Molecular Pathogens 2024, Vol.15, No.4, 179-188 http://microbescipublisher.com/index.php/mp 180 molecular functions, and cellular components (Tyagi et al., 2022). By examining the transcriptome, scientists can gain insights into gene expression patterns, regulatory mechanisms, and the functional roles of genes in various developmental stages and environmental conditions. This knowledge is crucial for improving breeding selection and cultivation practices, ultimately enhancing crop yield and resilience. 2.2 Advances in wheat transcriptomic technologies Recent advancements in transcriptomic technologies have significantly enhanced our ability to study wheat at the molecular level. Techniques such as RNA-Seq have been employed to characterize the transcriptomes of distinct cell types in biological tissues efficiently (Saini et al., 2021). For instance, the development of methods like Simplified Poly (A) Anchored Sequencing (SiPAS) has enabled large-scale gene expression quantification with high sensitivity, accuracy, and reproducibility, making transcriptomics a more powerful tool for deciphering genome function (Wang et al., 2021). Additionally, integrative analyses combining mRNA, noncoding RNA (ncRNA), and DNA methylation data have provided deeper insights into complex regulatory networks, such as those involved in preharvest sprouting resistance in wheat (Zhang et al., 2021). These technological advancements have paved the way for more comprehensive and detailed studies of wheat transcriptomes, facilitating the identification of key genes and pathways involved in disease resistance and other important traits. 2.3 Transcriptome analysis in the study of biotic stress Transcriptome analysis has been instrumental in understanding wheat's response to biotic stress, such as pathogen infections. For example, studies have utilized RNA-Seq to investigate the transcriptomic changes in wheat varieties with different resistances to pathogens like wheat yellow mosaic virus (WYMV) and wheat dwarf virus (WDV) (Sharaf et al., 2023). These analyses have revealed significant changes in gene expression and RNA modifications (Figure 1), such as N6-methyladenosine (m6A) methylation, which play crucial roles in plant defense responses. Furthermore, alternative splicing (AS) events have been shown to enhance transcript and protein diversity, contributing to stress adaptation in wheat during pathogen interactions (Zhang et al., 2019). By identifying differentially expressed transcripts and splicing variants, researchers can pinpoint specific genes and pathways that are activated or suppressed in response to biotic stress, providing valuable targets for breeding disease-resistant wheat varieties. Integrating transcriptomic data with genomic and phenotypic information has also proven effective in predicting resistance to diseases like fusarium head blight (FHB), demonstrating the potential of transcriptomics in enhancing predictive breeding strategies (Michel et al., 2021). 3 Key Pathogen-Responsive Genes in Wheat 3.1 Identification of major resistance genes The identification of major resistance genes in wheat has been significantly advanced through various genomic and transcriptomic studies. For instance, a meta-analysis of quantitative trait loci (QTL) mapping identified 63 meta-QTLs (MQTLs) associated with resistance to multiple diseases such as septoria tritici blotch, fusariumhead blight, and karnal bunt. This study also identified 194 differentially expressed genes (DEGs) linked to disease resistance, providing a valuable resource for marker-assisted breeding (Saini et al., 2021). Additionally, the wheat resistance gene Lr34, which encodes an ABCG-type transporter, has been shown to confer durable resistance against multiple pathogens. This gene's mode of action involves the constitutive activation of multiple defense pathways, including the induction of jasmonic acid and salicylic acid, which are crucial for plant defense (Chauhan et al., 2015). 3.2 Gene families involved in disease resistance Several gene families play pivotal roles in wheat disease resistance. The NB-ARC-encoding gene family, which includes nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes, is particularly noteworthy. A genome-wide identification study revealed 2151 NB-ARC-encoding genes in wheat, many of which are organized into clusters formed by tandem duplications. These genes are essential for recognizing pathogenic effectors and initiating immune responses (Andersen et al., 2020). Another significant gene family includes the pathogenesis-related (PR) proteins, such as PR-1, TLP, Chitinase, and β-1, 3-glucanase, which were found to be highly expressed in resistant wheat varieties, suggesting their crucial role in defense mechanisms against pathogens like fusarium equiseti (Manghwar et al., 2021).
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