Comparative transcriptomics reveals the difference in early endosperm development between maize with different amylose contents
- Published
- Accepted
- Subject Areas
- Developmental Biology, Plant Science
- Keywords
- Gene expression, Maize, Starch metabolism, RNA-sequence, Endosperm
- Copyright
- © 2019 Qu et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2019. Comparative transcriptomics reveals the difference in early endosperm development between maize with different amylose contents. PeerJ Preprints 7:e27577v1 https://doi.org/10.7287/peerj.preprints.27577v1
Abstract
The endosperm is a crucial organ for seeds that plays vital roles in supporting embryo development and determining seed weight and quality. Starch is the predominant storage carbohydrate of the endosperm and accounts for ~70% of the mature maize kernel weight. Nonetheless, because starch biosynthesis is a complex process that is orchestrated by multiple enzymes, the gene regulatory networks of starch biosynthesis, particularly amylose and amylopectin biosynthesis, have not been fully elucidated. Here, through high-throughput RNA sequencing, we developed a temporal transcriptome atlas of the endosperms of high-amylose maize and common maize at 5-, 10-, 15- and 20-day after pollination and found that 21,986 genes are involved in the programming of the high-amylose maize and common maize endosperm. A coexpression analysis identified multiple sequentially expressed gene sets that are closely correlated cellular and metabolic programs and provided valuable insight into the dynamic reprogramming of the transcriptome in common and high-amylose maize. In addition, a number of genes and transcription factors (TFs) were found to be strongly linked to starch synthesis, which might help elucidate the key mechanisms and regulatory networks underlying amylose and amylopectin biosynthesis. This study will aid the understanding of the spatiotemporal patterns and genetic regulation of endosperm development in different types of maize.
Author Comment
This is a submission to PeerJ for review.
Supplemental Information
Reads coverage of the SD609 and HS68 endosperms at the four developmental stages
Supplementary figure 1 Reads coverage of the SD609 and HS68 endosperms at the four developmental stages. From outside to inside of Circos image representing reads of 5, 10, 15 and 20 DAP mapped to maize reference genome sequences. Of which, red colour and green colour represents normalized reads number of SD609 and HS68, respectively.
Functional enrichment analysis of the shared genes among the four stages of endosperm development in SD609 and HS68
Supplementary figure 2 Functional enrichment analysis of the shared genes among the four stages of endosperm development in SD609 and HS68. (A) The enriched GO terms “biological process”, (B) “cellular component”, and (C) “molecular function” categories are shown.
Number of DEGs identified in SD609 and HS68
Supplementary figure 3 Number of DEGs identified in SD609 and HS68. A total of 1,193 DEGs were differentially expressed between SD609 and HS68, 7,813 DEGs were consistently expressed at the different development stages of SD609 and HS68, and 4,914 and 2,002 DEGs were specifically detected in SD609 and HS68, respectively.
Functional enrichment analysis of DEGs at different developmental stages
Supplementary figure 4 Functional enrichment analysis of DEGs at different developmental stages. (A) Functional annotation of 1,193 DEGs between SD609 and HS68. (B) Shared biological processes regulated by the material-specific DEGs of SD609 and HS68. (C) Specific biological processes of HS68 that are regulated by the material-specific DEGs of SD609 and HS68. (D) Specific biological processes of SD609 that are regulated by the material-specific DEGs of SD609 and HS68. Only biological processes with P values<0.0001 and FDR<0.01 are shown.
Functional enrichment analysis of the DEG sets of the coexpression clusters
Supplementary figure 5 Functional enrichment analysis of the DEG sets of the coexpression clusters. Only biological processes with a P value<0.0001 and FDR<0.01 are shown. (B) Functional analysis of coexpression clusters of SD609. (C) Functional analysis of coexpression clusters of HS68. (A) Functional analysis of shared DEGs in coexpression clusters between SD609 and HS68.
Expression patterns of shared DEGs between SD609 and HS68
Supplementary figure 6 Expression patterns of shared DEGs between SD609 and HS68. (A) Sixteen clusters were characterized by the fluctuating expression of gene sets at 5, 10, 15 and 20 DAP in both SD609 and HS68. The up- and downregulated gene sets are staggered or depicted consecutively during the developmental stages of the maize endosperm, and the same DEG sets with the same or different expression patterns in two different maize materials are shown. The scaled expression levels of the DEGs are provided on the y-axis, the developmental stages are shown on the x-axis, the coloured lines represent the individual gene expression clusters, and the trend in the expression of each gene set is depicted as a black line. “n” represents the number of DEGs.
Relationship between module eigengenes
Supplementary figure 7 Relationship between module eigengenes. The diagonals show the distribution. The lower left section shows a bivariate scatterplot with a fitting line, and the upper right section shows the correlation coefficient and the significance level.
List of primers used for the qRT-PCR gene detection analysis
Supplementary table 1 List of primers used for the qRT-PCR gene detection analysis.
Statistical analysis of the sequenced and mapped reads of SD609 and HS68
Supplementary table 2 Statistical analysis of the sequenced and mapped reads of SD609 and HS68.
Information on the expressed genes of SD609 and HS68
Supplementary table 3 Information on the expressed genes of SD609 and HS68.
Functional enrichment analysis of stage-specific gene expression
Supplementary table 4 Functional enrichment analysis of stage-specific gene expression.
Information of DEGs from SD609 and HS68
Supplementary table 5 Information of DEGs from SD609 and HS68.
GO enrichment analysis of the DEGs of SD609 and HS68
Supplementary table 6 GO enrichment analysis of the DEGs of SD609 and HS68.
qRT-PCR analysis of candidate genes
Supplementary table 7 qRT-PCR analysis of candidate genes.
Functional annotation of the WGCNA modules
Supplementary table 8 Functional annotation of the WGCNA modules.
Functional annotation of the hub genes
Supplementary table 9 Functional annotation of the hub genes.
Starch core gene networks
Supplementary table 10 Starch core gene networks.