Field genomics uncovers multi-gene resistance to cucumber viruses
image: Local LD study on the QTL controlling the CABYV maximum infection rate on chromosome 4 (upper part) [8.6–10.6 Mb] and on chromosome 7 (lower part). A. each dot represents an SNP, on the y-axis the r2 with the top SNP of the QTL represented by a dark dot. Grey dots represent SNPs with at least one missing data that were not studied by GWAS. The reddest dots reflect greater significance. B. Classification of genes located in the QTL interval according to the presence of SNPs in LD with the top SNP in coding or non-coding sequence.
Credit: Horticulture Research
Cucumber crops worldwide face major yield losses due to virus infections transmitted by aphids. A recent genome-wide association study (GWAS) uncovered multiple quantitative trait loci (QTLs) that regulate cucumber resistance to cucurbit aphid-borne yellows virus (CABYV) and cucumber mosaic virus (CMV) under natural field conditions. Researchers identified 35 QTLs linked to virus resistance and aphid attractiveness, revealing that field resistance is governed by numerous small-effect genes rather than single major ones. Some resistant alleles also reduced the attractiveness of cucumber leaves to Aphis gossypii, the main CABYV vector. These discoveries highlight the genetic complexity of virus defense in cucumbers and provide key targets for developing durable, pesticide-free varieties.
Viral diseases transmitted by aphids are among the most destructive threats to cucumber production. Cucumber mosaic virus (CMV) infects a broad range of host plants, while cucurbit aphid-borne yellows virus (CABYV) causes yellowing, flower abortion, and severe yield decline. Previous studies focused mainly on virus resistance under controlled inoculation conditions, which cannot fully capture the complex interactions in the field. Persistent viruses like CABYV have received little attention because their spread is closely linked to aphid vectors. However, as pesticide use declines in sustainable agriculture, controlling aphid-borne virus epidemics through genetic resistance has become increasingly important. Due to these challenges, there is a pressing need to investigate the genetic factors controlling cucumber resistance under real field conditions.
Researchers from INRAE (France) and Bayer Crop Science conducted a large-scale field experiment involving 256 cucumber lines to investigate the genetic basis of resistance to CABYV and CMV. The study, published (DOI: 10.1093/hr/uhaf016) on May 1, 2025, in Horticulture Research, used multilocus genome-wide association studies (GWAS) and a local score approach to identify QTLs influencing viral infection dynamics and aphid attractiveness. The results provide a comprehensive genetic map of cucumber–virus–vector interactions, offering new strategies for breeding virus-resistant cucumbers suited to low-pesticide cultivation systems.
The team assessed cucumber infection by CABYV and CMV using ELISA testing over six time points across the growing season. More than 8,800 virus detection assays were conducted on 1,575 plants. The study revealed widespread infection—81.9% of plants were infected by CABYV and 65.8% by CMV by harvest time. By integrating multilocus mixed linear models with a local score analysis, 35 QTLs were identified: 12 reducing CABYV epidemics, 7 reducing CMV epidemics, and 5 linked to lower aphid attractiveness. One key QTL on chromosome 4 reduced CABYV infection rates by 42%, while others delayed epidemic onset by up to 22 days. Interestingly, only one CMV resistance locus was shared between field and greenhouse conditions, suggesting that field resistance is controlled by distinct genetic mechanisms. Some QTLs overlapped with previously known mildew resistance genes, implying that virus resistance might have been unintentionally introduced during earlier breeding programs. The study also pinpointed genes involved in stress response, disease resistance, and extracellular signaling as potential regulators of these traits.
“Our research shows that cucumber resistance to viruses in the field depends on the combined effect of many small genetic factors rather than single dominant genes,” said Dr. Nathalie Boissot, senior researcher at INRAE and corresponding author of the study. “By revealing these multilocus interactions, we can now guide breeding strategies toward stacking or pyramiding multiple QTLs to achieve stable, durable resistance. This represents a shift from laboratory-based resistance screening to field-level genomic resilience, which is essential for future sustainable crop protection.”
The discovery of multiple resistance QTLs and their interactions with aphid behavior offers a roadmap for breeding cucumbers resilient to viral epidemics without relying on pesticides. Combining QTLs that reduce infection rates, delay virus spread, and decrease aphid attraction could enhance long-term crop resistance and stability under diverse environments. The researchers propose integrating these findings into genomic selection programs, enabling breeders to develop new elite cucumber cultivars with durable, broad-spectrum resistance. Beyond cucumbers, the study provides a methodological model for investigating polygenic resistance in other horticultural crops facing vector-borne virus challenges.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhaf016
Funding information
This work was supported by Bayer Crop Science in the framework of a CIFRE PhD fund.
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.