Comparative transcriptomics of atrazine-tolerant and sensitive alfalfa varieties under atrazine stress.

BACKGROUND: Alfalfa (Medicago sativa L.) is a vital forage crop with substantial economic and ecological significance in agriculture and animal husbandry. However, atrazine, a widely used herbicide, negatively impacts the growth and yield of alfalfa due to its residual presence in the environment. Transcriptomic analysis was performed to investigate the differences in tolerance and uncover the potential molecular regulatory mechanisms between the tolerant variety JN5010 and the sensitive variety WL363 when subjected to atrazine stress, using RNA-seq on pooled samples. RESULTS: Based on the analysis of gene expression profiles, significant differences were observed between the tolerant variety JN5010 and the sensitive variety WL363 under atrazine stress: 2,297 upregulated and 3,167 downregulated in the shoot parts, and 3,232 upregulated and 4,907 downregulated in the roots of JN5010. In WL363, 2,937 genes were upregulated and 4,237 genes were downregulated in the shoot parts, while 5,316 genes were upregulated and 7,977 genes were downregulated in the roots. The DEGs in the shoot parts were mainly involved in biological regulation, metabolic processes, and cellular processes, including proline metabolic processes and S-adenosylmethionine cycle. The DEGs in the roots were predominantly associated with nitric oxide synthesis and metabolism, as well as processes related to cell wall biosynthesis and degradation. In the shoot parts of JN5010, six DEGs were mapped onto the proline metabolic pathway, including four upregulated genes involved in proline biosynthesis and two downregulated genes involved in proline catabolism. In the roots of WL363, eleven DEGs were mapped onto the phenylpropanoid biosynthesis pathway, including seven upregulated genes involved in flavonoid biosynthesis and four downregulated genes associated with lignin biosynthesis. These findings highlight the distinct genetic responses of the two alfalfa varieties to atrazine stress, with JN5010 exhibiting more consistent gene expression patterns compared to the sensitive variety WL363. CONCLUSIONS: The tolerant variety JN5010 shows improved tolerance to atrazine stress by maintaining stable gene expression and precise regulation in various pathways, such as antioxidant processes, signaling, photosynthesis, and toxin removal. This differential gene expression helps JN5010 maintain stability in its functions under stress, demonstrating better adaptability. These findings enhance our understanding of how alfalfa tolerates atrazine stress and provide important insights for developing atrazine-tolerant varieties.