Identification and characterization of a cucumber accession resistant to tomato leaf curl New Delhi virus

Abstract Tomato leaf curl New Delhi virus (ToLCNDV) causes significant yield and fruit quality losses in cucurbit crops, particularly in the Mediterranean region. Sources of resistance to ToLCNDV have been identified in various cucurbits, including cucumber, where quantitative trait loci (QTLs) have been mapped to chromosomes 1, 2, and 6. A candidate gene encoding RNA‐dependent RNA polymerase 3 ( CsRDR3 ) has been identified and functionally validated in QTL1, and a candidate gene encoding heat shock factor A2 ( CsHSFA2 ) has been identified in QTL2. We performed a field screening of cucumber accessions and identified ABS.PE.045 as potentially resistant to ToLCNDV. Since prototype Mediterranean isolates (ToLCNDV‐ES) induce only mild symptoms in cucumber, we cloned ToLCNDV‐CsES, an aggressive isolate from cucumber. The proteins from ToLCNDV‐ES and ToLCNDV‐CsES differ by only 10 amino acids; however, ToLCNDV‐CsES induces severe symptoms in cucumber plants of the Wisconsin cultivar. We used ToLCNDV‐CsES to phenotype ABS.PE.045, Wisconsin, and their F 1 and F 2,3 progenies. ABS.PE.045 plants were highly resistant, F 1 plants showed symptoms and virus progression similar to those of Wisconsin plants, and F 2 individuals segregated, suggesting the involvement of two or more genes in resistance determination. A bulk segregant analysis coupled with RNA‐Seq suggested the involvement of four QTLs in resistance, with defined intervals on cucumber chromosomes 1, 2, 6, and 7. Our analysis suggested that CsRDR3 and CsHSF2A are bona fide candidates for QTLs 1 and 2, in agreement with previous studies. We propose CsaV3_7G022160 , annotated as encoding a CCCH zinc finger protein, as a candidate for QTL7. The new marker and cloned ToLCNDV‐CsES represent important tools for breeding resistance to this virus in cucumber.