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Organ size is an important agronomic trait that directly affects the biomass of rice (Oryza sativa L.), thus identification and characterization of genes involved in organ size control would contribute to basic biology, as well as provide target genes for genetic manipulation of rice yield potential. Although organism or organ size is of pivotal importance, the molecular and genetic mechanisms underlying it remain far from understood. Here we report the isolation and characterization of reduced organ size with early senescence1 (roses1) mutant in rice. The roses1 mutant was obtained by ethyl methanesulfonate mutagenesis, and genetic analysis revealed that roses1 mutation is controlled by a single recessive nuclear gene. Distinct reduction in the size of organs in roses1 mutant plants was attributed to decreased cell number and cell size detected by histological analysis and the early leaf senescence with green and pale brown stripes, probably due to elevated stomata density detected by microscopy analysis. The ROSES1 gene was isolated by using map-based cloning strategy, encoding a BEL1-like homeobox transcription factor containing a plant-specific peroxidase (POX) domain of unknown function. The b-glucuronidase (GUS) activity driven by the ROSES1 promoter was strongly detected at the root meristem and elongation zone, shoot meristem, node, intercalary meristem of internode, leaf, inflorescence branch, and developing caryopsis and embryo. Differential gene expression analysis revealed potential regulatory networks involved in organ size control and stomata functioning that could be affected by the expression of the ROSES1 protein. [ABSTRACT FROM AUTHOR]

Genomic and transcriptomic data on kiwifruit (Actinidia chinensis) in public databases are very limited despite its nutritional and economic value. Previously, we have constructed and sequenced nine fruit RNA-Seq libraries of A. chinensis "Hongyang" at immature, mature, and postharvest ripening stages of fruit development, and generated over 66.2 million paired-end and 24.4 million single-end reads. From this dataset, here we have identified 7051 long noncoding RNAs (lncRNAs), 29,327 alternative splicing (AS) events and 2980 novel protein-coding genes that were not annotated in the draft genome of "Hongyang." AS events were demonstrated in genes involved in the synthesis of nutritional metabolites in fruit, such as ascorbic acids, carotenoids, anthocyanins, and chlorophylls, and also in genes in the ethylene signaling pathway, which plays an indispensable role in fruit ripening. Additionally, transcriptome profiles and the contents of sugars, organic and main amino acids were compared between immature, mature, and postharvest ripening stages in kiwifruits. A total of 5931 differentially expressed genes were identified, including those associated with the metabolism of sugar, organic acid, and main amino acids. The data generated in this study provide a foundation for further studies of fruit development and ripening in kiwifruit, and identify candidate genes and regulatory elements that could serve as targets for improving important agronomic traits through marker assisted breeding and biotechnology. [ABSTRACT FROM AUTHOR]

The indeterminate gametophyte1 (ig1) mutation was first characterized to modulate female gametophyte development in maize (Zea mays). However, the function of its rice orthologue, OsIG1, remains unknown. For this, we first analysed OsIG1 localization from differential tissues in rice. Real-time quantitative PCR (qRT-PCR) and histochemical staining results demonstrated that the expression signal of OsIG1 was strongly detected in young inflorescence, moderately in mature flower and weakly in leaf. Furthermore, RNA in situ hybridization analyses exhibited that OsIG1 was strongly expressed in inflorescence meristems, floral meristems, empty-glume- and floret- primordia, especially in the primordia of stamens and immature ovules, and the micropylar side of the mature ovary. In OsIG1-RNAi lines, wrinkled blade formation was accompanied by increased leaf inclination angle. Cross-section further showed that the number of bulliform cells located between the vasculatures was significantly increased, indicating that OsIG1 is involved in division and differentiation of bulliform cell and lateral growth during leaf development. OsIG1-RNAi suppression lines showed pleiotropic phenotypes, including degenerated palea, glume-like features and open hull. In addition, a single OsIG1-RNAi floret is characterized by frequently developing double ovules with abnormal embryo sac development. Additionally, down-regulation of OsIG1 differentially affected the expression of genes associated with the floral organ development including EG1, OsMADS6 and OsMADS1. Taken together, these results demonstrate that OsIG1 plays an essential role in the regulation of empty-glume identity, floral organ number control and female gametophyte development in rice. [ABSTRACT FROM AUTHOR]

Epigenetic modification generally refers to phenotypic changes by a mechanism other than changes in DNA sequence and plays a significant role in developmental processes. In this study, we found that overexpression of one alternatively spliced tomato DDB1 transcript, DDB1F that is prevalently present in all tested tissues, resulted in reduction of organ size. Transgenic plants constitutively expressing the DDB1F from a strong cauliflower mosaic virus (CaMV) 35S promoter displayed moderately reduced size in vegetative organs (leaves and stems) and radically decreased size in reproductive organs (flowers, seeds and fruits), in which several genes encoding negative regulators for cell division were upregulated. Significantly, reduction of organ size conferred by overexpression of DDB1F transgene appears not to segregate in the subsequent generations, suggesting the phenotypic alternations are manipulated in an epigenetic manner and can be transmitted over generations. This notion was further substantiated by analysis of DNA methylation level at the SIWEE1 gene (encoding a negative regulator of cell division), revealing a correlation between less methylation in the promoter region and elevated expression level of this gene. Thus, our results suggest DDB1 plays an important role in regulation of the epigenetic state of genes involved in organogenesis, despite the underlying mechanism remains to be elucidated. [ABSTRACT FROM AUTHOR]

Abstract  Aldehyde dehydrogenases (ALDHs) play a central role in detoxification processes of aldehydes generated in plants when exposed to the stressed conditions. In order to identify genes required for the stresses responses in the grass crop Zea mays, an ALDH (ZmALDH22A1) gene was isolated and characterized. ZmALDH22A1 belongs to the family ALDH22 that is currently known only in plants. The ZmALDH22A1 encodes a protein of 593 amino acids that shares high identity with the orthologs from Saccharum officinarum (95%), Oryza sativa (89%), Triticum aestivum (87%) and Arabidopsis thaliana (77%), respectively. Real-time PCR analysis indicates that ZmALDH22A1 is expressed differentially in different tissues. Various elevated levels of ZmALDH22A1 expression have been detected when the seedling roots exposed to abiotic stresses including dehydration, high salinity and abscisic acid (ABA). Tomato stable transformation of construct expressing the ZmALDH22A1 signal peptide fused with yellow fluorescent protein (YFP) driven by the CaMV35S-promoter reveals that the fusion protein is targeted to plastid. Transgenic tobacco plants overexpressing ZmALDH22A1 shows elevated stresses tolerance. Stresses tolerance in transgenic plants is accompanied by a reduction of malondialdehyde (MDA) derived from cellular lipid peroxidation. [ABSTRACT FROM AUTHOR]

The various degrees of preharvest sprouting occurring in hybrid rice is a limiting factor in the propagation and production of hybrid rice seeds. The phenotype of sprouted rice is very similar to that of the maize (Zea mays) seed-specific mutation viviparous 1. VP1 has been shown to be a transcription factor essential for seed maturation and dormancy induction. In this study, numerous truncated transcripts of OsVP1 resulting from an unusual post-transcriptional processing, were detected in four rice (Oryza sativa) cultivars. The observed events took place at a region spanning exons 1 to 5, and led to a variety of deletions that resulted in the loss of functional domain and frame-shifts with premature termination by introducing a stop codon. Various proportions of the transcripts expressed in both immature and mature embryos were observed to be incorrectly processed and associated with the genetic variation of preharvest sprouting rates among various rice varieties. In sprouting-susceptible rice cultivars, G46B and HeiB, many more incorrectly processed OsVP1 transcripts were expressed in immature than in mature embryos, indicating that the unusual post-transcriptional processing of the OsVP1 gene was developmentally regulated. In addition, comprehensive sequence analyses demonstrated the presence of paired short direct repeats (SDRs) at the junctions of the unusual excision sites in exons of OsVP1 gene. Site selection for the deletion of exon materials was altered along with the genotypes and developmental stages. [ABSTRACT FROM PUBLISHER]

• Glycine betaine (GB), a quaternary ammonium solute, plays a crucial role in developing osmotic tolerance. Rice contains a choline monooxygenase ( CMO) and two betaine aldehyde dehydrogenase homologues that are required for GB synthesis, but usually no GB is accumulated in rice ( Oryza sativa). • To elucidate the molecular processes that underlie the GB deficiency in rice, an experiment involving rice and spinach ( Spinacia oleracea) was conducted to analyze the products transcribed from CMO genes. Reverse transcription-polymerase chain reaction (RT-PCR) was used to obtain CMO transcripts and a sequencing approach was employed to analyze the structural composition of various CMO transcripts. • The results showed that most rice CMO transcripts were processed incorrectly, retaining introns or deleted of coding sequences; the unusual deletion events occurred at sequence elements of the short-direct repeats. • In conclusion, the production of incorrect CMO transcripts results in a deficiency of the full-length CMO protein and probably reduces GB accumulation considerably in rice plants. Sequence comparison results also implied that the unusual deletion-site selection might be mediated by the short-direct repeats in response to stress conditions. [ABSTRACT FROM AUTHOR]

Various abilities to synthesize and accumulate glycine betaine (GB) are crucial for angiosperms to develop salt and drought tolerances. In higher plants, GB is synthesized by a two-step oxidation of choline via an intermediate form of betaine aldehyde, and catalyzed by choline monooxygenase and betaine aldehyde dehydrogenase (BADH). In this study, numerous truncated and/or recombinant transcripts of two BADH homologs resulting from an unusual posttranscriptional processing were detected in rice (Oryza sativa) and other cereal crops, including maize (Zea niays), wheat (Triticum aestivum), and barley (Hordeum vulgare). The observed events took place at the 5′ exonic region, and led to the insertion of exogenous gene sequences and a variety of deletions that resulted in the removal of translation initiation codon, loss of functional domain, and frameshifts with premature termination by introducing stop codon. By contrast, the BADH transcripts from dicotyledonous species, such as spinach (Spinacia oleracea), Arabidopsis (Arabidopsis thaliana), and tomato (Solanum lycopersicum), had correctly processed mRNA. This suggests the differentiation of posttranscriptional processing in BADH genes potentially contributes to the variation of GB-synthesizing capacities among various plant species. In addition, comprehensive sequence analyses demonstrated that extensive sequence similarities (named as short, direct repeats) are of paired presence surrounding the junctions of both the deletion and/or insertion sites in the unusual BADH transcripts. The site selection for the deletion/insertion was altered in response to the stress conditions. This indicates that the sequence elements of short, direct repeats are probably required for the recognition of the deletion/insertion sites. [ABSTRACT FROM AUTHOR]