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Analysis of global gene expression profiles to identify differentially expressed genes critical for embryo development in Brassica rapa

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Abstract

Embryo development represents a crucial developmental period in the life cycle of flowering plants. To gain insights into the genetic programs that control embryo development in Brassica rapa L., RNA sequencing technology was used to perform transcriptome profiling analysis of B. rapa developing embryos. The results generated 42,906,229 sequence reads aligned with 32,941 genes. In total, 27,760, 28,871, 28,384, and 25,653 genes were identified from embryos at globular, heart, early cotyledon, and mature developmental stages, respectively, and analysis between stages revealed a subset of stage-specific genes. We next investigated 9,884 differentially expressed genes with more than fivefold changes in expression and false discovery rate ≤0.001 from three adjacent-stage comparisons; 1,514, 3,831, and 6,633 genes were detected between globular and heart stage embryo libraries, heart stage and early cotyledon stage, and early cotyledon and mature stage, respectively. Large numbers of genes related to cellular process, metabolism process, response to stimulus, and biological process were expressed during the early and middle stages of embryo development. Fatty acid biosynthesis, biosynthesis of secondary metabolites, and photosynthesis-related genes were expressed predominantly in embryos at the middle stage. Genes for lipid metabolism and storage proteins were highly expressed in the middle and late stages of embryo development. We also identified 911 transcription factor genes that show differential expression across embryo developmental stages. These results increase our understanding of the complex molecular and cellular events during embryo development in B. rapa and provide a foundation for future studies on other oilseed crops.

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Acknowledgments

This work was supported by the State Key Basic Research and Development Plan of China (2013CB126900) and the National Natural Science Foundation of China (31370258).

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Authors and Affiliations

  1. State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China

    Yu Zhang, Lifang Peng, Ya Wu, Yanyue Shen & Jianbo Wang

  2. Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of CAAS, Wuhan, 430062, China

    Xiaoming Wu

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  1. Yu Zhang
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  3. Ya Wu
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Correspondence to Jianbo Wang.

Electronic supplementary material

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11103_2014_238_MOESM1_ESM.tif

Supplemental Fig. 1 Percent of coverage representing the percentage of genes which expressed in each of the four stages mapped in the Brassica rapa L. genome. cDNA libraries are taken from Brassica rapa L. embryo at globular (G), heart (H), early cotyledon (E) and mature (M) stage, respectively. Gene coverage is the percentage of a gene covered by reads. It is equal to the ratio of the number of bases in a gene covered by unique mapping reads to the total number of bases in that gene. Visual result is showed as percentage of the amount of genes (TIFF 1348 kb)

11103_2014_238_MOESM2_ESM.tif

Supplemental Fig. 2 The result of qRT-PCR validation. It shows the expression pattern of nine random selected genes in validation. The columns denote the mean relative expression level; the bars denote the standard deviation (TIFF 772 kb)

11103_2014_238_MOESM3_ESM.doc

Supplemental Table 1 Primers used in the qRT-PCR analysis of gene expression in B. rapa embryo development. ACT2/7 is used as internal control to standardize the results (DOC 36 kb)

11103_2014_238_MOESM4_ESM.xls

Supplemental Table 2 A total of 32,941 genes derived from four cDNA libraries. The Gene ID, length of gene, RPKM of four stages and expression pattern are presented in this table (XLS 4609 kb)

11103_2014_238_MOESM5_ESM.xls

Supplemental Table 3 A list of KEGG pathways mapped by 22,060 genes in our result. Pathways over-represented by genes were for metabolic pathways, biosynthesis of secondary metabolites, plant-pathogen interaction, and plant hormone signal transduction with 4953, 2760, 1663, and 1540 members, respectively (XLS 34 kb)

11103_2014_238_MOESM6_ESM.xls

Supplemental Table 4 A table listing 9,884 differentially expressed genes (DEGs) during Brassica rapa L. embryo development. We use FDR ≤ 0.001 and the absolute value of log2Ratio ≥ 2.322 as the threshold to judge the significance of gene expression difference. The RPKM of four stages and expression pattern of DEGs are presented in the table (XLS 1308 kb)

11103_2014_238_MOESM7_ESM.xls

Supplemental Table 5 Differentially expressed genes between globular and heart stage embryos. FDR: false discovery rate. We used FDR ≤ 0.001 and the absolute value of log2Ratio ≥ 2.322 (fold change greater than five folds) as the threshold to judge the significance of gene expression difference (XLS 199 kb)

11103_2014_238_MOESM8_ESM.xls

Supplemental Table 6 Differentially expressed genes between heart and early cotyledon-stage embryos. FDR: false discovery rate. We used FDR ≤ 0.001 and the absolute value of log2Ratio ≥ 2.322 (fold change greater than five folds) as the threshold to judge the significance of gene expression difference (XLS 407 kb)

11103_2014_238_MOESM9_ESM.xls

Supplemental Table 7 Differentially expressed genes between early cotyledon and mature embryos. FDR: false discovery rate. We used FDR ≤ 0.001 and the absolute value of log2Ratio ≥ 2.322 (fold change greater than five folds) as the threshold to judge the significance of gene expression difference (XLS 1176 kb)

11103_2014_238_MOESM10_ESM.xls

Supplemental Table 8 GO enrichment analysis for 9,884 DEGs. GO term classifications: C, Cellular Component; F, Molecular Function; P, Biological Process. GO terms with P-value ≤0.05 were regarded as significantly enriched GO terms (XLS 53 kb)

11103_2014_238_MOESM11_ESM.xls

Supplemental Table 9 Overview of all 127 KEGG pathways of 9,884 DEGs. All DEGs are assigned to 127 KEGG pathways. The KEGG functional class, number, RPKM of four stages and expression type are also presented in this table (XLS 50 kb)

11103_2014_238_MOESM12_ESM.xls

Supplemental Table 10 The detail of all 237 branch pathways in 35 MapMan major pathways. The MapMan functional class, number, RPKM of four stages and expression type are presented in the table (XLS 4073 kb)

11103_2014_238_MOESM13_ESM.xls

Supplemental Table 11 A list of putative transcription factor (TF) genes in our results. We queried Brassica rapa L. transcription factor genes in the Plant Transcription Factor Database (http://planttfda.cbi.edu.cn/). All 57 transcription factor (TF) gene families were found in the result. 2,502 putative TF genes are identified in 32,941 genes. Of the 2,502 putative TFs, 911 genes which showed significantly differential expression of four stages are marked by *. The TF gene family name, number, RPKM, GO function annotation of TF family’s members are presented in the table (XLS 551 kb)

11103_2014_238_MOESM14_ESM.xls

Supplemental Table 12 A summary of 57 transcription factor (TF) gene families differentially expressed during B. rapa embryo development. The TF gene family name, number, RPKM, expression pattern and expression pattern of TF family’s members are presented in the table (XLS 46 kb)

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Zhang, Y., Peng, L., Wu, Y. et al. Analysis of global gene expression profiles to identify differentially expressed genes critical for embryo development in Brassica rapa . Plant Mol Biol 86, 425–442 (2014). https://doi.org/10.1007/s11103-014-0238-1

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