Search

The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and noncoding genes. Our study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young 'AA' subclade containing the two domesticated species. This study highlights the prevalence of functionally coupled disease resistance genes and identifies many new haplotypes of potential use for future crop protection. Finally, this study marks a milestone in modern rice research with the release of a complete long-read assembly of IR 8 'Miracle Rice', which relieved famine and drove the Green Revolution in Asia 50 years ago.

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.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.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.

Author(s): Miyako Ueguchi-Tanaka [1, 8]; Motoyuki Ashikari [1, 8]; Masatoshi Nakajima [2, 8]; Hironori Itoh [1]; Etsuko Katoh [3]; Masatomo Kobayashi [4]; Teh-yuan Chow [5, 7]; Yue-ie C. Hsing [5]; [...]

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.

Rice, Oryza sativa L., is one of the most important crops in the world. With the rising world population, feeding people in a more sustainable and environmentally friendly way becomes increasingly important. Therefore, the rice research community needs to share resources to better understand the functions of rice genes that are the foundation for future agricultural biotechnology development, and one way to achieve this goal is via the extensive study of insertional mutants. We have constructed a large rice insertional mutant population in a japonica rice variety, Tainung 67. The collection contains about 93 000 mutant lines, among them 85% with phenomics data and 65% with flanking sequence data. We screened the phenotypes of 12 individual plants for each line grown under field conditions according to 68 subcategories and 3 quantitative traits. Both phenotypes and integration sites are searchable in the Taiwan Rice Insertional Mutants Database. Detailed analyses of phenomics data, T-DNA flanking sequences, and whole-genome sequencing data for rice insertional mutants can lead to the discovery of novel genes. In addition, studies of mutant phenotypes can reveal relationships among varieties, cultivation locations, and cropping seasons. [ABSTRACT FROM AUTHOR]

Two inter-subspecific segregating populations were constructed to map quantitative trait loci (QTLs) for plant height (PH) and heading date (HD) in rice. A total of 99 and 95 polymorphic SSR and STS markers were used to establish linkage maps in japonica TK8 × indica IR1545-339 and japonica Nipponbare × IR1545-339, respectively. By employing composite interval mapping verified by single point analysis, ten PH and seven HD QTLs were located on seven and six chromosomes, respectively; only Qph1.2 and Qhd3 were common in the two populations. The phenotypic variance explained (PVE) by major PH and HD QTLs was 22.07% (Qph6.1) and 12.98% (Qph6.2), and 35.74% (Qhd3) and 15.54% (Qhd3), for TK8/ IR1545-339 and Nipponbare/IR1545-339, respectively. Comparative genetic analysis of QTL intervals on rice pseudomolecules showing the convergence of QTLs affecting PH and HD across the Oryza genus revealed all QTLs uncovered in the two populations possibly allelic to QTLs previously published. By comparative mapping and candidate gene approach, we specified three PH, Qph1.2, Qph4, and Qph6.1, and one HD QTL, Qhd10, without high-resolution mapping, and the reality of QTLs identified by interval mapping were discussed herein. [ABSTRACT FROM AUTHOR]

The article presents a study on the mechanisms of plant drought tolerance or desiccation tolerance. It identified the role of late embryogenesis abundant (LEA) proteins in protecting plants from drought or desiccation. It was found that the LEA proteins may carry out a bipartitie function under different water stages, may establish a water shell and decrease ion strength, and may enhance the bioglass strength. LEA proteins may also act as a water replacement to stabilize cellular components.

With the completion of the rice genome sequencing project, the next major challenge is the large-scale determination of gene function. A systematic phenotypic profiling of mutant collections will provide major insights into gene functions important for crop growth or production. Thus, detailed phenomics analysis is the key to functional genomics. Currently, the two major types of rice mutant collections are insertional mutants and chemical or irradiation-induced mutants. Here we describe how to manipulate a rice mutant population, including conducting phenomics studies and the subsequent propagation and seed storage. We list the phenotypes screened and also describe how to collect data systematically for a database of the qualitative and quantitative phenotypic traits. Thus, data on mutant lines, phenotypes, and segregation rate for all kinds of mutant populations, as well as integration sites for insertional mutant populations, would be searchable, and the collection would be a good resource for rice functional genomics study.