Search

The apocarotenoid zaxinone promotes growth and suppresses strigolactone biosynthesis in rice. To shed light on the mechanisms underlying its growth-promoting effect, we employed a combined omics approach integrating transcriptomics and metabolomics analysis of rice seedlings treated with zaxinone, and determined the resulting changes at the cellular and hormonal levels. Metabolites as well as transcripts analysis demonstrate that zaxinone application increased sugar content and triggered glycolysis, the tricarboxylic acid cycle and other sugar-related metabolic processes in rice roots. In addition, zaxinone treatment led to an increased root starch content and induced glycosylation of cytokinins. The transcriptomic, metabolic and hormonal changes were accompanied by striking alterations of roots at cellular level, which showed an increase in apex length, diameter, and the number of cells and cortex cell layers. Remarkably, zaxinone did not affect the metabolism of roots in a strigolactone deficient mutant, suggesting an essential role of strigolactone in the zaxinone growth-promoting activity. Taken together, our results unravel zaxinone as a global regulator of the transcriptome and metabolome, as well as of hormonal and cellular composition of rice roots. Moreover, they suggest that zaxinone promotes rice growth most likely by increasing sugar uptake and metabolism, and reinforce the potential of this compound in increasing rice performance., Wang et al. report zaxinone as a global regulator of the transcriptome and metabolome, as well as of hormonal and cellular composition of rice roots. This study shows that zaxinone promotes rice growth by enhancing root sugar uptake and metabolism and modulation of cytokinin content, indicating the potential application of this compound in increasing rice performance.

Summary Grain/seed yield and plant stress tolerance are two major traits that determine the yield potential of many crops. In cereals, grain size is one of the key factors affecting grain yield. Here, we identify and characterize a newly discovered gene Rice Big Grain 1 (RBG1) that regulates grain and organ development, as well as abiotic stress tolerance. Ectopic expression of RBG1 leads to significant increases in the size of not only grains but also other major organs such as roots, shoots and panicles. Increased grain size is primarily due to elevated cell numbers rather than cell enlargement. RBG1 is preferentially expressed in meristematic and proliferating tissues. Ectopic expression of RBG1 promotes cell division, and RBG1 co‐localizes with microtubules known to be involved in cell division, which may account for the increase in organ size. Ectopic expression of RBG1 also increases auxin accumulation and sensitivity, which facilitates root development, particularly crown roots. Moreover, overexpression of RBG1 up‐regulated a large number of heat‐shock proteins, leading to enhanced tolerance to heat, osmotic and salt stresses, as well as rapid recovery from water‐deficit stress. Ectopic expression of RBG1 regulated by a specific constitutive promoter, GOS2, enhanced harvest index and grain yield in rice. Taken together, we have discovered that RBG1 regulates two distinct and important traits in rice, namely grain yield and stress tolerance, via its effects on cell division, auxin and stress protein induction.

The dispersal of rice (Oryza sativa) following domestication influenced massive social and cultural changes across South, East, and Southeast (SE) Asia. The history of dispersal across islands of SE Asia, and the role of Taiwan and the Austronesian expansion in this process remain largely unresolved. Here, we reconstructed the routes of dispersal of O. sativa ssp. japonica rice to Taiwan and the northern Philippines using whole-genome resequencing of indigenous rice landraces coupled with archaeological and paleoclimate data. Our results indicate that japonica rice found in the northern Philippines diverged from Indonesian landraces as early as 3,500 years before present (BP). In contrast, rice cultivated by the indigenous peoples of the Taiwanese mountains has complex origins. It comprises two distinct populations, each best explained as a result of admixture between temperate japonica that presumably came from northeast Asia, and tropical japonica from the northern Philippines and mainland SE Asia, respectively. We find that the temperate japonica component of these indigenous Taiwan populations diverged from northeast Asia subpopulations at about 2,600 BP, whereas gene flow from the northern Philippines had begun before ∼1,300 BP. This coincides with a period of intensified trade established across the South China Sea. Finally, we find evidence for positive selection acting on distinct genomic regions in different rice subpopulations, indicating local adaptation associated with the spread of japonica rice.

BackgroundEndosperm is a triploid tissue in seed resulting from a sperm nucleus fused with the binucleate central cell after double fertilization. Endosperm may be involved in metabolite production, solute transport, nutrient storage, and germination. In the legume family (Fabaceae), with the greatest number of domesticated crops, approximately 60% of genera contain well-differentiated endosperm in mature seeds. Soybean seeds, the most important legume crop in the worlds, have endosperm surrounding embryos during all stages of seed development. However, the function of soybean endosperm is still unknown.ResultsFlow cytometry assay confirmed that soybean endosperm was triploid. Cytobiological observation showed that soybean endosperm cells were alive with zigzag-shape cell wall. Soybean endosperm cells allowed fusion proteins (42 kDa) to move from bombarded cells to adjacent unbombarded-cells. Such movement is not simple diffusion because the fusion proteins failed to move into dead cells. We used symplastic tracers to test the transport potential of soybean endosperm. Small organic dye and low-molecular-weight symplastic tracers revealed fast symplastic transport. After a treatment of an inhibitor of ATPase,N,N′-dicyclohexylcarbodiimide (DCCD), symplastic transport was blocked, but all tracers still showed fast apolopastic transport. The transport speed of 8-hydroxypyrene-1,3,6-trisulfonic acid in endosperm was 1.5 to 3 times faster than in cotyledon cells or Arabidopsis embryos.ConclusionsSoybean endosperm is a membrane-like, semi-transparent, and fully active tissue located between the seed coat and cotyledon. Soybean endosperm cells allowed macromolecules to move fast via plasmodesmata transport. The size exclusion limit is larger for soybean endosperm cells than its cotyledon or even Arabidopsis embryo cells. Soybean endosperm may be involved in fast and horizontal transport during the mid-developmental stage of seeds.

The recent release of genomic sequences for 3000 rice varieties provides access to the genetic diversity at species level for this crop. We take advantage of this resource to unravel some features of the retrotranspositional landscape of rice. We develop software TRACKPOSON specifically for the detection of transposable elements insertion polymorphisms (TIPs) from large datasets. We apply this tool to 32 families of retrotransposons and identify more than 50,000 TIPs in the 3000 rice genomes. Most polymorphisms are found at very low frequency, suggesting that they may have occurred recently in agro. A genome-wide association study shows that these activations in rice may be triggered by external stimuli, rather than by the alteration of genetic factors involved in transposable element silencing pathways. Finally, the TIPs dataset is used to trace the origin of rice domestication. Our results suggest that rice originated from three distinct domestication events., Transposable elements (TE) are the dominant constituent of plant genomes. Here the authors develop a tool to analyze TE insertion sites in 3000 rice genomes and provide evidence for recent TE activity during cultivation and that external, rather than genetic, stimuli trigger most activations.

Key message Elevated expression of nucleotide-binding and leucine-rich repeat proteins led to closer vein spacing and higher vein density in rice leaves. Abstract To feed the growing global population and mitigate the negative effects of climate change, there is a need to improve the photosynthetic capacity and efficiency of major crops such as rice to enhance grain yield potential. Alterations in internal leaf morphology and cellular architecture are needed to underpin some of these improvements. One of the targets is to generate a “Kranz-like” anatomy in leaves that includes decreased interveinal spacing close to that in C4 plant species. As C4 photosynthesis has evolved from C3 photosynthesis independently in multiple lineages, the genes required to facilitate C4 may already be present in the rice genome. The Taiwan Rice Insertional Mutants (TRIM) population offers the advantage of gain-of-function phenotype trapping, which accelerates the identification of rice gene function. In the present study, we screened the TRIM population to determine the extent to which genetic plasticity can alter vein density (VD) in rice. Close vein spacing mutant 1 (CVS1), identified from a VD screening of approximately 17,000 TRIM lines, conferred heritable high leaf VD. Increased vein number in CVS1 was confirmed to be associated with activated expression of two nucleotide-binding and leucine-rich repeat (NB-LRR) proteins. Overexpression of the two NB-LRR genes individually in rice recapitulates the high VD phenotype, due mainly to reduced interveinal mesophyll cell (M cell) number, length, bulliform cell size and thus interveinal distance. Our studies demonstrate that the trait of high VD in rice can be achieved by elevated expression of NB-LRR proteins limited to no yield penalty.

[Background and Aims]: MicroRNAs (miRNAs) are small non-coding RNAs that act as post-transcriptional regulators of gene expression via sequence-specific cleavage or translational repression of target transcripts. They are transcribed as long single-stranded RNA precursors with unique stem–loop structures that are processed by a DICER-Like (DCL) ribonuclease, typically DCL1, to produce mature miRNAs. Although a plethora of miRNAs have been found to be regulated by pathogen infection in plants, the biological function of most miRNAs remains largely unknown. Here, the contribution of OsDCL1 to rice immunity was investigated., [Methods]: Activation-tagged Osdcl1a (Osdcl1a-Ac) rice mutants were examined for resistance to pathogen infection. mRNA and small RNA deep sequencing, quantitative real-time PCR (RT-qPCR) and stem–loop reverse tanscripion–PCR (RT–PCR) were used to examine DCL1a-mediated alterations in the rice transcriptome. Rice diterpene phytoalexins were quantified by liquid chromatography–tandem mass spectrometry (LC-MSMS). Accumulation of O2·– was determined by nitroblue tetrazolium (NBT) staining., [Key Results]: dcl1a-Ac mutants exhibit enhanced susceptibility to infection by fungal pathogens which was associated with a weaker induction of defence gene expression. Comparison of the mRNA and miRNA transcriptomes of dcl1a-Ac and wild-type plants revealed misregulation of genes involved in detoxification of reactive oxygen species. Consequently, dcl1a-Ac plants accumulated O2·– in their leaves and were more sensitive to methyl viologen-induced oxidative stress. Furthermore, dcl1a-Ac plants showed downregulation of diterpenoid phytoalexin biosynthetic genes, these genes also being weakly induced during pathogen infection. Upon pathogen challenge, dcl1a-Ac plants failed to accumulate major diterpenoid phytoalexins. OsDCL1a activation resulted in marked alterations in the rice miRNAome, including both upregulation and downregulation of miRNAs., [Conclusions]: OsDCL1a activation enhances susceptibility to infection by fungal pathogens in rice. Activation of OsDCL1a represses the pathogen-inducible host defence response and negatively regulates diterpenoid phytoalexin production. These findings provide a basis to understand the molecular mechanisms through which OsDCL1a mediates rice immunity., This work was supported by the Spanish Ministry of Economy and Competitiveness (MINECO, grants BIO2012-32838, BIO2015-67212-R), the CSIC/NSC (Spanish Research Council/National Science Council of Taiwan)-Formosa Program (2009TW0041) and the Japan Society for the Promotion of Science (JSPS KAKENHI, grant no. 17H03811 to K.O.). We also acknowledge support from the CERCA Programme (‘Generalitat de Catalunya’) and MINECO (‘Severo Ochoa Programme for Centres of Excellence in R&D’ 2016–2019, SEV-2015-0533). R.S.-G. was the recipient of a PhD grant from MINECO (BES-2013–065521).

Drought stress in plants causes differential expression of numerous genes. One of these differentially expressed genes in rice is a specific amidohydrolase. We characterized this amidohydrolase gene on the rice chromosome 12 as the first plant guanine deaminase (OsGDA1). The biochemical activity of GDA is known from tea and coffee plants where its catalytic product, xanthine, is the precursor for theine and caffeine. However, no plant gene that is coding for GDA is known so far. Recombinant OsGDA1 converted guanine to xanthine in vitro. Measurement of guanine and xanthine contents in the OsGDA1 knockout (KO) line and in the wild type Tainung 67 rice plants also suggested GDA activity in vivo. The content of cellular xanthine is important because of its catabolic products allantoin, ureides, and urea which play roles in water and nitrogen stress tolerance among others. The identification of OsGDA1 fills a critical gap in the S‐adenosyl‐methionine (SAM) to xanthine pathway. SAM is converted to S‐adenosyl‐homocysteine (SAH) and finally to xanthine. SAH is a potent inhibitor of DNA methyltransferases, the reduction of which leads to increased DNA methylation and gene silencing in Arabidopsis. We report that the OsGDA1 KO line exhibited a decrease in SAM, SAH and adenosine and an increase in rice genome methylation. The OsGDA1 protein phylogeny combined with mutational protein destabilization analysis suggested artificial selection for null mutants, which could affect genome methylation as in the KO line. Limited information on genes that may affect epigenetics indirectly requires deeper insights into such a role and effect of purine catabolism and related genetic networks.

Background Rice (Oryza sativa) is one of the main crops in the world, and more than 3.9 billion people will consume rice by 2025. Sterility significantly affects rice production and leads to yield defects. The undeveloped anthers or abnormal pollen represent serious defects in rice male sterility. Therefore, understanding the mechanism of male sterility is an important task. Here, we investigated a rice sterile mutant according to its developmental morphology and transcriptional profiles. Results An untagged T-DNA insertional mutant showed defective pollen and abnormal anthers as compared with its semi-sterile mutant (sstl) progeny segregates. Transcriptomic analysis of sterile sstl-s revealed several biosynthesis pathways, such as downregulated cell wall, lipids, secondary metabolism, and starch synthesis. This downregulation is consistent with the morphological characterization of sstl-s anthers with irregular exine, absence of intine, no starch accumulation in pollen grains and no accumulated flavonoids in anthers. Moreover, defective microsporangia development led to abnormal anther locule and aborted microspores. The downregulated lipids, starch, and cell wall synthesis-related genes resulted in loss of fertility. Conclusions We illustrate the importance of microsporangia in the development of anthers and functional microspores. Abnormal development of pollen grains, pollen wall, anther locule, etc. result in severe yield reduction. Electronic supplementary material The online version of this article (10.1186/s40529-019-0260-3) contains supplementary material, which is available to authorized users.

[Background] MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression at the post-transcriptional level in eukaryotes. In rice, MIR7695 expression is regulated by infection with the rice blast fungus Magnaporthe oryzae with subsequent down-regulation of an alternatively spliced transcript of natural resistance-associated macrophage protein 6 (OsNramp6). NRAMP6 functions as an iron transporter in rice., [Results] Rice plants grown under high iron supply showed blast resistance, which supports that iron is a factor in controlling blast resistance. During pathogen infection, iron accumulated in the vicinity of M. oryzae appressoria, the sites of pathogen entry, and in cells surrounding infected regions of the rice leaf. Activation-tagged MIR7695 rice plants (MIR7695-Ac) exhibited enhanced iron accumulation and resistance to M. oryzae infection. RNA-seq analysis revealed that blast resistance in MIR7695-Ac plants was associated with strong induction of defense-related genes, including pathogenesis-related and diterpenoid biosynthetic genes. Levels of phytoalexins during pathogen infection were higher in MIR7695-Ac than wild-type plants. Early phytoalexin biosynthetic genes, OsCPS2 and OsCPS4, were also highly upregulated in wild-type rice plants grown under high iron supply., [Conclusions] Our data support a positive role of miR7695 in regulating rice immunity that further underpin links between defense and iron signaling in rice. These findings provides a basis to better understand regulatory mechanisms involved in rice immunity in which miR7695 participates which has a great potential for the development of strategies to improve blast resistance in rice., This work was supported by the Spanish Ministry of Economy and Competitiveness (MINECO, BIO2015–67212-R) to BSS, the CSIC/NSC (Spanish Research Council/National Science Council of Taiwan)-Formosa Program (2009TW0041 and NSC 99–2923-B-001-002-MY3), the Academia Sinica Summit Project to YICH, and the Japan Society for the Promotion of Science (JSPS KAKENHI, 17H03811 to KO). We acknowledge support from the CERCA Programme (“Generalitat de Catalunya”) and the “Severo Ochoa Programme for Centres of Excellence in R&D” (MINECO, 2016–2019, SEV-2015-0533).

Rice (Oryza sativa) is one of the world's most important crops. Rice researchers make extensive use of insertional mutants for the study of gene function. Approximately half a million flanking sequence tags from rice insertional mutant libraries are publicly available. However, the relationship between genotype and phenotype is very weak. Transgenic plant assays have been used frequently for complementation, overexpression or antisense analysis, but sequence changes caused by callus growth, Agrobacterium incubation medium, virulence genes, transformation and selection conditions are unknown. We used high-throughput sequencing of DNA from rice lines derived from Tainung 67 to analyze non-transformed and transgenic rice plants for mutations caused by these parameters. For comparison, we also analyzed sequence changes for two additional rice varieties and four T-DNA tagged transformants from the Taiwan Rice Insertional Mutant resource. We identified single-nucleotide polymorphisms, small indels, large deletions, chromosome doubling and chromosome translocations in these lines. Using standard rice regeneration/transformation procedures, the mutation rates of regenerants and transformants were relatively low, with no significant differences among eight tested treatments in the Tainung 67 background and in the cultivars Taikeng 9 and IR64. Thus, we could not conclusively detect sequence changes resulting from Agrobacterium-mediated transformation in addition to those caused by tissue culture-induced somaclonal variation. However, the mutation frequencies within the two publically available tagged mutant populations, including TRIM transformants or Tos17 lines, were about 10-fold higher than the frequency of standard transformants, probably because mass production of embryogenic calli and longer callus growth periods were required to generate these large libraries.

Rice domestication/adaptation is a good model for studies of the development and spread of this important crop. Mutations that caused morphological and physiological change, followed by human selection/expansion, finally led to the improvement of phenotypes suitable for different kinds of environments. We used the sequence information for Heading date 1 (Hd1) gene to reveal the association between sequence changes and flowering phenotypes of rice in different regions. Seven loss-of-function hd1 haplotypes had been reported. By data-mining the genome sequencing information in the public domain, we discovered 3 other types. These loss-of-function allele haplotypes are present in subtropical and tropical regions, which indicates human selection. Some of these haplotypes are present locally. However, types 7 and 13 are present in more than one-third of the world's rice accessions, including landraces and modern varieties. In the present study, phylogenetic, allele network and selection pressure analyses revealed that these two haplotypes might have occurred early in Southeastern Asia and then were introgressed in many local landraces in nearby regions. We also demonstrate that these haplotypes are present in weedy rice populations, which again indicates that these alleles were present in rice cultivation for long time. In comparing the wild rice sequence information, these loss-of-function haplotypes occurred in agro but were not from wild rice.

This article was not made open access when initially published online, which was corrected before print publication. In addition, ORCID links were missing for 12 authors and have been added to the HTML and PDF versions of the article.

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.

Background Genetic data for traditional Taiwanese (Formosan) agriculture is essential for tracing the origins on the East Asian mainland of the Austronesian language family, whose homeland is generally placed in Taiwan. Three main models for the origins of the Taiwanese Neolithic have been proposed: origins in coastal north China (Shandong); in coastal central China (Yangtze Valley), and in coastal south China. A combination of linguistic and agricultural evidence helps resolve this controversial issue. Results We report on botanically informed linguistic fieldwork of the agricultural vocabulary of Formosan aborigines, which converges with earlier findings in archaeology, genetics and historical linguistics to assign a lesser role for rice than was earlier thought, and a more important one for the millets. We next present the results of an investigation of domestication genes in a collection of traditional rice landraces maintained by the Formosan aborigines over a hundred years ago. The genes controlling awn length, shattering, caryopsis color, plant and panicle shapes contain the same mutated sequences as modern rice varieties everywhere else in the world, arguing against an independent domestication in south China or Taiwan. Early and traditional Formosan agriculture was based on foxtail millet, broomcorn millet and rice. We trace this suite of cereals to northeastern China in the period 6000–5000 BCE and argue, following earlier proposals, that the precursors of the Austronesians, expanded south along the coast from Shandong after c. 5000 BCE to reach northwest Taiwan in the second half of the 4th millennium BCE. This expansion introduced to Taiwan a mixed farming, fishing and intertidal foraging subsistence strategy; domesticated foxtail millet, broomcorn millet and japonica rice; a belief in the sacredness of foxtail millet; ritual ablation of the upper incisors in adolescents of both sexes; domesticated dogs; and a technological package including inter alia houses, nautical technology, and loom weaving. Conclusion We suggest that the pre-Austronesians expanded south along the coast from that region after c. 5000 BCE to reach northwest Taiwan in the second half of the 4th millennium BCE. Electronic supplementary material The online version of this article (10.1186/s12284-018-0247-9) contains supplementary material, which is available to authorized users.

This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

Rice is an important crop and major model plant for monocot functional genomics studies. With the establishment of various genetic resources for rice genomics, the next challenge is to systematically assign functions to predicted genes in the rice genome. Compared with the robustness of genome sequencing and bioinformatics techniques, progress in understanding the function of rice genes has lagged, hampering the utilization of rice genes for cereal crop improvement. The use of transfer DNA (T-DNA) insertional mutagenesis offers the advantage of uniform distribution throughout the rice genome, but preferentially in gene-rich regions, resulting in direct gene knockout or activation of genes within 20-30 kb up- and downstream of the T-DNA insertion site and high gene tagging efficiency. Here, we summarize the recent progress in functional genomics using the T-DNA-tagged rice mutant population. We also discuss important features of T-DNA activation- and knockout-tagging and promoter-trapping of the rice genome in relation to mutant and candidate gene characterizations and how to more efficiently utilize rice mutant populations and datasets for high-throughput functional genomics and phenomics studies by forward and reverse genetics approaches. These studies may facilitate the translation of rice functional genomics research to improvements of rice and other cereal crops.

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.

Small RNAs (sRNAs) play important roles in plants under stress conditions. However, limited research has been performed on the sRNAs involved in plant wound responses. In the present study, a novel wounding-induced sRNA, sRNA8105, was identified in sweet potato (Ipomoea batatas cv. Tainung 57) using microarray analysis. It was found that expression of sRNA8105 increased after mechanical wounding. Furthermore, Dicer-like 1 (DCL1) is required for the sRNA8105 precursor (pre-sRNA8105) to generate 22 and 24 nt mature sRNA8105. sRNA8105 targeted the first intron of IbMYB1 (MYB domain protein 1) before RNA splicing, and mediated RNA cleavage and DNA methylation of IbMYB1. The interaction between sRNA8105 and IbMYB1 was confirmed by cleavage site mapping, agro-infiltration analyses, and use of a transgenic sweet potato over-expressing pre-sRNA8105 gene. Induction of IbMYB1-siRNA was observed in the wild-type upon wounding and in transgenic sweet potato over-expressing pre-sRNA8105 gene without wounding, resulting in decreased expression of the whole IbMYB1 gene family, i.e. IbMYB1 and the IbMYB2 genes, and thus directing metabolic flux toward biosynthesis of lignin in the phenylpropanoid pathway. In conclusion, sRNA8105 induced by wounding binds to the first intron of IbMYB1 RNA to methylate IbMYB1, cleave IbMYB1 RNA, and trigger production of secondary siRNAs, further repressing the expression of the IbMYB1 family genes and regulating the phenylpropanoid pathway.

Rice (Oryza sativa) is one of the most important crops in the world. Several rice insertional mutant libraries are publicly available for systematic analysis of gene functions. However, the tagging efficiency of these mutant resources-the relationship between genotype and phenotype-is very low. We used whole-genome sequencing to analyze a T-DNA-tagged transformant from the Taiwan Rice Insertional Mutants (TRIM) resource. The phenomics records for M0028590, one of the TRIM lines, revealed three phenotypes-wild type, large grains, and tillering dwarf-in the 12 T1 plants. Using the sequencing data for 7 plants from three generations of this specific line, we demonstrate that introgression from an indica rice variety might occur in one generation before the seed was used for callus generation and transformation of this line. In addition, the large-grain trait came from the GS3 gene of the introgressed region and the tillering dwarf phenotype came from a single nucleotide change in the D17 gene that occurred during the callus induction to regeneration of the transformant. As well, another regenerant showed completely heterozygous single-nucleotide polymorphisms across the whole genome. In addition to the known sequence changes such as T-DNA integration, single nucleotide polymorphism, insertion, deletion, chromosome rearrangement and doubling, spontaneous outcrossing occurred in the rice field may also explain some mutated traits in a tagged mutant population. Thus, the co-segregation of an integration event and the phenotype should be checked when using these mutant populations.

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., This work was supported by the Spanish Ministry of Economy and Competitiveness (MINECO) and the European Regional Development funds (FEDER) (BIO2012-32838, BIO2015-67212-R to B.S.S.) and the CSIC/NSC (Spanish National Research Council/National Science Council of Taiwan)-Cooperative Research Project-Formosa Program (2009TW0041 to B.S.S. and Y.I.C.H]. P.B. received a Ph.D. grant from the Ministerio de Ciencia e Innovación, Formación de Personal Investigador (BES-2010-032879).

To facilitate genetic research, we constructed two linkage maps by employing two F₂ populations derived from rice inter-subspecific crosses, japonica Tainung 67 (TNG67)/indica Taichung Sen 10 (TCS10) and japonica TNG67/indica Taichung Sen 17 (TCS17). We established linkage map lengths of 1481.6 cM and 1267.4 cM with average intervals of 13.8 cM and 14.4 cM by using 107 and 88 PCR markers for coverage of 88% of the rice genome in TNG67/TCS10 and TNG67/TCS17, respectively. The discrepancy in genetic maps in the two populations could be due to different cross combinations, crossing-over events, progeny numbers and/or markers. The most plausible explanation was segregation distortion; 18 markers (16.8%) distributed at nine regions of seven chromosomes and 10 markers (11.4%) at four regions of four chromosomes displayed severe segregation distortion (p < 0.01)in TNG67/TCS10 and TNG67/TCS17, respectively. All segregation-distorted markers in these two populations corresponded to reported reproductive barriers, either gametophytic or zygotic genes but not to hybrid breakdown genes. The observed recombination frequency, which was higher or lower than the intrinsic frequency, revealed the association of segregation distortion skewed to the same or different genotypes at the consecutive markers. The segregation distortion, possibly caused by reproductive barriers, affects the evaluation recombination frequencies and consequently the linkage analysis of QTLs and positional cloning.

Searches of sequenced genomes of diverse organisms revealed that the moss Physcomitrella patens is the most primitive organism possessing oleosin genes. Microscopy examination of Physcomitrella revealed that oil bodies (OBs) were abundant in the photosynthetic vegetative gametophyte and the reproductive spore. Chromatography illustrated the neutral lipids in OBs isolated from the gametophyte to be largely steryl esters and triacylglycerols, and SDS-PAGE showed the major proteins to be oleosins. Reverse transcription-PCR revealed the expression of all three oleosin genes to be tissue specific. This tissue specificity was greatly altered via alternative splicing, a control mechanism of oleosin gene expression unknown in higher plants. During the production of sex organs at the tips of gametophyte branches, the number of OBs in the top gametophyte tissue decreased concomitant with increases in the number of peroxisomes and level of transcripts encoding the glyoxylate cycle enzymes; thus, the OBs are food reserves for gluconeogenesis. In spores during germination, peroxisomes adjacent to OBs, along with transcripts encoding the glyoxylate cycle enzymes, appeared; thus, the spore OBs are food reserves for gluconeogenesis and equivalent to seed OBs. The one-cell-layer gametophyte could be observed easily with confocal microscopy for the subcellular OBs and other structures. Transient expression of various gene constructs transformed into gametophyte cells revealed that all OBs were linked to the endoplasmic reticulum (ER), that oleosins were synthesized in extended regions of the ER, and that two different oleosins were colocated in all OBs.

Rice ( Oryza sativa ) is the reference genome for the grasses, including cereals. The complete genome sequence lays the foundation for comparative genomics to the other grasses based on genome structure and individual gene function ([Devos, 2005][1]; [International Rice Genome Sequencing Project

The anthers in flowers perform important functions in sexual reproduction. Several recent studies used microarrays to study anther transcriptomes to explore genes controlling anther development. To analyze the secretion and other functions of the tapetum, we produced transcriptomes of anthers of rice (Oryza sativa subsp. japonica) at six progressive developmental stages and pollen with sequencing-by-synthesis technology. The transcriptomes included at least 18,000 unique transcripts, about 25% of which had antisense transcripts. In silico anther-minus-pollen subtraction produced transcripts largely unique to the tapetum; these transcripts include all the reported tapetum-specific transcripts of orthologs in other species. The differential developmental profiles of the transcripts and their antisense transcripts signify extensive regulation of gene expression in the anther, especially the tapetum, during development. The transcriptomes were used to dissect two major cell/biochemical functions of the tapetum. First, we categorized and charted the developmental profiles of all transcripts encoding secretory proteins present in the cellular exterior; these transcripts represent about 12% and 30% of the those transcripts having more than 100 and 1,000 transcripts per million, respectively. Second, we successfully selected from hundreds of transcripts several transcripts encoding potential proteins for lipid exine synthesis during early anther development. These proteins include cytochrome P450, acyltransferases, and lipid transfer proteins in our hypothesized mechanism of exine synthesis in and export from the tapetum. Putative functioning of these proteins in exine formation is consistent with proteins and metabolites detected in the anther locule fluid obtained by micropipetting.

Gibberellin 2-oxidases (GA2oxs) regulate plant growth by inactivating endogenous bioactive gibberellins (GAs). Two classes of GA2oxs inactivate GAs through 2β-hydroxylation: a larger class of C19 GA2oxs and a smaller class of C20 GA2oxs. In this study, we show that members of the rice (Oryza sativa) GA2ox family are differentially regulated and act in concert or individually to control GA levels during flowering, tillering, and seed germination. Using mutant and transgenic analysis, C20 GA2oxs were shown to play pleiotropic roles regulating rice growth and architecture. In particular, rice overexpressing these GA2oxs exhibited early and increased tillering and adventitious root growth. GA negatively regulated expression of two transcription factors, O. sativa homeobox 1 and TEOSINTE BRANCHED1, which control meristem initiation and axillary bud outgrowth, respectively, and that in turn inhibited tillering. One of three conserved motifs unique to the C20 GA2oxs (motif III) was found to be important for activity of these GA2oxs. Moreover, C20 GA2oxs were found to cause less severe GA-defective phenotypes than C19 GA2oxs. Our studies demonstrate that improvements in plant architecture, such as semidwarfism, increased root systems and higher tiller numbers, could be induced by overexpression of wild-type or modified C20 GA2oxs.

The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. Since the last publication of the RAP-DB, the IRGSP genome has been revised and reassembled. In addition, a large number of rice-expressed sequence tags have been released, and functional genomics resources have been produced worldwide. Thus, we have thoroughly updated our genome annotation by manual curation of all the functional descriptions of rice genes. The latest version of the RAP-DB contains a variety of annotation data as follows: clone positions, structures and functions of 31 439 genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc. Other annotation data such as Gnomon can be displayed along with those of RAP for comparison. We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/.

Promoters play key roles in conferring temporal, spatial, chemical, developmental, or environmental regulation of gene expression. Promoters that are subject to specific regulations are useful for manipulating foreign gene expression in plant cells, tissues, or organs with desirable patterns and under controlled conditions, and have been important for both basic research and applications in agriculture biotechnology. Recent advances in genomics technologies have greatly facilitated identification and study of promoters in a genome scale with high efficiency. Previously we have generated a large T-DNA tagged rice mutant library (TRIM), in which the T-DNA was designed with a gene/promoter trap system, by placing a promoter-less GUS gene next to the right border of T-DNA. GUS activity screens of this library offer in situ and in planta identifications and analyses of promoter activities in their native configurations in the rice genome. In the present study, we systematically performed GUS activity screens of the rice mutant library for genes/promoters constitutively, differentially, or specifically active in vegetative and reproductive tissues. More than 8,200 lines have been screened, and 11% and 22% of them displayed GUS staining in vegetative tissues and in flowers, respectively. Among the vegetative tissue active promoters, the ratio of leaf active versus root active is about 1.6. Interestingly, all the flower active promoters are anther active, but with varied activities in different flower tissues. To identify tissue specific ABA/stress up-regulated promoters, we compared microarray data of ABA/stress induced genes with those of tissue-specific expression determined by promoter trap GUS staining. Following this approach, we showed that the peroxidase 1 gene promoter was ABA up-regulated by 4 fold within 1 day of exposure to ABA and its expression is lateral root specific. We suggest that this be an easy bioinformatics approach in identifying tissue/cell type specific promoters that are up-regulated by hormones or other factors.

Sub-QTLs and multiple intra-QTL genes are hypothesized to underpin large-effect QTLs. Known QTLs over gene families, biosynthetic pathways or certain traits represent functional gene-clusters of genes of the same gene ontology (GO). Gene-clusters containing genes of different GO have not been elaborated, except in silico as coexpressed genes within QTLs. Here we demonstrate the requirement of multiple intra-QTL genes for the full impact of QTL qDTY12.1 on rice yield under drought. Multiple evidences are presented for the need of the transcription factor ‘no apical meristem’ (OsNAM12.1) and its co-localized target genes of separate GO categories for qDTY12.1 function, raising a regulon-like model of genetic architecture. The molecular underpinnings of qDTY12.1 support its effectiveness in further improving a drought tolerant genotype and for its validity in multiple genotypes/ecosystems/environments. Resolving the combinatorial value of OsNAM12.1 with individual intra-QTL genes notwithstanding, identification and analyses of qDTY12.1has fast-tracked rice improvement towards food security.

The repeat sequences occupied more than 50 % of soybean genome. In order to understand where these repeat sequences distributed in soybean genome and its related Glycine species, we examined three new repeat sequences—soybean repeat sequence (SBRS1, SBRS2 and SBRS3), some nonspecific repeat sequences and 45S rDNA on several Glycine species, including annual and perennial accessions in this study. In the annual species, G. soja, signals for SBRS1 and ATT repeat can be found on each chromosome in GG genome, but those for SBRS2 and SBRS3 were located at three specific loci. In perennial Glycine species, these three SBR repeat frequently co-localized with 45S rDNA, two major 45S rDNA loci were found in all tetraploid species. However, an extra minor locus was found in one accession of the G. pescadrensis (Tab074), but not in another accession (Tab004). We demonstrate that some repetitive sequences are present in all Glycine species used in the study, but the abundancy is different in annual or perennial species. We suggest this study may provide additional information in investigations of the phylogeny in the Glycine species. Electronic supplementary material The online version of this article (doi:10.1186/s40529-015-0103-9) contains supplementary material, which is available to authorized users.

Rice is a facultative short-day plant, and it requires a photoperiod shorter than the critical day length to get flowering. Sensitivity to photoperiod has been suggested as a major selection target in cultivated or weedy rice. The modern rice varieties in Taiwan may be cultivated twice a year. These varieties contain loss-of-function of two important flowering-time related genes, Heading date 1 (Hd1) and Early heading date 1 (Ehd1), and are mainly from a mega variety, Taichung 65. However, the parental lines of this variety were sensitive to photoperiod, thus, how Taichung 65 loss its sensitivity is a mystery. In this study, we used accession-specific single nucleotide polymorphism analysis to reveal the gene flow that occurred between different rice accessions decades ago and demonstrate that two landraces introgressed during the breeding process, which led to the loss of photoperiod sensitivity. Both Hd1 and Ehd1 may be important during artificial selection for flowering time, especially in a subtropical region such as Taiwan. This is a good example of introgression playing important roles during rice domestication.

Background Comparative evolutionary analysis of whole genomes requires not only accurate annotation of gene space, but also proper annotation of the repetitive fraction which is often the largest component of most if not all genomes larger than 50 kb in size. Results Here we present the Rice TE database (RiTE-db) - a genus-wide collection of transposable elements and repeated sequences across 11 diploid species of the genus Oryza and the closely-related out-group Leersia perrieri. The database consists of more than 170,000 entries divided into three main types: (i) a classified and curated set of publicly-available repeated sequences, (ii) a set of consensus assemblies of highly-repetitive sequences obtained from genome sequencing surveys of 12 species; and (iii) a set of full-length TEs, identified and extracted from 12 whole genome assemblies. Conclusions This is the first report of a repeat dataset that spans the majority of repeat variability within an entire genus, and one that includes complete elements as well as unassembled repeats. The database allows sequence browsing, downloading, and similarity searches. Because of the strategy adopted, the RiTE-db opens a new path to unprecedented direct comparative studies that span the entire nuclear repeat content of 15 million years of Oryza diversity. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1762-3) contains supplementary material, which is available to authorized users.

Two deep-coverage bacterial artificial chromosome (BAC) libraries of Oryza sativa japonica cv. Tainung 67 (TNG 67), a popular genetic stock in breeding programs and scientific research in Taiwan, have been constructed to facilitate positional cloning of rice genes and to analyze variety-specific genome composition, toward rice structural and functional genomic studies. Good high-molecular-weight DNA was produced well by nuclei preparation from two- to three-week-old seedlings, partially digested by either HindIII or EcoRI, and two cycles of size selection by pulsed-field gel electrophoresis (PFGE). The HindIII library consists of 45,312 clones, near lack of false positive clones, with an estimated average insert size of 138.4 kb and coverage of 15.1× haploid genome equivalents. The EcoRI library consists of 9984 clones, 2% of false positive clones, with an estimated average insert size of 137.8 kb and coverage of 3.2× haploid genome equivalents. Nine single-copy sequence tagged site (STS) markers, located on different chromosomes, were used to screen the two libraries, which a single BAC clone double-spotted on three filters, and hybridized 16–29, with an average of 21.2 BACs. As a result, these two libraries can complement each other and cover nearly 100% of the rice genome, consequently providing efficient tools to isolate any genes of interest. Resources, high-density filters, individual clones, and whole libraries, are available for public distribution and may be accessed at the Institute of Plant and Microbial Biology, Academia Sinica, or Arizona Genomic Institute (AGI).

A fine physical map of the rice (Oryza sativa spp. Japonica var. Nipponbare) chromosome 5 with bacterial artificial chromosome (BAC) and PI-derived artificial chromosome (PAC) clones was constructed through integration of 280 sequenced BAC/PAC clones and 232 sequence tagged site/expressed sequence tag markers with the use of fingerprinted contig data of the Nipponbare genome. This map consists of five contigs covering 99% of the estimated chromosome size (30.08 Mb). The four physical gaps were estimated at 30 and 20 kb for gaps 1-3 and gap 4, respectively. We have submitted 42.2-Mb sequences with 29.8 Mb of nonoverlapping sequences to public databases. BAC clones corresponding to telomere and centromere regions were confirmed by BAC-fluorescence in situ hybridization (FISH) on a pachytene chromosome. The genetically centromeric region at 54.6 cM was covered by a minimum tiling path spanning 2.1 Mb with no physical gaps. The precise position of the centromere was revealed by using three overlapping BAC/PACs for approximately 150 kb. In addition, FISH results revealed uneven chromatin condensation around the centromeric region at the pachytene stage. This map is of use for positional cloning and further characterization of the rice functional genomics.

Rice, one of the world's most important food plants, has important syntenic relationships with the other cereal species and is a model plant for the grasses. Here we present a map-based, finished quality sequence that covers 95% of the 389 Mb genome, including virtually all of the euchromatin and two complete centromeres. A total of 37,544 non-transposable-element-related protein-coding genes were identified, of which 71% had a putative homologue in Arabidopsis. In a reciprocal analysis, 90% of the Arabidopsis proteins had a putative homologue in the predicted rice proteome. Twenty-nine per cent of the 37,544 predicted genes appear in clustered gene families. The number and classes of transposable elements found in the rice genome are consistent with the expansion of syntenic regions in the maize and sorghum genomes. We find evidence for widespread and recurrent gene transfer from the organelles to the nuclear chromosomes. The map-based sequence has proven useful for the identification of genes underlying agronomic traits. The additional single-nucleotide polymorphisms and simple sequence repeats identified in our study should accelerate improvements in rice production.

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.

This special issue of Rice presents a selection of papers from the international symposium “Rice and Language Across Asia: Crops, Movement, and Social Change,” held at Cornell University, Ithaca, USA, on September 22–25, 2011. The goal of this meeting was to reexamine the relationship between the beginnings and spread of rice agriculture and cultural, social, and linguistic developments of early Asian societies. Rice farming is but one aspect of the development of early agriculture inAsia, which of course also involved animal domestication and the adoption of other crops such as millets, tubers, and other vegetables, but the special focus on rice is justified because of the highly significant role of rice in the agricultural transformations and expansions across Asia over the last ten millennia. This included the growth and dispersal of early human populations, as well as the dramatic influences on social organization that accompanied the introduction, development, and increased reliance on rice farming. Recent years have seen rapid advances in the multiple related fields of research that bear on these questions: in linguistics and historical linguistics, in particular in the fields of language reconstruction and subgrouping; in both human genetics and plant genetics; in archaeology, including especially in the burgeoning subfield of archaeobotany; in anthropology (see O’Connor this volume and O’Connor 1995), deploying a deep historical and regional approach of a certain kind that had become uncommon in anthropology), as well as in other related fields, such as economic history, climate research, and others. For some time now, scholars in these disparate yet related disciplines have grappled with the pursuit of data and the comparison with results from other disciplines: see for example the collected essays volumes by Sagart et al. (2005), Sanchez-Mazas et al. (2008), Petraglia and Allchin (2007), Peregrine et al. (2009), Enfield and White (2011) and others. All face the problems of how to compare research results and how to achieve interdisciplinary communication and mutual reinforcement between scholars addressing the problems of shared concern, across different disciplines. All of the contributions to our September 2011 symposium, including those presented here, were contributed in the spirit of extending these discussions and exchanging views between disciplines on the complex relationship between crops, language, and sociocultural developments in early Asia. Because of the interrelated lines of evidence emerging from linguistics, genetics, biology and environmental studies, archaeology, anthropology, and history, the complexity of the issues cannot be avoided, and further interdisciplinary engagement will continue to be necessary. This includes a need for further effort to facilitate the communication between disciplines, and a need for reflection on the adequacy of indiscipline terminology and ways of thinking that may be taken for granted within disciplines, but the limits of which become even more apparent in interdisciplinary encounters than M. Fiskesjo (*) Department of Anthropology, Cornell University, McGraw Hall, Room 204, Ithaca, NY 14853, USA e-mail: magnus.fiskesjo@cornell.edu

A cDNA clone GmPM4 which encodes mRNA species in mature or dry soybean seeds was characterized. DNA sequence analysis shows that the deduced polypeptides have a molecular mass of 68 kDa. GmPM4 proteins have a relatively high amino acid sequence homology with a major biotinylated protein isolated from pea seeds, SBP65, but both of these proteins differ markedly from that of presently known biotin enzymes. The accumulation of GmPM4 mRNA is detectable in the leaf primodium and the vascular tissues of the hypocotyl-radicle axis of mature seeds, and the GmPM4 proteins are present at high levels in dry and mature soybean seeds, but not in fresh immature seeds. It degrades rapidly at the early stage of seed germination. These proteins are boiling-soluble and biotinylated when they are present endogenously in soybean seeds; however, the same recombinant protein expressed in Escherichia coli is boiling-soluble, but it is not biotinylated.

In the past 15 years a large international effort of generation of mutant collections has been accomplished in rice, the model plant for cereals and grasses. Physical and chemical mutagenesis as well as insertion mutagenesis using Agrobacterium T-DNA, endogenous Tos17 retro-element, and maize transposon systems have been used to create lesions in the 39,000 non-transposable genes annotated in the rice genome. Nowadays, 72 % of the rice genes have at least one sequence-indexed insert while 22 % have three, allelic, sequence-indexed inserts. Despite their yet incomplete coverage, these resources have already been instrumental in unraveling the function of numerous genes underlying important developmental and physiological traits through forward or reverse genetics strategies. Together with sequence-specific inactivation approaches (RNA interference and nuclease-based gene editing), mutant collections will contribute to the elucidation of the function of all agronomically important genes in rice by year 2020, an objective shared by the rice community.

The protein and mRNA levels of late embryogenesis abundant (LEA) genes may be linked to osmotic stresses. Here, we characterized three soybean hydrophilic LEA proteins – GmPM11 (LEA I), GmPM6 (LEA II), and GmPM30 (LEA III) – by circular dichroism and Fourier transform infrared spectroscopy. Structural analysis revealed that the LEA proteins adopted high amounts of disordered conformations in solution and underwent conformational changes with hydrophobicity and desiccation induction. Macromolecular interaction studies revealed that the GmPM proteins interact with non-reducing sugars and phospholipids. GmPM6 and GmPM30 but not GmPM11 could prevent beta-aggregation of poly-l-lysine after slow drying. We discuss the possible functions of hydrophilic LEA proteins in maturing seeds.

Flowering is an important and highly regulated process. Taiwanese researchers have contributed significantly to understanding flowering biology, including cell biology, cytogenetics and functional genomics, in rice, lily and especially orchids. In recognition of this effort, the PCP Editorial Board is publishing a special issue on flowering research in Taiwan. This issue contains seven articles on cutting-edge topics or reviews of flowering research carried out in Taiwan, focusing on research into orchids and lily. An anther consists of sporophytic tissues of three outer cell layers and an innermost layer, the tapetum. The tapetum has attracted the most attention. Tapetum cells are important in nurturing the maturing microspores, and their ablation leads to microspore death and thus male sterility (Hesse et al. 1993). In a review paper, M.-D. Huang et al. (pp. 1459–1466) provide information about current studies on the transcriptome of the anther sporophyte, including microarray and next-generation sequencing data. The authors illustrate a proposed gene regulation network of anther development in Arabidopsis using the most updated references. In addition, they point out potential studies worthwhile pursuing, including those of ‘secretomes’, antisense transcripts and small RNAs. Finally, they propose a model for exine precursor biosynthesis in tapetum cells and transport of these precursors from the tapetum cell to the microspore surface. With an estimated >25,000 species, orchids are the most species-rich of all angiosperm families (Leitch et al. 2009). They show a wide diversity of epiphytic and terrestrial growth forms and have successfully colonized almost every habitat on earth. The expansion of the orchid family probably took place in a comparatively short period as compared with that of most flowering plant families, which suggests exceptionally high speciation rates (Gill 1989). The production of orchids in the world has increased 12–18% every year since 2000. Taiwan is one of the world-renowned countries exporting orchids, because the climate is congenial to the growth of orchids and because of the rich resource of native species and advances in breeding techniques to produce more beautiful and elegant new varieties. Taiwan’s orchid industry has been recognized by the international community as prosperous in terms of sales volume, orchid plantation, orchid-growing technologies and financial resources. The most popular potted flowering plants are Phalaenopsis hybrids, and Oncidium are the top-traded cut flowers. Most, if not all, orchid flowers on the market are hybrids, such as Phalaenopsis spp., although most researchers use inbred lines such as Phalaenopsis equestris as materials for detailed studies. Fig. 1 illustrates several examples of orchid varieties, their mutants, disease and insect infection, as well as orchid production. In the second review paper of this issue, Hsiao et al. (pp. 1467–1486) provide an overview of the research activities in orchid biology and biotechnology, including the status of genomics, transformation technology, flowering regulation, molecular regulatory mechanisms of floral development, scent production and color presentation. The authors also point out the pros and cons of using orchids for genome research. Oncidium is a valuable floral genus of orchid. The yellow color is most often seen in the flower market. The largest flower structure is the labellum, also known as the lip (fig. 1E, p. 1533). Chang et al. (pp. 1532–1545) used 454 sequencing to perform deep sequencing of the Oncidium transcriptome using six organs. A value-added expressed sequence tag (EST) database, OncidiumOrchidGenomeBase (http://predictor.nchu. edu.tw/oogb/), was constructed and provides a foundation for molecular genetics and functional genomics for modifying the flowering quality and desirable agronomic traits of Oncidium. The authors also identified flowering time-associated genes, including photoreceptors and floral pathway integrators. Su et al. (pp. 1501–1514) performed transcriptome analysis of mixed vegetative and reproductive tissues of the moth orchid Phalaenopsis aphrodite and constructed the Orchidstra genome database (http://orchidstra.abrc.sinica.edu.tw) for searching and linking to corresponding Pfam, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Fu et al. (2011) prepared an EST database from 11 tissues collected from three orchid species, i.e. P. equestris, P. aphrodite and P. bellina, using both traditional and next-generation sequencing. This OrchidBase is freely available at http://lab.fhes.tn.edu.tw/est. Altogether, these three transcriptome databases consist of about 100,000 contigs from four orchid species and thus provide tremendous resources for orchid functional genomics studies as well as breeding application. Although the floral ABCDE model is generally thought to be ubiquitous in the core eudicots, studies of basal angiosperms

An anther includes sporophytic tissues of three outer cell layers and an innermost layer, the tapetum, which encloses a locule where the gametophytic microspores mature to become pollen. The sporophytic tissues also comprise some vascular cells and specialized cells of the stomium aligning the long anther axis for anther dehiscence. Studies of the anther sporophytic cells, especially the tapetum, have recently expanded from the use of microscopy to molecular biology and transcriptomes. The available sequencing technologies, plus the use of laser microdissection and in silico subtraction, have produced high-quality anther sporophyte transcriptomes of rice, Arabidopsis and maize. These transcriptomes have been used for research discoveries and have potential for future discoveries in diverse areas, including developmental gene activity networking and changes in enzyme and metabolic domains, prediction of protein functions by quantity, secretion, antisense transcript regulation, small RNAs and promoters for generating male sterility. We anticipate that these studies with rice and other transcriptomes will expand to encompass other plants, whose genomes will be sequenced soon, with ever-advancing sequencing technologies. In comprehensive gene activity profiling of the anther sporophyte, studies involving transcriptomes will spearhead investigation of the downstream gene activity with proteomics and metabolomics.

Summary Lipid metabolism in maize (Zea mays L.) tissue culture was studied using 7 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 kernels, but 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. Also, embryogenic calli were used to select cell lines resistant to ceruleni an inhibitor of fatty-acid synthesis. While it was hypothesized that the cerulenin-resistant calli might give rise to an overproducing-oil line, the selected resistant calli did not exhibit an increase in lipid content relative to the control calli.

Proteins abundant in seeds during the late stages of development, late embryogenesis abundant (LEA) proteins, are associated with desiccation tolerance. More than 100 of the group I LEA genes, also termed Em genes, have been identified from plants, bacteria and animals. The wide distribution indicates the functional importance of these genes. In the present study, we characterized a novel Em-like gene, OsLEA1a of rice (Oryza sativa). The encoded OsLEA1a protein has an N-terminal sequence similar to that of other plant Em proteins but lacks a 20-mer motif that is the most significant feature of typical Em proteins. The location of the sole intron indicates that the second exon of OsLEA1a is the mutated product of a typical Em gene. Transcriptome analysis revealed OsLEA1a mainly expressed in embryos, with no or only a few transcripts in osmotic stress-treated vegetative tissues. Structural analysis revealed that the OsLEA1a protein adopts high amounts of disordered conformations in solution and undergoes desiccation-induced conformational changes. Macromolecular interaction studies revealed that OsLEA1a protein interacts with non-reducing sugars and phospholipids but not poly-L-lysine. Thus, although the OsLEA1a protein lost its 20-mer motif, it is still involved in the formation of bioglasses with non-reducing sugars or plasma membrane. However, the protein does not function as a chaperone as do other groups of hydrophilic LEA proteins. The orthologs of the OsLEA1a gene had been indentified from various grasses but not in dicot plants. Genetic analysis indicated that rice OsLEA1a locates at a 193 kb segment in chromosome 1 and is conserved in several published cereal genomes. Thus, the ancestor of Em-like genes might have evolved after the divergence of monocot plants.

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.

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.