Broomcorn millet (Panicum miliaceum L.), known for its traits of drought resistance, adaptability to poor soil, short growth period, and high photosynthetic efficiency as a C₄ plant, represents one of the earliest domesticated crops globally. This study reports the telomere-to-telomere (T2T) gap-free reference genome for broomcorn millet (AJ8) using PacBio high-fidelity (HiFi) long reads, Oxford Nanopore long-read technologies and high-throughput chromosome conformation capture (Hi-C) sequencing data. The size of AJ8 genome was approximately 834.7 Mb, anchored onto 18 pseudo-chromosomes. Notably, 18 centromeres and 36 telomeres were obtained. The assembled genome showed high quality in terms of completeness (BUSCO score: 99.6%, QV: 61.7, LAI value: 20.4). In addition, 63,678 protein-coding genes and 433.8 Mb (~52.0%) repetitive sequences were identified. The complete reference genome for broomcorn millet provides a valuable resource for genetic studies and breeding of this important cereal crop.

Foxtail millet is a vital nutritional cereal. The de-husked grain is usually yellow and mainly contains carotenoids, which directly reflects the millet quality. In this study, the impact of ultraviolet-B(UV-B) on millet color and carotenoid content was determined using two foxtail millet varieties, HuaJinZao (HJZ) and Qinhuang 2 (QH). The b* value at different stages of grain development and the content of carotenoids (primarily lutein and zeaxanthin) in foxtail millet grains decreased when the plants were exposed to low UV-B intensity. A total of 3113 and 96 differentially expressed genes were identified in HJZ and QH, respectively, and were found to be associated with the metabolism of tryptophan, starch, and sucrose as well as the biosynthesis of amino acids, which was relatively consistent with the functional annotation of differential metabolites. Furthermore, we evaluated the changes in the expression of seven and eight genes associated with carotenoid and starch metabolism, respectively, in the kernels of foxtail millet exposed to UV-B and found that appropriate UV-B intensity could promote the expression levels of genes involved in carotenoid synthesis and repress the expression of genes involved in carotenoid degradation. This study lays a theoretical foundation for cultivating new foxtail millet varieties with high carotenoid content.

Cryptochromes (CRYs), as essential blue-light photoreceptors, play pivotal roles in modulating plant growth, development, and stress responses. Although CRY-mediated light signaling has been extensively studied in model species, their functions remain limited in wheat. In this work, a comprehensive analysis of the TaCRY gene family was performed in wheat, identifying 12 TaCRY members localized to distinct chromosomes 2, 6, and 7. TaCRYs contain the conserved PHR and CCT domains and diverse gene structures. Collinearity relationships indicated their dynamic evolution patterns during polyploidization. Cis-acting elements of TaCRY members associated with light responsiveness, phytohormone signaling, and abiotic stress were also identified. Transcriptome analysis revealed that the differential expression patterns of TaCRY members under seed vigor process. This study expands our understanding of TaCRY diversity and provides valuable molecular information for marker-assisted selection in wheat improvement.

Sucrose nonfermenting 1-related protein kinase 2 (SnRK2) proteins constitute a family of plant-specific serine/threonine kinases that play critical roles in mediating abscisic acid (ABA) signaling and responses to abiotic stresses, including drought and salinity. Nevertheless, systematic bioinformatics analysis and expression profiling of the SnRK2 gene family in broomcorn millet (Panicum miliaceum L.) have not yet been reported. A total of 16 PmSnRK2 genes were identified in the broomcorn millet genome, unevenly distributed across 12 chromosomes and phylogenetically classified into three subfamilies (I–III). Gene structure analysis revealed that the majority of PmSnRK2 genes harbor seven to eight introns. Promoter region mining uncovered abundant cis-elements responsive to hormones and abiotic stresses. Synteny analysis detected 12 PmSnRK2–PmSnRK2 paralogous pairs, with duplication events dated between ~ 1.28 and 219.36 million years ago; all Ka/Ks ratios were below 1, consistent with strong purifying selection. Multiple sequence alignment confirmed the presence of the conserved serine/threonine kinase active-site motif, the ATP-binding signature, and two characteristic C-terminal domains (I and II) across all family members. Structural superimposition of four representative PmSnRK2 proteins (PmSnRK2.6.2, PmSnRK2.11.1, PmSnRK2.13.1, PmSnRK2.15.1) onto Arabidopsis AtSnRK2.3 (PDB: 3UC3) yielded RMSD values of 0.922–1.134 Å within the kinase domain, underscoring three-dimensional conservation. Expression profiling using public RNA-seq datasets demonstrated that all 16 genes are transcribed in at least one of eight tissues, with individual members peaking in shoots, leaf blades, stems, inflorescences, roots, or seeds. Under exogenous ABA (50–100 µM), salt (100 mM NaCl), and PEG (20%) treatments, PmSnRK2 genes exhibited distinct induction and repression dynamics, revealing functional divergence in stress-response pathways. Our study provides comprehensive insights into the genomic characteristics, evolutionary patterns, and potential functional roles of the PmSnRK2 gene family in broomcorn millet. These results enhance the current understanding of how PmSnRK2 genes may contribute to abiotic stress tolerance, offering a valuable foundation for further functional validation and targeted improvement in broomcorn millet breeding programs.

The ABCB subfamily, a subset transporter of the ATP-binding cassette (ABC) superfamily, is vital for various plant life processes, especially in the transport of polar auxin and brassinosteroids. Although ABCB transporters have been characterized in diverse plant species, their specific functions in wheat remain largely unexplored. In this study, we identified 99 TaABCB members in wheat and categorized them into four groups based on their conserved domains and phylogenetic relationships. These members were found to be unevenly distributed across all 21 wheat chromosomes. We conducted a comprehensive genome-wide analysis encompassing gene structure, protein motifs, gene duplication events, collinearity, and cis-acting elements. Transcriptome analysis revealed that different TaABCB members displayed distinct expression patterns under phosphate starvation stress. Notably, we discovered that TaABCB7 might play a role in regulating wheat's phosphate starvation. Crucially, we pinpointed an elite haplotype, H001, of the candidate gene TaABCB7, which has been progressively selected and employed in wheat breeding improvement programs. Overall, this study enhances our comprehensive understanding of TaABCB members and offers a potential gene resource for molecular marker-assisted selection breeding in wheat.

Background: Carotenoids are essential phytonutrients for human health and plant adaptation. In plastids, carotenoid storage and turnover occur in plastoglobules, whose core structural components are Fibrillin (FBN) proteins. The FBN family remains uncharacterized in foxtail millet ( Setaria italica ), a nutritious C4 cereal whose grain carotenoid content strongly correlates with color. The genetic basis of carotenoid variation in foxtail millet is largely unknown. Results: We identified 12 SiFBN genes in foxtail millet, which were phylogenetically classified into 11 subfamilies. Expression analysis revealed three major patterns: constitutive ( SiFBN1b ), development-dependent ( SiFBN6 , SiFBN10 ), and differentially expressed between varieties ( SiFBN3 ). SiFBN3 was significantly upregulated in the high-carotenoid yellow-grain variety JG21 compared to JG25, though haplotype analysis in a 152-accession panel revealed no sequence polymorphism in this gene. Furthermore, a candidate-gene association analysis in a 152-accession panel identified a natural polymorphism in SiFBN10 (A/T at position 40085873) associated with carotenoid content. The T allele (Hap2, frequency 30.3%) was strongly associated with high carotenoid accumulation across two independent years, whereas the A allele (Hap1, 69.7%) linked to low content. Both SiFBN3 and SiFBN10 were experimentally confirmed to localize to chloroplasts. Conclusions: This study suggests that carotenoid accumulation in foxtail millet grains involves multiple regulatory layers. SiFBN3 shows differential expression between the yellow-grain variety JG21 and the white-grain variety JG25, though the genetic basis of this difference remains to be elucidated given the absence of sequence polymorphism in the 152-accession panel. In addition, a natural polymorphism in SiFBN10 is associated with carotenoid content variation in the natural population and may contribute to phenotypic differences among accessions.