Abstract
Seed aging is a complex and irreversible process that occurs during seed development and storage. The quality of Allium mongolicum Regel seeds directly impacts its cultivation and production. However, the mechanism of aging seeds in A. mongolicum Regel is not well understood. Germination and physiological indicators were assessed, and RNA-Seq technique was performed on samples stored for 1, 4, and 8 years. In total, 5723, 7347 and 5293 differentially expressed genes (DEGs) were identified in 1 year old (S1) versus 4 year old (S2), S1 versus 8 year old (S4), and S2 versus S4, respectively. The number of DEGs increased as the storage time increased. The analysis revealed that the majority of the these DEGs were involved in a wide range of processes, such as protein synthesis, degradation and targeting; RNA processing and regulation; transport; DNA; signaling; stress; metabolism; amino acid metabolism; secondary metabolism; and hormone metabolism. The germination rate of A. mongolicum seeds remained consistently high, exceeding 80%, even after four years of storage. This observation indicates a potential correlation with the increased expression levels of aspartic proteases. However, as the storage time surpassed the seed’s lifespan, there was a notable decline in the expression levels of genes that encode aspartic proteases, cysteine proteases, and serine proteases. Conducting further research on these candidate genes could enhance our comprehension of the regulatory mechanisms involved in seed aging during storage for varying durations.
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Funding
This work was supported by a National Natural Science Foundations of China (311,760,081), Science Fund of Inner Mongolia of China (2019MS03055), Animal and Plant Breeding Special projects of Inner Mongolia Agricultural University (YZGC2017016), The Major Seed Industry Science and Technology Innovation Demonstration Project of the Autonomous Region Unveiled in Command, The Special Fund Project for the Transformation of Scientific and Technological Achievements of the Inner Mongolia Autonomous Region (2021CG0023), The Science and Technology Plan of the Inner Mongolia Autonomous Region (2021GG0084), The Major Science and Technology Project of the Inner Mongolia Autonomous Region (2021ZD0001), Major Science and Technology Project (2019ZD016).
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H, LZ, H, XM and Y, ZR supervised the experiment. Z, XY, G, F, Z, D, L, Z, N, KZ and W, PC performed the experiment work and prepared the figures and tables. Z, XY wrote the manuscript. Z, FL edited the final version of the manuscript.All authors have approved the final manuscript.
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10681_2023_3259_MOESM1_ESM.docx
Supplementary file1 Figure S1 (A) Length distribution of Allium mongolicum unigenes; (B)All samples Pearson; (C)PCA plot analysis of all samples; (D) The number of DEGs after different storage times (1, 4, 8 years).
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Supplementary file3 Figure S3 Histogram of gene ontology classification. The results have been summarized into three main GO categories: biological processes, cellular components and molecular function. The x-axis indicates the sub-categories, and the y-axis indicates the number of DEGs. (A) GO terms of S1 vs S4; (B) GO terms of S2 vs S4.
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Supplementary file4 Figure S4 Heatmap of DEGs involved in pathways both in S1 vs S4 and S2 vs S4 (A) hormone; (B) signaling; (C) redox and secondary metabolism. The expression levels of DEGs in RPKM were compiled using Excel 2007, normalized using a log2 base method, and exported to the HemItoolkit 124. The heatmap was generated using default parameters. The expression levels are presented as different colours and values are defined in the scale bar.
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Supplementary file6 Table S2 Basic information on transcriptome data from A. mongolicum seeds stored for 1, 4 and 8 year. (A) Summary of sequences analysis; (B) Statistics of assembly results; (C) Statistical tables for the four databases annotated.
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Supplementary file8 Table S4 Differentially expressed genes involved in protein and energy metabolism in both S1 vs S4 and S2 vs S4
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Zhang, X., Guo, F., Huang, X. et al. Combined physiological and transcriptomic analyses to identify candidate genes involved in aging during storage of Allium mongolicum Regel. seeds. Euphytica 220, 14 (2024). https://doi.org/10.1007/s10681-023-03259-1
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DOI: https://doi.org/10.1007/s10681-023-03259-1