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Grass pea has the potential to become a miracle crop if the stigma attached to it as a toxic plant is ignored. In light of the following, we conducted transcriptome analyses on the high and low ODAP-containing cultivars i.e., Nirmal and Bidhan respectively in both normal and salt stress conditions. In this study, genes that work upstream and downstream to β-ODAP have been found. Among these genes, AAO3 and ACL5 were related to ABA and polyamine biosynthesis, showing the relevance of ABA and polyamines in boosting the β-ODAP content in Nirmal. Elevated β-ODAP levels in salt stress-treated Bidhan may have evolved tolerance by positively regulating the expression of genes involved in phenylpropanoid and jasmonic acid biosynthesis. Although the concentration of β-ODAP in Bidhan increased under salt stress, it was lower than in stress-treated Nirmal. Despite this, the expression of stress-related genes that work downstream to β-ODAP was found higher in stress-treated Bidhan. This could be because stress-treated Nirmal has lower GSH, proline, and higher H 2 O 2 , resulting in the development of severe oxidative stress. Overall, our research not only identified new genes linked with β-ODAP, but also revealed the molecular mechanism by which a low β-ODAP-containing cultivar developed tolerance against salinity stress. • Bidhan is a low-β-ODAP cultivar having salinity stress tolerance. • β-ODAP production is largely regulated by genes involved in ABA and polyamine biosynthesis. • Elevated β-ODAP in stress-treated Bidhan develops tolerance by positive regulation of phenylpropanoid and jasmonic acid biosynthesis related genes. • Elevated level of GSH and proline provides salinity stress tolerance to Bidhan. [ABSTRACT FROM AUTHOR]