Skip to main content
SpringerLink
Log in

Inheritance analysis and identification of SNP markers associated with ZYMV resistance in Cucurbita pepo

  • Published:
Molecular Breeding Aims and scope Submit manuscript

Abstract

Cucurbit crops are economically important worldwide. One of the most serious threats to cucurbit production is Zucchini yellow mosaic virus (ZYMV). Several resistant accessions were identified in Cucurbita moschata and their resistance was introgressed into Cucurbita pepo. However, the mode of inheritance of ZYMV resistance in C. pepo presents a great challenge to attempts at introgressing resistance into elite germplasm. The main goal of this work was to analyze the inheritance of ZYMV resistance and to identify markers associated with genes conferring resistance. An Illumina GoldenGate assay allowed us to assess polymorphism among nine squash genotypes and to discover six polymorphic single-nucleotide polymorphisms (SNPs) between two near-isogenic lines, “True French” (susceptible to ZYMV) and Accession 381e (resistant to ZYMV). Two F2 and three BC1 populations obtained from crossing the ZYMV-resistant Accession 381e with two susceptible ones, the zucchini True French and the cocozelle “San Pasquale,” were assayed for ZYMV resistance. Molecular analysis revealed an approximately 90% association between SNP1 and resistance, which was confirmed using High Resolution Melt (HRM) and a CAPS marker. Co-segregation up to 72% in populations segregating for resistance was observed for two other SNP markers that could be potentially linked to genes involved in resistance expression. A functional prediction of proteins involved in the resistance response was performed on genome scaffolds containing the three SNPs of interest. Indeed, 16 full-length pathogen recognition genes (PRGs) were identified around the three SNP markers. In particular, we discovered that two nucleotide-binding site leucine-rich repeat (NBS-LRR) protein-encoding genes were located near the SNP1 marker. The investigation of ZYMV resistance in squash populations and the genomic analysis performed in this work could be useful for better directing the introgression of disease resistance into elite C. pepo germplasm.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Addinsoft (2007) XLSTAT, Analyse de données et statistique avec MS Excel. Addinsoft, NY

    Google Scholar 

  • Andolfo G, Ercolano MR (2015) Plant innate immunity multicomponent model. Front Plant Sci 6:987

    Article  PubMed  PubMed Central  Google Scholar 

  • Andolfo G, Sanseverino W, Rombauts S et al (2013) Overview of tomato (Solanum lycopersicum) candidate pathogen recognition genes reveals important Solanum R locus dynamics. New Phytol 197:223–237

    Article  CAS  PubMed  Google Scholar 

  • Andolfo G, Ferriello F, Tardella L et al (2014) Tomato genome-wide transcriptional responses to fusarium wilt, and tomato mosaic virus. PLoS One 9:e94963

    Article  PubMed  PubMed Central  Google Scholar 

  • Blanca J, Cañizares J, Roig C, Ziarsolo P, Nuez F, Picó B (2011) Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae). BMC Genomics 12:104

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brown RN, Bolanos-Herrera A, Myers JR, Jahn MM (2003) Inheritance of resistance to four cucurbit viruses in Cucurbita moschata. Euphytica 129:253–258

    Article  CAS  Google Scholar 

  • Burge CB, Karlin S (1998) Finding the genes in genomic DNA. Curr Opin Struct Biol 8:346–354

    Article  CAS  PubMed  Google Scholar 

  • Cipollini D (2008) Constitutive expression of methyl jasmonate-inducible responses delays reproduction and constrains fitness responses to nutrients in Arabidopsis thaliana. Evol Ecol 24:59–68

    Article  Google Scholar 

  • Cohen R, Hanan A, Paris HS (2003) Single-gene resistance to powdery mildew in zucchini squash (Cucurbita pepo). Euphytica 130:433–441

    Article  CAS  Google Scholar 

  • Collum TD, Padmanabhan MS, Hsieh YC, Culver JN (2016) Tobacco mosaic virus-directed reprogramming of auxin/indole acetic acid protein transcriptional responses enhances virus phloem loading. Proc Natl Acad Sci U S A 113:E2740–E2749

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Desbiez C, Lecoq H (1997) Zucchini yellow mosaic virus. Plant Pathol 46:809–829

    Article  Google Scholar 

  • Ercolano MR, Sanseverino W, Carli P, Ferriello F, Frusciante L (2012) Genetic and genomic approaches for R-gene mediated disease resistance in tomato: retrospects and prospects. Plant Cell Rep 31:973–985

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Esteras C, Gómez P, Monforte AJ, Blanca J, Vicente-Dólera N, Roig C, Nuez F, Picó B (2012) High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping. BMC Genomics 13:80

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Formisano G, Paris HS, Frusciante L, Ercolano MR (2010) Commercial Cucurbita pepo squash hybrids carrying disease resistance introgressed from Cucurbita moschata have high genetic similarity. Plant Genet Resour 8:198–203

    Article  CAS  Google Scholar 

  • Fulton TM, Chunwongse J, Tanksley SD (1995) Microprep protocol for extraction of DNA from tomato and other herbaceous plants. Plant Mol Biol Report 13:207–209

    Article  CAS  Google Scholar 

  • Gal-On A (2007) Zucchini yellow mosaic virus: insect transmission and pathogenicity—the tails of two proteins. Mol Plant Pathol 8:139–150

    Article  CAS  PubMed  Google Scholar 

  • Gilbert-Albertini F, Lecoq H, Pitrat M, Nicolet JL (1993) Resistance of Cucurbita moschata to watermelon mosaic virus type 2 and its genetic relation to resistance to zucchini yellow mosaic virus. Euphytica 69:231–237

    Article  Google Scholar 

  • Gómez P, Rodríguez-Hernández AM, Moury B, Aranda MA (2009) Genetic resistance for the sustainable control of plant virus diseases: breeding, mechanisms and durability. Eur J Plant Pathol 125:1–22

    Article  Google Scholar 

  • Gong L, Stift G, Kofler R, Pachner M, Lelley T (2008a) Microsatellites for the genus Cucurbita and an SSR-based genetic linkage map of Cucurbita pepo L. Theor Appl Genet 117:37–48

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gong L, Pachner M, Kalai K, Lelley T (2008b) SSR-based genetic linkage map of Cucurbita moschata and its synteny with Cucurbita pepo. Genome 51:878–887

    Article  CAS  PubMed  Google Scholar 

  • Iovieno P, Andolfo G, Schiavulli A, Catalano D, Ricciardi L, Frusciante L et al. (2015) Structure, evolution and functional inference on the MildewLocusO (MLO) gene family in three cultivated Cucurbitaceae. BMC Genomics 16:1112. doi:10.1186/s12864-015-2325-3

  • Ishibashi K, Kezuka Y, Kobayashi C, Kato M, Inoue T, Nonaka T et al (2014) Structural basis for the recognition–evasion arms race between Tomato mosaic virus and the resistance gene Tm-1. PNAS 111:E3486–E3495

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lecoq H, Pitrat M, Clément M (1981) Identification et caractérisation d’un potyvirus provoquant la maladie du rabougrissement jaune du melon. Agronomie 1:827–834

    Article  Google Scholar 

  • Lefebvre V, Palloix A (1996) Both epistatic and additive effects of QTLs are involved in polygenic induced resistance to disease: a case study, the interaction pepper—Phytophthora capsici Leonian. Theor Appl Genet 93:503–511

    Article  CAS  PubMed  Google Scholar 

  • Levi A, Thomas CE, Newman M, Zhan X, Xu Y, Wehner TC (2003) Massive preferential segregation and nonrandom assortment of linkage-groups produce quasi-linkage in an F2 mapping population of watermelon. Hortscience 38:782

    Google Scholar 

  • Lisa V, Lecoq H (1984) Zucchini yellow mosaic virus. Descriptions of Plant Viruses, Commonwealth Mycological Institute and Association of Applied Biologists 282

  • Lisa V, Boccardo G, D'Agostino G, Dellavalle G, d’Aquilio M (1981) Characterization of a potyvirus that causes zucchini yellow mosaic. Phytopathology 71:667–672

    Article  CAS  Google Scholar 

  • MacQueen A, Bergelson J (2016) Modulation of R-gene expression across environments. J Exp Bot 67:2093–2105

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209–220

    CAS  PubMed  Google Scholar 

  • Munger HM, Provvidenti R (1987) Inheritance of resistance to zucchini yellow mosaic virus in Cucurbita moschata. Cucurbit Genet Coop Rep 10:8–81

    Google Scholar 

  • Nameth ST, Dodds JA, Paulus AO, Laemmlen FF (1986) Cucurbit viruses of California: an ever-changing problem. Plant Dis 70:8–12

    Article  Google Scholar 

  • Ott J, Wang J, Leal SM (2015) Genetic linkage analysis in the age of whole-genome sequencing. Nat Rev Genet 16(5):275–284

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pachner M, Lelley T (2004) Different genes for resistance to zucchini yellow mosaic virus (ZYMV) in Cucurbita moschata. In: Lebeda A, Paris HS (eds) Progress in cucurbit genetics and breeding research: Proceedings of Cucurbitaceae 2004. Palacky University, Olomouc (Czech Republic), pp 237–243

    Google Scholar 

  • Pachner M, Paris HS, Lelley T (2011) Genes for resistance to zucchini yellow mosaic in tropical pumpkin. J Hered 102:330–335

    Article  CAS  PubMed  Google Scholar 

  • Pachner M, Paris HS, Winkler J, Lelley T (2015) Phenotypic and marker-assisted pyramiding of genes for resistance to zucchini yellow mosaic virus in oilseed pumpkin (Cucurbita pepo). Plant Breed 134:121–128

    Article  CAS  Google Scholar 

  • Paris HS (1986) A proposed subspecific classification for Cucurbita pepo. Phytologia 61:133–138

    Google Scholar 

  • Paris HS (2001) Characterization of the Cucurbita pepo collection at the Newe Ya‘ar Research Center, Israel. Plant Genet Resour Newsl 126:41–45

    Google Scholar 

  • Paris HS (2008) Summer squash. In: Prohens J, Nuez F (eds) Handbook of plant breeding, Vegetables I: 351–379

  • Paris HS, Cohen S (2000) Oligogenic inheritance for resistance to zucchini yellow mosaic virus in Cucurbita pepo. Ann Appl Biol 136:209–214

    Article  Google Scholar 

  • Paris HS, Cohen S, Burger Y, Joseph R (1988) Single-gene resistance to zucchini yellow mosaic virus in Cucurbita moschata. Euphytica 37:27–29

    Article  Google Scholar 

  • Peakall PE, Smouse R (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics 28:2537–2539

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sakamoto T, Deguchi M, Brustolini OJ, Santos AA, Silva FF, Fontes EP (2012) The tomato RLK superfamily: phylogeny and functional predictions about the role of the LRRII-RLK subfamily in antiviral defense. BMC Plant Biol 12:229

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sanseverino W, Ercolano MR (2012) In silico approach to predict candidate R proteins and to define their domain architecture. BMC Res Notes 5:678

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Teare MD, Santibanez Koref MF (2014) Linkage analysis and the study of Mendelian disease in the era of whole exome and genome sequencing. Brief Funct Genomics 13(5):378–383

    Article  PubMed  Google Scholar 

  • Valkonen JPT, Wiegmann K, Hämäläinen JH, Marczewski W, Watanabe KN (2008) Evidence for utility of the same PCR-based markers for selection of extreme resistance to Potato virus Y controlled by Rysto of Solanum stoloniferum derived from different sources. Ann Appl Biol 152:121–130

    Article  CAS  Google Scholar 

  • Wessel-Beaver L (2005) Cultivar and germplasm release. Release of ‘Soler’ tropical pumpkin. J Agric Univ P R 89:263–266

    Google Scholar 

  • Whitaker TW, Davis GN (1962) Cucurbits: botany, cultivation and utilization. Interscience, New York, pp 105–116

    Google Scholar 

  • Whitaker TW, Robinson RW (1986) Squash breeding. In: Bassett MJ (ed) Breeding vegetable crops. Avi, Westport, pp 209–242

    Google Scholar 

  • Xu Y, Crouch JH (2008) Marker-assisted selection in plant breeding: from publications to practice. Crop Sci 48:391–407

    Article  Google Scholar 

  • Xu R, Zhang S, Huang J, Zheng C (2013) Genome-wide comparative in silico analysis of the RNA helicase gene family in Zea mays and Glycine max: a comparison with Arabidopsis and Oryza sativa. PLoS One 8:e78982

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ye G, Smith KF (2008) Marker-assisted gene pyramiding for inbred line development: basic principles and practical guidelines. Int J Plant Breed 2:1–10

    Article  Google Scholar 

  • Zdobnov EM, Apweiler R (2001) InterProScan—an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17:847–848

    Article  CAS  PubMed  Google Scholar 

  • Zraidi A, Stift G, Pachner M, Shojaeiyan A, Gong L, Lelley T (2007) A consensus map for Cucurbita pepo. Mol Breed 20:375–388

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by the Ministry of University and Research (GenHORT project).

We thank La Semiorto Sementi S.r.l. for plant material.

Author information

Author notes

  1. Claudio Capuozzo and Gelsomina Formisano contributed equally to this work.

Authors and Affiliations

  1. Department of Agricultural Sciences, University of Naples ‘Federico II’, Via Università 100, 80055, Naples, Portici, Italy

    Claudio Capuozzo, Paolo Iovieno, Giuseppe Andolfo, Maria Mafalda Barbella & Maria Raffaella Ercolano

  2. La Semiorto Sementi S.r.l. Sarno, Via Vecchia Lavorate 81-85, 84087, Salerno, Sarno, Italy

    Claudio Capuozzo & Gelsomina Formisano

  3. Council for Agricultural Research and Agricultural Economy Analysis (CREA), Plant Pathology Research Centre, Via Bertero 22, 00156, Rome, Italy

    Laura Tomassoli

  4. Universidad Politecnica de Valencia, Edificio 8 Escalera J Cpi Cammino de Vera SN Univeridad Politecna de Valencia, 46022, Valencia, Spain

    Belen Pico

  5. Department of Vegetable Crops and Plant Genetics, Agricultural Research Organization, Newe Ya‘ar Research Center, 30-095, Ramat Yishay, Israel

    Harry S. Paris

Authors
  1. Claudio Capuozzo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Gelsomina Formisano
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Paolo Iovieno
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Giuseppe Andolfo
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Laura Tomassoli
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Maria Mafalda Barbella
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Belen Pico
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Harry S. Paris
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Maria Raffaella Ercolano
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Maria Raffaella Ercolano.

Electronic supplementary material

ESM 1

(ODS 9 kb)

Supplementary figure 1

High Resolution Melting Real-Time PCR (HRM) profiles. The profiles of the melting curves of amplicons containing SNP1 (panel A) of the resistant parent (Accession 381e), homozygous A/A, (green curves), the susceptible parent (‘True French’), homozygous G/G (red curves) and derived hybrid, heterozygous A/G (blue curves). A and G represent the alternative nucleotide of the identified SNP1. In panels B and C, the melting curves of amplicons containing SNP2 and SNP3 are shown, respectively. The green curves show the homozygous individuals (C/C and T/T, in B and C, respectively), such as the resistant parent (Accession 381e), meanwhile the red curves those (A/A and C/C, in B and C, respectively) such as the susceptible parent (‘True French’). The derived F1s, heterozygous A/C for SNP2 and C/T for SNP3, are depicted as blue curves. (GIF 126 kb)

High resolution image (TIFF 396 kb)

Supplementary figure 2

A Cleaved Amplified Polymorphism Sequence (CAPS) marker. The polymorphism of the marker SNP1 is shown in the segregating F2 population generated by crossing Accession 381e (resistant to ZYMV, R) and ‘True French’ (susceptible to ZYMV, r). In lane 5: resistant homozygous genotypes (R/R - 400 bp); in lanes 1, 3, 9, 10, 11 and 12: susceptible homozygous genotype (r/r – 200 bp); in lanes 2, 4, 6, 7 and 8: resistant heterozygous genotypes (R/r - 400 bp and 200 bp), M: ladder (1Kb+, Life technologies Invitrogen). (GIF 32 kb)

High resolution image (TIFF 426 kb)

Supplementary figure 3

A linkage analysis among markers was performed. SNP2 and SNP3 are on a single linkage group, at genetic distance 39.1 cM, for the ‘True French’ × Accession 381e F2 population (panel A) whilst are at a distance of 18.7 cM for the BC1 from Plant 28 of the F2 of ‘San Pasquale’ × Accession 381e (panel B). (GIF 45 kb)

High resolution image (TIFF 49 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Capuozzo, C., Formisano, G., Iovieno, P. et al. Inheritance analysis and identification of SNP markers associated with ZYMV resistance in Cucurbita pepo . Mol Breeding 37, 99 (2017). https://doi.org/10.1007/s11032-017-0698-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s11032-017-0698-5

Keywords

Search

Navigation