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Small RNA and Degradome Sequencing Reveal Complex Roles of miRNAs and Their Targets in Developing Wheat Grains.

Li T, Ma L, Geng Y, Hao C, Chen X, Zhang X - PLoS ONE (2015)

Bottom Line: A comparison of the miRNAomes revealed that 55 miRNA families were differentially expressed during the grain development.Predicted and validated targets of these development-related miRNAs are involved in different cellular responses and metabolic processes including cell proliferation, auxin signaling, nutrient metabolism and gene expression.This study provides insight into the complex roles of miRNAs and their targets in regulating wheat grain development.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture / Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.

ABSTRACT
Plant microRNAs (miRNAs) have been shown to play critical roles in plant development. In this study, we employed small RNA combined with degradome sequencing to survey development-related miRNAs and their validated targets during wheat grain development. A total of 186 known miRNAs and 37 novel miRNAs were identified in four small RNA libraries. Moreover, a miRNA-like long hairpin locus was first identified to produce 21~22-nt phased siRNAs that act in trans to cleave target mRNAs. A comparison of the miRNAomes revealed that 55 miRNA families were differentially expressed during the grain development. Predicted and validated targets of these development-related miRNAs are involved in different cellular responses and metabolic processes including cell proliferation, auxin signaling, nutrient metabolism and gene expression. This study provides insight into the complex roles of miRNAs and their targets in regulating wheat grain development.

No MeSH data available.


Related in: MedlinePlus

Expression correlation between development-related miRNAs and their targets.(A) qRT-PCR analysis of miRNA expression in developing grains. The dots represent the relative abundances of sequence reads in four small RNA libraries. (B) qRT-PCR analysis of target expression in the developing grains. Data represent the mean values ± SD of three replicates.
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pone.0139658.g006: Expression correlation between development-related miRNAs and their targets.(A) qRT-PCR analysis of miRNA expression in developing grains. The dots represent the relative abundances of sequence reads in four small RNA libraries. (B) qRT-PCR analysis of target expression in the developing grains. Data represent the mean values ± SD of three replicates.

Mentions: Based on sequencing data and cluster analysis (Fig 3), we selected ten development-ralated miRNAs (eight known and two new miRNAs) to detect their expression in developing grains by quantitative real-time PCR (qRT-PCR). Almost all the miRNAs determined by qRT-PCR followed similar expression trends in terms of read abundances in the libraries (Figs 6A and S5). For example, miR156 and miR164 from Group II both showed high expression levels at 14 DPA, miR166, miR393 and Ta-miRn8 from Group I showed gradual decreases in expression from 7 to 28 DPA, whereas expression of miR9666 from Group IV increased gradually from 7 to 28 DPA (Figs 6A and S5). These changes were consistent with relative changes in sequence abundance. Some minor discrepancy between qPCR and sequencing data was also observed for miR827 from Group III, which demonstrated a relatively low expression level at 21 DPA by qPCR compared with sequencing data (Fig 6A). Consistent with previous studies in wheat grains [18,19], similar expression patterns were observed for several development-ralated miRNAs such as miR156, miR167 and miR827. Overall, our results indicated that a high-throughput sequencing approach is a useful tool for profiling miRNA expression with good reproducibility.


Small RNA and Degradome Sequencing Reveal Complex Roles of miRNAs and Their Targets in Developing Wheat Grains.

Li T, Ma L, Geng Y, Hao C, Chen X, Zhang X - PLoS ONE (2015)

Expression correlation between development-related miRNAs and their targets.(A) qRT-PCR analysis of miRNA expression in developing grains. The dots represent the relative abundances of sequence reads in four small RNA libraries. (B) qRT-PCR analysis of target expression in the developing grains. Data represent the mean values ± SD of three replicates.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4591353&req=5

pone.0139658.g006: Expression correlation between development-related miRNAs and their targets.(A) qRT-PCR analysis of miRNA expression in developing grains. The dots represent the relative abundances of sequence reads in four small RNA libraries. (B) qRT-PCR analysis of target expression in the developing grains. Data represent the mean values ± SD of three replicates.
Mentions: Based on sequencing data and cluster analysis (Fig 3), we selected ten development-ralated miRNAs (eight known and two new miRNAs) to detect their expression in developing grains by quantitative real-time PCR (qRT-PCR). Almost all the miRNAs determined by qRT-PCR followed similar expression trends in terms of read abundances in the libraries (Figs 6A and S5). For example, miR156 and miR164 from Group II both showed high expression levels at 14 DPA, miR166, miR393 and Ta-miRn8 from Group I showed gradual decreases in expression from 7 to 28 DPA, whereas expression of miR9666 from Group IV increased gradually from 7 to 28 DPA (Figs 6A and S5). These changes were consistent with relative changes in sequence abundance. Some minor discrepancy between qPCR and sequencing data was also observed for miR827 from Group III, which demonstrated a relatively low expression level at 21 DPA by qPCR compared with sequencing data (Fig 6A). Consistent with previous studies in wheat grains [18,19], similar expression patterns were observed for several development-ralated miRNAs such as miR156, miR167 and miR827. Overall, our results indicated that a high-throughput sequencing approach is a useful tool for profiling miRNA expression with good reproducibility.

Bottom Line: A comparison of the miRNAomes revealed that 55 miRNA families were differentially expressed during the grain development.Predicted and validated targets of these development-related miRNAs are involved in different cellular responses and metabolic processes including cell proliferation, auxin signaling, nutrient metabolism and gene expression.This study provides insight into the complex roles of miRNAs and their targets in regulating wheat grain development.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture / Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.

ABSTRACT
Plant microRNAs (miRNAs) have been shown to play critical roles in plant development. In this study, we employed small RNA combined with degradome sequencing to survey development-related miRNAs and their validated targets during wheat grain development. A total of 186 known miRNAs and 37 novel miRNAs were identified in four small RNA libraries. Moreover, a miRNA-like long hairpin locus was first identified to produce 21~22-nt phased siRNAs that act in trans to cleave target mRNAs. A comparison of the miRNAomes revealed that 55 miRNA families were differentially expressed during the grain development. Predicted and validated targets of these development-related miRNAs are involved in different cellular responses and metabolic processes including cell proliferation, auxin signaling, nutrient metabolism and gene expression. This study provides insight into the complex roles of miRNAs and their targets in regulating wheat grain development.

No MeSH data available.


Related in: MedlinePlus