Geng Shiwei, Gao Wenju, Sun Fenglei, Yang Ni, Ma Teng, Wang Tingwei, Wang Bingyue, Wang Junhao, Qian Shuaishuai, Li Shengmei, Zhao Jieyin
Xinjiang Cotton Technology Innovation Center/Xinjiang Key Laboratory of Cotton Genetic Improvement and Intelligent Production/National Cotton Engineering Technology Research Center, Cotton Research Institute of Xinjiang Uyghur Autonomous Region Academy of Agricultural Sciences, Wulumuqi, Xinjiang, China.
National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang, China.
Front Plant Sci. 2025 Jun 3;16:1604606. doi: 10.3389/fpls.2025.1604606. eCollection 2025.
Cotton, one of the most important economic crops worldwide, has long been bred mainly for improvements in yield and quality, with relatively little focus on salt-alkali resistance.
In this study, transcriptomic and metabolomic sequencing were performed on exposed to alkaline stress for different durations.
The results of sample clustering, principal component analysis (PCA), and the number of differentially expressed genes (DEGs) revealed that 12 hours and 24 hours were the periods during which upland cotton presented the strongest response to salt stress, with flavonoid biosynthesis and alpha-linolenic acid metabolism playing significant roles during this time. A total of 6,610 DEGs were identified via comparison to the 0 h time point, including 579 transcription factors (TFs) that were significantly enriched in pathways such as flavonoid biosynthesis, the cell cycle, the cytochrome P450 pathway, phenylalanine metabolism, phototransduction, and alpha-linolenic acid metabolism. Through ultrahigh-performance liquid chromatography-MS (UPLC-MS), 4,225 metabolites were identified, and 1,684 differentially accumulated metabolites (DAMs) were identified by comparison to the levels at 0 h. A joint analysis of RNA-seq and metabolomic data revealed that the flavonoid biosynthesis and alpha-linolenic acid metabolism pathways play key roles in the response of to alkaline stress, and the key genes in these pathways were identified. The weighted gene correlation network analysis (WGCNA) revealed 15 candidate genes associated with alkali tolerance in cotton, including 4 TFs and 4 genes related to flavonoid and anthocyanin biosynthesis.
In conclusion, our study provides a theoretical foundation for understanding the molecular mechanisms underlying alkali tolerance in cotton and offers new gene resources for future research.
棉花是全球最重要的经济作物之一，长期以来主要致力于提高产量和品质，而对耐盐碱能力的关注相对较少。
本研究对暴露于碱性胁迫不同时长的棉花进行了转录组和代谢组测序。
样本聚类、主成分分析（PCA）以及差异表达基因（DEG）数量的结果表明，12小时和24小时是陆地棉对盐胁迫反应最强的时期，在此期间黄酮类生物合成和α-亚麻酸代谢发挥了重要作用。与0小时时间点相比，共鉴定出6610个DEG，其中包括579个转录因子（TF），这些转录因子在黄酮类生物合成、细胞周期、细胞色素P450途径、苯丙氨酸代谢、光转导和α-亚麻酸代谢等途径中显著富集。通过超高效液相色谱-质谱联用仪（UPLC-MS）鉴定出4225种代谢物，并与0小时的水平相比，鉴定出1684种差异积累代谢物（DAM）。RNA测序和代谢组数据的联合分析表明，黄酮类生物合成和α-亚麻酸代谢途径在棉花对碱性胁迫的反应中起关键作用，并鉴定出了这些途径中的关键基因。加权基因共表达网络分析（WGCNA）揭示了15个与棉花耐碱性相关的候选基因，包括4个TF和4个与黄酮类和花青素生物合成相关的基因。
总之，我们的研究为理解棉花耐碱性的分子机制提供了理论基础，并为未来的研究提供了新的基因资源。
