Multi-omics integrative analysis provided new insights into alkaline stress in alfalfa.

Saline-alkali stress is one of the main abiotic stresses that limits plant growth. Salt stress has been widely studied, but alkaline salt degradation caused by NaHCO 3 has rarely been investigated. In the present study, the alfalfa cultivar 'Zhongmu No. 1′ was treated with 50 mM NaHCO 3 (0, 4, 8, 12 and 24 h) to study the resulting enzyme activity and changes in mRNA, miRNA and metabolites in the roots. The results showed that the enzyme activity changed significantly after alkali stress treatment. The genomic analysis revealed 14,970 differentially expressed mRNAs (DEMs), 53 differentially expressed miRNAs (DEMis), and 463 differentially accumulated metabolites (DAMs). Combined analysis of DEMs and DEMis revealed that 21 DEMis negatively regulated 42 DEMs. In addition, when combined with Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of DEMs and DAMs, we found that phenylpropanoid biosynthesis, flavonoid biosynthesis, starch and sucrose metabolism and plant hormone signal transduction played important roles in the alkali stress response. The results of this study further elucidated the regulatory mechanism underlying the plant response to alkali stress and provided valuable information for the breeding of new saline-alkaline tolerance plant varieties. [Display omitted] • Integrate transcriptome and metabolomics to analyse the alkaline stress of alfalfa. • Candidate genes, miRNAs and metabolites in response to alkaline stress in alfalfa were identified. • Alfalfa response to alkali is related to abscisic acid, ethylene, jasmonic acid and auxin signal transduction pathways. • Flavonoid synthesis was found to be associated with alkaline stress in alfalfa. • Five new miRNAs were identified, which could respond to alkaline stress. [ABSTRACT FROM AUTHOR]