Drought caused by extreme climate change has become more severe and unpredictable, causing imperceptible effects on leaf photosynthesis in foxtail millet. To investigate the damage, we performed light drought (LD) and heavy drought (HD) treatments at both the elongation (Y) and booting stages to obtain a comprehensive understanding of the morphological, anatomical, physiological, transcriptome, and metabolome levels. Under drought stress, the length and area of leaves decreased, especially during the HD treatment at the booting stage. The number of mesophyll cells and the area of large vascular bundles decreased under LD and HD treatments at the booting stage, with more blurring vascular bundle structure and Kranz anatomy. However, these numbers decreased with no significance under Y-LD and Y-HD treatments at the elongation stage. The net photosynthetic rate, stomatal conductivity, transpiration rate, and intercellular CO₂ concentration significantly decreased at the booting stage. In addition, the efficiency of electron transfers in photosystem II (PSII) decreased. Conjunction analyses of the transcriptome and metabolome were utilized to uncover the underlying mechanism at the booting stage. The results showed no common differentially enriched pathway in the transcriptome and metabolome under LD treatment. However, 32 pathways were enriched in both the transcript and metabolome under HD treatment. Among these, three pathways, including arginine and proline metabolism, tyrosine metabolism, and ubiquinone, along with other terpenoid-quinone biosynthesis pathways, were differentially enriched in both the transcript and metabolome. The accumulation of homogentisate, salidroside, homoprotocatechuate, L-DOPA, tyramine, and L-tyrosine increased under drought stress. Although genes related to PSII and the Calvin cycle were slightly up-regulated under LD conditions, they were down-regulated under HD conditions. The metabolites of ribose-5P, glycerate-3P, D-fructose-1, 6P₂, and D-fructose-6P were all decreased in both the LD and HD treatments, especially D-fructose-6P, confirming that drought stress harmed the Calvin cycle. The results revealed that regardless of the severity of drought, the photosynthetic function was compromised not only at the morphological and anatomical levels but also in terms of impaired ATP synthase and inhibited photosynthetic CO₂ assimilation.

Salt stress is a major constraint to crop productivity and quality. The limited availability of salt-tolerant genes poses significant challenges to breeding programs aimed at enhancing salt tolerance. Sorghum displays a remarkable ability to withstand saline conditions; therefore, elucidating the genetic underpinnings of this trait is crucial. This study entailed a comprehensive resequencing of 186 sorghum accessions to perform a genome-wide association study (GWAS) focusing on relative root length (RL) and root fresh weight (RFW) under salt stress conditions. We identified eight candidate genes within a co-localized region, among which SbTEF1 - a gene encoding a transcription elongation factor protein - was deemed a potential candidate due to its annotation and expression pattern alterations under salt stress. Haplotype analysis, gene cloning, linkage disequilibrium (LD) analysis, and allele effect analysis revealed that PAV284, located in the promoter region of SbTEF1, modulated gene expression under salt stress, which, in turn, influenced sorghum seedlings’ salt tolerance. PAV284 holds promise as a genetic marker for selecting salt-tolerant germplasm via marker-assisted breeding, enhancing the development of salt-tolerant sorghum cultivars.