RNA-Seq Transcriptome Analysis Provides Candidate Genes for Resistance to Tomato Leaf Curl New Delhi Virus in Melon

Abstract

Tomato leaf curl New Delhi virus (ToLCNDV) emerged in the Mediterranean Basin in 2012 as the first DNA bipartite begomovirus (Geminiviridae family), causing severe yield and economic losses in cucurbit crops. A major resistance locus was identified in the wild melon accession WM-7 (Cucumis melo kachri group), but the mechanisms involved in the resistant response remained unknown. In this work, we used RNA-sequencing to identify disease-associated genes that are differentially expressed in the course of ToLCNDV infection and could contribute to resistance. Transcriptomes of the resistant WM-7 genotype and the susceptible cultivar Piñonet Piel de Sapo (PS) (C. melo ibericus group) in ToLCNDV and mock inoculated plants were compared at four time points during infection (0, 3, 6, and 12 days post inoculation). Different gene expression patterns were observed over time in the resistant and susceptible genotypes in comparison to their respective controls. Differentially expressed genes (DEGs) in ToLCNDV-infected plants were classified using gene ontology (GO) terms, and genes of the categories transcription, DNA replication, and helicase activity were downregulated in WM-7 but upregulated in PS, suggesting that reduced activity of these functions reduces ToLCNDV replication and intercellular spread and thereby contributes to resistance. DEGs involved in the jasmonic acid signaling pathway, photosynthesis, RNA silencing, transmembrane, and sugar transporters entail adverse consequences for systemic infection in the resistant genotype, and lead to susceptibility in PS. The expression levels of selected candidate genes were validated by qRT-PCR to corroborate their differential expression upon ToLCNDV infection in resistant and susceptible melon. Furthermore, single nucleotide polymorphism (SNPs) with an effect on structural functionality of DEGs linked to the main QTLs for ToLCNDV resistance have been identified. The obtained results pinpoint cellular functions and candidate genes that are differentially expressed in a resistant and susceptible melon line in response to ToLCNDV, an information of great relevance for breeding ToLCNDV-resistant melon cultivars.

The haplotype-resolved T2T reference genome highlights structural variation underlying agronomic traits of melon

“…However, we did not detect differences in the expression levels of these R genes after artificial inoculation with ToLCNDV to resistant and susceptible melon germplasm reported in a previous study ( Fig. S12 , see online supplementary material) [ 63 ]. Furthermore, previous research indicated that the ToLCNDV transcription activator protein could be degraded through the autophagy pathway [ 52 ].…”

Coat protein is responsible for tomato leaf curl New Delhi virus pathogenicity in tomato

“…The ToLCNDV outbreak caused losses of over 20% of zucchini and melons in Spain and 80% of pumpkins in Italy ( Sáez et al., 2017 ; Panno et al., 2019 ; Crespo et al., 2020 ), whereas no significant losses of tomatoes have been reported in these regions due to this virus to date. Most studies have focused on different adaptations in susceptible or resistant/tolerant hosts to identify candidate genes against this virus using molecular techniques or high-throughput sequencing ( Kushwaha et al., 2015 ; Romero-Masegosa et al., 2021 ; Sáez et al., 2022 ). To date, no studies have been conducted to compare the biological characteristics and reveal the precise molecular mechanisms by which different ToLCNDV strains display distinct adaptations in the same hosts.…”

Spanish Melon Landraces: Revealing Useful Diversity by Genomic, Morphological, and Metabolomic Analysis

“…Another SNP change was detected in MELO3C022339 (Glutaredoxin protein) with a moderate change in Trigonus (G/T) and a low change (C/T) in some Flexuosus, Ibericus 21AM, Trigonus, and WM7. This last change has already been linked to resistance DEGs (differential expressed genes) associated with the response to Tomato Leaf Curl New Delhi Virus (ToLCNDV), with the SNP being present in resistant WM7 but not in the susceptible Piel de Sapo variant Piñonet [33].…”