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Genome-wide expression profiles of seasonal bud dormancy at four critical stages in Japanese apricot

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Abstract

Dormancy is one of the most important adaptive mechanisms developed by perennial plants. To reveal the comprehensive mechanism of seasonal bud dormancy at four critical stages in Japanese apricot (Prunus persica), we applied Illumina sequencing to study differentially expressed genes (DEGs) at the transcriptional level. As a result, 19,759, 16,375, 19,749 and 20,800 tag-mapped genes were sequenced from libraries of paradormancy (R1), endodormancy (R2), ecodormancy (R3) and dormancy release (R4) stages based on the P. persica genome. Moreover, 6,199, 5,539, and 5,317 genes were differentially expressed in R1 versus R2, R2 versus R3, and R3 versus R4, respectively. Gene Ontology analysis of dormancy-related genes showed that these were mainly related to the cytoplasm, cytoplasmic part metabolism, intracellular metabolism and membrane-bound organelle metabolism. Pathway-enrichment annotation revealed that highly ranked genes were involved in ribosome pathways and protein processing in the endoplasmic reticulum. The results demonstrated that hormone response genes such as auxin, abscisic acid, ethylene and jasmonic acid, as well as zinc finger family protein genes are possibly involved in seasonal bud dormancy in Japanese apricot. The expression patterns of DEGs were verified using real-time quantitative RT-PCR. These results contribute to further understanding of the mechanism of bud dormancy in Japanese apricot.

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Acknowledgments

We gratefully acknowledge the Natural Science Foundation of Jiangsu Province (BK2011642) and the National Science Foundation of China (31101526) for providing financial support, as well as the Jiangsu Province Agriculture Independent Innovation System Project [CX(12)2011] for funding part of this study.

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  1. College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095, People’s Republic of China

    Wenjun Zhong, Zhihong Gao, Weibing Zhuang, Ting Shi, Zhen Zhang & Zhaojun Ni

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  1. Wenjun Zhong
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Correspondence to Zhihong Gao.

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Wenjun Zhong and Zhihong Gao contributed equally to this work.

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Table S1 Genes selected for real-time RT-PCR. (DOC 40 kb)

Table S2 Auxin-related genes changed by two-fold or more in R1 vs. R2, R2 vs. R3 and R3 vs. R4 libraries. (DOC 48 kb)

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Table S3 Ethylene-related genes changed by two-fold or more in R1 vs. R2, R2 vs. R3 and R3 vs. R4 libraries. (DOC 35 kb)

Table S4 ABA-related genes changed by two-fold or more in R1 vs. R2, R2 vs. R3 and R3 vs. R4 libraries. (DOC 35 kb)

Table S5 JA-related genes changed by two-fold or more in R1 vs. R2, R2 vs. R3 and R3 vs. R4 libraries. (DOC 27 kb)

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Table S6 Gibberellin-related genes changed by two-fold or more in R1 vs. R2, R2 vs. R3 and R3 vs. R4 libraries. (DOC 27 kb)

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Table S7 Expression of DAMs genes changed by two-fold or more in R1 vs. R2, R2 vs. R3 and R3 vs. R4 libraries. (DOC 34 kb)

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Table S8 Zinc finger family protein genes changed by eight-fold or more in R1 vs. R2, R2 vs. R3 and R3 vs. R4 libraries. (DOC 30 kb)

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Table S9 Calcium-related genes changed by five-fold or more in R1 vs. R2, R2 vs. R3 and R3 vs. R4 libraries. (DOC 39 kb)

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Fig. S1 Comparison of gene expression levels between R1 vs. R2, R2 vs. R3 and R3 vs. R4. To compare gene expression levels, each library was normalised to one million tags. Red dots represent transcripts more prevalent in the front library, green dots show those present at a lower frequency in the front library and blue dots indicate transcripts that did not change significantly. The parameters FDR <0.001 and log2 ratio >1 were used as the threshold to judge the significance of differences in gene expression. Fig. S1a: Gene expression level in R1 vs. R2. (TIFF 277 kb)

Fig. S1b: Gene expression level in R2 vs. R3. (TIFF 273 kb)

Fig. S1c: Gene expression level in R3 vs. R4. (TIFF 270 kb)

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Fig. S2 Differentially expressed tags in R1 vs. R2, R2 vs. R3 and R3 vs. R4 libraries. The x-axis represents the fold-change in differentially expressed unique tags in each library. The y-axis represents the number of unique tags (log10). Differentially accumulating unique tags with a five-fold difference between the libraries are shown in the red region. The blue and green regions represent unique tags that are up- or down-regulated more than five-fold in each library, respectively. Fig. S2a: Differentially expressed tags in R1 vs. R2. (PNG 32 kb)

Fig. S2b: Differentially-expressed tags in R2 vs. R3. (PNG 32 kb)

Fig. S2c: Differentially expressed tags in R3 vs. R4. (PNG 32 kb)

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Fig. S3 Saturation evaluation of differential expression. Fig. S3a: sequencing saturation analysis of paradormancy. (TIFF 183 kb)

Fig. S3b: sequencing saturation analysis of endodormancy. (TIFF 185 kb)

Fig. S3c: sequencing saturation analysis of ecodormancy. (TIFF 183 kb)

Fig. S3d: sequencing saturation analysis of dormancy release. (TIFF 185 kb)

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Fig. S4 Numbers of up-regulated and down-regulated differentially expressed genes between different samples. (DOC 23 kb)

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Fig. S5 Histogram illustrating Gene Ontology functional enrichment analysis of differentially expressed genes. Fig. S5a: GO functional enrichment analysis of R1 vs. R2. (DOC 125 kb)

Fig. S5b: GO functional enrichment analysis of R2 vs. R3. (DOC 137 kb)

Fig. S5c: GO functional enrichment analysis of R3 vs. R4. (DOC 134 kb)

Fig. S6 Histogram showing pathway enrichment analysis for differentially expressed genes. (DOC 133 kb)

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Fig. S7 The expression levels of DAM3, DAM5 and DAM6 genes in R1, R2, R3 and R4, respectively. The x-axis indicates the different genes. The y-axis shows the expression level as determined by DGE (The results of tag mapping based on the Prunus persica genome). (TPM: number of transcripts per million clean tags). (TIFF 81 kb)

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Zhong, W., Gao, Z., Zhuang, W. et al. Genome-wide expression profiles of seasonal bud dormancy at four critical stages in Japanese apricot. Plant Mol Biol 83, 247–264 (2013). https://doi.org/10.1007/s11103-013-0086-4

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