Joint Analysis of Transcriptome and Metabolome of a Wheat(Triticum aestivum) Seed Dormancy Mutant
ZHU Sha-Sha1,2,*, LI Xing-Yan1,*, LI Xiao-Long1,2, HAN Yang1,2, DANG Meng-Yuan1,2, YANG Yan1,2,**
1 College of Life Sciences, Inner Mongolia Agricultural University, Hohhot 010029, China; 2 Inner Mongolia Key Lab of Biomanufacturing Technology, Hohhot 010029, China
Abstract：The dormancy characteristics of wheat(Triticum aestivum) seeds determine its germination uniformity after sowing and regulates pre-harvest sprouting resistance of grains at harvest. In this study, the wheat mutant 1813WH, previously generated by our research team with enhanced seed dormancy and antioxidant capacity as well as decreased energy metabolism, was used as experimental material. Integrated transcriptomic and metabolomic analyses were performed on seeds at the waxy ripening stage; differentially expressed genes(DEGs) and differentially accumulated metabolites(DAMs) were screened based on multi-omics data, with subsequent verification of the associated pathways. The results showed that, compared with the wild type(WT), 1813WH showed altered expression of genes involved in nitrogen metabolism and differential accumulation of corresponding metabolites. Differentially expressed genes(DEGs) and differentially accumulated metabolites(DAMs) were enriched in pathways including arginine synthesis, amino acid metabolism, and plant hormone signaling. The relative content of the non-reducing sugar—sucrose was significantly higher in 1813WH than in the wild type(P<0.05), while the levels of reducing sugars including glucose-6-phosphate(G6P), fructose-1,6-bisphosphate(FBP), and fructose-6-phosphate(F6P), were significantly lower than in the wild type(P<0.05). In addition, the relative contents of jasmonic acid(Jasmonic acid, JA) and abscisic acid(abscisic acid, ABA) were lower in 1813WH than in WT, whereas the relative cytokinin content was higher than that in WT. These results indicated that the seeds of 1813WH actively inhibited core energy metabolism pathways such as the tricarboxylic acid(TCA) cycle at the waxy ripe stage, redirecting nitrogen resources toward the synthesis of polyamines and inert nitrogen compounds such as asparagine. It was hypothesized that the 1813WH mutant might regulate the core metabolic network, alter the carbon-nitrogen metabolic balance and internal hormone levels in wheat, thereby potentially optimize its growth and stress resistance strategies. Based on this, it is speculated that seeds might maintain deep dormancy through a "resource sequestration" strategy. This study provides a new theoretical basis for subsequent elucidation of its molecular mechanism and further regulation of wheat dormancy and pre-harvest sprouting resistance.
朱莎莎, 李星岩, 李晓龙, 韩洋, 党梦圆, 杨燕. 一个小麦种子休眠突变体的转录组和代谢组联合分析[J]. 农业生物技术学报, 2026, 34(8): 1597-1611.
ZHU Sha-Sha, LI Xing-Yan, LI Xiao-Long, HAN Yang, DANG Meng-Yuan, YANG Yan. Joint Analysis of Transcriptome and Metabolome of a Wheat(Triticum aestivum) Seed Dormancy Mutant. 农业生物技术学报, 2026, 34(8): 1597-1611.
[1] 段若昕, 陈盈盈, 林金星, 等. 2025. 种子休眠及其调控机制研究进展[J]. 生物技术通报, 41(12): 16-26. (Duan R X, Chen Y Y, Lin J X, et al.2025. Advance on seed dormancy and its regulation mechanism[J]. Biotechnology Bulletin, 41(12): 16-26.) [2] 郝丙青, 曲春浦, 刘忠野, 等. 2016. 植物氮代谢中天冬酰胺合成酶B的研究进展[J]. 山东农业科学, 48(01):142-149. (Hao B Q, Qu C P, Liu Z Y, et al.2016. Research advancement of asparagine synthetase B in plant nitrogen metabolism[J]. Shandong Agricultural Sciences, 48(01): 142-149.) [3] 蒋纪芸, 阎世理, 潘世禄, 等. 1988. 品种、栽培条件对旱地小麦产量及其品质的影响[J]. 北京农学院学报,(02):149-157. (Jiang J Y, Yan S L, Pan S L, et al. 1988. Effects of cultivars and cultural measures on the grain yield and quality of dry land wheat[J]. Journal of Beijing University of Agriculture,(02): 149-157.) [4] Dogramaci M, Sarkar D, Datir S, et al.2024. Methyl jasmonate and 1,4-dimethylnaphthalene differentially impact phytohormonal and stress protective pathway regulation involved in potato tuber dormancy[J]. Postharvest Biology and Technology, 213: 112931. [5] Dourmap C, Baud S, Eubel H, et al.2026, Pyrroline-5-carboxylate dehydrogenase is a key actor of nitrogen metabolism in maturing seeds of Arabidopsis thaliana[J]. Journal of Experimental Botany, 77(6): 1827-1843. [6] El-Maarouf-Bouteau H, Bailly C.2008. Oxidative signaling in seed germination and dormancy[J]. Plant Signaling & Behavior, 3(3): 175-182. [7] Fait A, Angelovici R, Less H, et al.2006. Arabidopsis seed development and germination is associated with temporally distinct metabolic switches[J]. Plant Physiology, 142(3): 839-854. [8] Finch-Savage W E, Leubner-Metzger G.2006. Seed dormancy and the control of germination[J]. New Phytologist, 171(3): 501-523. [9] Fußeder A, Ziegler P, Peters W, et al.1982. Turnover of O-glucosides of dihydrozeatin and dihydrozeatin-9-riboside during the cell growth cycle of photoautotrophic cell suspension cultures of Chenopodium rubrum[J]. Journal of the German Botanical Society, 102: 335-340. [10] Gao J W, Su Y, Zhang X H, et al.2025. GABA-regulated transamination generates alternative carbon skeleton for root nitrogen assimilation of wheat under waterlogging stress[J]. Environmental and Experimental Botany, 241: 106284. [11] Huo S, Chang L, Liu Y, et al.2025. Polyamine-activated carbonyl stress nanoplatform synergistically reverses biofilm-driven immunosuppressive microenvironment[J]. ACS Nano, 19(33): 30254-30274. [12] Ikeda Y, Fujii J.2023. The emerging roles of γ-glutamyl peptides produced by γ-glutamyltransferase and the glutathione synthesis system[J]. Cells, 12(24): 2831. [13] Khan A, Tian R, Bean S R, et al.2024. Transcriptome and metabolome analyses reveal regulatory networks associated with nutrition synthesis in Sorghum seeds[J]. Communications Biology, 7(1): 841. [14] Lea P J, Sodek L, Parry M A, et al.2007. Asparagine in plants[J]. Annals of Applied Biology, 150(1): 1-26. [15] Li G, Zhang Y, Xu J, et al.2025a. Nitrogen uptake and carbon-nitrogen synergistic translocation improve yield and nitrogen use efficiency in the dep1 rice line[J]. Journal of Integrative Agriculture, 24(12): 4787-4809. [16] Li X Y, Li X L, Zhu S S, et al.2025b. Characterization of a wheat mutant line 1813WH presenting increased seed dormancy and longevity, and reduced pre-harvest sprouting[J]. BMC Plant Biology, 25(1): 1563. [17] Linkies A, Leubner-Metzger G.2012. Beyond gibberellins and abscisic acid: How ethylene and jasmonates control seed germination[J]. Plant Cell Reports, 31(2): 253-270. [18] Liu H, Gao X, Fan W, et al.2025a. Optimizing carbon and nitrogen metabolism in plants: From fundamental principles to practical applications[J]. Journal of Integrative Plant Biology, 67(6): 1447-1466. [19] Liu Q, Liu H, Sun L, et al.2025b. Precise control of chromatin loop extrusion enhances sustainable green revolution yield in rice[J]. Nature Genetics, 57(11): 2798-2807. [20] Liu Y, Duan X, Zhao X, et al.2021. Diverse nitrogen signals activate convergent ROP2-TOR signaling in Arabidopsis[J]. Developmental Cell, 56(9): 1283-1295. [21] Livak K J, Schmittgen T D.2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method[J]. Methods, 25(4): 402-408. [22] Love M I, Huber W, Anders S.2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2[J]. Genome Biology, 15(12): 550. [23] Martin R C, Mok M C, Mok D W.1999. Isolation of a cytokinin gene, ZOG1, encoding zeatin O-glucosyltransferase from Phaseolus lunatus[J]. Proceedings of the National Academy of Sciences of the USA, 96(1): 284-289. [24] Men Y, Wei P, Zhang F, et al.2025. Spermidine improves seed viability in Allium mongolicum by regulating AmCS-mediated metabolic and antioxidant networks[J]. Frontiers in Plant Science, 16: 1683362. [25] Nishizawa-Yokoi A, Yabuta Y, Shigeoka S.2008. The contribution of carbohydrates including raffinose family oligosaccharides and sugar alcohols to protection of plant cells from oxidative damage[J]. Plant Signaling & Behavior, 3(11): 1016-1018. [26] Oracz K, Stawska M.2016. Cellular recycling of proteins in seed dormancy alleviation and germination[J]. Frontiers in Plant Science, 7: 1128. [27] Pulletikurti S, Yadav M, Springsteen G, et al.2022. Prebiotic synthesis of α-amino acids and orotate from α-ketoacids potentiates transition to extant metabolic pathways[J]. Nature Chemistry, 14(10): 1142-1150. [28] Rosental L, Nonogaki H, Fait A.2014. Activation and regulation of primary metabolism during seed germination[J]. Seed Science Research, 24(1): 1-15. [29] Sohn S I, Pandian S, Kumar T S, et al.2021. Seed dormancy and pre-harvest sprouting in rice-an updated overview[J]. International Journal of Molecular Sciences, 22(21): 11804. [30] Tarkowski ŁP, Van den Ende W.2015. Cold tolerance triggered by soluble sugars: A multifaceted countermeasure[J]. Frontiers in Plant Science, 6: 203. [31] Tuma T T, Nyamdari B, Hsieh C, et al.2024. Perturbation of tonoplast sucrose transport alters carbohydrate utilization for seasonal growth and defense metabolism in coppiced poplar[J]. Tree Physiology, 44(7): tpae061. [32] Varet H, Brillet-Guéguen L, Coppée J Y, et al.2016. SARTools: A DESeq2- and EdgeR-based R pipeline for comprehensive differential analysis of RNA-Seq data[J]. Public Library of Science ONE, 11(6): e0157022. [33] Wang J, Ma X M, Kojima M, et al.2013. Glucosyltransferase UGT76C1 finely modulates cytokinin responses via cytokinin N-glucosylation in Arabidopsis thaliana[J]. Plant Physiology and Biochemistry, 65: 9-16. [34] Wang Y P, Li L, Ye T T, et al.2011. Cytokinin antagonizes ABA suppression to seed germination of Arabidopsis by downregulating ABI5 expression[J]. The Plant Journal, 68(2): 249-261. [35] Whillier S, Garcia B, Chapman B E, et al.2011. Glutamine and α-ketoglutarate as glutamate sources for glutathione synthesis in human erythrocytes[J]. The FEBS Journal, 278(17): 3152-3163. [36] Wu X, Cheng R, Xue S, et al.2013. Precise mapping of a quantitative trait locus interval for spike length and grain weight in bread wheat(Triticum aestivum L.)[J]. Molecular Breeding, 33: 129-138. [37] Yao Y Y, Guo W L, Gou J Y, et al.2025. Wheat2035: Integrating pan-omics and advanced biotechnology for future wheat design[J]. Molecular Plant, 18(2): 272-297.
