[Show abstract][Hide abstract] ABSTRACT: Soybean cyst nematode (SCN), Heterodera glycines, is the most devastating pathogen of soybean worldwide. MicroRNAs (miRNAs) are a class of small, non-coding RNAs that are known to play important role in plant stress response. However, there are few reports profiling the miRNA expression patterns during pathogen stress. We sequenced four small RNA libraries from two soybean cultivar (Hairbin xiaoheidou, SCN race 3 resistant, Liaodou 10, SCN race 3 susceptible) that grown under un-inoculated and SCN-inoculated soil. Small RNAs were mapped to soybean genome sequence, 364 known soybean miRNA genes were identified in total. In addition, 21 potential miRNA candidates were identified. Comparative analysis of miRNA profiling indicated 101 miRNAs belong to 40 families were SCN-responsive. We also found 20 miRNAs with different express pattern even between two cultivars of the same species. These findings suggest that miRNA paly important role in soybean response to SCN and have important implications for further identification of miRNAs under pathogen stress.
PLoS ONE 01/2012; 7(6):e39650. · 3.73 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: To gain insight into the changes in the transcriptome of soybean roots during soybean cyst nematode (SCN) infection, we conducted
genome-wide gene expression profiling using serial analysis of gene expression (SAGE) combined with Solexa sequencing. More
than 3 million tags were generated from the SCN-infected and uninfected roots, and 366941 and 314591 clean UniTags were obtained
from SCN-infected and uninfected samples, respectively. In the SCN-infected sample, 48249 UniTags represented 18114 reference
genes. In the uninfected control, 46290 UniTags represented 19323 reference genes. Comparison of tag frequencies identified
1405 genes that were expressed at greater levels in SCN-infected roots than in uninfected roots, and 1191 genes that were
expressed at lower levels. Quantitative real-time PCR analyses confirmed the changes in mRNA levels observed in our sequencing
analyses. A comparable number of genes were up- and down-regulated in response to nematode infection, indicating that down-regulation
of some genes might be essential in the plant response to nematodes. Our SAGE results showed significant changes in expression
of many unreported genes involved in nematode infection. Approximately 7% of tags mapped to the antisense strand of genes,
indicating widespread antisense transcription.
–soybean cyst nematode–gene expression profile–SAGE–Solexa sequencing
Chinese Science Bulletin 01/2011; 56(18):1904-1911. · 1.37 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Transgenic Bacillus thuringiensis (Bt) rice expressing cry1C gene showed a high level of resistance to leaffolders (Cnaphalocrocis medinalis) and stemborers. Till now, no detection method based on the plasmid molecule as the calibrator has been reported. In this study, one plasmid molecule containing the rice root-specific gene (gos9) endogenous sequence and the cry1C rice 5′ event-specific sequence was developed. Real-time polymerase chain reaction (PCR) method was established using the developed plasmid molecule as the calibrator. Two standard curves for gos9 and the cry1C rice 5′ event-specific sequence showed high PCR efficiency and good linear regression. Limit of quantification of the plasmid molecule in quantitative PCR assays was 40 copies. Biases for 5 and 0.25 % content samples’ quantification were −6.01 and −3.55 % with acceptable standard deviation and repeatability standard deviation, respectively. Comparing with genomic DNA, the plasmid molecule was suitable for cry1C rice quantification as the calibrator. Furthermore, the present study provided a reliable and stable identification and quantification system for monitoring cry1C rice.
European Food Research and Technology 237(2). · 1.39 Impact Factor