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Temporal small RNA transcriptome profiling unraveled partitioned miRNA expression in developing maize endosperms between reciprocal crosses.

Xin M, Yang G, Yao Y, Peng H, Hu Z, Sun Q, Wang X, Ni Z - Front Plant Sci (2015)

Bottom Line: In addition, we found a subset of distinct tandem miRNAs are generated from a single stem-loop structure in maize that might be conserved in monocots.Furthermore, a SNP variation of Zma-miR408-5p at 11th base position was characterized between B73 and Mo17 which might lead to completely different functions in repressing targets.Together, this study suggests that miRNA plays a crucial role in regulating endosperm development, and exhibited distinct expression patterns in developing endosperm between maize reciprocal crosses.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University Beijing, China.

ABSTRACT
In angiosperms, the endosperm nurtures the embryo and provides nutrients for seed germination. To identify the expression pattern of small interfering RNA in the developing maize endosperm, we have performed high-throughput small RNA transcriptome sequencing of kernels at 0, 3, and 5 days after pollination (DAP) and endosperms at 7, 10, and 15 DAP using B73 and Mo17 reciprocal crosses in previous study. Here, we further explored these small RNA-seq data to investigate the potential roles of miRNAs in regulating the gene expression process. In total, 57 conserved miRNAs and 18 novel miRNAs were observed highly expressed in maize endosperm. Temporal expression profiling indicated that these miRNAs exhibited dynamic and partitioned expression patterns at different developmental stages between maize reciprocal crosses, and quantitative RT-PCR results further confirmed our observation. In addition, we found a subset of distinct tandem miRNAs are generated from a single stem-loop structure in maize that might be conserved in monocots. Furthermore, a SNP variation of Zma-miR408-5p at 11th base position was characterized between B73 and Mo17 which might lead to completely different functions in repressing targets. More interestingly, Zma-miR408-5p exhibited B73-biased expression pattern in the B73 and Mo17 reciprocal hybrid endosperms at 7, 10, and 15 DAP according to the reads abundance with SNPs and CAPS experiment. Together, this study suggests that miRNA plays a crucial role in regulating endosperm development, and exhibited distinct expression patterns in developing endosperm between maize reciprocal crosses.

No MeSH data available.


Related in: MedlinePlus

Developmentally dependent expression patterns of newly identified maize miRNAs negatively correlated with their targets expression. (A) 18 novel miRNAs were identified in 7-, 10-, and 15-DAP maize endosperms, which can be clustered into four groups according to their expression patterns, namely, one-step-down, one-step-up, two-step-down-up, and two-step-up-down. (B) Quantitative RT-PCR results of Zma-miR2006 and Zma-miR2011. Zma-miR2006 showed gradually decreased expression patterns in 7-, 10-, and 15-DAP endosperms in both reciprocal crosses, whereas Zma-miR2011 reached its lowest expression level in 10-DAP endosperm. (C) Boxplot of expression levels of novel miRNA and their putative targets in kernels and endosperms. MiRNA shows higher abundance in endosperm stages compared to kernel stages; in contrast, their targets exhibited lower expression levels in endosperm stages than in kernel stages, which is consistent with the negative correlation between miRNAs and their targets.
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Figure 3: Developmentally dependent expression patterns of newly identified maize miRNAs negatively correlated with their targets expression. (A) 18 novel miRNAs were identified in 7-, 10-, and 15-DAP maize endosperms, which can be clustered into four groups according to their expression patterns, namely, one-step-down, one-step-up, two-step-down-up, and two-step-up-down. (B) Quantitative RT-PCR results of Zma-miR2006 and Zma-miR2011. Zma-miR2006 showed gradually decreased expression patterns in 7-, 10-, and 15-DAP endosperms in both reciprocal crosses, whereas Zma-miR2011 reached its lowest expression level in 10-DAP endosperm. (C) Boxplot of expression levels of novel miRNA and their putative targets in kernels and endosperms. MiRNA shows higher abundance in endosperm stages compared to kernel stages; in contrast, their targets exhibited lower expression levels in endosperm stages than in kernel stages, which is consistent with the negative correlation between miRNAs and their targets.

Mentions: Upon double fertilization, endosperm undergoes a series of biological processes to form the nutritive tissue, which provides nutrients to support embryogenesis and seedling germination. To identify high-confidence miRNAs and investigate their expression profiles during developmental endosperms, we only focused on 21 nt small RNAs with T at the beginning of the 5′ end and reads number exceeding 100 rpm in 12 libraries. Finally, 18 novel putative miRNAs were identified in these six developmental stages based on the mirdeep-p program with the default algorithm (Yang and Li, 2011). Unexpectedly, all 18 miRNAs exhibit significantly increased expression levels in the endosperm compared to the kernels, corresponding to an average of 53.1-fold (2.4 ~ 410.0-fold) higher, although their expression levels among 7-, 10-, and 15-DAP endosperms varied (Table 1). Specifically, after combining the reads amount between two reciprocal crosses, four temporal gene-expression patterns were identified according to their expression trends in endosperms that we described as one-step-up, one-step-down (miRNA level transitions from low to high or high to low, respectively, in the consecutive 7-, 10-, 15-DAP stages), two-step-up-down or two step-down-up (miRNA level transitions from low to high and back down or from high to low and back up, respectively, in a series of endosperm developmental stages). The majority of newly identified miRNAs (14, 77.8%) exhibited a single transition point, of which 27.8% showed the one-step-up pattern, whereas 50% exhibited the one-step down pattern. In contrast, only 22.2% of miRNAs reached their expression peak or trough at 10 DAP (two-step-up-down or two step-down-up) (Figure 3A). Of these newly identified maize miRNAs, the most enriched is Zma-miR2001, whose abundance peaks at 7 DAP and then declines at 10 and 15 DAP; overall, its expression level in endosperms is significantly higher than in kernels by approximately 410.0-fold (Figure 3A). To validate the expression patterns of the newly identified miRNAs, quantitative RT-PCR were performed on mature miRNAs of Zma-miR2006 and Zma-miR2011, and their expression profiles were similar to the results obtained from RNA-seq data (Figure 3B).


Temporal small RNA transcriptome profiling unraveled partitioned miRNA expression in developing maize endosperms between reciprocal crosses.

Xin M, Yang G, Yao Y, Peng H, Hu Z, Sun Q, Wang X, Ni Z - Front Plant Sci (2015)

Developmentally dependent expression patterns of newly identified maize miRNAs negatively correlated with their targets expression. (A) 18 novel miRNAs were identified in 7-, 10-, and 15-DAP maize endosperms, which can be clustered into four groups according to their expression patterns, namely, one-step-down, one-step-up, two-step-down-up, and two-step-up-down. (B) Quantitative RT-PCR results of Zma-miR2006 and Zma-miR2011. Zma-miR2006 showed gradually decreased expression patterns in 7-, 10-, and 15-DAP endosperms in both reciprocal crosses, whereas Zma-miR2011 reached its lowest expression level in 10-DAP endosperm. (C) Boxplot of expression levels of novel miRNA and their putative targets in kernels and endosperms. MiRNA shows higher abundance in endosperm stages compared to kernel stages; in contrast, their targets exhibited lower expression levels in endosperm stages than in kernel stages, which is consistent with the negative correlation between miRNAs and their targets.
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Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4584948&req=5

Figure 3: Developmentally dependent expression patterns of newly identified maize miRNAs negatively correlated with their targets expression. (A) 18 novel miRNAs were identified in 7-, 10-, and 15-DAP maize endosperms, which can be clustered into four groups according to their expression patterns, namely, one-step-down, one-step-up, two-step-down-up, and two-step-up-down. (B) Quantitative RT-PCR results of Zma-miR2006 and Zma-miR2011. Zma-miR2006 showed gradually decreased expression patterns in 7-, 10-, and 15-DAP endosperms in both reciprocal crosses, whereas Zma-miR2011 reached its lowest expression level in 10-DAP endosperm. (C) Boxplot of expression levels of novel miRNA and their putative targets in kernels and endosperms. MiRNA shows higher abundance in endosperm stages compared to kernel stages; in contrast, their targets exhibited lower expression levels in endosperm stages than in kernel stages, which is consistent with the negative correlation between miRNAs and their targets.
Mentions: Upon double fertilization, endosperm undergoes a series of biological processes to form the nutritive tissue, which provides nutrients to support embryogenesis and seedling germination. To identify high-confidence miRNAs and investigate their expression profiles during developmental endosperms, we only focused on 21 nt small RNAs with T at the beginning of the 5′ end and reads number exceeding 100 rpm in 12 libraries. Finally, 18 novel putative miRNAs were identified in these six developmental stages based on the mirdeep-p program with the default algorithm (Yang and Li, 2011). Unexpectedly, all 18 miRNAs exhibit significantly increased expression levels in the endosperm compared to the kernels, corresponding to an average of 53.1-fold (2.4 ~ 410.0-fold) higher, although their expression levels among 7-, 10-, and 15-DAP endosperms varied (Table 1). Specifically, after combining the reads amount between two reciprocal crosses, four temporal gene-expression patterns were identified according to their expression trends in endosperms that we described as one-step-up, one-step-down (miRNA level transitions from low to high or high to low, respectively, in the consecutive 7-, 10-, 15-DAP stages), two-step-up-down or two step-down-up (miRNA level transitions from low to high and back down or from high to low and back up, respectively, in a series of endosperm developmental stages). The majority of newly identified miRNAs (14, 77.8%) exhibited a single transition point, of which 27.8% showed the one-step-up pattern, whereas 50% exhibited the one-step down pattern. In contrast, only 22.2% of miRNAs reached their expression peak or trough at 10 DAP (two-step-up-down or two step-down-up) (Figure 3A). Of these newly identified maize miRNAs, the most enriched is Zma-miR2001, whose abundance peaks at 7 DAP and then declines at 10 and 15 DAP; overall, its expression level in endosperms is significantly higher than in kernels by approximately 410.0-fold (Figure 3A). To validate the expression patterns of the newly identified miRNAs, quantitative RT-PCR were performed on mature miRNAs of Zma-miR2006 and Zma-miR2011, and their expression profiles were similar to the results obtained from RNA-seq data (Figure 3B).

Bottom Line: In addition, we found a subset of distinct tandem miRNAs are generated from a single stem-loop structure in maize that might be conserved in monocots.Furthermore, a SNP variation of Zma-miR408-5p at 11th base position was characterized between B73 and Mo17 which might lead to completely different functions in repressing targets.Together, this study suggests that miRNA plays a crucial role in regulating endosperm development, and exhibited distinct expression patterns in developing endosperm between maize reciprocal crosses.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University Beijing, China.

ABSTRACT
In angiosperms, the endosperm nurtures the embryo and provides nutrients for seed germination. To identify the expression pattern of small interfering RNA in the developing maize endosperm, we have performed high-throughput small RNA transcriptome sequencing of kernels at 0, 3, and 5 days after pollination (DAP) and endosperms at 7, 10, and 15 DAP using B73 and Mo17 reciprocal crosses in previous study. Here, we further explored these small RNA-seq data to investigate the potential roles of miRNAs in regulating the gene expression process. In total, 57 conserved miRNAs and 18 novel miRNAs were observed highly expressed in maize endosperm. Temporal expression profiling indicated that these miRNAs exhibited dynamic and partitioned expression patterns at different developmental stages between maize reciprocal crosses, and quantitative RT-PCR results further confirmed our observation. In addition, we found a subset of distinct tandem miRNAs are generated from a single stem-loop structure in maize that might be conserved in monocots. Furthermore, a SNP variation of Zma-miR408-5p at 11th base position was characterized between B73 and Mo17 which might lead to completely different functions in repressing targets. More interestingly, Zma-miR408-5p exhibited B73-biased expression pattern in the B73 and Mo17 reciprocal hybrid endosperms at 7, 10, and 15 DAP according to the reads abundance with SNPs and CAPS experiment. Together, this study suggests that miRNA plays a crucial role in regulating endosperm development, and exhibited distinct expression patterns in developing endosperm between maize reciprocal crosses.

No MeSH data available.


Related in: MedlinePlus