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.
Highlights
In flowering plants, the triploid endosperm is derived from the fertilization of the central cell (2n) and the sperm cell (1n) (Yadegari and Drews, 2004)
MiR390 targets a non-protein coding gene and triggers the production of TAS3, and as a consequence, which in turn causes the degradation of AUXIN RESPONSE FACTOR3 (ARF3) and ARF4 mRNAs, and advance the process of precocious maturation
These miRNA regulation networks were previously observed in Arabidopsis, these interplay nodes might be applicable during maize kernel and endosperm development according to the miRNA expression profile determined here
Summary
The triploid endosperm is derived from the fertilization of the central cell (2n) and the sperm cell (1n) (Yadegari and Drews, 2004). The misexpression of the endosperm-specific gene Meg results in malformed transfer cells, which in turn adversely regulates nutrient uptake, sucrose partitioning, and seed biomass yield (Costa et al, 2012). Gene ontology (GO) enrichment analysis demonstrated that the putative targets of these grainabundant miRNAs could be involved in the regulation of carbohydrate and protein metabolism, transcription, and cellular transport functional groups, suggesting their crucial roles in gene regulatory networks in seed development (Xue et al, 2009; Lan et al, 2012; Gu et al, 2013; Meng et al, 2013). Our data demonstrated that Zma-miR408-5p exhibited a parentbiased expression pattern based on the SNP information and Cleaved Amplified Polymorphic Sequence (CAPS) experiment, further suggesting that parental genomes might not contribute to controlling endosperm development in terms of miRNA-mediated regulation networks
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