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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.

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Biased expression pattern of Zma-miR408-5p in 7-, 10-, and 15-DAP endosperms in B73 and Mo17 reciprocal crosses. (A) SNP of Zma-miR408-5p between B73 and Mo17 confirmed by re-sequencing. (B)Zma-miR408-5p of B73 was more highly expressed compared to that of Mo17 during endosperm developmental stages in both reciprocal crosses based on the sequencing data. (C) Validation of biased expression pattern of Zma-miR408-5p using CAPS in 7, 10, and 15 DAP endosperms of reciprocal crosses.
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Figure 6: Biased expression pattern of Zma-miR408-5p in 7-, 10-, and 15-DAP endosperms in B73 and Mo17 reciprocal crosses. (A) SNP of Zma-miR408-5p between B73 and Mo17 confirmed by re-sequencing. (B)Zma-miR408-5p of B73 was more highly expressed compared to that of Mo17 during endosperm developmental stages in both reciprocal crosses based on the sequencing data. (C) Validation of biased expression pattern of Zma-miR408-5p using CAPS in 7, 10, and 15 DAP endosperms of reciprocal crosses.

Mentions: A proportion of small interfering RNAs exhibited possible parent-biased expression patterns in the developing plant endosperm between B73 and Mo17 reciprocal crosses (Xin et al., 2014), leading us to investigate whether miRNAs also showed allele-biased expression patterns. We first examined the SNPs located in the endosperm-abundant miRNAs between B73 and Mo17 cultivars. However, no informative SNPs were identified in these small regulatory molecules between the two inbred lines, probably because of their high evolutionary conservation, except for Zma-miR408*. Further comparison found Zma-miR408* was more abundantly expressed than Zma-miR408 in both kernels and endosperms, consistent with previous reports (Jiao et al., 2011; Gu et al., 2013) and indicating Zma-miR408* probably also has a biological relevance rather than the useless, degraded sequences. Therefore, we designed the original Zma-miR408 and Zma-miR408* to be Zma-miR408-3p and Zma-miR408-5p, respectively, based on 3′- or 5′-arm derivation of the miRNA species. Although the well-known conservation of miRNA, a SNP (A/G) between B73 and Mo17 inbred lines in mature Zma-miR408-5p sequence was identified and confirmed by sequencing (Figure 6A). Based on the SNP information, we next examined whether this miRNA is subjected to allele-biased expression between the two reciprocal crosses. Interestingly, Zma-miR408-5p showed a significantly B73-allele biased expression pattern in 7-, 10-, and 15-DAP reciprocal endosperms (Figure 6B, χ2-test, p-value ≤ 0.01), which was further confirmed by CAPS experiments (Figure 6C). Moreover, the SNP of Zma-miR408-5p was located at the 11th base position from the 5′ end between B73 and Mo17, indicating that this polymorphism was likely to cause functional variation of Zma-miR408-5p. Thus, these two should target complete different genes based on the principle of complementary base pairing because the 10/11 base position is very important for miRNA-directed mRNA cleavage (Figure 6B). The target prediction of B73 and Mo17 Zma-miR408-5p by the psRNATarget server is also consistent with our speculation. The putative targets of B73 Zma-miR408-5p were GRMZM2G034896, GRMZM2G093526, and GRMZM2G177518, while Mo17 Zma-miR408-5p likely negatively modulates five other targets, including AC196575.3_FG007, GRMZM2G169005, GRMZM2G162065, AC198481.3_FG004, and GRMZM2G349554.


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)

Biased expression pattern of Zma-miR408-5p in 7-, 10-, and 15-DAP endosperms in B73 and Mo17 reciprocal crosses. (A) SNP of Zma-miR408-5p between B73 and Mo17 confirmed by re-sequencing. (B)Zma-miR408-5p of B73 was more highly expressed compared to that of Mo17 during endosperm developmental stages in both reciprocal crosses based on the sequencing data. (C) Validation of biased expression pattern of Zma-miR408-5p using CAPS in 7, 10, and 15 DAP endosperms of reciprocal crosses.
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Figure 6: Biased expression pattern of Zma-miR408-5p in 7-, 10-, and 15-DAP endosperms in B73 and Mo17 reciprocal crosses. (A) SNP of Zma-miR408-5p between B73 and Mo17 confirmed by re-sequencing. (B)Zma-miR408-5p of B73 was more highly expressed compared to that of Mo17 during endosperm developmental stages in both reciprocal crosses based on the sequencing data. (C) Validation of biased expression pattern of Zma-miR408-5p using CAPS in 7, 10, and 15 DAP endosperms of reciprocal crosses.
Mentions: A proportion of small interfering RNAs exhibited possible parent-biased expression patterns in the developing plant endosperm between B73 and Mo17 reciprocal crosses (Xin et al., 2014), leading us to investigate whether miRNAs also showed allele-biased expression patterns. We first examined the SNPs located in the endosperm-abundant miRNAs between B73 and Mo17 cultivars. However, no informative SNPs were identified in these small regulatory molecules between the two inbred lines, probably because of their high evolutionary conservation, except for Zma-miR408*. Further comparison found Zma-miR408* was more abundantly expressed than Zma-miR408 in both kernels and endosperms, consistent with previous reports (Jiao et al., 2011; Gu et al., 2013) and indicating Zma-miR408* probably also has a biological relevance rather than the useless, degraded sequences. Therefore, we designed the original Zma-miR408 and Zma-miR408* to be Zma-miR408-3p and Zma-miR408-5p, respectively, based on 3′- or 5′-arm derivation of the miRNA species. Although the well-known conservation of miRNA, a SNP (A/G) between B73 and Mo17 inbred lines in mature Zma-miR408-5p sequence was identified and confirmed by sequencing (Figure 6A). Based on the SNP information, we next examined whether this miRNA is subjected to allele-biased expression between the two reciprocal crosses. Interestingly, Zma-miR408-5p showed a significantly B73-allele biased expression pattern in 7-, 10-, and 15-DAP reciprocal endosperms (Figure 6B, χ2-test, p-value ≤ 0.01), which was further confirmed by CAPS experiments (Figure 6C). Moreover, the SNP of Zma-miR408-5p was located at the 11th base position from the 5′ end between B73 and Mo17, indicating that this polymorphism was likely to cause functional variation of Zma-miR408-5p. Thus, these two should target complete different genes based on the principle of complementary base pairing because the 10/11 base position is very important for miRNA-directed mRNA cleavage (Figure 6B). The target prediction of B73 and Mo17 Zma-miR408-5p by the psRNATarget server is also consistent with our speculation. The putative targets of B73 Zma-miR408-5p were GRMZM2G034896, GRMZM2G093526, and GRMZM2G177518, while Mo17 Zma-miR408-5p likely negatively modulates five other targets, including AC196575.3_FG007, GRMZM2G169005, GRMZM2G162065, AC198481.3_FG004, and GRMZM2G349554.

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