Large-scale identification and functional analysis ofNLRgenes in blast resistance in the Tetep rice genome sequence

Tetep is a rice cultivar known for broad-spectrum resistance to blast, a devastating fungal disease. The molecular basis for its broad-spectrum resistance is still poorly understood. Is it because Tetep has many moreNLRgenes than other cultivars? Or does Tetep possess multiple majorNLRgenes that can individually confer broad-spectrum resistance to blast? Moreover, are there many interactingNLRpairs in the Tetep genome? We sequenced its genome, obtained a high-quality assembly, and annotated 455 nucleotide-binding site leucine-rich repeat (NLR) genes. We cloned and tested 219NLRgenes as transgenes in 2 susceptible cultivars using 5 to 12 diversified pathogen strains; in many cases, fewer than 12 strains were successfully cultured for testing. Ninety clonedNLRs showed resistance to 1 or more pathogen strains and each strain was recognized by multipleNLRs. However, fewNLRs showed resistance to >6 strains, so multipleNLRs are apparently required for Tetep’s broad-spectrum resistance to blast. This was further supported by the pedigree analyses, which suggested a correlation between resistance and the number of Tetep-derivedNLRs. In developing a method to identifyNLRpairs each of which functions as a unit, we found that >20% of theNLRs in the Tetep and 3 other rice genomes are paired. Finally, we designed an extensive set of molecular markers for rapidly introducing clustered and pairedNLRs in the Tetep genome for breeding new resistant cultivars. This study increased our understanding of the genetic basis of broad-spectrum blast resistance in rice.

Transcription factors–DNA interactions in rice: identification and verification

The completion of the rice genome sequence paved the way for rice functional genomics research. Additionally, the functional characterization of transcription factors is currently a popular and crucial objective among researchers. Transcription factors are one of the groups of proteins that bind to either enhancer or promoter regions of genes to regulate expression. On the basis of several typical examples of transcription factor analyses, we herein summarize selected research strategies and methods and introduce their advantages and disadvantages. This review may provide some theoretical and technical guidelines for future investigations of transcription factors, which may be helpful to develop new rice varieties with ideal traits.

Pengembangan Populasi Mutan Penanda Aktivasi: I. Transformasi Padi Japonica Tropis Lokal Sulawesi cv. Asemandi dengan bantuan Agrobacterium tumefaciens

<p>The rice transformation technology<br />is not only provides valuable methods for the introduction<br />of useful genes into rice plant to improve important<br />agronomic traits, but also helps in studying gene function<br />and regulation based on rice genome sequence information.<br />Knockout of genes by insertional mutagenesis is a straightforward<br />method to identify gene functions. One of the<br />methods to develop rice mutants is through genetic transformation<br />mediated by Agrobacterium using activation<br />tagging by Ac-Ds system. A study was done with an objective<br />to obtain mutant rice of local tropical japonica cv. Asemandi<br />through genetic trans-formation mediated by Agrobacterium<br />tumefaciens. The transformation was conducted using<br />Agrobacterium vector with the strain of Agl-1 containing<br />activation tag construct. The result of experiment showed<br />that it has been obtained 17 independent line (304 plants)<br />transgenic Asemandi containing activation tag construct.<br />These starter lines will be used as materials to develop<br />several generations of stabil rice mutant through selfing.</p>

Genome-Wide Transcriptome Analysis of Cadmium Stress in Rice

Rice growth is severely affected by toxic concentrations of the nonessential heavy metal cadmium (Cd). To elucidate the molecular basis of the response to Cd stress, we performed mRNA sequencing of rice following our previous study on exposure to high concentrations of Cd (Oono et al., 2014). In this study, rice plants were hydroponically treated with low concentrations of Cd and approximately 211 million sequence reads were mapped onto the IRGSP-1.0 reference rice genome sequence. Many genes, including some identified under high Cd concentration exposure in our previous study, were found to be responsive to low Cd exposure, with an average of about 11,000 transcripts from each condition. However, genes expressed constitutively across the developmental course responded only slightly to low Cd concentrations, in contrast to their clear response to high Cd concentration, which causes fatal damage to rice seedlings according to phenotypic changes. The expression of metal ion transporter genes tended to correlate with Cd concentration, suggesting the potential of the RNA-Seq strategy to reveal novel Cd-responsive transporters by analyzing gene expression under different Cd concentrations. This study could help to develop novel strategies for improving tolerance to Cd exposure in rice and other cereal crops.