Integrated miRNAome and transcriptome analysis validates the role of the vvi-miR395a– VvExpA10 module in saline-alkali stress tolerance of grape

Abstract

Soil salinization restricts agricultural production. Identifying key regulatory genes and molecular mechanisms underlying saline-alkali stress is crucial for developing tolerant crops. In this study, the grapevine cultivars ‘Hotan Red’ (HTR) and ‘Yongyou No. 1’ (YY), which differ in saline-alkali tolerance, were used for physiological, microRNA, and transcriptomic analyses. HTR accumulated more osmotic regulatory substances and maintained relatively intact chloroplast structures, exhibiting stress resistance superior to YY. Fourier transform infrared (FTIR) analysis revealed that saline-alkali treatment did not alter the basic composition of functional groups in the leaf cell wall, but affected their relative contents. 26 miRNAs notably responsive to saline-alkali stress were identified. In HTR, vvi-miR395a expression was significantly downregulated under the saline-alkali stress, whereas the repression of vvi-miR395a in YY was less pronounced. RLM-5′RACE and GUS histochemical staining indicated that vvi-miR395a directly targets VvExpA10. Overexpression of vvi-miR395a suppressed VvExpA10 expression and reduced pectin and cellulose contents in grape calli and roots, but increased malondialdehyde contents. Simultaneous overexpression of VvExpA10-OE and STTM395a in transgenic calli led to significant enhancement of saline-alkali tolerance. These findings indicate that suppression of vvi-miR395a impaired its targeted cleavage of VvExpA10, thereby enhancing the levels of cell wall components and significantly improving grapevine tolerance to saline-alkali stress. This study validated the regulatory effect of the vvi-miR395a-VvExpA10 module in grapevine response to saline-alkali stress, offering potential targets used for the genetic improvement of grape with enhanced tolerance to saline-alkali stress.