Genome-wide association studies to assess genetic factors controlling cucumber resistance to CABYV and CMV in crop fields and the attractiveness for their Aphis gossypii vector

Abstract

Cucumber crops face high pressure from pathogens, including various viral species. Mapping quantitative trait loci (QTL) for vegetable resistance to viruses has primarily been conducted after mechanical inoculation in controlled environments, but not in crop field conditions. Moreover, viruses that cannot be mechanically inoculated, e.g. the cucurbit aphid-borne yellows virus (CABYV), have been overlooked in resistance studies. Here, we aimed to identify QTLs reducing epidemics of two prevalent cucumber viruses: CABYV and the cucumber mosaic virus (CMV). We evaluated the resistance of 256 elite cucumber lines and landraces in crop field conditions by screening for the presence of both viruses six-times during the season. We mapped twelve QTLs reducing CABYV epidemics and seven QTLs reducing CMV epidemics by combining multiloci genome-wide association studies and local score approach analyses. We also examined the attractiveness of this cucumber panel for Aphis gossypii, a major cucumber virus vector. We identified five QTLs that reduced the attractiveness, including one co-localizing with a QTL reducing CABYV epidemics. Interestingly, some accessions deemed CMV-resistant after mechanical inoculation in controlled environments showed high infection rates in crop field conditions. Only one QTL for CMV resistance was detected in both conditions, indicating that these phenotypes are regulated by independent QTLs. Local linkage disequilibrium study findings suggested that certain QTLs reducing epidemics were introduced early into elite lines through serendipity or selection. QTLs could be pyramided with other low-effect QTLs through genomic selection to obtain cucumber cultivars with enhanced field resistance to viruses.

Acknowledgements

We thank Salomé Roels, Nathalie Giovinazzo, and Marie-Claire Le Coant for their help in ELISA. We thank Abdelmalek Azahaf, Léa Bigonville, and Olivier Pages for their help in the CABYV sampling. We thank Denis Garcia, Amaury Lerude, Jamal Azahaf, Yves Calvez, and Lucie Amouroux for their help in the protocol design and management of the OPFs. We thank Marie Coustary and Jenny Santin for help in cucumber sowing. We thank Marc Gini for designing our special sample grinder. We thank Dr Cécile Desbiez and Dr Alexandra Schoeny for productive discussions during the project preparation. Finally, we thank David Manley for his careful English language review. We thank the R community, and especially the authors of the software packages that were intensively used in this study, including Dr Endelman, Dr Segura, Dr Gao, and Dr Bonhomme.

Author Contributions

S.M., N.B., M.C., and P.M. designed the study. Data collection was performed by S.M., P.M., L.K., A.R., and E.C. J.C. contributed to the functional analysis. Data analyses were performed by S.M., A.R., and E.C. S.M. and N.B. wrote and finalized the manuscript with advice from M.C., J.C., E.C., and A.R. All authors read and approved the final manuscript.

Data availability

Phenotyping data are in supplementary table file. Genetic data are in Monnot, S.; Cantet, M.; Mary-Huard, T.; Moreau, L.; Lowdon, R.; Van Haesendonck, M.; Ricard, A.; Boissot, N. Unravelling Cucumber Resistance to Several Viruses via Genome-Wide Association Studies Highlighted Resistance Hotspots and New QTLs. Horticulture Research 2022.

Funding

This work was supported by Bayer Crop Science in the framework of a CIFRE PhD fund.

Conflict of interest statement

S.M. and M.C. are Bayer employees.

Supplementary Data

Supplementary data is available at Horticulture Research online.

References

[1] Che G, Zhang X. Molecular basis of cucumber fruit domestica-tion. Curr Opin Plant Biol. 2019;47:38-46

[2] Wang X, Bao K, Reddy UK. et al. The USDA cucumber (Cucumis Sativus L.. collection: genetic diversity, population structure, genome-wide association studies, and Core collection develop-ment. Hortic Res. 2018;5:64

[3] Lin X, Zhang N, Song H. et al. Population-specific, recent positive selection signatures in cultivated Cucumis Sativus L. (cucum-ber). G3 Genes|Genomes|Genetics. 2022;12:jkac119.

[4] Pitrat M, Foury C, eds. Histoires de légumes: Des Origines à l’orée du XXIe siècle. Paris: Institut National de la Recherche Agronomique; 2003:

[5] Liang D, Chen M, Qi X. et al. QTL mapping by SLAF-seq and expression analysis of candidate genes for aphid resistance in cucumber. Front Plant Sci. 2016;7:1000

[6] Brault V, Uzest M, Monsion B. et al. Aphids as transport devices for plant viruses. CRBiol. 2010;333:524-38

[7] Ng JCK, Falk BW. Virus-vector interactions mediating nonpersis-tent and semipersistent transmission of plant viruses. Annu Rev Phytopathol. 2006;44:183-212

[8] Schnieder N, Känel A, Zimmermann M. et al. So similar yet so different: the distinct contributions of Extrafascicular and fas-cicular phloem to transport and exudation in cucumber plants. J Plant Physiol. 2022;271:153643.

[9] Moreno A, Garzo E, Fernandez-Mata G. et al. Aphids secrete watery saliva into plant tissues from the onset of stylet pene-tration. Entomol Exp Appl. 2011;139:145-53

[10] Perring TM, Gruenhagen NM, Farrar CA. Management of Plant Viral Diseases through chemical control of insect vectors. Annu Rev Entomol. 1999;44:457-81

[11] Lecoq H, Bourdin D, Wipf-Scheibel C. et al. A new yellowing disease of cucurbits caused by a Luteovirus, cucurbit aphid-borne yellows virus. Plant Pathol. 1992;41:749-61

[12] Menzel W, Maeritz U, Seigner L. First report of cucurbit aphid-borne yellows virus infecting cucurbits in Germany. New Dis Rep. 2020;41:1-1

[13] Kuypers M. Dangerous Cucumber CABYV Virus Is Spreading to North-ern Europe. innovationorigins.com. http://www.fao.org/faostat/en/#data/QCL (05October 2021, date last accessed)

[14] Gómez P, Rodríguez-Hernández AM, Moury B. et al. Genetic resistance for the sustainable control of plant virus diseases: breeding, mechanisms and durability. Eur J Plant Pathol. 2009;125: 1-22

[15] Monnot S, Desaint H, Mary-Huard T. et al. Deciphering the genetic architecture of plant virus resistance by GWAS, state of the art and potential advances. Cells. 2021;10:3080

[16] Korte A, Farlow A. The advantages and limitations of trait anal-ysis with GWAS: a review. Plant Methods. 2013;9:29

[17] Bonhomme M, Fariello MI, Navier H. et al. A local score approach improves GWAS resolution and detects minor QTL: applica-tion to Medicago Truncatula quantitative disease resistance to multiple Aphanomyces Euteiches isolates. Heredity. 2019;123: 517-31

[18] Moury B, Selassie KG, Marchoux G. et al. High temperature effects on hypersensitive resistance to tomato spotted wilt Tospovirus (TSWV) in pepper (capsicum Chinense Jacq.). Eur J Plant Pathol. 1998;104:489-98

[19] Wang Y, Lee KC, Gaba V. et al. Breakage of resistance to cucumber mosaic virus by Co-infection with zucchini yellow mosaic virus: enhancement of CMV accumulation independent of symptom expression. Arch Virol. 2004;149:379-96

[20] Martín-Hernández AM, Picó B. Natural resistances to viruses in cucurbits. Agronomy. 2021;11:23

[21] Monnot S, Cantet M, Mary-Huard T. et al. Unravelling cucum-ber resistance to several viruses via genome-wide association studies highlighted resistance hotspots and new QTLs. Hortic Res. 2022;9:uhac184

[22] Leibman D, Wolf D, Saharan V. et al. A high level of transgenic viral small RNA is associated with broad potyvirus resistance in cucurbits. MPMI. 2011;24:1220-38

[23] Leibman D, Kravchik M, Wolf D. et al. Differential expres-sion of cucumber RNA-dependent RNApolymerase 1 genes dur-ing antiviral Defence and resistance. Mol Plant Pathol. 2018;19: 300-12

[24] Chandrasekaran J, Brumin M, Wolf D. et al. Development of broad virus resistance in non-transgenic cucumber using CRISPR/Cas9 technology. Mol Plant Pathol. 2016;17:1140-53

[25] Simko I, Piepho H-P. The area under the disease Progress stairs: calculation, advantage, and application. Phytopathology. 2011;102:381-9

[26] Schoeny A, Rimbaud L, Gognalons P. et al. Can winged aphid abundance Be a predictor of cucurbit aphid-borne yellows virus epidemics in melon crop. Viruses. 2020;12:911

[27] Fariello MI, Boitard S, Mercier S. et al. Accounting for linkage disequilibrium in genome scans for selection without individual genotypes: the local score approach. Mol Ecol. 2017;26:3700-14

[28] Gao X. Multiple testing corrections for imputed SNPs. Genet Epidemiol. 2011;35:154-8

[29] Li Q, Li H, Huang W. et al. A chromosome-scale genome assembly of cucumber (Cucumis Sativus L.). GigaScience. 2019;8:giz072

[30] Guan J, Miao H, Zhang Z. et al. A near-complete cucumber reference genome assembly and cucumber-DB, a multi-omics database. Mol Plant. 2024;17:1178-82

[31] Wang Y, Bo K, Gu X. et al. Molecularly tagged genes and quan-titative trait loci in cucumber with recommendations for QTL nomenclature. Hortic Res. 2020;7:3

[32] Bartoli C, Roux F. Genome-wide association studies in plant Pathosystems: toward an ecological genomics approach. Front Plant Sci. 2017;8:763

[33] Desbiez C, Wipf-Scheibel C, Millot P. et al. Distribution and evolution of the major viruses infecting cucurbitaceous and solanaceous crops in the French Mediterranean area. Virus Res. 2020;286:198042.

[34] Cheval C, Aldon D, Galaud J-P. et al. Calcium/calmodulin-mediated regulation of plant immunity. Biochimica et Biophysica acta (BBA) - molecular. Cell Res. 2013;1833:1766-71

[35] Giner A, Pascual L, Bourgeois M. et al. Amutationinthe melon vacuolar protein sorting 41prevents systemic infection of cucumber mosaic virus. Sci Rep. 2017;7:10471

[36] Shi L, Yang Y, Xie Q. et al. Inheritance and QTL mapping of cucumber mosaic virus resistance in cucumber (Cucumis Sativus L.). PLoS One. 2018;13:1-12

[37] Mistral P, Vanlerberghe-Masutti F, Elbelt S. et al. Aphis gossypi-i/aphis Frangulae collected worldwide: microsatellite markers data and genetic cluster assignment. Data Brief. 2021;36:106967

[38] Tjallingii WF. Salivary secretions by aphids interacting with proteins of phloem wound responses. JExp Bot. 2006;57:739-45

[39] Zaffaroni M, Papaix J, Rimbaud L. et al. Combining single-gene-resistant and pyramided cultivars in agricultural landscape compromises the benefits of pyramiding in Most, but not all, productions situations. Phytopathology. 2024;114:2310-21

[40] McElroy MS, Navarro AJR, Mustiga G. et al. Prediction of cacao (Theobroma Cacao) resistance to Moniliophthora Spp. diseases via genome-wide association analysis and genomic selection. Front Plant Sci. 2018;9:343

[41] Schoeny A, Desbiez C, Millot P. et al. Impact of vat resistance in melon on viral epidemics and genetic structure of virus populations. Virus Res. 2017;241:105-15

[42] Dogimont C. Sources of resistance to cucurbit aphid-borne yel-lows Luteovirus in a melon germ plasm collection. Plant Dis. 1996;80:1379

[43] Cucurbit Aphid-Borne Yellows Virus. sediag.fr. https://sediag.fr/boutique/type-de-culture/legumes/cucurbit-aphid-borne-yellows-virus-cabyv/ (accessed 2022-06-27)

[44] Sutula CL, Gillett J, Morrissey S. et al. Interpreting ELISA data and establishing the positive-negative threshold. Plant Dis. 1986;70: 722-6

[45] Boissot N, Schoeny A, Vanlerberghe-Masutti F. Vat, an amaz-ing gene conferring resistance to aphids and viruses they carry: from molecular structure to field effects. Front Plant Sci. 2016;7:1420

[46] BioBam Bioinformatics. OmicsBox - Bioinformatics Made Easy. https://www.biobam.com/omicsbox