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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

Distribution features of small RNA species in kernel and endosperm small RNA libraries. (A) Proportions of distinct small RNA spceies in 12 sequencing libraries. (B) Proportions of abundance for 21-nt small RNAs with A, C, G, and U at the beginning of the sequence, during kernel and endosperm developmental stages. (C) Proportions of abundance for 24-nt small RNAs with A, C, G, and U at the beginning of the sequenceduring kernel and endosperm developmental stages. DAP, days after pollination.
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Figure 1: Distribution features of small RNA species in kernel and endosperm small RNA libraries. (A) Proportions of distinct small RNA spceies in 12 sequencing libraries. (B) Proportions of abundance for 21-nt small RNAs with A, C, G, and U at the beginning of the sequence, during kernel and endosperm developmental stages. (C) Proportions of abundance for 24-nt small RNAs with A, C, G, and U at the beginning of the sequenceduring kernel and endosperm developmental stages. DAP, days after pollination.

Mentions: To study the potential roles of miRNAs in developing maize kernels and endosperms, 12 siRNA libraries of 0-, 3-, and 5-DAP kernels and 7-, 10-, and 15-DAP endosperms from the B73 and Mo17 reciprocal crosses were sequenced (Xin et al., 2014)to observe key events in endosperm development such as cellularization, proliferation, differentiation, and nutrient accumulation (Lopes and Larkins, 1993; Sabelli and Larkins, 2009). The majority siRNAs of our dataset were 24 nt in length and accounted for approximately 68% of total distinct reads, whereas ~12.5% siRNA reads belong to the 21-nt family, this result is similar to those of previous studies (Jiao et al., 2011; Gu et al., 2013) (Figure 1A). Further investigation revealed that a large proportion of 24-nt siRNA reads begin with A at the 5′ end (46.0% average, 29.2 ~ 60.3%), whereas more 21-nt siRNAs begin with T (54.4% average, 40.2 ~ 66.6%) (Figures 1B,C).


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)

Distribution features of small RNA species in kernel and endosperm small RNA libraries. (A) Proportions of distinct small RNA spceies in 12 sequencing libraries. (B) Proportions of abundance for 21-nt small RNAs with A, C, G, and U at the beginning of the sequence, during kernel and endosperm developmental stages. (C) Proportions of abundance for 24-nt small RNAs with A, C, G, and U at the beginning of the sequenceduring kernel and endosperm developmental stages. DAP, days after pollination.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 1: Distribution features of small RNA species in kernel and endosperm small RNA libraries. (A) Proportions of distinct small RNA spceies in 12 sequencing libraries. (B) Proportions of abundance for 21-nt small RNAs with A, C, G, and U at the beginning of the sequence, during kernel and endosperm developmental stages. (C) Proportions of abundance for 24-nt small RNAs with A, C, G, and U at the beginning of the sequenceduring kernel and endosperm developmental stages. DAP, days after pollination.
Mentions: To study the potential roles of miRNAs in developing maize kernels and endosperms, 12 siRNA libraries of 0-, 3-, and 5-DAP kernels and 7-, 10-, and 15-DAP endosperms from the B73 and Mo17 reciprocal crosses were sequenced (Xin et al., 2014)to observe key events in endosperm development such as cellularization, proliferation, differentiation, and nutrient accumulation (Lopes and Larkins, 1993; Sabelli and Larkins, 2009). The majority siRNAs of our dataset were 24 nt in length and accounted for approximately 68% of total distinct reads, whereas ~12.5% siRNA reads belong to the 21-nt family, this result is similar to those of previous studies (Jiao et al., 2011; Gu et al., 2013) (Figure 1A). Further investigation revealed that a large proportion of 24-nt siRNA reads begin with A at the 5′ end (46.0% average, 29.2 ~ 60.3%), whereas more 21-nt siRNAs begin with T (54.4% average, 40.2 ~ 66.6%) (Figures 1B,C).

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