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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.


The 55 wheat grain development-related miRNAs.Hierarchical cluster analysis of 55 differentially expressed miRNAs in wheat grains (7–28 DPA) was performed by comparing miRNA abundances (TPM) in each library to the average of the four libraries. Color scale indicates fold-change as log2, from high (red) to low (green). Five miRNA clusters are shown on the right.
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pone.0139658.g003: The 55 wheat grain development-related miRNAs.Hierarchical cluster analysis of 55 differentially expressed miRNAs in wheat grains (7–28 DPA) was performed by comparing miRNA abundances (TPM) in each library to the average of the four libraries. Color scale indicates fold-change as log2, from high (red) to low (green). Five miRNA clusters are shown on the right.

Mentions: To explore the potential regulatory roles of miRNAs in grain development, we analyzed differential expression profiles of miRNA families including known and novel miRNAs. To minimize noise and improve accuracy, we selected only the miRNAs with abundances over 10 TPM in at least one library for comparison. After statistical assessment (P < 0.01) and cluster analysis (Fig 3), 55 miRNA families including 45 known and 10 novel miRNAs exhibited differential expression during grain development and clustered into five groups (I–V) with similar profiles. miRNAs with a single expression peak at 7 DPA, 14 DPA, 21 DPA or 28 DPA were classified as Group I, II, III or IV. Group V included miRNAs with two separate expression peaks at 14 DPA and 28 DPA. For 13 highly conserved miRNA families differentially expressed in wheat grain development (Fig 3), five (miR165/166, miR171, miR393, miR396 and miR444), three (miR156, miR164 and miR168), two (miR319 and miR827), one (miR408) and two miRNAs (miR159 and miR167) belonged to Group I, II, III, IV and V, respectively. The different expression patterns of these miRNAs indicate that they control grain development in a temporal manner. It is noted that some development-related miRNAs including miR156, miR167 and miR827 were also indentified by previous studies [18,19], demonstrating their important regulatory roles in wheat grain development.


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)

The 55 wheat grain development-related miRNAs.Hierarchical cluster analysis of 55 differentially expressed miRNAs in wheat grains (7–28 DPA) was performed by comparing miRNA abundances (TPM) in each library to the average of the four libraries. Color scale indicates fold-change as log2, from high (red) to low (green). Five miRNA clusters are shown on the right.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0139658.g003: The 55 wheat grain development-related miRNAs.Hierarchical cluster analysis of 55 differentially expressed miRNAs in wheat grains (7–28 DPA) was performed by comparing miRNA abundances (TPM) in each library to the average of the four libraries. Color scale indicates fold-change as log2, from high (red) to low (green). Five miRNA clusters are shown on the right.
Mentions: To explore the potential regulatory roles of miRNAs in grain development, we analyzed differential expression profiles of miRNA families including known and novel miRNAs. To minimize noise and improve accuracy, we selected only the miRNAs with abundances over 10 TPM in at least one library for comparison. After statistical assessment (P < 0.01) and cluster analysis (Fig 3), 55 miRNA families including 45 known and 10 novel miRNAs exhibited differential expression during grain development and clustered into five groups (I–V) with similar profiles. miRNAs with a single expression peak at 7 DPA, 14 DPA, 21 DPA or 28 DPA were classified as Group I, II, III or IV. Group V included miRNAs with two separate expression peaks at 14 DPA and 28 DPA. For 13 highly conserved miRNA families differentially expressed in wheat grain development (Fig 3), five (miR165/166, miR171, miR393, miR396 and miR444), three (miR156, miR164 and miR168), two (miR319 and miR827), one (miR408) and two miRNAs (miR159 and miR167) belonged to Group I, II, III, IV and V, respectively. The different expression patterns of these miRNAs indicate that they control grain development in a temporal manner. It is noted that some development-related miRNAs including miR156, miR167 and miR827 were also indentified by previous studies [18,19], demonstrating their important regulatory roles in wheat grain development.

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.