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.

Background: Ammonium nitrogen (NH₄⁺) serves as a vital nitrogen source, playing pivotal regulatory roles in plant growth, development, and high-yield formation. Ammonium transporters (AMTs), encoded by the AMT gene family, are central to NH₄⁺ transport. However, the functional roles of AMT genes in wheat remain poorly understood. Methods: A comprehensive genome-wide analysis of the TaAMT gene family numbers was conducted, encompassing investigations into gene structure, protein motif composition, gene duplication events, collinearity relationships, and cis-acting regulatory elements. Furthermore, the expression patterns of distinct TaAMT members were examined under varying ammonium supply conditions and pathogen stress. Results: In this study, a total of 21 TaAMT members were identified. Additionally, all TaAMT proteins were localized to the plasma membrane. Phylogenetic analysis clustered these genes into four distinct subgroups. Comparative analyses of gene structure and conserved motifs revealed conserved domain composition and motif organization within each subgroup. Interspecific synteny analysis highlighted evolutionary conservation across species. Promoter region analysis identified multiple cis-regulatory elements associated with hormone signaling, light responsiveness, and abiotic stress adaptation. Expression profiling demonstrated that TaAMT members exhibit both tissue-specific and constitutive expression patterns across developmental stages. RT-qPCR further revealed that the expression of TaAMT members responds to varying concentrations of ammonium nitrogen supply, as well as infection stresses caused by stripe rust and powdery mildew. Conclusions: Collectively, this study uncovered the functional diversity of TaAMT members, offering novel molecular targets and theoretical foundations for breeding wheat varieties with enhanced nitrogen use efficiency and disease resistance.

Background: Ammonium nitrogen (NH₄⁺) serves as a vital nitrogen source, playing pivotal regulatory roles in plant growth, development, and high-yield formation. Ammonium transporters (AMTs), encoded by the AMT gene family, are central to NH4+ transport. However, the functional roles of AMT genes in wheat remain poorly understood.Methods: In this study, a total of 21 TaAMT members were identified. A comprehensive genome-wide analysis was conducted, encompassing investigations into gene structure, protein motif composition, gene duplication events, collinearity relationships, and cis-acting regulatory elements. Furthermore, the expression patterns of distinct TaAMT members were examined under varying ammonium supply conditions and pathogen stress. Results: All TaAMT proteins exhibited hydrophobic characteristics and localized to the plasma membrane. Phylogenetic analysis clustered these genes into four distinct subgroups. Comparative analyses of gene structure and conserved motifs revealed conserved domain composition and motif organization within each subgroup. Interspecific synteny analysis highlighted evolutionary conservation across species. Promoter region analysis identified multiple cis-regulatory elements associated with hormone signaling, light responsiveness, and abiotic stress adaptation. Expression profiling demonstrated that TaAMT members exhibit both tissue-specific and constitutive expression patterns across developmental stages. RT-qPCR further revealed that the expression of TaAMT members responds to varying concentrations of ammonium nitrogen supply, as well as infection stresses caused by stripe rust and powdery mildew. Conclusions: Collectively, this study provides the useful molecular information into the roles of TaAMT members in nitrogen use efficiency and disease resistance, offering valuable genetic resources for wheat breeding programs aimed at enhancing agronomic traits.

INDETERMINATE DOMAIN (IDD) transcription factors are plant-specific regulators essential for plant development and stress adaptation. As a globally important staple crop, common wheat (Triticum aestivum L.) is frequently threatened by fungal diseases such as powdery mildew and stripe rust. To date, however, the IDD gene family in wheat has not been systematically characterized, and its roles in biotic stress responses remain unclear. In this study, we performed genome-wide identification and a comprehensive analysis of the TaIDD gene family. A total of 41 TaIDD genes were identified, which were unevenly distributed across 15 chromosomes and divided into four phylogenetic groups. Synteny and selective pressure analyses demonstrated that segmental duplication was the main driver of family expansion and that TaIDD genes underwent strong purifying selection during evolution. Cis-acting element analysis revealed abundant hormone- and stress-related elements in their promoter regions. Transcriptome and RT-qPCR analyses indicated that TaIDD genes exhibited distinct expression patterns under abiotic and biotic stress. Notably, TaIDD13, TaIDD19, TaIDD27, TaIDD37, TaIDD39, and TaIDD41 were significantly induced by multiple fungal pathogens, suggesting their potential involvement in stress-responsive pathways that may be related to disease resistance. Subcellular localization analysis further confirmed that TaIDD39 was exclusively localized in the nucleus, consistent with its function as a transcriptional regulator. Our findings provide insights into the evolutionary characteristics and stress-response mechanisms of TaIDD genes and highlight TaIDD39 and other potential candidates that may serve as valuable resources for wheat molecular breeding to enhance broad-spectrum disease resistance and stress tolerance.

Vacuolar processing enzymes (VPEs) are legumain-type cysteine proteases regulating plant protein processing, programmed cell death, seed maturation and stress responses. Nevertheless, the VPE family remains poorly characterized in hexaploid wheat (Triticum aestivum L.), and its possible roles in grain pigmentation are unclear. Here, we genome-wide identified 27 TaVPE genes and performed multi-omics analyses. Phylogenetic classification separated TaVPE proteins into four clades, all possessing conserved Peptidase_C13 and legumain_C domains, with similar motif patterns within each clade. These 27 TaVPE genes were unevenly located across 12 chromosomes of homoeologous groups 2, 3, 5 and 6. Collinearity analysis uncovered 26 intra-wheat collinear blocks and 47 orthologous gene pairs between wheat and rice, maize and foxtail millet, while no collinear counterparts were found in Arabidopsis. All duplicated pairs had Ka/Ks values less than 1, suggesting strong purifying selection. Numerous cis-acting elements related to hormones (ABA, MeJA, SA), stresses, and MYB/bHLH transcription factor binding sites were detected in TaVPE promoters. Expression data from public databases and transcriptomes of purple-grained Donghei-1 and white-grained Jinmai-66 (17, 31, 36 and 41 days after flowering) demonstrated predominant TaVPE expression at anthesis and grain-filling stages. Five TaVPE genes were retained as candidate genes associated with purple grain colour: TaVPE6, TaVPE15, TaVPE18, TaVPE25 and TaVPE26. All five showed significantly higher expression in the purple-grained cultivar than in the white-grained one at one or more mid-to-late grain-filling stages. This work establishes the first systematic profile of wheat VPE family and identifies candidate genes potentially associated with anthocyanin accumulation, supporting future functional research and molecular breeding for anthocyanin-enriched wheat.

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.