Multi-omics analysis provides preliminary insights into the mechanisms involved in dormancy and germination in asparagus (Asparagus officinalis)

IF 4.2 2区农林科学 Q1 HORTICULTURE

Scientia Horticulturae Pub Date : 2025-08-01 DOI:10.1016/j.scienta.2025.114363

Yinchao Zhang , Yuzhen Sheng , Jia Lai , Yong Liu , Qianfang Zhang , Jia Liu , Xiaoli Shi , Haitao Huang , Peng sheng Ye , Shugu Wei , Ling Huang

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引用次数: 0

Abstract

Dormancy and germination are critical physiological processes in asparagus (Asparagus officinalis) bud development, yet their molecular regulatory networks remain poorly understood. Here, we integrated transcriptomic and metabolomic analyses to characterize gene expression and metabolic dynamics during these stages. Principal component analysis (PCA) of 12 samples revealed distinct clustering of three biological replicates for dormancy and germination. Transcriptome analysis identified 2510 common differentially expressed genes (DEGs) during dormancy release and sprouting in asparagus rhizomes. Among these, 92 transcription factors (TFs) were significantly regulated, dominated by ZF-HD (19 members), MYB (18), and WRKY (13). Gene ontology analysis (GO) enrichment highlighted microtubule-based processes, carbohydrate metabolism, and photosynthesis, while kyoto encyclopedia of genes and genomes (KEGG) analysis revealed significant pathways in phenylpropanoid biosynthesis and starch/sucrose metabolism. Metabolomic profiling detected 331 (GS vs DS) and 173 (GR vs DR) differential metabolites, with 93 shared metabolites. Integrative analysis via Procrustes (M² = 0.1828, p-value = 0.001) and O2PLS identified four key candidate genes (AoAHG1, AoGA3ox2, AoHB13, AoPRH132) linking transcriptional and metabolic regulation. These findings unravel potential molecular mechanisms underlying dormancy regulation and germination activation, highlighting TF-hormone-signaling crosstalk and key metabolites in asparagus bud development. We also identified two common KEGG pathways in the transcriptome and metabolome, flavonoid biosynthesis (ko00941) and starch/sucrose metabolism (ko00500), suggesting that these two pathways play important roles in dormancy and germination. This study provides a comprehensive framework for dissecting the regulatory networks governing perennial plant dormancy and sprouting, offering targets for agricultural optimization of asparagus production.

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多组学分析为芦笋（asparagus officinalis）休眠和萌发机制提供了初步见解。

休眠和萌发是芦笋芽发育的关键生理过程，但其分子调控网络尚不清楚。在这里，我们整合了转录组学和代谢组学分析来表征这些阶段的基因表达和代谢动力学。主成分分析（PCA）表明，12个样品在休眠和萌发过程中存在3个不同的生物重复。转录组分析鉴定了2510个芦笋根茎休眠释放和发芽过程中的共同差异表达基因（deg）。其中，有92个转录因子（TFs）受到显著调控，以ZF-HD（19个成员）、MYB（18个成员）和WRKY（13个成员）为主。基因本体分析（GO）强调了基于微管的过程、碳水化合物代谢和光合作用，而京都基因和基因组百科全书（KEGG）分析揭示了苯丙类生物合成和淀粉/蔗糖代谢的重要途径。代谢组学分析检测到331种（GS vs DS）和173种（GR vs DR）差异代谢物，93种共享代谢物。通过Procrustes （M²= 0.1828，p值= 0.001）和O2PLS进行整合分析，鉴定出4个关键候选基因（AoAHG1, AoGA3ox2, AoHB13, AoPRH132）与转录和代谢调控相关。这些发现揭示了休眠调节和发芽激活的潜在分子机制，突出了芦笋芽发育中tf -激素信号串扰和关键代谢物。我们还在转录组和代谢组中发现了两个常见的KEGG通路，类黄酮生物合成（ko00941）和淀粉/蔗糖代谢（ko00500），表明这两个通路在休眠和萌发中起重要作用。该研究为剖析多年生植物休眠和发芽的调控网络提供了一个全面的框架，为芦笋生产的农业优化提供了目标。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Scientia Horticulturae 农林科学-园艺

CiteScore

8.60

自引率

4.70%

发文量

796

审稿时长

47 days

期刊介绍： Scientia Horticulturae is an international journal publishing research related to horticultural crops. Articles in the journal deal with open or protected production of vegetables, fruits, edible fungi and ornamentals under temperate, subtropical and tropical conditions. Papers in related areas (biochemistry, micropropagation, soil science, plant breeding, plant physiology, phytopathology, etc.) are considered, if they contain information of direct significance to horticulture. Papers on the technical aspects of horticulture (engineering, crop processing, storage, transport etc.) are accepted for publication only if they relate directly to the living product. In the case of plantation crops, those yielding a product that may be used fresh (e.g. tropical vegetables, citrus, bananas, and other fruits) will be considered, while those papers describing the processing of the product (e.g. rubber, tobacco, and quinine) will not. The scope of the journal includes all horticultural crops but does not include speciality crops such as, medicinal crops or forestry crops, such as bamboo. Basic molecular studies without any direct application in horticulture will not be considered for this journal.