Assessment of tomato germplasms for Mi-1.2-mediated resistance to Meloidogyne incognita: Integrating in-silico dynamics and bioinformatic approaches

Abstract

Meloidogyne incognita poses a significant threat to global tomato production, causing substantial yield losses. Utilizing resistance genes, particularly Mi-1.2, has emerged as an effective strategy to mitigate the impact of root-knot nematodes (RKNs) in tomatoes. The objective of this study was to identify tomato genotypes resistant to M. incognita, evaluate the nematode's effect on tomato physiological parameters, and investigate the molecular dynamics of the Mi-1.2 gene using in-silico approaches. Greenhouse screening of 28 genotypes identified four (18273, 18275, PONY EXPRESS, and CARRMEN) as highly resistant, with no gall formation observed on their roots. PCR amplification confirmed the presence of the Mi-1.2 gene in these genotypes. An evaluation of varietal responses revealed that nematode infestation significantly impacted physiological attributes, reducing fruit yield by 23 %, while increasing fresh root weight by 14 %. Promoter analysis of the Mi-1.2 gene identified seven cis-regulatory elements, including binding sites for WRKY transcription factors. Protein-protein interaction analysis predicted critical functional partners, such as pto, Wifi1, PTI5, and SGT1, which play key roles in signal transduction and cellular defense mechanisms. Molecular docking revealed that the Mi-1.2 protein exhibited the most stable interaction with the Cg-1 effector protein, characterized by the lowest interaction energy and optimal binding orientation, compared to other candidate effectors Map-1 and 16D10. This study provides valuable information for breeding programs in Pakistan, as new resistant tomato cultivars were identified, which could be used for future breeding programs to enhance resistance to RKNs.