October 2011, Volume 53 Issue 10, Pages 770ĘC844.

Cover Caption: Petal Development in Lotus japonicus
About the cover: Flowers of Lotus japonicus (WT) exhibit dorsoventral asymmetry, with three types of petals. In this issue, Weng et al. (pp 770ĘC782) examined the entire course of petal development. At the stage 2 (as showed by a scanning electron microscopy photo), CYC-like TCP genes control floral primordium initiation along the dorsoventral axis; at the late stage, they regulate the expression level of MIXTA-like genes and determine the shape and size of these petals. The cover pictures show the phenotypes of mutations in TCP genes.


          Cell and Developmental Biology
Petal Development in Lotus japonicus
Author: Lin Weng, Zhaoxia Tian, Xianzhong Feng, Xin Li, Shilei Xu, Xiaohe Hu, Da Luo and Jun Yang
Journal of Integrative Plant Biology 2011 53(10): 770-782
Published Online: September 9, 2011
DOI: 10.1111/j.1744-7909.2011.01072.x

Previous studies have demonstrated that petal shape and size in legume flowers are determined by two separate mechanisms, dorsoventral (DV) and organ internal (IN) asymmetric mechanisms, respectively. However, little is known about the molecular mechanisms controlling petal development in legumes. To address this question, we investigated petal development along the floral DV axis in Lotus japonicus with respect to cell and developmental biology by comparing wild-type legumes to mutants. Based on morphological markers, the entire course of petal development, from initiation to maturity, was grouped to define 3 phases or 13 stages. In terms of epidermal micromorphology from adaxial surface, mature petals were divided into several distinct domains, and characteristic epidermal cells of each petal differentiated at stage 9, while epidermal cells of all domains were observed until stage 12. TCP and MIXTA-like genes were found to be differentially expressed in various domains of petals at stages 9 and 12. Our results suggest that DV and IN mechanisms interplay at different stages of petal development, and their interaction at the cellular and molecular level guides the elaboration of domains within petals to achieve their ideal shape, and further suggest that TCP genes determine petal identity along the DV axis by regulating MIXTA-like gene expression.

Keywords: CYC-like TCP genes; epidermal cell; <i>Lotus japonicus</i>; MIXTA-like genes; petal.

Weng L, Tian Z, Feng X, Li X, Xu S, Hu X, Luo D, Yang J (2011) Petal development in <i>Lotus japonicus</i>. J. Integr. Plant Biol. 53(10), 770–782.

Abstract (Browse 2465)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Transcript Accumulation Dynamics of Phenylpropanoid Pathway Genes in the Maturing Xylem and Phloem of Picea abies during Latewood Formation
Author: Giovanni Emiliani, Maria Laura Traversi, Monica Anichini, Guido Giachi and Alessio Giovannelli
Journal of Integrative Plant Biology 2011 53(10): 783ĘC799
Published Online: July 18, 2011
DOI: 10.1111/j.1744-7909.2011.01069.x

In temperate regions, latewood is produced when cambial activity declines with the approach of autumnal dormancy. The understanding of the temporal (cambium activity vs dormancy) and spatial (phloem, cambial region, maturing xylem) regulation of key genes involved in the phenylpropanoid pathway during latewood formation represents a crucial step towards providing new insights into the molecular basis of xylogenesis. In this study, the temporal pattern of transcript accumulation of 12 phenylpropanoid genes (PAL1, C4H3/5, C4H4, 4CL3, 4CL4, HCT1, C3H3, CCoAOMT1, COMT2, COMT5, CCR2) was analyzed in maturing xylem and phloem of Picea abies during latewood formation. Quantitative reverse transcription-polymerase chain reaction analyses revealed a well-defined RNA accumulation pattern of genes involved in the phenylpropanoid pathway during latewood formation. Differences in the RNA accumulation patterns were detected between the different tissue types analyzed. The results obtained here demonstrated that the molecular processes involved in monolignol biosynthesis are not restricted to the cambial activity timeframe but continued after the end of cambium cell proliferation. Furthermore, since it has been shown that lignification of maturing xylem takes place in late autumn, we argue on the basis of our data that phloem could play a key role in the monolignol biosynthesis process.

Keywords: cambial region; gene expression; latewood formation; xylogenesis.

Emiliani G, Traversi ML, Anichini M, Giachi G, Giovannelli A (2011) Transcript accumulation dynamics of phenylpropanoid pathway genes in the maturing xylem and Phloem of <i>Picea abies</i> during latewood formation. J. Integr. Plant Biol. 53(10), 783–799.

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          Molecular Ecology and Evolution
Exploring the Transcriptome Landscape of Pomegranate Fruit Peel for Natural Product Biosynthetic Gene and SSR Marker Discovery  
Author: Nadia Nicole Ono, Monica Therese Britton, Joseph Nathaniel Fass, Charles Meyer Nicolet, Dawei Lin and Li Tian
Journal of Integrative Plant Biology 2011 53(10): 800-813
Published Online: September 12, 2011
DOI: 10.1111/j.1744-7909.2011.01073.x

Pomegranate fruit peel is rich in bioactive plant natural products, such as hydrolyzable tannins and anthocyanins. Despite their documented roles in human nutrition and fruit quality, genes involved in natural product biosynthesis have not been cloned from pomegranate and very little sequence information is available on pomegranate in the public domain. Shotgun transcriptome sequencing of pomegranate fruit peel cDNA was performed using RNA-Seq on the Illumina Genome Analyzer platform. Over 100 million raw sequence reads were obtained and assembled into 9,839 transcriptome assemblies (TAs) (>200 bp). Candidate genes for hydrolyzable tannin, anthocyanin, flavonoid, terpenoid and fatty acid biosynthesis and/or regulation were identified. Three lipid transfer proteins were obtained that may contribute to the previously reported IgE reactivity of pomegranate fruit extracts. In addition, 115 SSR markers were identified from the pomegranate fruit peel transcriptome and primers were designed for 77 SSR markers. The pomegranate fruit peel transcriptome set provides a valuable platform for natural product biosynthetic gene and SSR marker discovery in pomegranate. This work also demonstrates that next-generation transcriptome sequencing is an economical and effective approach for investigating natural product biosynthesis, identifying genes controlling important agronomic traits, and discovering molecular markers in non-model specialty crop species.

Ono NN, Britton MT, Fass JN, Nicolet CM, Lin D , Tian L (2011) Exploring the transcriptome, landscape of pomegranate fruit peel for natural product biosynthetic gene and SSR marker discovery. J. Integr. Plant Biol. 53(10), 800–813.

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          Plant-environmental Interactions
Induced Pib Expression and Resistance to Magnaporthe grisea are Compromised by Cytosine Demethylation at Critical Promoter Regions in Rice  
Author: Yuan Li, Qiong Xia, Hongping Kou, Dan Wang, Xiuyun Lin, Ying Wu, Chunming Xu, Shaocheng Xing and Bao Liu
Journal of Integrative Plant Biology 2011 53(10): 814-823
Published Online: July 21, 2011
DOI: 10.1111/j.1744-7909.2011.01070.x

Pib is a well-characterized rice blast-resistance gene belonging to the nucleotide binding site (NBS) and leucine-rich repeat (LRR) superfamily. Expression of Pib was low under non-challenged conditions, but strongly induced by the blast-causing fungal pathogen Magnaporthe grisea, thereby conferring resistance to the pathogen. It is generally established that cytosine methylation of the promoter-region often plays a repressive role in modulating expression of the gene in question. We report here that two critical regions of the Pib promoter were heavily CG cytosine-methylated in both cultivars studied. Surprisingly, induced expression of Pib by M. grisea infection did not entail its promoter demethylation, and partial demethylation by 5-azacytidine-treatment actually reduced Pib expression relative to wild-type plants. Accordingly, the blast disease-resistance was compromised in the 5′-azaC-treated plants relative to wild-type. In contrast, the disease susceptibility was not affected by the 5′-azaC treatment in another two rice cultivars that did not contain the Pib gene, ruling out effects of other R genes and non-specific genotoxic effects by the drug-treatment as a cause for the compromised Pib-conditioned blast-resistance. Taken together, our results suggest that promoter DNA methylation plays a novel enhancing role in conditioning high-level of induced expression of the Pib gene in times of M. grisea infection, and its conferred resistance to the pathogen.

Keywords: DNA methylation; Magnaporthe grisea; blast-resistance; induced Pib expression.

Li Y, Xia Q, Kou H, Wang D, Lin X, Wu Y, Xu C, Xing S and Liu B (2011) Induced Pib expression and resistance to Magnaporthe grisea are compromised by cytosine demethylation at critical promoter regions in rice. J. Integr. Plant Biol. 53(10), 814-823.

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Clustering of Pathogen-Response Genes in the Genome of Arabidopsis Thaliana
Author: Olga A. Postnikova, Natalia Y. Minakova, Alexander M. Boutanaev and Lev G. Nemchinov
Journal of Integrative Plant Biology 2011 53(10): 824-834
Published Online: August 2, 2011
DOI: 10.1111/j.1744-7909.2011.01071.x

Previously, we used heterologous expressed sequence tag (EST) mapping to generate a profile of 4 935 pathogen-response genes of Arabidopsis thaliana. In this work, we performed a computer analysis of this profile, revealing 1 594 non-homologous clustered genes distributed among all A. thaliana chromosomes, whose co-regulation may be related to host responses to pathogens. To supplement computer data, we arbitrarily selected two clusters and analyzed their expression levels in A. thaliana ecotypes Col-0 and C24 during infection with the yellow strain of Cucumber mosaic virus CMV(Y). Ecotype Col-0 is susceptible to CMV(Y), whereas C24 contains the dominant resistance gene RCY1. Upon infection with CMV(Y), all clustered genes were significantly activated in the resistant ecotype C24. In addition, we demonstrated that posttranslational histone modifications associated with trimethylation of histone H3 lysine 27 are most likely involved in regulation of several cluster genes described in this study. Overall, our experiments indicated that pathogen-response genes in the genome of A. thaliana may be clustered and co-regulated.

Keywords: CMV; H3K27me3; heterologous EST mapping; clustering of defense-related genes.

Postnikova OA, Minakova NY, Boutanaev AM, Nemchinov LG (2011) Clustering of pathogen-response genes in the genome of Arabidopsis thaliana. J. Integr. Plant Biol. 53(10), 824-834.

Abstract (Browse 1438)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Gene Expression Profile Changes in Germinating Rice
Author: Dongli He, Chao Han and Pingfang Yang
Journal of Integrative Plant Biology 2011 53(10): 835-844
Published Online: September 12, 2011
DOI: 10.1111/j.1744-7909.2011.01074.x

Water absorption is a prerequisite for seed germination. During imbibition, water influx causes the resumption of many physiological and metabolic processes in growing seed. In order to obtain more complete knowledge about the mechanism of seed germination, two-dimensional gel electrophoresis was applied to investigate the protein profile changes of rice seed during the first 48 h of imbibition. Thirty-nine differentially expressed proteins were identified, including 19 down-regulated and 20 up-regulated proteins. Storage proteins and some seed development- and desiccation-associated proteins were down regulated. The changed patterns of these proteins indicated extensive mobilization of seed reserves. By contrast, catabolism-associated proteins were up regulated upon imbibition. Semi-quantitative real time polymerase chain reaction analysis showed that most of the genes encoding the down- or up-regulated proteins were also down or up regulated at mRNA level. The expression of these genes was largely consistent at mRNA and protein levels. In providing additional information concerning gene regulation in early plant life, this study will facilitate understanding of the molecular mechanisms of seed germination.

Keywords: rice seed; two-dimensional gel electrophoresis; matrix assisted laser desorption; ionization time of flight; semi-quantitative real time polymerase chain reaction; germination; proteomics; imbibition.

He D, Han C, Yang P (2011) Gene expression profile changes in germinating rice. J. Integr. Plant Biol. 53(10), 835–844.

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