Integrated analysis of the transcriptome and metabolome reveals the molecular mechanism regulating cotton boll abscission under low light intensity

Abstract

Background Cotton boll shedding is one of the main factors adversely affecting the cotton yield. During the cotton plant growth period, low light conditions can cause cotton bolls to fall off prematurely. In this study, we clarified the regulatory effects of low light intensity on cotton boll abscission by comprehensively analyzing the transcriptome and metabolome. Results When the fruiting branch leaves were shaded after pollination, all of the cotton bolls fell off within 5 days. Additionally, H2O2 accumulated during the formation of the abscission zone. Moreover, 10,172 differentially expressed genes (DEGs) and 81 differentially accumulated metabolites (DAMs) were identified. A KEGG pathway enrichment analysis revealed that the identified DEGs and DAMs were associated with plant hormone signal transduction and flavonoid biosynthesis pathways. The results of the transcriptome analysis suggested that the expression of ethylene (ETH) and abscisic acid (ABA) signaling-related genes was induced, which was in contrast to the decrease in the expression of most of the IAA signaling-related genes. A combined transcriptomics and metabolomics analysis revealed that flavonoids may help regulate plant organ abscission. A weighted gene co-expression network analysis detected two gene modules significantly related to abscission. The genes in these modules were mainly related to exosome, flavonoid biosynthesis, ubiquitin-mediated proteolysis, plant hormone signal transduction, photosynthesis, and cytoskeleton proteins. Furthermore, TIP1;1, UGT71C4, KMD3, TRFL6, REV, and FRA1 were identified as the hub genes in these two modules. Conclusions In this study, we elucidated the mechanisms underlying cotton boll abscission induced by shading on the basis of comprehensive transcriptomics and metabolomics analyses of the boll abscission process. The study findings have clarified the molecular basis of cotton boll abscission under low light intensity, and suggested that H2O2, phytohormone, and flavonoid have the potential to affect the shedding process of cotton bolls under low light stress.

Recent advances in exploring transcriptional regulatory landscape of crops

“…Several high-ranking causal genes identified from the GRN were validated for their functional impacts on cotton seed development (Zhao et al, 2023). (Fu et al, 2024) Cotton Biology question Oil accumulation (Ma et al, 2024) Cotton Biology question Low light intensity (Zhao et al, 2024) Cotton Biology question Seed yield (Zhao et al, 2023) Rapeseed Biology question Oleic acid content (Yao et al, 2020) Soybean Biology question Salt stress (Yang et al, 2019) Tomato Biology question Drought-responsive (Chowdhury et al, 2023) Sweet potato Biology question Chlorogenic acid biosynthesis (Xu et al, 2022a) Banana Biology question Fruit ripening (Kuang et al, 2021) Multiple species Methodology cisDynet software (Zhu et al, 2023a)…”

“…Additionally, several studies integrate a large amount of omics data, including both physical interactions and functional regulation relationships, in wheat (Chen et al, 2023;Tang et al, 2023). Similar integrated analysis has also been conducted in cotton (Zhao et al, 2024).…”