Gene Co-Expression Analysis Reveals the Transcriptome Changes and Hub Genes of Fructan Metabolism in Garlic under Drought Stress

Abstract

Drought has become a serious environmental factor that affects the growth and yield of plants. Fructan, as an important storage compound in garlic, plays an important role in drought tolerance. Genomic changes in plants under drought stress clarify the molecular mechanism of plants’ responses to stress. Therefore, we used RNA-seq to determine the transcriptomic changes in garlic under drought stress and identified the key module related to fructan metabolism by weighted gene co-expression network analysis. We conducted a comprehensive analysis of the garlic transcriptome under drought stress over a time course (0, 3, 6, 9, 12, 15 d). Drought significantly induces changes in gene expression. The number of specifically expressed genes were 1430 (3 d), 399 (6 d), 313 (9 d), 351 (12 d), and 1882 (15 d), and only 114 genes responded at each time point. The number of upregulated DEGs was higher than the number of downregulated DEGs. Gene ontology and a Kyoto Encyclopedia of Genes and Genomes analysis showed that garlic was more likely to cause changes in carbohydrate metabolism pathways under drought stress. Fructan content measurements showed that drought stress significantly induced fructan accumulation in garlic. To determine whether there were modules involved in the transcriptional regulation of fructan content in garlic, we further analyzed the genes related to fructan metabolism using WGCNA. They were enriched in two modules, with F-box protein and GADPH as hub genes, which are involved in garlic fructan metabolism in response to drought stress. These results provide important insights for the future research and cultivation of drought-tolerant garlic varieties.

Garlic (Allium sativum L.) Invertase Genes: Genome-Wide Identification and Expression in Response to Abiotic Stresses and Phytohormones

“…Protection from stress-related effects is facilitated by changes in the content of hexoses through hydrolysis of sucrose by all invertases and fructans by acid invertases and FEHs [14,15]. Consistent with these data, transcriptomic analyses indicate that the adaptive response of garlic under salt stress includes regulation of sucrose metabolism [27,28] and that fructans, which along with sucrose are important storage sugars, can stimulate garlic resistance to low temperatures [26] and drought [29].…”

“…Garlic (Allium sativum L.) is a popular spice plant with considerable medicinal properties due to the presence of a large number of biologically active compounds with beneficial health effects [21]; it is also used to improve soil quality through intercropping and crop rotation [22]. Garlic is cultivated all over the world, which, given its non-sexual reproduction, suggests high adaptive plasticity of the genome and a well-developed stress response system [23][24][25]; it is known to be sensitive to various abiotic stresses, including low temperatures [26], soil salinity [27,28], and drought [29]. Transcriptomic and metabolomic studies have revealed that stresses affect the metabolism of sucrose and fructans, which contribute to garlic yield and quality [26][27][28][29].…”

“…Garlic is cultivated all over the world, which, given its non-sexual reproduction, suggests high adaptive plasticity of the genome and a well-developed stress response system [23][24][25]; it is known to be sensitive to various abiotic stresses, including low temperatures [26], soil salinity [27,28], and drought [29]. Transcriptomic and metabolomic studies have revealed that stresses affect the metabolism of sucrose and fructans, which contribute to garlic yield and quality [26][27][28][29]. Thus, cold exposure results in an increase in the content of fructans, the main reserve carbohydrates in Allium species, and in the upregulation of key genes controlling fructan metabolism, including FEH, which encodes fructan exohydrolase [26].…”

Promoting the Aging Process and Enhancing the Production of Antioxidant Components of Garlic through Pulsed Electric Field Treatments

“…Such conditions facilitate the accumulation of carbohydrates, particularly affecting carbohydrate metabolism pathways in garlic. A preceding study reported that garlic mitigates oxidative damage from drought stress primarily through the induction of fructan synthesis and catabolism, with noted fluctuations in fructan levels initially increasing and subsequently decreasing [ 54 ]. The degradation and synthesis of fructans are related to FEH, 1-fructosyltransferase (1-FFT), and sucrose 1-fructosyltransferase (1-SST).…”