SRA

In angiosperms, endosperm plays a crucial role in coordinating seed development through genetic balance and molecular interaction, and is the primary tissue where genomic imprinting occurs. To identify small interfering RNA (siRNA) “imprintome” and its paternal transcriptome activation in early developing maize endosperms, we performed high-throughput small RNA sequencing of whole kernels at 0, 3 and 5 days after pollination (DAP) and endosperms at 7, 10 and 15 DAP, using B73 by Mo17 reciprocal crosses. We observed gradually increased expression of paternal siRNAs in 3- and 5-DAP kernels and balanced contribution of parental siRNA transcriptome in 7-DAP endosperm, followed by identification 460 imprinted siRNA loci with majority (456/460, 99.1%) being maternally expressed that occurred at 10 DAP. Genome-wide scanning found 13 imprinted genes harboring imprinted siRNA loci within their 2-Kb flanking regions, which was significantly different from random probability based on simulation analysis. Finally, gene ontology categories of “response to auxin stimulus”, “response to brassinosteroid stimulus” and “regulation of gene expression” for genes harboring 10-DAP specific siRNAs and “nutrient reservoir activity”, “protein localization to vacuole” and “secondary metabolite biosynthetic process” for genes harboring 15-DAP specific siRNAs indicated that siRNAs could be involved in influencing specific cellular or biochemical processes that are essential for endosperm development, e.g. nutrient uptake and allocation. Although the mechanism of how these siRNAs regulating endosperm key events remains unclear, this study provided us an alternative perspective of siRNA function in plant. Overall design: The unpollinated kernels (0 DAP), the kernels of 3, 5 DAP and endosperms of 7 10, 15 DAP from the B73 and Mo17 reciprocal crosses were used to perform high-throughput sequencing using the Illumina HiSeq2000 platform