The early maize (Zea mays) seed undergoes several developmental stages after double fertilization to become fully differentiated within a short period of time, but the genetic control of this highly dynamic and complex developmental process remains largely unknown. Here, we report a high temporal-resolution investigation of transcriptomes using 31 samples collected at an interval of 4 or 6 h within the first six days of seed development. These time-course transcriptomes were clearly separated into four distinct groups corresponding to the stages of double fertilization, coenocyte formation, cellularization, and differentiation. A total of 22,790 expressed genes including 1415 transcription factors (TFs) were detected in early stages of maize seed development. In particular, 1093 genes including 110 TFs were specifically expressed in the seed and displayed high temporal specificity by expressing only in particular period of early seed development. There were 160, 22, 112, and 569 seed-specific genes predominantly expressed in the first 16 h after pollination, coenocyte formation, cellularization, and differentiation stage, respectively. In addition, network analysis predicted 31,256 interactions among 1317 TFs and 14,540 genes. The high temporal-resolution transcriptome atlas reported here provides an important resource for future functional study to unravel the genetic control of seed development.

Long-range chromatin interactions are important for transcriptional regulation of genes, many of which are related to complex agronomics traits. However, the pattern of three-dimensional chromatin interactions remains unclear in plants. Here we report the generation of chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) data and the construction of extensive H3K4me3- and H3K27ac-centered chromatin interaction maps in maize. Results show that the interacting patterns between proximal and distal regulatory regions of genes are highly complex and dynamic. Genes with chromatin interactions have higher expression levels than those without interactions. Genes with proximal-proximal interactions prefer to be transcriptionally coordinated. Tissue-specific proximal–distal interactions are associated with tissue-specific expression of genes. Interactions between proximal and distal regulatory regions further interweave into organized network communities that are enriched in specific biological functions. The high-resolution chromatin interaction maps will help to understand the transcription regulation of genes associated with complex agronomic traits of maize.

VQ motif-containing proteins play crucial roles in abiotic stress responses in plants. Recent studies have shown that some VQ proteins physically interact with WRKY transcription factors to activate downstream genes. In the present study, we identified and characterized genes encoding VQ motif-containing proteins using the most recent version of the maize genome sequence. In total, 61VQ genes were identified. In a cluster analysis, these genes clustered into nine groups together with their homologous genes in rice and Arabidopsis. Most of the VQ genes (57 out of 61 numbers) identified in maize were found to be single-copy genes. Analyses of RNA-seq data obtained using seedlings under long-term drought treatment showed that the expression levels of most ZmVQ genes (41 out of 61 members) changed during the drought stress response. Quantitative real-time PCR analyses showed that most of the ZmVQ genes were responsive to NaCl treatment. Also, approximately half of the ZmVQ genes were co-expressed with ZmWRKY genes. The identification of these VQ genes in the maize genome and knowledge of their expression profiles under drought and osmotic stresses will provide a solid foundation for exploring their specific functions in the abiotic stress responses of maize.

BackgroundDrought is one of the major factors limiting global maize production. Exposure to long-term drought conditions inhibits growth and leads to yield losses. Although several drought-responsive genes have been identified and functionally analyzed, the mechanisms underlying responses to drought and water recovery treatments have not been fully elucidated. To characterize how maize seedling respond to drought stress at the transcriptional level, we analyzed physiological responses and differentially expressed genes (DEGs) in the inbred line B73 under water deficit and recovery conditions.ResultsThe data for relative leaf water content, leaf size, and photosynthesis-related parameters indicated that drought stress significantly repressed maize seedling growth. Further RNA sequencing analysis revealed that 6107 DEGs were responsive to drought stress and water recovery, with more down-regulated than up-regulated genes. Among the DEGs, the photosynthesis- and hormone-related genes were enriched in responses to drought stress and re-watering. Additionally, transcription factor genes from 37 families were differentially expressed among the three analyzed time-points. Gene ontology enrichment analyses of the DEGs indicated that 50 GO terms, including those related to photosynthesis, carbohydrate metabolism, oxidoreductase activities, nutrient metabolism and other drought-responsive pathways, were over-represented in the drought-treated seedlings. The content of gibberellin in drought treatment seedlings was decreased compared to that of control seedlings, while abscisic acid showed accumulated in the drought treated plants. The deep analysis of DEGs related to cell wall development indicated that these genes were prone to be down-regulated at drought treatment stage.ConclusionsMany genes that are differentially expressed in responses to drought stress and water recovery conditions affect photosynthetic systems and hormone biosynthesis. The identified DEGs, especially those encoding transcription factors, represent potential targets for developing drought-tolerant maize lines.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1281-x) contains supplementary material, which is available to authorized users.

SummaryCircadian clocks are endogenous auto-regulatory mechanisms that allow organisms, from bacteria to humans, to advantageously time a wide range of activities within 24 h environmental cycles. Here we report the identification and characterization of an MYB-related gene, designated Circadian 1 (CIR1), that is involved in circadian regulation in Arabidopsis. Expression of CIR1 is transiently induced by light and oscillates with a circadian rhythm. The rhythmic expression of CIR1 is controlled by the central oscillator. Constitutive expression of CIR1 resulted in a shorter period length for the rhythms of four central oscillator components, and much lower amplitude for the rhythms of central oscillator components CCA1 and LHY. Furthermore, CIR1 over-expression severely affected the circadian rhythms of its own RNA and those of the slave oscillator EPR1 and effector genes Lhcb and CAT3. Plants that constitutively expressed CIR1 displayed delayed flowering, longer hypocotyls and reduced seed germination in the dark. These results suggest that CIR1 is possibly part of a regulatory feedback loop that controls a subset of the circadian outputs and modulates the central oscillator.