Transcriptome-wide identification of imprinting genes at the seed dehydration stage in maize

Seeds harvested at lower moisture contents (MC) are advantageous, leading to both high-efficiency drying and high-vigor seed production. While maize is the most successful crop in utilizing heterosis, the regulatory mechanism governing seed MC in hybrids remains largely unknown. Here, three pairs of reciprocal hybrids were constructed using four distinct inbred lines: the fast-dehydration line PH4CV (P) and Zheng30 (Z2), and the slow lines Zheng58 (Z1) and Dan360 (D). Field experiments demonstrated that hybrids crossed using the faster lines as maternal parents (PZ1, Z2Z1, and PD) exhibited a faster dehydration rate during seed development compared to their corresponding reciprocal hybrids (Z1P, Z1Z2, and DP). Seeds were then collected from the PZ1 and Z1P reciprocal hybrids at 55 days after pollination (DAP) for transcriptome analysis. The results showed that 68.3% of the Different Expression Genes (DEGs) between reciprocal hybrids overlapped with the DEGs between parental lines. By comparing the Allele Specific Expression (ASE) of the expressed genes within each hybrid, an average maternal allele proportion of 0.524 was determined in these 55 DAP seeds. Furthermore, 226 Maternally Expressed Genes (MEGs), and 112 Paternally Expressed Genes (PEGs) were identified, and the ASE of two candidate imprinting genes, Zm00001d040697 and Zm00001d052744, were subsequently verified in the reciprocal hybrids by qPCR. Expression analyses indicated that the imprinted genes are likely distinct from the genes differentially expressed between the reciprocal hybrids. Together, these results confirm a maternal effect on seed dehydration rate, and provide a strong set of candidate imprinting genes potentially regulating seed MC.