Genomic basis for light control of plant development

Light is one of the key environmental signals regulating plant growth and development.Therefore,understanding the mechanisms by which light controls plant development has long been of great interest to plant biologists.Traditional genetic and molecular approaches have successfully identified key regulatory factors in light signaling,but recent genomic studies have revealed massive reprogramming of plant transcriptomes by light,identified binding sites across the entire genome of several pivotal transcription factors in light signaling,and discovered the involvement of epigenetic regulation in light-regulated gene expression.This review summarizes the key genomic work conducted in the last decade which provides new insights into light control of plant development.

Genome-wide association study dissects the genetic bases of salt tolerance in maize seedlings

Excess salinity is a natural stress that causes crop yield losses worldwide. The genetic bases of maize salt tolerance remain largely unknown. Here we investigated the survival rates of 445 maize natural accessions after salt treatments. A skewed distribution of the salttolerant phenotypes was observed in this population.Genome-wide association studies(GWAS) revealed 57 loci significantly associated with salt tolerance. Forty-nine candidate genes were detected from these loci. About10% of these genes were co-localized with loci from QTL mapping. Forty four percent of the candidate genes were involved in stress responses, ABA signaling,stomata division, DNA binding/transcription regulation and auxin signaling, suggesting that they are key genetic mechanisms of maize salt tolerance. Transgenic studies showed that two genes, the salt-tolerance-associatedgene 4(SAG4, GRMZM2 G077295) and SAG6(GRMZM2 G106056), which encode a protein transport protein and the double-strand break repair protein MRE11,respectively, had positive roles in plant salt tolerance,and their salt-tolerant haplotypes were revealed. The genes we identified in this study provide a list of candidate targets for further study of maize salt tolerance, and of genetic markers and materials that may be used for breeding salt-tolerance in maize.

Enhanced Vitamin C Production Mediated by an ABA-Induced PTP-like Nucleotidase Improves Plant Drought Tolerance in Arabidopsis and Maize

Abscisic acid(ABA)is a key phytohormone that mediates environmental stress responses.Vitamin C,or L-ascorbic acid(AsA),is the most abundant antioxidant protecting against stress damage in plants.How the ABA and AsA signaling pathways interact in stress responses remains elusive.In this study,we characterized the role of a previously unidentified gene,PTPN(PTP-like Nucleotidase)in plant drought tolerance.In Arabidopsis,(AtPTPN was expressed in multiple tissues and upregulated by ABA and drought treatments.Loss-of-function mutants oiAtPTPN were hyposensitive to ABA but hypersensitive to drought stresses,whereas plants with enhanced expression AtPTPN showed opposite phenotypes to.Overexpression of maize PTPN(ZmPTPN)promoted,while knockdown oiZmPTPN inhibited plant drought tolerance,indicating conserved and positive roles of PTPN in plant drought tolerance.We found that both AtPTPN and ZmPTPN release Pi by hydrolyzing GDP/GMP/dGMP/IMP/dIMP,and that AtPTPN positively regulated AsA production via endogenous Pi content control.Consistently,overexpression of VTC2,the rate-limiting synthetic enzyme in AsA biosynthesis,promoted AsA production and plant drought tolerance,and these effects were largely dependent on AtPTPN activity.Furthermore,we demonstrated that the heat shock transcription factor HSFA6a directly binds the AtPTPN promoter and activates AtPTPN expression.Genetic analyses showed that AtPTPN is required for HSFA6a to regulate ABA and drought responses.Taken together,our data indicate that PTPN-mediated crosstalk between the ABA signaling and AsA biosynthesis pathways positively controls plant drought tolerance.

Genomic Features and Regulatory Roles of Intermediate-Sized Non-Coding RNAs in Arabidopsis

ABSTRACT Recent advances in genome-wide techniques allowed the identification of thousands of non-coding RNAs with various sizes in eukaryotes, some of which have further been shown to serve important functions in many biologi- cal processes. However, in model plant Arabidopsis, novel intermediate-sized ncRNAs （im-ncRNAs） （50-300 nt） have very limited information. By using a modified isolation strategy combined with deep-sequencing technology, we identified 838 im-ncRNAs in Arabidopsis globally. More than half （58%） are new ncRNA species, mostly evolutionary divergent. Interestingly, annotated protein-coding genes with 5＇-UTR-derived novel im-ncRNAs tend to be highly expressed. For intergenic im-ncRNAs, their average abundances were comparable to mRNAs in seedlings, but subsets exhibited signifi- cantly lower expression in senescing leaves. Further, intergenic im-ncRNAs were regulated by similar genetic and epige- netic mechanisms to those of protein-coding genes, and some showed developmentally regulated expression patterns. Large-scale reverse genetic screening showed that the down-regulation of a number of im-ncRNAs resulted in either obvious molecular changes or abnormal developmental phenotypes in vivo, indicating the functional importance of im-ncRNAs in plant growth and development. Together, our results demonstrate that novel Arabidopsis im-ncRNAs are developmentally regulated and functional components discovered in the transcriptome.

Integration of light and temperature signaling pathways in plants

As two of the most important environmental factors,light and temperature regulate almost all aspects of plant growth and development.Under natural conditions,light is accompanied by warm temperatures and darkness by cooler temperatures,suggesting that light and temperature are tightly associated signals for plants.Indeed,accumulating evidence shows that plants have evolved a wide range of mechanisms to simultaneously perceive and respond to dynamic changes in light and temperature.Notably,the photoreceptor phytochrome B(phy B)was recently shown to function as a thermosensor,thus reinforcing the notion that light and temperature signaling pathways are tightly associated in plants.In this review,we summarize and discuss the current understanding of the molecular mechanisms integrating light and temperature signaling pathways in plants,with the emphasis on recent progress in temperature sensing,light control of plant freezing tolerance,and thermomorphogenesis.We also discuss the questions that are crucial for a further understanding of the interactions between light and temperature signaling pathways in plants.

PHYTOCHROME-INTERACTING FACTORS Interact with the ABA Receptors PYL8 and PYL9 to Orchestrate ABA Signaling in Darkness

PHYTOCHROME-INTERACTING FACTORS(PIFs)are a group of basic helix-loop-helix transcription factors that can physically interact with photoreceptors,including phytochromes and cryptochromes.It was previously demonstrated that PIFs accumulated in darkness and repressed seedling photomorphogenesis,and that PIFs linked different photosensory and hormonal pathways to control plant growth and development.In this study,we show that PIFs positively regulate the ABA signaling pathway during the seedling stage specifically in darkness.We found that PIFs positively regulate ABI5 transcript and protein levels in darkness in response to exogenous ABA treatment by binding directly to the G-box motifs in the ABI5 promoter.Consistently,PIFs and the G-box motifs in the ABI5 promoter determine ABI5 expression in darkness,and overexpression of ABI5 could rescue the ABA-insensitive phenotypes of pifq mutants in the dark.Moreover,we discovered that PIFs can physically interact with the ABA receptors PYL8 and PYL9,and that this interaction is not regulated by ABA.Further analyses showed that PYL8 and PYL9 promote PIF4 protein accumulation in the dark and enhance PIF4 binding to the ABI5 promoter,but negatively regulate PIF4-mediated ABI5 activation.Taken together,our data demonstrate that PIFs interact with ABA receptors to orchestrate ABA signaling in darkness by controlling ABI5 expression,providing new insights into the pivotal roles of PIFs as signal integrators in regulating plant growth and development.

UV-B-induced photomorphogenesis in Arabidopsis

Ultraviolet-B(UV-B)is a relatively minor component of sunlight,but can induce stress-related physiological pro-cesses or UV-B-specifi c photomorphogenic responses in plants.In the last decade,signifi cant progress has been made in understanding the UV-B photomorphogenic pathway,including identifi cation of the key components in the pathway,molecular characterization of UV-B pho-toreceptor and perception mechanism,and elucidation of the signal transduction mechanisms from the photo-activated UV-B receptor to downstream gene expression.This review summarizes the key players identifi ed to date in the UV-B photomorphogenic pathway and their roles in mediating UV-B signal transduction.

Arabidopsis DET1 Represses Photomorphogenesis in Part by Negatively Regulating DELLA Protein Abundance in Darkness

Arabidopsis De-etiolated 1 （DET1） is one of the key repressors that maintain the etiolated state of seedlings in darkness. The plant hormone gibberellic acid （GA） also participates in this process, and plants deficient in GA synthesis or signaling show a partially de.etiolated phenotype in darkness. However, how DET1 and the GA pathway work in concert in repressing photomorphogenesis remains largely unknown. In this study, we found that the abundance of DELLA proteins in detl-1 was increased in comparison with that in the wildtype plants. Mutation in DET1 changed the sensitivity of hypocotyl elongation of mutant seedlings to GA and paclobutrazol （PAC）, an inhibitor of GA synthesis. However, we did not find obvious differences between detl-1 and wild-type plants with regard to the bioactive GA content or the GA signaling upstream of DELLAs. Genetic data showed that removal of several DELLA proteins suppressed the detl-1 mutant phenotype more obviously than GA treatment, indicating that DET1 can regulate DELLA proteins via some other mechanisms. In addition, a large-scale transcriptomic analysis revealed that DET1 and DELLAs play antagonistic roles in regulating expression of photosynthetic and cell elongation-related genes in etiolated seedlings. Taken together, our results show that DET1 represses photomorphogenesis in darkness in part by reducing the abundance of DELLA proteins.

OsPKpa_1 encodes a plastidic pyruvate kinase that affects starch biosynthesis in the rice endosperm

Pyruvate kinase （PK） is a key enzyme in glycolysis and carbon metabolism. Here, we isolated a rice （Oryza sativa） mutant, w59, with a white-core floury endosperm. Map-based cloning of w59 identified a mutation in OsPKpα1, which encodes a plastidic isoform of PK （PKp）. OsPKpα1 localizes to the amyloplast stroma in the developing endosperm, and the mutation of OsPKpα1 in w59 decreases the plastidic PK activity, resulting in dramatic changes to the lipid biosynthesis in seeds. The w59 grains were also characterized by a marked decrease in starch content. Consistent with a decrease in number and size of the w59 amyloplasts, large empty spaces were observed in the central region of the w59 endosperm, at the early grain-filling stage. Moreover, a phylogenetic analysis revealed four potential rice isoforms of OsPKp. We validated the in vitro PK activity of these OsPKps through reconstituting active PKp complexes derived from inactive individual OsPKps, revealing the heteromeric structure of rice PKps, which was further confirmed using a protein- protein interaction analysis. These findings suggest a functional connection between lipid and starch synthesis in rice endosperm amyloplasts.

Integration of Cytological Features with Molecular and Epigenetic Properties of Rice Chromosome 4

It has been reported that rice chromosome 4 has eight major heterochromatic knobs within the heterochromatic half and that this organization correlates with chromosomal-level transcriptional activity. To better understand this chromosomal organization, we created a model based on the statistical distribution of various types of gene models to divide chromosome 4 into 17 euchromatic and heterochromatic regions that correspond with the cytological staining. Fluorescence in-situ hybridization （FISH） experiments using a set of bacterial artificial chromosome （BAC） clones from chromosome 4 placed all 18 clones in the region predicted by the model. Elevated levels of H3K4 di- and tri-methylation detected by chromatin-immunoprecipitation （CHIP） on chip were correlated with euchromatic regions whereas lower levels of these two modifications were detected in heterochromatic regions. Small RNAs were more abundant in the heterochromatic regions. To validate these findings, H3K4 trimethylation, H3K9 acetylation, H4K12 acetylation, and H3K9 di- and tri-methylation of 19 individual genes were measured by ChlP-PCR. Genes in heterochromatic regions had elevated H3K9 di- and tri-methylation while genes in euchromatic regions had elevated levels of the other three modifications. We also assayed cytosine methylation of these genes using the restriction enzymes McrBC, Hapll, and Msp I. This analysis indicated that cytosines of transposable elements and some genes located in heterochromatic regions were methylated while cytosines of the other genes were unmethylated. These results suggest that local transcriptional activity may reflect the organization of the corresponding part of the chromosome. They also indicate that epigenetic regulation plays an important role in correlating chromosomal organization with transcriptional activity.