Stripe rust (Puccinia striiformis f. sp. tritici; Pst) and powdery mildew (Blumeria graminis f. sp. tritici; Bgt) are important diseases of wheat (Triticum aestivum) worldwide. Increasingly evidences suggest that long intergenic ncRNAs (lincRNAs) are developmentally regulated and play important roles in development and stress responses of plants. However, identification of lincRNAs in wheat is still limited comparing with functional gene expression. The transcriptome of the hexaploid wheat line N9134 inoculated with the Chinese Pst race CYR31 and Bgt race E09 at 1, 2, and 3 days post-inoculation was recapitulated to detect the lincRNAs. Here, 283 differential expressed lincRNAs were identified from 58218 putative lincRNAs, which account for 31.2 % of transcriptome. Of which, 254 DE-LincRNAs responded to the Bgt stress, and 52 lincRNAs in Pst. Among them, 1328 SnRNP motifs (sm sites) were detected and showed RRU4–11RR sm site element and consensus RRU1–9VU1–7RR SnRNP motifs, where the total number of uridine was more than 3 but less than 11. Additionally, 101 DE-lincRNAs were predicted as targets of miRNA by psRNATarget, while 5 target mimics were identified using target mimicry search in TAPIR. Taken together, our findings indicate that the lincRNA of wheat responded to Bgt and Pst stress and played important roles in splicesome and inter-regulating with miRNA. The sm site of wheat showed a more complex construction than that in mammal and model plant. The mass sequence data generated in this study provide a cue for future functional and molecular research on wheat–fungus interactions.

Aegilops geniculata Roth has been used as a donor of disease-resistance genes, to enrich the gene pool for wheat (Triticum aestivum) improvement through distant hybridization. In this study, the wheat–Ae. geniculata alien disomic substitution line W16998 was obtained from the BC₁F₈ progeny of a cross between the common wheat ‘Chinese Spring’ (CS) and Ae. geniculata Roth (serial number: SY159//CS). This line was identified using cytogenetic techniques, analysis of genomic in situ hybridization (GISH), functional molecular markers (Expressed sequence tag-sequence-tagged site (EST–STS) and PCR-based landmark unique gene (PLUG), fluorescence in situ hybridization (FISH), sequential fluorescence in situ hybridization–genomic in situ hybridization (sequential FISH–GISH), and assessment of agronomic traits and powdery mildew resistance. During the anaphase of meiosis, these were evenly distributed on both sides of the equatorial plate, and they exhibited high cytological stability during the meiotic metaphase and anaphase. GISH analysis indicated that W16998 contained a pair of Ae. geniculata alien chromosomes and 40 common wheat chromosomes. One EST–STS marker and seven PLUG marker results showed that the introduced chromosomes of Ae. geniculata belonged to homoeologous group 7. Nullisomic–tetrasomic analyses suggested that the common wheat chromosome, 7A, was absent in W16998. FISH and sequential FISH–GISH analyses confirmed that the introduced Ae. geniculata chromosome was 7M^g. Therefore, W16998 was a wheat–Ae. geniculata 7M^g (7A) alien disomic substitution line. Inoculation of isolate E09 (Blumeria graminis f. sp. tritici) in the seedling stage showed that SY159 and W16998 were resistant to powdery mildew, indeed nearly immune, whereas CS was highly susceptible. Compared to CS, W16998 exhibited increased grain weight and more spikelets, and a greater number of superior agronomic traits. Consequently, W16998 was potentially useful. Germplasms transfer new disease-resistance genes and prominent agronomic traits into common wheat, giving the latter some fine properties for breeding.

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.

Lesion mimic phenotypes, characterized by leaf spots formed in the absence of pathogens or pests, are often associated with reactive oxygen species (ROS) accumulation and cell necrosis. This study identified a novel and stable homozygous spotted phenotype (HSP) from the F₈ population of common wheat (XN509 × N07216). The yellow spots that appeared at the booting stage were light-sensitive, and accompanied by cell necrosis and H₂O₂ accumulation. Compared with homozygous normal plants (HNPs), HSPs exhibited enhanced resistance to stripe rust and powdery mildew without compromising yield. RNA-Seq analysis at three stages revealed that differentially expressed genes (DEGs) between HSPs and HNPs were significantly enriched in KEGG pathways related to photosynthesis and photosynthesis-antenna proteins. GO analysis highlighted chloroplast and light stimulus-related down-regulated DEGs. Fine mapping identified TaSpl1 within a 0.91 Mb interval on chromosome 3DS, flanked by the markers KASP188 and KASP229, using two segregating populations comprising 1117 individuals. The candidate region contained 42 annotated genes, including 14 DEGs based on previous BSR-Seq data. PCR amplification and qRT-PCR verification identified the expression of TraesCS3D02G022100 was consistent with RNA-Seq data. Gene homology analysis and silencing experiments confirmed that TraesCS3D02G022100 was associated with stay-green traits. These findings provide new insights into the genetic regulation of lesion mimics, photosynthesis, and disease resistance in wheat.

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.