GRAS proteins belong to a plant-specific transcription factor family. Currently, 33 GRAS members including a putative expressed pseudogene have been identified in the Arabidopsis genome. With a reverse genetic approach, we have constructed a ''phenome-ready unimutant collection'' of the GRAS genes in Arabidopsis thaliana. Of this collection, we focused on loss-of-function mutations in 23 novel GRAS members. Under standard conditions, homozygous mutants have no obvious morphological phenotypes compared with those of wild-type plants. Expression analysis of GRAS genes using quantitative realtime RT-PCR (qRT-PCR), microarray data mining, and promoter::GUS reporter fusions revealed their tissuespecific expression patterns. Our analysis of protein-protein interaction and subcellular localization of individual GRAS members indicated their roles as transcription regulators. In our yeast two-hybrid (Y2H) assay, we confirmed the protein-protein interaction between SHORT-ROOT (SHR) and SCARECROW (SCR). Furthermore, we identified a new SHR-interacting protein, SCARECROW-LIKE23 (SCL23), which is the most closely related to SCR. Our large-scale analysis provides a comprehensive evaluation on the Arabidopsis GRAS members, and also our phenome-ready unimutant collection will be a useful resource to better understand individual GRAS proteins that play diverse roles in plant growth and development.

BackgroundTongil (IR667-98-1-2) rice, developed in 1972, is a high-yield rice variety derived from a three-way cross between indica and japonica varieties. Tongil contributed to the self-sufficiency of staple food production in Korea during a period known as the `Korean Green Revolution'. We analyzed the nucleotide-level genome structure of Tongil rice and compared it to those of the parental varieties.ResultsA total of 17.3 billion Illumina Hiseq reads, 47× genome coverage, were generated for Tongil rice. Three parental accessions of Tongil rice, two indica types and one japonica type, were also sequenced at approximately 30x genome coverage. A total of 2,149,991 SNPs were detected between Tongil and Nipponbare varieties. The average SNP frequency of Tongil was 5.77 per kb. Genome composition was determined based on SNP data by comparing Tongil with three parental genome sequences using the sliding window approach. Analyses revealed that 91.8% of the Tongil genome originated from the indica parents and 7.9% from the japonica parent. Copy numbers of SSR motifs, ORF gene distribution throughout the whole genome, gene ontology (GO) annotation, and some yield-related QTLs or gene locations were also comparatively analyzed between Tongil and parental varieties using sequence-based tools. Each genetic factor was transferred from the parents into Tongil rice in amounts that were in proportion to the whole genome composition.ConclusionsTongil was derived from a three-way cross among two indica and one japonica varieties. Defining the genome structure of Tongil rice demonstrates that the Tongil genome is derived primarily from the indica genome with a small proportion of japonica genome introgression. Comparative gene distribution, SSR, GO, and yield-related gene analysis support the finding that the Tongil genome is primarily made up of the indica genome.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-014-0022-5) contains supplementary material, which is available to authorized users.

Methyl jasmonate, the methyl ester of jasmonic acid, is a volatile plant hormone that acts as an important cellular regulator, mediating diverse developmental processes and defense responses. Methyl jasmonate is synthesized by methylation of jasmonic acid; this reaction is catalyzed by jasmonic acid carboxyl methyltransferase (JMT). Although JMT cDNA had previously been described only for Arabidopsis thaliana, here we used PCR to isolate it from Capsicum annuum L. The 389-amino-acid sequence deduced for the JMT gene showed 92% identity to that from A. thaliana. Southern blot analysis revealed thatJMT is present in the genome as two copies. Our preliminary northern blot detected no JMT transcript, but, through RT-PCR and subsequent Southern blot analysis of products using gene. specific probes, we found that transcript levels increased after leaf-wounding, Likewise, 10 ~M methyl jasmonate inducedJMTgene expressio n in leaves. Transcription levels began to increase 10 rain after wounding, and were maintained for I to 4 h. Moreover, expression of the CaJMT and PIN2 genes was increased by both wounding and MeJA applications, but was not enhanced by treatment with H202.

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