Guojun Feng

Drought limits the stability of foxtail millet production and the efficient use of germplasm resources, yet whether drought-tolerant and drought-sensitive accessions engage fundamentally distinct pathways or a shared, quantitatively reprogrammed network remains unclear. We generated 36 leaf transcriptomes from three drought-sensitive (DSEN) and three drought-tolerant (DTOL) accessions under well-watered (WW) and drought-stress (DS) conditions, retaining 25,099 genes for downstream analyses. Principal component analysis confirmed water treatment as the primary driver of global expression variation. DS-versus-WW comparisons identified 10,635 and 6215 drought-responsive DEGs in the DSEN and DTOL groups, respectively, with 5195 shared and a genome-wide response correlation of 0.791. Crucially, accession-level tests revealed no significant DEGs between groups under WW, only 22 under DS, and none for the group × drought-response interaction, underscoring the absence of qualitative pathway shifts. Functional enrichment analyses jointly indicated suppression of photosynthesis and translation, accompanied by reprogramming of carbohydrate metabolism, membrane lipid remodeling, phenylpropanoid and secondary metabolism, protein homeostasis, and stress signaling. WGCNA partitioned 10,000 highly variable genes into 16 modules. The blue module, which showed the strongest drought response in DSEN, was enriched for cell-wall and carbohydrate metabolism, membrane lipid processes, and stress-protection pathways, whereas the brown module, which responded most robustly in DTOL, was enriched for calcium signaling, protein phosphorylation/dephosphorylation, transcriptional regulation, proline biosynthesis, and dehydration protection. The yellow and cyan modules exhibited the largest between-group effect sizes under drought but failed multiple-testing correction, remaining candidate networks. Collectively, our results support a model of shared core response with divergent regulatory intensity, where sensitive accessions undergo broader transcriptional perturbation, while tolerant ones deploy more concentrated and coordinated modules. This study provides modular targets for drought-tolerance breeding and highlights the necessity of accession-level replication and conservative statistical inference in comparative transcriptomics.

Abiotic stresses caused by climate change pose a significant challenge to global food security, making it necessary to develop stress-resistant crops. Foxtail millet (Setaria italica (L.) P. Beauv.) is a drought-tolerant C₄ cereal and serves as a model crop for elucidating stress adaptation mechanisms and promoting climate-resilient agricultural solutions. This paper reviews the tolerance mechanisms of foxtail millet to abiotic stresses. Physiologically, the species exhibits excellent water-use efficiency, requiring 75% less irrigation than traditional cereals, achieved through enhanced osmotic adjustment via soluble substance accumulation and the maintenance of ion homeostasis. Morphological adaptations include reduced leaf area, adjusted stomatal density, well-developed root systems, and specialized anatomical features that optimize water conservation. At the molecular level, stress tolerance involves complex transcriptional networks mediated by multiple transcription factor family members, including those (NF-Y, DREB, NAC, WRKY, MYB) that coordinate stress-responsive gene expression, antioxidant defense systems, and osmotic adjustment pathways. Furthermore, this review summarizes multi-omics characteristics, including genomics (such as QTL mapping and GWAS), proteomics, transcriptomics, metabolomics, and regulatory networks, for foxtail millet under abiotic stress tolerance. Additionally, reproductive resilience is maintained through efficient mobilization of stem reserves to panicles, phenological plasticity in flowering timing, and preserved gametic viability under thermal stress. Combining advanced molecular breeding with the inherent tolerance of foxtail millet positions this crop as both a solution to climate change and a genetic resource for enhancing the stress resistance of other cereals. These findings establish foxtail millet as a valuable model for developing sustainable agricultural technologies essential for food security under projected climate scenarios.

A significant number of crop species and their associated agricultural landscapes are impacted by soil salinity, which severely hampers germination and seedling establishment. Developing salt-tolerant germplasm and improving screening methods are critical priorities for plant breeding programs. This study used sorghum as a model to evaluate germination and early growth responses in 100 accessions under control and 150 mM NaCl conditions. Multiple indices were used to develop a numeric salt tolerance score (STS), minimizing baseline growth effects to better reflect true stress responses. Multivariate approaches, including PCA, cluster analysis, and machine learning, were employed to assess salt tolerance. Salt stress significantly reduced germination traits such as germination index, rate, and vigor. The STS proved effective in ranking accessions for salt tolerance. Salt-tolerant accession showed upregulation of ion transport and homeostasis genes ( SbNHXLP , SbHKT1;4 , SbHKT1;5 , and SbCLCc ), and downregulation of certain transcription factors. Physiological analyses revealed lower sodium accumulation, higher K+/Na+ ratios, and enhanced antioxidant and osmotic regulation in tolerant accessions. These findings suggest that coordinated ion homeostasis and stress responses are likely determinants of salt tolerance during germination. This integrated screening system offers a valuable tool for early-stage breeding of salt-tolerant sorghum.

Drought is the primary factor contributing to crop yield loss. Therefore, enhancing the drought tolerance of foxtail millet, a globally significant food crop, is essential for ensuring global food security. We analyzed 425 foxtail millet samples from the Xinjiang Academy of Agricultural Sciences using 1,304,248 highly polymorphic SNPs for a genome-wide association study, and a total of 77 QTL regions were detected across three environments. Linkage disequilibrium (LD) analysis, population genetic structure analysis, K-means clustering, and phylogenetic tree construction revealed that foxtail millet in different subgroups exhibited certain regional differences. The secondary screening of QTL region genes combined with transcriptome analysis identified six genes with significant expression differences. These drought-responsive genes in foxtail millet function as protein kinases, glycosyltransferases, CTP synthetases, and transcription factors. Haplotype analysis identified 8 phenotypically distinct haplotypes in candidate genes associated with drought stress. Expression levels of genes associated with drought tolerance and yield, validated by RT-qPCR, were largely consistent with transcriptome analysis results. This study’s results offer a scientifically significant reference for genetic research and improvement in foxtail millet yield under drought stress.

Drought stress critically constrains agricultural productivity in arid and semi-arid regions, necessitating the development of drought-tolerant crop varieties for sustainable food security. This study evaluated drought tolerance in 222 foxtail millet (Setaria italica) germplasms from diverse Chinese agroecological zones from 2021–2023 at a specialized identification site in Xinjiang. Field experiments used a randomized complete block design comparing normal irrigation (3000 m³/ha) with drought stress (1800 m³/ha) across 12 morpho-agronomic traits including plant height, spike characteristics, biomass, and yield components. Drought stress significantly reduced all parameters, with yield exhibiting the highest sensitivity (drought tolerance coefficient = 0.58). Principal component analysis indicated that the first three components explained 82.70% of phenotypic variance, with yield-related parameters contributing the most to genotypic differentiation. Integrated evaluation using comprehensive drought tolerance coefficient (DTC), drought resistance index (DRI), and D-values classified germplasms into five categories: highly resistant (4.50%), resistant (11.71%), moderately resistant (57.21%), sensitive (16.22%), and highly sensitive (10.36%). Correlation and stepwise regression analyses identified five critical indicators: stem basal thickness, single plant biomass, spike weight, grain weight per spike, and yield. The predictive model demonstrated exceptional accuracy (R² = 0.9998), enabling efficient screening using the targeted traits. The elite germplasms T125 (92) and Baogu 23 (135) consistently ranked as the most drought-tolerant across all methods. These findings establish a robust methodological framework for evaluating drought tolerance in foxtail millet and provide practical selection criteria for developing climate-resilient cultivars. The identified germplasms and evaluation indices significantly contribute to agricultural sustainability in water-limited environments, supporting food security in regions that are increasingly affected by climate-induced drought stress.