7(1) 2014 issue
January 2014 issue
Southern Cross Publishing Group©2014

Plant Omics | January 2014
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Transcriptomic landscape of chrysanthemums infected by Chrysanthemum stunt viroid

Yeonhwa Jo
#, Kyoung-Min Jo#, Sang-Ho Park, Kook-Hyung Kim*, and Won Kyong Cho*

Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea


CSVd is one of the main pathogens infecting chrysanthemum species and is responsible for serious economic losses. To identify the genes involved in viroid infection, we obtained the ESTs of chrysanthemums infected by CSVd using a high-throughput next generation sequencing method. The cDNA library was prepared from the total RNAs extracted from leaves of chrysanthemum infected with CSVd. The prepared cDNA library was sequenced using the FLX 454 sequencer. As a result, a total of 11,600 ESTs were obtained from 99,750 reads after de novo assembly. A BLAST search was performed to annotate the functions of the 11,600 chrysanthemum ESTs. In addition, GO terms, enzyme codes, and InterPro domains for each chrysanthemum EST were obtained using the Blast2GO program with default parameters. Gene ontology enrichment analysis identified 144 significantly enriched GO terms, which were further divided into biological processes (93 GO terms), cellular components (19 GO terms), and molecular functions (32 GO terms). CSVd infection affected the mRNAs involved in various metabolic pathways, stresses, transcription, translation, transport, chloroplasts, plasmodesmata, actins, and microtubules. Comparative analysis revealed 70% of the chrysanthemum ESTs were orthologous to those of five representative plant species. The current study provides information on a large number of chrysanthemum genes. The obtained information will be valuable for studying plant-viroid interactions.

Pages 1-11 | Full Text PDF | Supplementary data Xls
Fine-mapping and candidate gene analysis of BLACK HULL1 in rice (Oryza sativa L.)

Chao CHEN1,2, Wei WU1, Xingming SUN1, Ben LI1, Guanglong HU1,3, Qiang ZHANG1,4, Jinjie LI1, Hongliang ZHANG1, Zichao LI1*

Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvment, China Agricultural University, Beijing 100193, China

2China National Seed Group Co., Ltd., Beijing 100045, China
3Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100093, China
4Rice Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China

Black hull, as a kind of visual traits which can be easily identified after heading, plays a crucial role in the study of rice domestication. Previous studies have shown that the gene for phenol reaction may be responsible for the phenotype of black hull. To further explore the molecular mechanism of the formation of black hull, a near-isogenic line was constructed with black hull phenotype and by gene mapping and cloning from the cross between the indica rice 05048 and the japonica rice Nipponbare according to recombinant inbreeding method. The segregation ratio of F6 population indicated that the black hull trait is controlled by a dominant gene, which is called BLACK HULL1 (BH1). Through the map-based cloning method, BH1 was fine-mapped in a 24.2-kb interval between SSR marker RM6629 and SNP marker SNP6-1 on the long arm of chromosome 4. In this region, 5 genes were annotated by the MSU Rice Genome Annotation Project Database. Sequence analysis and phenol color reaction test showed that Phr1, one of the two polyphenol oxidase gene in rice genome, has the high possibility for being the candidate gene of BH1 and involved in the formation of black hull. These findings contribute to facilitate the illumination of molecular mechanism in rice domestication.

Pages 12-18 | Full Text PDF
Overlapping sets of transcripts from host and non-host interactions of tomato are expressed early during non-host resistance

Battepati Uma and Appa Rao Podile*

Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad-500 046, India

Natural immunity present in all the plants against most of the pathogens is called as non-host resistance (NHR). Although NHR is most durable form of resistance, it was less studied compared to other forms of resistance. We compared transcriptional changes in tomato during non-host (Magnaporthe grisea) and compatible (Alternaria alternata f. sp. lycopersici) interactions using Agilent microarray GeneChip containing ~44,000 probe sets. The experiment was designed to understand the early and late responses of tomato leaves inoculated with non-host and compatible pathogens. Microarray data revealed that the expression profiles in the non-host and compatible interactions at 6 h post inoculation (hpi) and 24 hpi largely overlapped indicating  that a set of genes are activated during plant-pathogen interaction. However, these genes were expressed much earlier in NHR compared to a compatible interaction. NHR is, therefore, an accelerated and amplified basal defense response. Transcripts involved in energy production (carbohydrate metabolism and photosynthesis) were down-regulated, whereas transcripts associated with catabolic processes (starch and sucrose hydrolysis) were up-regulated in both the interactions at 6 and 24 hpi. We have also identified that the pathway involved in synthesis of volatile compounds like 2-phenylethanol was induced during NHR in tomato. This is the first report of transcriptome profile in tomato during non-host interactions against M. grisea.

Pages 19-27 | Full Text PDF | Supplementary data
Heterologous expression of a rice RNA-recognition motif gene OsCBP20 in Escherichia coli confers abiotic stress tolerance

Chao Zhou, Rong-Jun Chen, Xiao-Ling Gao, Li-Hua Li, Zheng-Jun Xu*

Rice Institute, Sichuan Agriculture of University, Chengdu 611130, PR China

Diverse RNA-binding proteins (RBPs) have been determined to play a crucial role in post-transcriptional regulation of RNA metabolism during plant response to abiotic stresses. In this report we characterize a rice (Oryza sativa L.) protein, named OsCBP20, which is similar to subunits of a nuclear cap-binding protein 20 (CBP20), it contains a canonical RNA recognition motif (RRM). We compared the survivability of Escherichia coli (BL21) cells transformed with a recombinant plasmid with control E. coli under different concentration NaCl and mannitol. In addition, we also investigated the high temperature (50C) impact on survival of E. coil. The OsCBP20 gene was isolated from rice (Oryza sativa L.) cDNA, encoding protein of 243 amino acids with a calculated molecular mass of 28.6 KDa and a PI of 5.14. On the basis of multiple sequence alignment and phylogenetic analysis, OsCBP20 is classified in RRM family. Recombinant OsCBP20 protein can be highly expressed in E. coli. The OsCBP20 protein can enhance the tolerance of E. coli recombinant to high salinity, heat, and dehydration, which suggested that OsCBP20 protein, may play a protective role under stressed conditions. Our work provides new evidence on CBP20 response to abiotic stresses.

Pages 28-34 | Full Text PDF
Regularities in simple sequence repeat variations induced by a cross of resynthesized Brassica napus and natural Brassica napus

Caihua Gao1, Jiaming Yin1, Annaliese S. Mason2, Zhanglin Tang1, Xiaodong Ren1, Chao Li3, Zeshan An1, Donghui Fu4*, Jiana Li1*

1Engineering Research Center of South Upland Agriculture of Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
2Centre for Integrative Legume Research and School of Agriculture and Food Sciences, The University of Queensland, Brisbane 4072, Australia
3Institute of Oil Croups of Guizhou Province, Jinzhu Town, Xiaohe district
, Guiyang 550006, China
4Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China

Interspecific hybridization can induce extensive variation in genome sequences, including simple sequence repeat (SSR) regions. To determine the characteristics of SSR variation induced by interspecific hybridization and the possible effect of SSR variation on gene function, we constructed a Brassica napus doubled-haploid (DH) population from a cross between natural B. napus and resynthesized B. napus (B. oleracea B. rapa) and identified, located, sequenced and functionally annotated SSR variants. The results showed that novel SSR variants were generated in the F1 generation and maintained in the introgressed DH population. Elimination of sequences carrying SSRs also occurred in the F1 hybrids, with three times as many sequences lost in the introgressed DH population compared to in the F1 hybrids, probably due to non-homologous recombination. The degree of SSR variation observed depended primarily on the number of SSR repeats and secondarily on the nucleotide composition of the SSR motifs. In the introgressed DH population, many genes containing SSRs exhibited frameshift mutations (62.5%) due to the expansion or contraction of the SSR motifs following deletion (25%) or insertion (12.5%) mutations. Most genes harboring SSR variants were associated with vital metabolic processes, such as protein or DNA metabolic processes. The SSR variation induced by interspecific hybridization reflects an intrinsic property of species adaptability post-hybridization through variation. This study is beneficial to understanding the origin of SSRs and the effects of SSR mutation on polyploid genomes.

Pages 35-46 | Full Text PDF | Supplementary data
Expedient identification of Magnoliaceae species by DNA barcoding

Hua Yu1,2, Kongyun Wu1,3, Jingyuan Song1, Yingjie Zhu1, Hui Yao1*, Kun Luo1, Yong Dai4, Shijun Xu4, Yulin Lin1*

1Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing 100193, China
2Shandong Center of Crop Germplasm Resources, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China
3Guiyang College of Traditional Chinese Medicine, Guiyang 550005, China
4Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China

Magnoliaceae species have high ornamental and medicinal importance, but they are morphologically similar. DNA barcoding has been regarded as a rapid and effective approach for species identification. To determine the efficiency of expedient identification in Magnoliaceae species by DNA barcoding, in this study, we collected 83 samples belonging to 68 species in 10 genera of Magnoliaceae. Candidate DNA regions (i.e., psbA-trnH, matK, rbcL, ITS, ITS2, rpoB, and rpoC1) were amplified and sequenced for the evaluation of their PCR amplification, sequencing efficiency, intra- and inter-specific divergence and barcoding gap by sequence alignment and Kimura 2-Parameter (K2P) distance analysis
, and the rate of correct identification was assessed by BLAST analysis. The results showed that psbA-trnH and matK exhibited high performance in efficiency of PCR amplification and the rate of successful sequencing, followed by rbcL. Associated with the analysis of 199 sequences for 96 species in 9 genera of Magnoliaceae retrieved from GenBank, it was discovered that psbA-trnH was highest in inter-specific divergence and rate of correct identification, indicating its efficiency in the identification of Magnoliaceae species. Besides, matK was also easy to amplify and had high rate of correct identification, suggesting its potential to distinguish Magnoliaceae species. This study indicates that DNA barcoding provides an effective technique for the expedient identification of morphologically similar species, and it is a powerful aid to the conventional methods for species identification.

Pages 47-53 | Full Text PDF
| Supplementary data
Overexpression of a new cellulose synthase gene (PuCesA6) from Ussuri poplar (Populus ussuriensis) exhibited a dwarf phenotype in transgenic tobacco

Lei Xu*

Key Laboratory of Bio-Based Material Science and Technology, Northeast Forestry University, Harbin, 150040, China

Cellulose is synthesized in plant cell walls by cellulose synthase (CesA) genes. The characterization of a new cellulose synthase gene (PuCesA6) (GenBank Accession No. HQ686077) from an economically important tree, Ussuri Poplar (Populus ussuriensis) is reported here. The predicted PuCesA6 protein is highly similar to Populus tremuloides PtrCesA6 (99%) expressing in all expanding cells depositing primary cell wall. The domain structures of PuCesA6 was predicted by multiple alignment analysis, which contained a N-terminal cysteine rich zinc binding domain, 8 putative transmembrane helices (TMH), a signature D, D, D, QxxRW motif, 5 alternating conserved regions (CR-P) and 2 hypervariable regions (HVR). Subcellular localization analysis showed that PuCesA6 protein was localized in the cytomembrane. Ectopic expression of PuCesA6 in tobacco significantly exhibited "dwarf" phenotype, with final aerial height less than 35 cm (
approximately two-thirds height of wild type). The phenomenon could be explained by post-transcriptional gene silencing (PTGS) of the expression of the homologous genes in tobacco. Thus, identification of new CesA genes from poplar tree genomes is essential for enhancing knowledge of cellulose biosynthesis in trees that has many fundamental and commercial implications.

Pages 54
-62 | Full Text PDF