The impact of transposable elements on the structure, evolution and function of the rice genome

International audienc

International Consortium of Rice Mutagenesis: Resources and beyond

Rice is one of the most important crops in the world. The rice community needs to cooperate and share efforts and resources so that we can understand the functions of rice genes, especially those with a role in important agronomical traits, for application in agricultural production. Mutation is a major source of genetic variation that can be used for studying gene function. We will present here the status of mutant collections affected in a random manner by physical/chemical and insertion mutageneses. As of early September 2013, a total of 447, 919 flanking sequence tags from rice mutant libraries with T-DNA, Ac/Ds, En/Spm, Tos17, nDART/aDART insertions have been collected and publicly available. From these, 336,262 sequences are precisely positioned on the japonica rice chromosomes, and 67.5% are in gene interval. We discuss the genome coverage and preference of the insertion, issues limiting the exchange and use of the current collections, as well as new and improved resources. We propose a call to renew all mutant populations as soon as possible. We also suggest that a common web portal should be established for ordering seeds. (Résumé d'auteur

The Polycistronic miR166k-166h positively regulates rice immunity via post-transcriptional control of EIN2

MicroRNAs (miRNAs) are small RNAs acting as regulators of gene expression at the post-transcriptional level. In plants, most miRNAs are generated from independent transcriptional units, and only a few polycistronic miRNAs have been described. miR166 is a conserved miRNA in plants targeting the HD-ZIP III transcription factor genes. Here, we show that a polycistronic miRNA comprising two miR166 family members, miR166k and miR166h, functions as a positive regulator of rice immunity. Rice plants with activated MIR166k-166h expression showed enhanced resistance to infection by the fungal pathogens Magnaporthe oryzae and Fusarium fujikuroi, the causal agents of the rice blast and bakanae disease, respectively. Disease resistance in rice plants with activated MIR166k-166h expression was associated with a stronger expression of defense responses during pathogen infection. Stronger induction of MIR166k-166h expression occurred in resistant but not susceptible rice cultivars. Notably, the ethylene-insensitive 2 (EIN2) gene was identified as a novel target gene for miR166k. The regulatory role of the miR166h-166k polycistron on the newly identified target gene results from the activity of the miR166k-5p specie generated from the miR166k-166h precursor. Collectively, our findings support a role for miR166k-5p in rice immunity by controlling EIN2 expression. Because rice blast is one of the most destructive diseases of cultivated rice worldwide, unraveling miR166k-166h-mediated mechanisms underlying blast resistance could ultimately help in designing appropriate strategies for rice protection

The Rice Paradox: Multiple Origins but Single Domestication in Asian Rice

The origin of domesticated Asian rice (Oryza sativa) has been a contentious topic, with conflicting evidence for either single or multiple domestication of this key crop species. We examined the evolutionary history of domesticated rice by analyzing de novo assembled genomes from domesticated rice and its wild progenitors. Our results indicate multiple origins, where each domesticated rice subpopulation (japonica, indica, and aus) arose separately from progenitor O. rufipogon and/or O. nivara. Coalescence-based modeling of demographic parameters estimate that the first domesticated rice population to split off from O. rufipogon was O. sativa ssp. japonica, occurring at ∼13.1–24.1 ka, which is an order of magnitude older then the earliest archeological date of domestication. This date is consistent, however, with the expansion of O. rufipogon populations after the Last Glacial Maximum ∼18 ka and archeological evidence for early wild rice management in China. We also show that there is significant gene flow from japonica to both indica (∼17%) and aus (∼15%), which led to the transfer of domestication alleles from early-domesticated japonica to proto-indica and proto-aus populations. Our results provide support for a model in which different rice subspecies had separate origins, but that de novo domestication occurred only once, in O. sativa ssp. japonica, and introgressive hybridization from early japonica to proto-indica and proto-aus led to domesticated indica and aus rice

Early iron production in the Levant: Smelting and smithing at early 1st millennium BC Tell Hammeh, Jordan, and Tel Beth-Shemesh, Israel

The use of iron in the Near East is first attested by the sporadic occurrence of iron artefacts during the Bronze Age. By the end of the Late Bronze Age, however, use of iron metal gradually increases to such a level that one can assume a reasonably regular production of iron metal from terrestrial ores by smelting. However, very few iron metallurgical workshops or installations have been discovered in the Near East thus far. Of these, most are apparently related to secondary smithing, and very few if any have clear evidence for iron smelting. Recent fieldwork at Tell Hammeh, Jordan, identified a major iron smelting operation dated to ca. 930 Cal BC. Excavations in 2001 and 2003 at Tel Beth- Shemesh, Israel, uncovered remains of a full-scale smithing operation, dating to ca. 900 Cal BC. Dedicated excavation techniques were developed and refined for both sites, aiming at optimal recovery of both technological and archaeological information. The excavated materials were comprehensively analysed using relevant scientific analytical techniques, which included the development and application of a calibration method for quantitative bulk chemical analysis of iron- rich materials by XRF. Combining laboratory data and fieldwork, this thesis explores the particular lime- rich and iron-oxide-poor nature of the Hammeh slags as a function of the composition of the local ore and the sacrificial contribution of technical ceramics (tuyeres and furnace wall). Furthermore, it compares the smelting operations at Tell Hammeh with the smithing at Tel Beth-Shemesh, both in terms of their respective archaeological contexts as well as of their technological residues. This aims at the identification and reconstruction of the chaine operatoire of the technologies at both sites. The reconstructed technological processes are discussed in terms of their place in the socio-economic and cultural context of the early first millennium BC of the Levant. Beyond providing new data about early iron metallurgy, the integrated archaeological and laboratory approach, the excavation methods applied, the analytical methodology, as well as the archaeometric data presented here may serve as a model for the excavation, interpretation, or comparison of future (and previous) discoveries of iron metallurgy in the Near East

Direct calibration of PICKY-designed microarrays

Abstract Background Few microarrays have been quantitatively calibrated to identify optimal hybridization conditions because it is difficult to precisely determine the hybridization characteristics of a microarray using biologically variable cDNA samples. Results Using synthesized samples with known concentrations of specific oligonucleotides, a series of microarray experiments was conducted to evaluate microarrays designed by PICKY, an oligo microarray design software tool, and to test a direct microarray calibration method based on the PICKY-predicted, thermodynamically closest nontarget information. The complete set of microarray experiment results is archived in the GEO database with series accession number GSE14717. Additional data files and Perl programs described in this paper can be obtained from the website http://www.complex.iastate.edu under the PICKY Download area. Conclusion PICKY-designed microarray probes are highly reliable over a wide range of hybridization temperatures and sample concentrations. The microarray calibration method reported here allows researchers to experimentally optimize their hybridization conditions. Because this method is straightforward, uses existing microarrays and relatively inexpensive synthesized samples, it can be used by any lab that uses microarrays designed by PICKY. In addition, other microarrays can be reanalyzed by PICKY to obtain the thermodynamically closest nontarget information for calibration

Lipid Metabolism in Corn Tissue Culture and Molecular Biology of Soybean Seed Maturation

127 p.Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 1988.Lipid metabolism of corn (Zea mays) tissue culture was studied using seven strains or inbred lines. The lipid content from the embryogenic callus derived from these lines followed the same trend as the lipid content found in the seeds, however there was no consistent lipid pattern observed for the leaf or root callus from these same lines relative to the tissue that it originated from. Therefore corn embryogenic callus provides an ideal tissue to study lipid metabolism. Embryogenic calli were also used to select cell lines resistant to cerulenin, an inhibitor of fatty acid synthesis. While it was hypothesized that the cerulenin-resistant calli might be an overproducing-oil line, the selected resistant calli did not exhibit an increase in lipid content relative to the control calli.A variant corn callus induced from etiolated corn leaves from Illinois High Oil strain was identified. The variant callus has increased lipid content concomitant with increased acetyl-CoA carboxylase activity and altered biotin-containing protein patterns relative to the wild type callus. The variant callus also exhibited an altered fatty acid composition concomitant with decreased oleic acid desaturase activity. Thus it appears that acetyl-CoA carboxylase and oleic acid desaturase are important regulatory enzymes in lipid metabolism.Gene expression during precocious and natural maturation of soybean (Glycine max) seeds was investigated by cloning the cDNAs corresponding to the mRNAs which were expressed only during maturation. The cDNA clones were isolated by construction of a cDNA library from poly(A)\sp+RNA from four days pod dried 35 days after flowering (DAF) soybean seeds followed by differential hybridization. The soybean seed maturation polypeptide gene appears to be switched on in precociously dried immature (35 DAF) seeds or naturally maturing seeds. The maturation cDNA clones were shown to encode a 31 kD protein and this protein is encoded by a single copy or relatively low copy genes.U of I OnlyRestricted to the U of I community idenfinitely during batch ingest of legacy ETD

Genome-wide analysis of polycistronic microRNAs in cultivated and wild rice

MicroRNAs (miRNAs) are small noncoding RNAs that direct posttranscriptional gene silencing in eukaryotes. They are frequently clustered in the genomes of animals and can be independently transcribed or simultaneously transcribed into single polycistronic transcripts. Only a few miRNA clusters have been described in plants, and most of them are generated from independent transcriptional units. Here, we used a combination of bioinformatic tools and experimental analyses to discover new polycistronic miRNAs in rice. A genome-wide analysis of clustering patterns of MIRNA loci in the rice genome was carried out using a criterion of 3 kb as the maximal distance between two miRNAs. This analysis revealed 28 loci with the ability to form the typical hairpin structure of miRNA precursors in which 2 or more mature miRNAs mapped along the same structure. RT-PCR provided evidence for the polycistronic nature of seven miRNA precursors containing homologous or nonhomologous miRNA species. Polycistronic miRNAs and candidate polycistronic miRNAs are located across different rice chromosomes, except chromosome 12, and resided in both duplicated and nonduplicated chromosomal regions. Finally, most polycistronic and candidate polycistronic miRNAs showed a pattern of conservation in the genome of rice species with an AA genome. The diversity in the organization of MIR genes that are transcribed as polycistrons suggests a versatile mechanism for the control of gene expression in different biological processes and supports additional levels of complexity in miRNA functioning in plants