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

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.