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• The landscape of AS modulation in wheat- Pst and - Bgt interaction. • Differential splice variants were activated against Pst and Bgt stress. • Specific induced AS genes were differential enriched in Pst -resistant and -susceptible plants. Alternative splicing (AS) enhances the diversities of both transcripts and proteins in eukaryotes, which contribute to stress adaptation. To catalog wheat (Triticum aestivum L.) AS genes, we characterized 45 RNA-seq libraries from wheat seedlings infected by powdery mildew, Blumeria graminis f. sp. tritici (Bgt) or stripe rust fungus, Puccinia striiformis f. sp. tritici (Pst). We discovered that 11.2% and 10.4% of the multiexon genes had AS transcripts during Bgt and Pst infections, respectively. In response to fungal infection, wheat modulated AS not only in disease resistance proteins, but also in splicing related factors. Apart from the stress induced or activated splicing variants by pathogen, the differential expression profiles were fold increased through changing the ratio of full spliced transcripts versus intron retention (IR) transcripts. Comparing AS transcripts produced by the same gene in Bgt with Pst stress, the spliced terminal exons and the stranded introns are independent and different. This demonstrated that differential induction of specific splice variants were activated against two fungal pathogens. The specific induced AS genes in the Pst -resistant plants were enriched in improving the membrane permeability and protein modification ability, whereas gene expression involved in protein translation and transport were strengthened in Pst -susceptible plants. [ABSTRACT FROM AUTHOR]

• TaSpl1 , a dominant gene, was usually suppressed by dominant-negative regulators. • TaSpl1 simulated a regulated cell death phenotype in the absence of pathogen. • TaSpl1 activated defense genes that enhance Pst and Bgt resistance in adult plants. The spotted leaf lesion mimic trait simulates cell death in a plant responding to pathogen infection. Some spotted leaf genes are recessive, while others are dominant. A small number of plants with a lesion mimic phenotype appeared in a segregating population obtained by crossing two normal green wheat strains, XN509 and N07216. Here, we clarified the genetic model and its breeding value. Phenotyping of the consecutive progeny populations over six cropping seasons showed that the spotted leaf lesion mimic phenotype was controlled by a dominant gene designated TaSpl1 , which was inhibited by two other dominant genes, designated TaSpl1-I 1 and TaSpl1-I 2. Using bulked segregant analysis RNA-seq (BSR-Seq) and newly developed KASP-PCR markers, the TaSpl1 and TaSpl1-I 1 loci in N07216 were mapped to the end of chromosomes 3DS and 3BS, respectively. Plants with the spotted phenotype showed lower levels of stripe rust and powdery mildew than those with the normal green phenotype. Compared with normal leaves, the differentially expressed genes in spotted leaves were significantly enriched in plant-pathogen interaction and endocytosis pathways. There were no differences in the yield parameters of the F 5 and F 6 sister lines, N13039S with TaSpl1 and N13039 N without TaSpl1. These results provide a greater understanding of spotted leaf phenotyping and the breeding value of the lesion mimic allele in developing disease-resistance varieties. [ABSTRACT FROM AUTHOR]