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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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Differential expressed miRNAs in response to SCN.
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pone-0110051-g004: Differential expressed miRNAs in response to SCN.

Mentions: To verify the miRNA-guided target cleavage, RLM-5′ RACE experiments were performed to detect cleavage products of the four predicted gma-miRNAs. As shown in Figure 4, all four gma-miRNA guided target cleavages occurred at nucleotide 10 or 11 (Figure 4). Thus, all four predicted targets had specific cleavage sites corresponding to the miRNA complementary sequences.


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)

Differential expressed miRNAs in response to SCN.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0110051-g004: Differential expressed miRNAs in response to SCN.
Mentions: To verify the miRNA-guided target cleavage, RLM-5′ RACE experiments were performed to detect cleavage products of the four predicted gma-miRNAs. As shown in Figure 4, all four gma-miRNA guided target cleavages occurred at nucleotide 10 or 11 (Figure 4). Thus, all four predicted targets had specific cleavage sites corresponding to the miRNA complementary sequences.

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