RNA-seq transcriptome analysis provides candidate genes for resistance to Tomato leaf cur New Delhi virus in melon

[EN] 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.This work was supported by grants AGL201785563-C2-1-R and RTA2017-00061-C03-03 funded by MCIN/AEI/10.13039/501100011033 and by "ERDF A way of making Europe," by grant PID2020-116055RB-C21 funded by MCIN/AEI/10.13039/501100011033; and by PROMETEO projects 2017/078 and 2021/072 (to promote excellence groups) by the Conselleria d'Educacio, Investigacio, Cultura i Esports (Generalitat Valenciana).Sáez-Sánchez, C.; Flores-León, A.; Montero-Pau, J.; Sifres, A.; Dhillon N.P.S:; López, C.; Picó, B. (2022). RNA-seq transcriptome analysis provides candidate genes for resistance to Tomato leaf cur New Delhi virus in melon. Frontiers in Plant Science. 12:1-26. https://doi.org/10.3389/fpls.2021.7988581261

Resistance to tomato leaf curl New Delhi virus in melon is controlled by a major QTL located in chromosome 11

[EN] Key message Identification of three genomic regions and underlying candidate genes controlling the high level of resistance to ToLCNDV derived from a wild melon. SNP markers appropriated for MAS management of resistance. Tomato leaf curl New Delhi virus (ToLCNDV) is a bipartite begomovirus that severely affects melon crop (Cucumis melo) in the main production areas of Spain since 2012. In this work, we evaluated the degree of resistance of four accessions (two belonging to the subsp. agrestis var. momordica and two to the wild agrestis group) and their corresponding hybrids with a susceptible commercial melon belonging to the subsp. melo (Piel de Sapo, PS). The analysis using quantitative PCR (qPCR) allowed us to select one wild agrestis genotype (WM-7) with a high level of resistance and use it to construct segregating populations (F (2) and backcrosses). These populations were phenotyped for symptom severity and virus content using qPCR, and genotyped with different sets of SNP markers. Phenotyping and genotyping results in the F (2) and BC1s populations derived from the WM-7 x PS cross were used for QTL analysis. Three genomic regions controlling resistance to ToLCNDV were found, one major locus in chromosome 11 and two additional regions in chromosomes 12 and 2. The highest level of resistance (no or mild symptoms and very low viral titer) was obtained with the homozygous WM-7WM-7 genotype at the major QTL in chromosome 11, even with PSPS genotypes at the other two loci. The resistance derived from WM-7 is useful to develop new melon cultivars and the linked SNPs selected in this paper will be highly useful in marker-assisted breeding for ToLCNDV resistance in melon.CS was the recipient of a predoctoral fellowship (ACIF/2016/188) from Generalitat Valenciana, and CM was the recipient of a Juan de la Cierva contract from the Spanish Ministerio de Economia y Competitividad (FJCI-2014-19817). This work was supported by Project E_ RTA2013-00020-C04-03 from the Spanish Instituto Nacional de Investigaciones Agrarias (INIA) cofunded with FEDER funds. We also thank Maureen Mecozzi for helpful edits and the USDA genebank for providing seeds of some of the accessions used in this study.Sáez-Sánchez, C.; Esteras Gómez, C.; Martínez-Martínez, C.; Ferriol Molina, M.; Dhillon, N.; López Del Rincón, C.; Picó Sirvent, MB. (2017). Resistance to tomato leaf curl New Delhi virus in melon is controlled by a major QTL located in chromosome 11. 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