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Novel miRNA and phasiRNA biogenesis networks in soybean roots from two sister lines that are resistant and susceptible to SCN race 4.

Xu M, Li Y, Zhang Q, Xu T, Qiu L, Fan Y, Wang L - PLoS ONE (2014)

Bottom Line: In addition, we found that six miRNAs (gma-miR393, 1507, 1510, 1515, 171, 2118) guide targets to produce secondary phasiRNAs (phased, secondary, small interfering RNAs) in soybean root.Importantly, we also found that the expression of 34 miRNAs differed significantly between the two lines.These findings suggest that miRNAs play an important role in the soybean response to SCN.

View Article: PubMed Central - PubMed

Affiliation: Biotechnology Research Institute, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.

ABSTRACT
The soybean cyst nematode (SCN), Heterodera glycines, is the most devastating pathogen of soybean worldwide. SiRNAs (small interfere RNAs) have been proven to induce the silencing of cyst nematode genes. However, whether small RNAs from soybean root have evolved a similar mechanism against SCN is unknown. Two genetically related soybean sister lines (ZP03-5373 and ZP03-5413), which are resistant and susceptible, respectively, to SCN race 4 infection were selected for small RNA deep sequencing to identify small RNAs targeted to SCN. We identified 71 less-conserved miRNAs-miRNAs* counterparts belonging to 32 families derived from 91 loci, and 88 novel soybean-specific miRNAs with distinct expression patterns. The identified miRNAs targeted 42 genes representing a wide range of enzymatic and regulatory activities. Roots of soybean conserved one TAS (Trans-acting siRNA) gene family with a similar but unique trans-acting small interfering RNA (tasiRNA) biogenesis profile. In addition, we found that six miRNAs (gma-miR393, 1507, 1510, 1515, 171, 2118) guide targets to produce secondary phasiRNAs (phased, secondary, small interfering RNAs) in soybean root. Multiple targets of these phasiRNAs were predicted and detected. Importantly, we also found that the expression of 34 miRNAs differed significantly between the two lines. Seven ZP03-5373-specific miRNAs were differentially expressed after SCN infection. Forty-four transcripts from SCN were predicted to be potential targets of ZP03-5373-specific differential miRNAs. These findings suggest that miRNAs play an important role in the soybean response to SCN.

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Predicted schematic model of miRNA-SCN system in soybean root.
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pone-0110051-g005: Predicted schematic model of miRNA-SCN system in soybean root.

Mentions: The sequencing frequencies for miRNAs in the two libraries were used as an index for estimation of the relative abundance. The expression levels in SCN-resistant soybean root and SCN-sensitive soybean root were compared based on the “reads per million” genome-matched reads (RPM) of miRNAs. Using ZP03-5373 (RPM)/ZP03-5413 (RPM) values >5 or <5, a total of 34 miRNAs belonging to 27 families were identified to be significantly differentially expressed. The results are shown in Table S4. Most of the differentially expressed miRNAs were up regulated in the roots of the SCN-resistant line ZP03-5373 (Table S4). Although the absolute expression level of miRNA is useful, the identification of differential expression profiles at the whole-genome level in response to endogenous cues or stresses is often desirable to detect miRNA function in particular cell processes. In order to examine if the miRNAs might play a role in SCN resistance, the expression pattern of 14 miRNAs that were expressed specifically in ZP03-5373 were analysed using qRT-PCR in SCN-infected and uninfected ZP03-5373 plants. Seven miRNAs were up regulated significantly after the SCN-infection (Figure 5), and therefore appeared to be important in SCN infection and re-generation. A search of the SCN genome sequences identified 44 potential target genes in SCN by these seven SCN-inducible soybean miRNAs, suggesting a possible function of these miRNAs in regulating the expression of these SCN genes (Table 4).


Novel miRNA and phasiRNA biogenesis networks in soybean roots from two sister lines that are resistant and susceptible to SCN race 4.

Xu M, Li Y, Zhang Q, Xu T, Qiu L, Fan Y, Wang L - PLoS ONE (2014)

Predicted schematic model of miRNA-SCN system in soybean root.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4214822&req=5

pone-0110051-g005: Predicted schematic model of miRNA-SCN system in soybean root.
Mentions: The sequencing frequencies for miRNAs in the two libraries were used as an index for estimation of the relative abundance. The expression levels in SCN-resistant soybean root and SCN-sensitive soybean root were compared based on the “reads per million” genome-matched reads (RPM) of miRNAs. Using ZP03-5373 (RPM)/ZP03-5413 (RPM) values >5 or <5, a total of 34 miRNAs belonging to 27 families were identified to be significantly differentially expressed. The results are shown in Table S4. Most of the differentially expressed miRNAs were up regulated in the roots of the SCN-resistant line ZP03-5373 (Table S4). Although the absolute expression level of miRNA is useful, the identification of differential expression profiles at the whole-genome level in response to endogenous cues or stresses is often desirable to detect miRNA function in particular cell processes. In order to examine if the miRNAs might play a role in SCN resistance, the expression pattern of 14 miRNAs that were expressed specifically in ZP03-5373 were analysed using qRT-PCR in SCN-infected and uninfected ZP03-5373 plants. Seven miRNAs were up regulated significantly after the SCN-infection (Figure 5), and therefore appeared to be important in SCN infection and re-generation. A search of the SCN genome sequences identified 44 potential target genes in SCN by these seven SCN-inducible soybean miRNAs, suggesting a possible function of these miRNAs in regulating the expression of these SCN genes (Table 4).

Bottom Line: In addition, we found that six miRNAs (gma-miR393, 1507, 1510, 1515, 171, 2118) guide targets to produce secondary phasiRNAs (phased, secondary, small interfering RNAs) in soybean root.Importantly, we also found that the expression of 34 miRNAs differed significantly between the two lines.These findings suggest that miRNAs play an important role in the soybean response to SCN.

View Article: PubMed Central - PubMed

Affiliation: Biotechnology Research Institute, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.

ABSTRACT
The soybean cyst nematode (SCN), Heterodera glycines, is the most devastating pathogen of soybean worldwide. SiRNAs (small interfere RNAs) have been proven to induce the silencing of cyst nematode genes. However, whether small RNAs from soybean root have evolved a similar mechanism against SCN is unknown. Two genetically related soybean sister lines (ZP03-5373 and ZP03-5413), which are resistant and susceptible, respectively, to SCN race 4 infection were selected for small RNA deep sequencing to identify small RNAs targeted to SCN. We identified 71 less-conserved miRNAs-miRNAs* counterparts belonging to 32 families derived from 91 loci, and 88 novel soybean-specific miRNAs with distinct expression patterns. The identified miRNAs targeted 42 genes representing a wide range of enzymatic and regulatory activities. Roots of soybean conserved one TAS (Trans-acting siRNA) gene family with a similar but unique trans-acting small interfering RNA (tasiRNA) biogenesis profile. In addition, we found that six miRNAs (gma-miR393, 1507, 1510, 1515, 171, 2118) guide targets to produce secondary phasiRNAs (phased, secondary, small interfering RNAs) in soybean root. Multiple targets of these phasiRNAs were predicted and detected. Importantly, we also found that the expression of 34 miRNAs differed significantly between the two lines. Seven ZP03-5373-specific miRNAs were differentially expressed after SCN infection. Forty-four transcripts from SCN were predicted to be potential targets of ZP03-5373-specific differential miRNAs. These findings suggest that miRNAs play an important role in the soybean response to SCN.

Show MeSH
Related in: MedlinePlus