weedy rice in wet-seeding culture. The CPS package for rice consists of three main components namely Clearfield certified seeds, OnDuty herbicide (imazapic/imazapyr) and the Stewardship Guide. The seeds are supplied in standard 20 kg bags while the OnDuty herbicide is packed in a box of 4 sachets of 31 g each. The seed rate per ha is 7 bags (140 kg/ha) which is the normal seed rate used by farmers. The seeds and OnDuty herbicide are sold together as a package to ensure that; a) both seeds and herbicides are available together at all times, b) OnDuty herbicide and seeds are applied at the correct rate, and c) the correct variety together with the correct herbicide are used. To ensure successful crop establishment and attainment of high yield of Clearfield rice varieties, standard good agricultural practices have to be implemented and followed from sowing to harvesting. All these practices are basically similar to practices currently adopted by farmers in Malaysia.

2005 - Nature

Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5′- and 3′-halves

Analysis of the genome sequence of the small hyperthermophilic archaeal parasite Nanoarchaeum equitans has not revealed genes encoding the glutamate, histidine, tryptophan and initiator methionine transfer RNA species. Here we develop a computational approach to genome analysis that searches for widely separated genes encoding tRNA halves that, on the basis of structural prediction, could form intact tRNA molecules. A search of the N. equitans genome reveals nine genes that encode tRNA halves; together they account for the missing tRNA genes. The tRNA sequences are split after the anticodon-adjacent position 37, the normal location of tRNA introns. The terminal sequences can be accommodated in an intervening sequence that includes a 12–14-nucleotide GC-rich RNA duplex between the end of the 5′ tRNA half and the beginning of the 3′ tRNA half. Reverse transcriptase polymerase chain reaction and aminoacylation experiments of N. equitans tRNA demonstrated maturation to full-size tRNA and acceptor activity of the tRNAHis and tRNAGlu species predicted in silico. As the joining mechanism possibly involves tRNA trans-splicing, the presence of an intron might have been required for early tRNA synthesis.

2008 - Proceedings of the National Academy of Sciences

A transcript profiling approach reveals an epicatechin-specific glucosyltransferase expressed in the seed coat of Medicago truncatula

Expression of the Arabidopsis TRANSPARENT TESTA 2 (TT2) MYB family transcription factor leads to massive accumulation of proanthocyanidins (PAs) in hairy roots of Medicago truncatula. Microarray analysis showed that TT2 induces genes for flavonoid/PA biosynthesis, transcription factors, and a large number of genes of unknown function. A second microarray dataset identified genes that were preferentially expressed in the M. truncatula seed coat. Comparison of the two datasets defines target genes for steps that are yet unidentified in PA biosynthesis and accumulation. Of these genes, a glycosyltransferase, UGT72L1, was active specifically toward the PA precursor (−)−epicatechin, and its expression pattern in developing seeds correlated with the presence of epicatechin glucoside and accumulation of PAs. UGT72L1 may be involved in the production of epicatechin 3′-O-glucoside in the seed coat as a key step in PA biosynthesis or its regulation.

2002 - Trends in microbiology

Surface proteins and the pathogenic potential of Listeria monocytogenes.

On the basis of the recently determined genome sequence of Listeria monocytogenes, we performed a global analysis of the surface-protein-encoding genes. Only proteins displaying a signal peptide were taken into account. Forty-one genes encoding LPXTG proteins, including the previously known internalin gene family, were detected. Several genes encoding proteins that, like InlB and Ami, possess GW modules that attach them to lipoteichoic acids were also identified. Additionally, the completed genome sequence revealed genes encoding proteins potentially anchored in the cell membrane by a hydrophobic tail as well as genes encoding P60-like proteins and lipoproteins. We describe these families and discuss their putative implications for host-pathogen interactions.

2012 - Plant Physiology

Dynamic Nucleotide-Binding Site and Leucine-Rich Repeat-Encoding Genes in the Grass Family1[C][W][OA]

The proper use of resistance genes (R genes) requires a comprehensive understanding of their genomics and evolution. We analyzed genes encoding nucleotide-binding sites and leucine-rich repeats in the genomes of rice (Oryza sativa), maize (Zea mays), sorghum (Sorghum bicolor), and Brachypodium distachyon. Frequent deletions and translocations of R genes generated prevalent presence/absence polymorphism between different accessions/species. The deletions were caused by unequal crossover, homologous repair, nonhomologous repair, or other unknown mechanisms. R gene loci identified from different genomes were mapped onto the chromosomes of rice cv Nipponbare using comparative genomics, resulting in an integrated map of 495 R loci. Sequence analysis of R genes from the partially sequenced genomes of an African rice cultivar and 10 wild accessions suggested that there are many additional R gene lineages in the AA genome of Oryza. The R genes with chimeric structures (termed type I R genes) are diverse in different rice accessions but only account for 5.8% of all R genes in the Nipponbare genome. In contrast, the vast majority of R genes in the rice genome are type II R genes, which are highly conserved in different accessions. Surprisingly, pseudogene-causing mutations in some type II lineages are often conserved, indicating that their conservations were not due to their functions. Functional R genes cloned from rice so far have more type II R genes than type I R genes, but type I R genes are predicted to contribute considerable diversity in wild species. Type I R genes tend to reduce the microsynteny of their flanking regions significantly more than type II R genes, and their flanking regions have slightly but significantly lower G/C content than those of type II R genes.

2011 - Plant Cell

Positive Autoregulation of a KNOX Gene Is Essential for Shoot Apical Meristem Maintenance in Rice[W][OA]

This work reveals that rice KNOX genes OSH1 and OSH15 are required for shoot apical meristem (SAM) formation and maintenance and that KNOX gene expression is positively and directly regulated by OSH1 through evolutionarily conserved cis-elements. This is thought to be a novel mechanism that is indispensable for self-maintenance of the SAM. Self-maintenance of the shoot apical meristem (SAM), from which aerial organs are formed throughout the life cycle, is crucial in plant development. Class I Knotted1-like homeobox (KNOX) genes restrict cell differentiation and play an indispensable role in maintaining the SAM. However, the mechanism that positively regulates their expression is unknown. Here, we show that expression of a rice (Oryza sativa) KNOX gene, Oryza sativa homeobox1 (OSH1), is positively regulated by direct autoregulation. Interestingly, loss-of-function mutants of OSH1 lose the SAM just after germination but can be rescued to grow until reproductive development when they are regenerated from callus. Double mutants of osh1 and d6, a loss-of-function mutant of OSH15, fail to establish the SAM both in embryogenesis and regeneration. Expression analyses in these mutants reveal that KNOX gene expression is positively regulated by the phytohormone cytokinin and by KNOX genes themselves. We demonstrate that OSH1 directly binds to five KNOX loci, including OSH1 and OSH15, through evolutionarily conserved cis-elements and that the positive autoregulation of OSH1 is indispensable for its own expression and SAM maintenance. Thus, the maintenance of the indeterminate state mediated by positive autoregulation of a KNOX gene is an indispensable mechanism of self-maintenance of the SAM.

2010 - BMC Research Notes

Expression analysis of flavonoid biosynthesis genes during Arabidopsis thaliana silique and seed development with a primary focus on the proanthocyanidin biosynthetic pathway

BackgroundThe coordinated activity of different flavonoid biosynthesis genes in Arabidopsis thaliana results in tissue-specific accumulation of flavonols, anthocyanins and proanthocyanidins (PAs). These compounds possess diverse functions in plants including light-attenuation and oxidative stress protection. Flavonoids accumulate in a stimulus- and/or development-dependent manner in specific parts of the plant. PAs accumulate in the seed coat (testa).FindingsWe describe the biological material and the preparation of total RNA for the AtGenExpress developmental silique and seed series. AtGenExpress ATH1 GeneChip expression data from the different stages were reanalyzed and verified using quantitative real time PCR (qPCR). We observed organ-specific transcript accumulation of specific flavonoid biosynthetic genes consistent with previously published data and our PA compound accumulation data. In addition, we investigated the regulation of PA accumulation in developing A. thaliana seeds by correlating gene expression patterns of specific flavonoid biosynthesis genes with different seed embryonic developmental stages and organs and present two useful marker genes for isolated valve and replum organs, as well as one seed-specific marker.ConclusionsPotential caveats of array-based expression data are discussed based on comparisons with qPCR data. Results from ATH1 microarray and qPCR experiments revealed a shift in gene activity from general flavonoid biosynthesis at early stages of seed development to PA synthesis at late (mature) stages of embryogenesis. The examined PA accumulation-associated genes, including biosynthetic and regulatory genes, were found to be exclusively expressed in immature seeds. Accumulation of PAs initiates at the early heart stage of silique and seed development. Our findings provide new insights for further studies targeting the PA pathway in seeds.

2000 - Plant Cell

The Complete Sequence of 340 kb of DNA around the Rice Adh1–Adh2 Region Reveals Interrupted Colinearity with Maize Chromosome 4

A 2.3-centimorgan (cM) segment of rice chromosome 11 consisting of 340 kb of DNA sequence around the alcohol dehydrogenase Adh1 and Adh2 loci was completely sequenced, revealing the presence of 33 putative genes, including several apparently involved in disease resistance. Fourteen of the genes were confirmed by identifying the corresponding transcripts. Five genes, spanning 1.9 cM of the region, cross-hybridized with maize genomic DNA and were genetically mapped in maize, revealing a stretch of colinearity with maize chromosome 4. The Adh1 gene marked one significant interruption. This gene mapped to maize chromosome 1, indicating a possible translocation of Adh1 after the evolutionary divergence leading to maize and sorghum. Several other genes, most notably genes similar to known disease resistance genes, showed no cross-hybridization with maize genomic DNA, suggesting sequence divergence or absence of these sequences in maize, which is in contrast to several other well-conserved genes, including Adh1 and Adh2. These findings indicate that the use of rice as the model system for other cereals may sometimes be complicated by the presence of rapidly evolving gene families and microtranslocations. Seven retrotransposons and eight transposons were identified in this rice segment, including a Tc1/Mariner–like element, which is new to rice. In contrast to maize, retroelements are less frequent in rice. Only 14.4% of this genome segment consist of retroelements. Miniature inverted repeat transposable elements were found to be the most frequently occurring class of repetitive elements, accounting for 18.8% of the total repetitive DNA.

2014 - Ecotoxicology and environmental safety

Protective roles of nitric oxide on seed germination and seedling growth of rice (Oryza sativa L.) under cadmium stress.

Nitric oxide (NO) is a bioactive molecule in plants which mediates a variety of physiological processes and responses to biotic and abiotic stresses including heavy metals. In the present study, the effects of exogenous NO donor sodium nitroprusside (SNP) on rice seed germination and seedlings growth were investigated under Cd stress and a possible mechanism was postulated. The results indicated that 100μM Cd significantly decreased rice seed germination index, vigor index, root and shoot lengths as well as fresh weight compared to control. Exogenous SNP dose-dependently attenuated the inhibition of rice seed germination and thereafter seedling growth caused by Cd. The promoting effect was most pronounced at 30μM SNP. Cd exposure caused oxidative stress by elevating hydrogen peroxide (H2O2) and malondialdehyde (MDA) contents in root and shoot of rice seedlings. 30μM SNP counteracted partly Cd toxicity by reducing the H2O2 and MDA contents of Cd-exposed seedlings. Meanwhile, application of SNP markedly stimulated the activities of superoxide dismutases (SOD), ascorbate peroxidases (APX), guaiacol peroxidase (POD) and catalases (CAT) compared with Cd treatment alone, thereby indicating the enhancement of the antioxidative capacity in the root and shoot under Cd stress. In addition, addition of 30μM SNP increased accumulation of proline in both root and shoot. The Cd accumulation in seedlings was significant reduced by SNP, implicating that the protective role of SNP was responsible for preventing Cd accumulation. However, the effects of SNP were reverted by addition of cPTIO, a NO scavenger, suggesting the protective roles of SNP might be related to the induction of NO. Furthermore, K3Fe(CN)6 and [Formula: see text] / [Formula: see text] had no similar roles as SNP. Based on these results, it can be concluded that SNP exerted an advantageous effect on alleviating the inhibitory effect of Cd on rice seed germination and seedling growth, which might interact with NO.

2005 - Seed Science and Technology

Physiological and biochemical aspects of pre-sowing seed treatments in fine rice (Oryza sativa L.)

The effects of pre-sowing seed treatments on the germination and emergence of fine rice and on reducing, nonreducing and total sugars and α-amylase activity were studied. Fine rice seeds were either soaked in tap water by a traditional method, hardened for 18 or 24 h (two cycles) or osmoconditioned (-1.1 MPa KNO3) for 24 or 48 h. Seed hardening (24 h) and the traditional soaking treatments resulted in a higher germination percentage, germination index and energy of germination and lower mean germination time and mean emergence time. Performance was slightly better in seeds subjected to hardening for 24 h than the traditional soaking because of lower T50 and non-reducing sugars and higher reducing and total sugars and α-amylase activity. In seeds subjected to osmoconditioning for 48 h seed performance was impaired possibly because of KNO3 toxicity.

Transgenic rice seed synthesizing diverse flavonoids at high levels: a new platform for flavonoid production with associated health benefits.

Transgenic cereals: Current status and future prospects

Tricin levels and expression of flavonoid biosynthetic genes in developing grains of purple and brown pericarp rice

Plant Synthetic Metabolic Engineering for Enhancing Crop Nutritional Quality

Molecular and Functional Characterization of Oryza sativa Flavonol Synthase (OsFLS), a Bifunctional Dioxygenase.

An evidence-based review on the likely economic and environmental impact of genetically modified cereals and oilseeds for UK agriculture

Sustainable Cultivation of GM Crops in the Age of Climate Change: A Global Perspective

How rice organs are colored: The genetic basis of anthocyanin biosynthesis in rice

A multi-omics approach to lignocellulolytic enzyme discovery reveals a new ligninase activity from Parascedosporium putredinis NO1

Metabolic Engineering of Isoflavones: An Updated Overview

Polyphenols in foods: Classification, methods of identification, and nutritional aspects in human health.

Influence of the Lignin Extraction Methods on the Content of Tricin in Grass Lignins

Genetic Engineering for Increasing Antioxidant Content in Rice: Recent Progress and Future Perspectives

Biofortification of Cereals and Pulses Using New Breeding Techniques: Current and Future Perspectives

Tricin Biosynthesis and Bioengineering

Genetic mapping identifies a rice naringenin O-glucosyltransferase that influences insect resistance.

Comparative Analysis Reveals the Metabolic Characteristics of Astringent Seeds of Chinese Fir (Cunninghamia lanceolata (Lamb) Hook) during Astringent Compounds Accumulation Stages

Biofortification Under Climate Change: The Fight Between Quality and Quantity

Nutrition and antioxidant profiling in the unpolished and polished grains of eleven indigenous aromatic rice cultivars

Chemical Composition and Biosynthesis of Dietary Fiber Components

A flavonoid monomer tricin in Gramineous plants: Metabolism, bio/chemosynthesis, biological properties, and toxicology.