Panicle traits are important factors affecting yield, and their improvement has long been a critical goal in foxtail millet breeding. In order to understand the genetic basis of panicle formation, a large-scale genome-wide association study (GWAS) was performed in this study for six panicle-related traits based on 706,646 high-polymorphism SNP loci in 407 accessions. As a result, 87 quantitative trait loci (QTL) regions with a physical distance of less than 100 kb were detected to be associated with these traits in three environments. Among them, 27 core regions were stably detected in at least two environments. Based on rice–foxtail millet homologous comparison, expression, and haplotype analysis, 27 high-confidence candidate genes in the QTL regions, such as Si3g11200 (OsDER1), Si1g27910 (OsMADS6), Si7g27560 (GS5), etc., affected panicle-related traits by involving multiple plant growth regulator pathways, a photoperiod response, as well as panicle and grain development. Most of these genes showed multiple effects on different panicle-related traits, such as Si3g11200 affecting all six traits. In summary, this study clarified a strategy based on the integration of GWAS, a homologous comparison, and haplotype analysis to discover the genomic regions and candidate genes for important traits in foxtail millet. The detected QTL regions and candidate genes could be further used for gene clone and marker-assisted selection in foxtail millet breeding.

The excessive content of heavy metals and the deficiency of beneficial trace elements in cereals have threatened global food security and human health. As important metal transporters, Natural resistance-associated macrophage proteins (Nramps) are involved in the absorption and transport of various metal ions in plants, including beneficial elements and hazardous heavy metals, yet little is known about their roles in foxtail millet. In this study, 12 Nramps were identified in foxtail millet genome and divided into three clades. Expansion and functional differentiation of SiNramp gene family is evident in the high proportion of gene duplication as well as the diversity in protein structure and expression characteristics. The SiNramp genes exhibited different response patterns to Cd stress in different tissues. Based on the integration of ionome, RNA-seq and orthologous analysis, the association of SiNramp genes with the accumulation of different metal ions was investigated, and the possible functions of several SiNramp genes were predicted, such as SiNramp6 and SiNramp12. In general, this study provides a comprehensive theoretical framework for the study of Nramp genes in foxtail millet and other minor gramineous crops, which will lay a foundation for further research on the mechanism of metal transport and accumulation.

Essential mineral elements such as zinc and iron play a crucial role in maintaining crop growth and development, as well as ensuring human health. Foxtail millet is an ancient food crop rich in mineral elements and constitutes an important dietary supplement for nutrient-deficient populations. The ZIP (ZRT, IRT-like protein) transporters are primarily responsible for the absorption, transportation and accumulation of Zn, Fe and other metal ions in plants. Here, we identified 14 ZIP transporters in foxtail millet (SiZIP) and systematically characterized their phylogenetic relationships, expression characteristics, sequence variations, and responses to various abiotic stresses. As a result, SiZIPs display rich spatiotemporal expression characteristics in foxtail millet. Multiple SiZIPs demonstrated significant responses to Fe, Cd, Na, and K metal ions, as well as drought and cold stresses. Based on homologous comparisons, expression characteristics and previous studies, the functions of SiZIPs were predicted as being classified into several categories: absorption/efflux, transport/distribution and accumulation of metal ions. Simultaneously, a schematic diagram of SiZIP was drawn. In general, SiZIPs have diverse functions and extensively involve in the transport of metal ions and osmotic regulation under abiotic stresses. This work provides a fundamental framework for the transport and accumulation of mineral elements and will facilitate the quality improvement of foxtail millet.

Global climate change, which includes drought, extreme temperatures, and adverse soil conditions such as salinity and heavy metal pollution, has had a profound impact on crop yields and quality, thereby posing a substantial threat to global food security Notwithstanding the fact that a multitude of strategies and significant genes involved in plants' responses to abiotic stress have been reported in both model and non-model plants through the application of these advanced techniques, thereby augmenting our comprehension of the mechanisms underlying the abiotic stress tolerance of major crops, there still exist lacunae in knowledge. We instituted the research topic "Advances in crop breeding for abiotic stress tolerance" with the objective of bridging these gaps. Analyzing the responses of various crops to abiotic stress, especially identifying the relatively conserved metabolic pathways or important homologous genes in different species, is of crucial importance for the improvement of stress resistance breeding in important crops. In this research topic, the U-box, Dof, Di19, bZIP, and LLRLK gene families have been identified as potentially involved in the response process of crops to abiotic stress in different species. Multiple pathways related to transcriptional regulation, hormone regulation, energy metabolism, and secondary metabolite synthesis have also been found to be closely associated with abiotic stress. The interactions among these pathways/genes may be crosstalk, synergistic, or antagonistic, all of which have a certain impact on the abiotic stress resistance of crops. In the future, more advanced technologies and analytical strategies need to be further utilized to gain a deeper understanding of the molecular responses of crops to abiotic stress and ultimately promote the breeding improvement of crop stress resistance.

Foxtail millet is a plant that is highly drought-resistant and rich in nutrients. Its grain structure traits are linked with water uptake during grain germination, which is closely related to plant density for high yield under rain fed regions; however, there is no related research. Using Micro-CT technology, we investigated a total of 15 internal structure traits of foxtail millet grains, such as the volume and surface area of the embryo, endosperm, cavity, hull, and whole grain, and mapped relevant quantitative trait loci (QTLs) using recombination inbred lines (RILs). With phenotypic variations in these traits and genome sequences of 100 foxtail millet RILs, four QTLs were identified. In combination with transcriptome profiling during grain development, we identified seven candidate genes that may play a role in the regulation of grain structure in foxtail millet.