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Identification of MicroRNAs in Response to Different Day Lengths in Soybean Using High-Throughput Sequencing and qRT-PCR.

Li W, Wang P, Li Y, Zhang K, Ding F, Nie T, Yang X, Lv Q, Zhao L - PLoS ONE (2015)

Bottom Line: Furthermore, the results of GO and KEGG analyses indicated that most of the miRNA targets were transcription factors.The results indicated that the expression patterns of the selected miRNAs and miRNA targets showed no differences between the qRT-PCR and sequencing results.These results provided an important molecular basis to understand the regulation of flowering time through photoperiodic pathways in soybean.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Soybean Biology of Chinese Education Ministry (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin 150030, China.

ABSTRACT
MicroRNAs (miRNAs) are short, non-coding single-strand RNA molecules that play important roles in plant growth, development and stress responses. Flowering time affects the seed yield and quality of soybean. However, the miRNAs involved in the regulation of flowering time in soybean have not been reported until recently. Here, high-throughput sequencing and qRT-PCR were used to identify miRNAs involved in soybean photoperiodic pathways. The first trifoliate leaves of soybean that receive the signal of light treatment were used to construct six libraries (0, 8, and 16 h under short-day (SD) treatment and 0, 8, and 16 h under long-day (LD) treatment). The libraries were sequenced using Illumina Solexa. A total of 318 known plant miRNAs belonging to 163 miRNA families and 81 novel predicted miRNAs were identified. Among these, 23 miRNAs at 0 h, 65 miRNAs at 8 h and 83 miRNAs at 16 h, including six novel predicted miRNAs at 8 h and six novel predicted miRNAs at 16 h, showed differences in abundance between LD and SD treatments. Furthermore, the results of GO and KEGG analyses indicated that most of the miRNA targets were transcription factors. Seven miRNAs at 0 h, 23 miRNAs (including four novel predicted miRNAs) at 8 h, 16 miRNAs (including one novel predicted miRNA) at 16 h and miRNA targets were selected for qRT-PCR analysis to assess the accuracy of the sequencing and target prediction. The results indicated that the expression patterns of the selected miRNAs and miRNA targets showed no differences between the qRT-PCR and sequencing results. In addition, 23 miRNAs at 0 h, 65 miRNAs at 8 h and 83 miRNAs at 16 h responded to day length changes in soybean, including six novel predicted miRNAs at 8 h and six novel predicted miRNAs at 16 h. These results provided an important molecular basis to understand the regulation of flowering time through photoperiodic pathways in soybean.

No MeSH data available.


Differential expression analysis of soybean miRNAs identified using Solexa sequencing.The software IDE6 was used to analyze the known and novel predicted miRNAs obtained through high-throughput sequencing. Panels a to f show LD to SD abundance differences for time points A to C.
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pone.0132621.g004: Differential expression analysis of soybean miRNAs identified using Solexa sequencing.The software IDE6 was used to analyze the known and novel predicted miRNAs obtained through high-throughput sequencing. Panels a to f show LD to SD abundance differences for time points A to C.

Mentions: There were 23, 59 and 77 known miRNAs showing different abundance profiles at the time points 0, 8 and 16 h, respectively (Fig 4). At 0 h, 13 known miRNAs were decreased, while another 10 known miRNAs increased under LD treatments. At 8 h, only five known miRNAs were up-regulated, while another 54 known miRNAs were down-regulated under LD treatment. At 16 h, 26 known miRNAs were down-regulated, while another 51 known miRNAs were up-regulated under LD treatment.


Identification of MicroRNAs in Response to Different Day Lengths in Soybean Using High-Throughput Sequencing and qRT-PCR.

Li W, Wang P, Li Y, Zhang K, Ding F, Nie T, Yang X, Lv Q, Zhao L - PLoS ONE (2015)

Differential expression analysis of soybean miRNAs identified using Solexa sequencing.The software IDE6 was used to analyze the known and novel predicted miRNAs obtained through high-throughput sequencing. Panels a to f show LD to SD abundance differences for time points A to C.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4498749&req=5

pone.0132621.g004: Differential expression analysis of soybean miRNAs identified using Solexa sequencing.The software IDE6 was used to analyze the known and novel predicted miRNAs obtained through high-throughput sequencing. Panels a to f show LD to SD abundance differences for time points A to C.
Mentions: There were 23, 59 and 77 known miRNAs showing different abundance profiles at the time points 0, 8 and 16 h, respectively (Fig 4). At 0 h, 13 known miRNAs were decreased, while another 10 known miRNAs increased under LD treatments. At 8 h, only five known miRNAs were up-regulated, while another 54 known miRNAs were down-regulated under LD treatment. At 16 h, 26 known miRNAs were down-regulated, while another 51 known miRNAs were up-regulated under LD treatment.

Bottom Line: Furthermore, the results of GO and KEGG analyses indicated that most of the miRNA targets were transcription factors.The results indicated that the expression patterns of the selected miRNAs and miRNA targets showed no differences between the qRT-PCR and sequencing results.These results provided an important molecular basis to understand the regulation of flowering time through photoperiodic pathways in soybean.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Soybean Biology of Chinese Education Ministry (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin 150030, China.

ABSTRACT
MicroRNAs (miRNAs) are short, non-coding single-strand RNA molecules that play important roles in plant growth, development and stress responses. Flowering time affects the seed yield and quality of soybean. However, the miRNAs involved in the regulation of flowering time in soybean have not been reported until recently. Here, high-throughput sequencing and qRT-PCR were used to identify miRNAs involved in soybean photoperiodic pathways. The first trifoliate leaves of soybean that receive the signal of light treatment were used to construct six libraries (0, 8, and 16 h under short-day (SD) treatment and 0, 8, and 16 h under long-day (LD) treatment). The libraries were sequenced using Illumina Solexa. A total of 318 known plant miRNAs belonging to 163 miRNA families and 81 novel predicted miRNAs were identified. Among these, 23 miRNAs at 0 h, 65 miRNAs at 8 h and 83 miRNAs at 16 h, including six novel predicted miRNAs at 8 h and six novel predicted miRNAs at 16 h, showed differences in abundance between LD and SD treatments. Furthermore, the results of GO and KEGG analyses indicated that most of the miRNA targets were transcription factors. Seven miRNAs at 0 h, 23 miRNAs (including four novel predicted miRNAs) at 8 h, 16 miRNAs (including one novel predicted miRNA) at 16 h and miRNA targets were selected for qRT-PCR analysis to assess the accuracy of the sequencing and target prediction. The results indicated that the expression patterns of the selected miRNAs and miRNA targets showed no differences between the qRT-PCR and sequencing results. In addition, 23 miRNAs at 0 h, 65 miRNAs at 8 h and 83 miRNAs at 16 h responded to day length changes in soybean, including six novel predicted miRNAs at 8 h and six novel predicted miRNAs at 16 h. These results provided an important molecular basis to understand the regulation of flowering time through photoperiodic pathways in soybean.

No MeSH data available.