Abstract
The endosperm is a major organ of the seed that plays vital roles in determining seed weight and quality. However, genome-wide transcriptome patterns throughout maize endosperm development have not been comprehensively investigated to date. Accordingly, we performed a high-throughput RNA sequencing (RNA-seq) analysis of the maize endosperm transcriptome at 5, 10, 15 and 20 days after pollination (DAP). We found that more than 11,000 protein-coding genes underwent alternative splicing (AS) events during the four developmental stages studied. These genes were mainly involved in intracellular protein transport, signal transmission, cellular carbohydrate metabolism, cellular lipid metabolism, lipid biosynthesis, protein modification, histone modification, cellular amino acid metabolism, and DNA repair. Additionally, 7,633 genes, including 473 transcription factors (TFs), were differentially expressed among the four developmental stages. The differentially expressed TFs were from 50 families, including the bZIP, WRKY, GeBP and ARF families. Further analysis of the stage-specific TFs showed that binding, nucleus and ligand-dependent nuclear receptor activities might be important at 5 DAP, that immune responses, signalling, binding and lumen development are involved at 10 DAP, that protein metabolic processes and the cytoplasm might be important at 15 DAP, and that the responses to various stimuli are different at 20 DAP compared with the other developmental stages. This RNA-seq analysis provides novel, comprehensive insights into the transcriptome dynamics during early endosperm development in maize.
Highlights
Maize (Zea mays) is one of the world’s most important crops and is used for food, animal feed and biofuel [1]
Coverage of the reads mapped to the maize genome sequences varied across the four stages (S2 Fig), indicating that the transcriptome is dynamic during the early stage of maize endosperm development
Gene Ontology (GO) enrichment analysis showed that the differentially expressed transcription factors (DETFs) that were highly expressed at 5 days after pollination (DAP) were mainly involved in binding processes, such as water, ice, zinc ion, protein, cation, ion, metal ion and transition metal ion binding, as well as nucleus and ligand-dependent nuclear receptor activity (S18 Table)
Summary
Maize (Zea mays) is one of the world’s most important crops and is used for food, animal feed and biofuel [1]. 60% (30/50) of the TF families included relatively fewer DETFs, with most exhibiting either up- or down-regulation at specific stages of endosperm development (Fig 7A). A total of 473 DETFs could be grouped into 12 clusters; of these DETFs, 39 (R2, R5, R7-9 and R11), 44 (R1-5), 40 (R1, R6-7 and R12) and 44 (R1, R4-5, R8 and R10-12) were highly expressed at 5, 10, 15 and 20 DAP, respectively (Fig 7B and S17 Table). GO enrichment analysis showed that the DETFs that were highly expressed at 5 DAP were mainly involved in binding processes, such as water, ice, zinc ion, protein, cation, ion, metal ion and transition metal ion binding, as well as nucleus and ligand-dependent nuclear receptor activity (S18 Table). Dof, E2F/DP, GATA, GRF, SRS, WOX and ZF-HD family members have important roles in regulating the above functions, and the functions of some of doi:10.1371/journal.pone.0163814.g007
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
