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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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Expression levels of gma-miRNAs by two methods.Profile of sequencing frequencies for gma-miRNAs (left column of A, B and C); Profile of qRT-PCR Ct values for gma-miRNAs (right column of A, B and C).
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pone-0110051-g002: Expression levels of gma-miRNAs by two methods.Profile of sequencing frequencies for gma-miRNAs (left column of A, B and C); Profile of qRT-PCR Ct values for gma-miRNAs (right column of A, B and C).

Mentions: A total of 71 miRNAs-miRNAs* counterparts belonging to 32 families derived from 91 loci (Table 1 and Figure S1), that had previously been identified and reported in at least one plant species or family [11] were identified from the 258 miRNA candidates. A canonical predicted stem-loop structure could be identified in all 32 less-conserved miRNA families (Figure S1). Overall, all less-conserved miRNAs displayed lower expression levels than the conserved miRNAs, with the exception of gma-miR482C2, which was expressed at abundances of 4,000 RPM and 8,000 RPM in ZP03-5373 and ZP03-5413, respectively (Table 1). However, as with the conserved miRNAs, some of the less-conserved miRNAs were expressed differentially between ZP03-5373 and ZP03-5413. For example, ZP03-5413-biased expression was observed for gma-miR395C1, while ZP03-5373-biased expression was apparent for gma-miR393C1 and gma-miR2109C1 (Table 1). To validate the miRNA RPM data, we performed stem-stoop-based qRT-PCR analysis for selected miRNAs representing conserved, less-conserved and soybean-specific (discussed below) examples in the two lines. We found that while the qRT-PCR results for most of the miRNAs (miR1509a, miR1509b, miR2111 (Figure 2A) and miR395C1 (Figure 2B), miRC2, miRC6, miRC20 (Figure 2C), etc.) were reflective of the relative abundances of the sequenced RNAs in the two lines, others displayed varying degrees of divergence between the two analyses. For example, the miRC18 RPM value for ZP03-5373 was fourfold higher than for miRC10, while the abundances of miRC18 and miRC10 were in agreement, based on qRT-PCR results (Figure 2C). For miR482C2 the opposite pattern between qRT-PCR and miRNA sequencing was observed (Figure S2), which may have resulted from deep-sequencing deviation.


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)

Expression levels of gma-miRNAs by two methods.Profile of sequencing frequencies for gma-miRNAs (left column of A, B and C); Profile of qRT-PCR Ct values for gma-miRNAs (right column of A, B and C).
© Copyright Policy
Related In: Results  -  Collection

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

pone-0110051-g002: Expression levels of gma-miRNAs by two methods.Profile of sequencing frequencies for gma-miRNAs (left column of A, B and C); Profile of qRT-PCR Ct values for gma-miRNAs (right column of A, B and C).
Mentions: A total of 71 miRNAs-miRNAs* counterparts belonging to 32 families derived from 91 loci (Table 1 and Figure S1), that had previously been identified and reported in at least one plant species or family [11] were identified from the 258 miRNA candidates. A canonical predicted stem-loop structure could be identified in all 32 less-conserved miRNA families (Figure S1). Overall, all less-conserved miRNAs displayed lower expression levels than the conserved miRNAs, with the exception of gma-miR482C2, which was expressed at abundances of 4,000 RPM and 8,000 RPM in ZP03-5373 and ZP03-5413, respectively (Table 1). However, as with the conserved miRNAs, some of the less-conserved miRNAs were expressed differentially between ZP03-5373 and ZP03-5413. For example, ZP03-5413-biased expression was observed for gma-miR395C1, while ZP03-5373-biased expression was apparent for gma-miR393C1 and gma-miR2109C1 (Table 1). To validate the miRNA RPM data, we performed stem-stoop-based qRT-PCR analysis for selected miRNAs representing conserved, less-conserved and soybean-specific (discussed below) examples in the two lines. We found that while the qRT-PCR results for most of the miRNAs (miR1509a, miR1509b, miR2111 (Figure 2A) and miR395C1 (Figure 2B), miRC2, miRC6, miRC20 (Figure 2C), etc.) were reflective of the relative abundances of the sequenced RNAs in the two lines, others displayed varying degrees of divergence between the two analyses. For example, the miRC18 RPM value for ZP03-5373 was fourfold higher than for miRC10, while the abundances of miRC18 and miRC10 were in agreement, based on qRT-PCR results (Figure 2C). For miR482C2 the opposite pattern between qRT-PCR and miRNA sequencing was observed (Figure S2), which may have resulted from deep-sequencing deviation.

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