Deciphering the Intricate Regulatory Network of Rust (Uromyces viciae-fabae) Resistance in Lentil (Lens culinaris Medik.) Through Comparative RNA-Seq Analysis

The lentil (Lens culinaris Medikus), a significant pulse crop with high nutritional value for food and animal feed, is grown throughout the world. Lentil is abundant in proteins, carbohydrates, dietary fiber, minerals, vitamins, and antioxidants. Lentil yield is still low despite its nutritional advantages because of a number of biotic and abiotic problems. Multiple diseases that can harm growth and yield can affect lentils. Rust in lentils is caused by the destructive disease Uromyces viciae-fabae and is a threat to the production of lentils. The study's objective was to investigate the intricate molecular mechanisms underlying lentil resistance to the harmful rust infection caused by U. vicia-fabae. Utilizing cutting-edge sequencing methods like RNA-Seq, we examined two genotypes that had been inoculated with rust spores: rust-resistant L4147 and rust-susceptible LLS 18-109. The RNA-Seq method produced useful insights by comparing resistant control (RC), susceptible non-inoculated (SNI), resistant inoculated (RI), and susceptible inoculated (SI) samples. In six comparisons, differentially expressed genes (DEGs) were found, totaling 12,316 DEGs in all possible combinations. In rust-infected plants, functional gene classes related to defense were noticeably impacted. DEGs took part in a variety of biological processes, as evidenced by the enriched terms "metabolic process," "cellular process," and "response to stimulus."Highlighting metabolic pathways, secondary metabolite biosynthesis, and interactions between plants and pathogens, enriched KEGG pathways shed light on combinations. Notably, the expression of several ethylene-responsive genes, R genes, and genes related to ionic activity and metabolic processes varied, possibly strengthening defense. The number of DEGs was reduced through functional analysis to 34, which included LRR receptor-like kinases, transcription factors (WRKY, TIFY, AP2-EREBP, etc.), pathogenesis-related proteins (PR1-like protein), hormone signaling proteins (GH3 family protein, auxin-induced protein, ethylene-responsive factors, ABA receptors), R proteins (CC-NBS-LRR class), etc. Intricate connections between proteins involved in hormone signaling pathways, ubiquitin-mediated proteolysis, and other independent genes putatively linked to defense response were discovered through protein-protein interaction analysis. The significance of the genes identified in response was highlighted by the validation of 16 genes between RNA-Seq and qRT-PCR results, which confirmed credibility. Overall, by using cutting-edge techniques to identify important genes and pathways that control the defense response, this extensive study has shed light on the molecular basis of lentil rust resistance.