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Tong C.,Key Laboratory of Biology and Genetic Improvement of Oil Crops | Tong C.,Chinese Academy of Agricultural Sciences | Wang X.,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops | Wang X.,Chinese Academy of Agricultural Sciences | And 13 more authors.
BMC Genomics | Year: 2013

Background: The species Brassica rapa (2n=20, AA) is an important vegetable and oilseed crop, and serves as an excellent model for genomic and evolutionary research in Brassica species. With the availability of whole genome sequence of B. rapa, it is essential to further determine the activity of all functional elements of the B. rapa genome and explore the transcriptome on a genome-wide scale. Here, RNA-seq data was employed to provide a genome-wide transcriptional landscape and characterization of the annotated and novel transcripts and alternative splicing events across tissues. Results: RNA-seq reads were generated using the Illumina platform from six different tissues (root, stem, leaf, flower, silique and callus) of the B. rapa accession Chiifu-401-42, the same line used for whole genome sequencing. First, these data detected the widespread transcription of the B. rapa genome, leading to the identification of numerous novel transcripts and definition of 5'/3' UTRs of known genes. Second, 78.8% of the total annotated genes were detected as expressed and 45.8% were constitutively expressed across all tissues. We further defined several groups of genes: housekeeping genes, tissue-specific expressed genes and co-expressed genes across tissues, which will serve as a valuable repository for future crop functional genomics research. Third, alternative splicing (AS) is estimated to occur in more than 29.4% of intron-containing B. rapa genes, and 65% of them were commonly detected in more than two tissues. Interestingly, genes with high rate of AS were over-represented in GO categories relating to transcriptional regulation and signal transduction, suggesting potential importance of AS for playing regulatory role in these genes. Further, we observed that intron retention (IR) is predominant in the AS events and seems to preferentially occurred in genes with short introns. Conclusions: The high-resolution RNA-seq analysis provides a global transcriptional landscape as a complement to the B. rapa genome sequence, which will advance our understanding of the dynamics and complexity of the B. rapa transcriptome. The atlas of gene expression in different tissues will be useful for accelerating research on functional genomics and genome evolution in Brassica species. © 2013 Tong et al.; licensee BioMed Central Ltd. Source


Zhang P.-J.,Zhejiang Academy of Agricultural Sciences | Xu C.-X.,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops | Zhang J.-M.,Zhejiang Academy of Agricultural Sciences | Lu Y.-B.,Zhejiang Academy of Agricultural Sciences | And 5 more authors.
Functional Ecology | Year: 2013

Herbivore attack induces plants to mobilize chemical defences, including the release of volatiles that attract natural enemies of the herbivore. This commonly involves the jasmonic acid (JA) pathway. However, phloem-feeding whiteflies specifically trigger salicylic acid (SA)-signalling, thereby suppressing JA-based defences and enhancing host plant suitability. Here, we show with Arabidopsis thaliana plants that the whitefly parasitoid Encarsia formosa outsmarts this apparent host plant manipulation by exploiting the SA-triggered emission of β-myrcene. Assays with various Arabidopsis mutants and phytohormone and gene-expression analyses reveal that the whiteflies induce the accumulation of endogenous SA, thereby enhancing the expression of SA-regulated genes, one of which encodes ocimene/myrcene synthase, which resulted in the recruitment of parasitoids under greenhouse conditions. Performance assays confirmed that whiteflies directly benefit from suppressing JA-based defences. Taken together, we conclude that by activating SA-signalling whitefly feeding suppresses direct, JA-based defences, but that parasitoids can adapt to this by exploiting specific, SA-induced volatile emissions for host location. Our work further confirms that herbivory contributes to selective pressure governing the evolution of inducible volatile signals as indirect plant defences. © 2013 British Ecological Society. Source


Wang Z.,China Agricultural University | Wang Z.,Chinese Academy of Agricultural Sciences | Wang Z.,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops | Meng D.,China Agricultural University | And 7 more authors.
Plant Physiology | Year: 2013

Varieties of the European pear (Pyrus communis) can produce trees with both red- and green-skinned fruits, such as the Max Red Bartlett (MRB) variety, although little is known about the mechanism behind this differential pigmentation. In this study, we investigated the pigmentation of MRB and its green-skinned sport (MRB-G). The results suggest that a reduction in anthocyanin concentration causes the MRB-G sport. Transcript levels of PcUFGT (for UDP-glucose:flavonoid 3-O-glucosyltransferase), the key structural gene in anthocyanin biosynthesis, paralleled the change of anthocyanin concentration in both MRB and MRB-G fruit. We cloned the PcMYB10 gene, a transcription factor associated with the promoter of PcUFGT. An investigation of the 2-kb region upstream of the ATG translation start site of PcMYB10 showed the regions 2604 to 2911 bp and 21,218 to 21,649 bp to be highly methylated. A comparison of the PcMYB10 promoter methylation level between the MRB and MRB-G forms indicated a correlation between hypermethylation and the green-skin phenotype. An Agrobacterium tumefaciens infiltration assay was conducted on young MRB fruits by using a plasmid constructed to silence endogenous PcMYB10 via DNA methylation. The infiltrated fruits showed blocked anthocyanin biosynthesis, higher methylation of the PcMYB10 promoter, and lower expression of PcMYB10 and PcUFGT. We suggest that the methylation level of PcMYB10 is associated with the formation of the green-skinned sport in the MRB pear. The potential mechanism behind the regulation of anthocyanin biosynthesis is discussed. © 2013 American Society of Plant Biologists. All Rights Reserved. Source


Wang S.,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops | Wang S.,Chinese Academy of Agricultural Sciences | Xue J.,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops | Xue J.,Chinese Academy of Agricultural Sciences | And 8 more authors.
Canadian Journal of Plant Science | Year: 2014

Container culture and flower forcing are used for off-season production of tree peony for the Chinese Spring Festival. Storage of potted tree peony for 10 d at 12°C in a refrigerator before 4°C chilling treatment can help new root growth and promote leaf development. Development from bud swelling to anthesis was divided into nine stages. Some aborted flower buds usually emerge in Stage III. Removal of two to four leaflets in an alternating pattern and applying gibberellic acid 3 (GA3) around the flower bud at Stage III can decrease the flower bud abortion rate and promote flower formation rate. Two MADS-box genes with homology to Arabidopsis SVP, designated PsSVP1 and PsSVP2, which probably caused flower-bud abortion, were isolated by reverse transcription-PCR. Sequence comparison analysis showed that PsSVP was most similar to SVP-like gene in apple. Phylogenetic analysis indicates that PsSVP was evolutionarily close to SVP-like genes from Malus domestica, SVP genes from Cruciferae and SVP-like genes from Vitis vinifera. The qRT-PCR results suggested that expression of PsSVP was high in vegetative growth phase, especially in the leaves of tree peony, and its expression was regulated by GA3. Further analysis showed that more PsSVP transcripted in the aborted flower bud, especially in the buds where leaflets grew well. It was deduced that PsSVP can promote vegetative growth and suppress flowering in tree peony. Thus, it is very important to further investigate PsSVP and decipher the mechanisms of flower-bud abortion to improve forcing culture of tree peony. Source


Bai M.,Hunan Agricultural University | Yang G.-S.,Hunan Agricultural University | Chen W.-T.,Hunan Agricultural University | Mao Z.-C.,Chinese Academy of Agricultural Sciences | And 8 more authors.
Gene | Year: 2012

Dicer, Argonaute and RNA-dependent RNA polymerase form the core components to trigger RNA silencing. Although tomato (. Solanum lycopersicum) is a dicotyledon model plant, no systematic analysis and expression profiling of these genes in tomato has been undertaken previously. In this study, seven Dicer-like (SlDCLs), 15 Argonaute (SlAGOs) and six RNA-dependent RNA polymerase (SlRDRs) genes were identified in tomato. These genes were categorized into four subgroups based on phylogenetic analyses. Comprehensive analyses of gene structure, genomic localization and similarity among these genes were performed. Their expression patterns were investigated by means of expression models in different tissues and organs using online data and semi-quantitative RT-PCR. Many of the candidate genes were up-regulated in response to Tomato yellow leaf curl virus infection and abiotic stresses. The expression models of tandem gene duplications among SlDCL2s indicated the DCL2 family plays an important role in the evolution of tomato. © 2012 Elsevier B.V.. Source

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