Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

Genetic mapping and QTL analysis of horticultural traits in cucumber (Cucumis sativus L.) using recombinant inbred lines


A set of 171 recombinant inbred lines (RIL) were developed from a narrow cross in cucumber (Cucumis sativus L.; 2n = 2x = 14) using the determinate (de), gynoecious (F), standard-sized leaf line G421 and the indeterminate, monoecious, little-leaf (ll) line H-19. A 131-point genetic map was constructed using these RILs and 216 F2 individuals to include 14 SSRs, 24 SCARs, 27 AFLPs, 62 RAPDs, 1 SNP, and three economically important morphological [F (gynoecy), de (determinate habit), ll (little leaf)] markers. Seven linkage groups spanned 706 cM with a mean marker interval of 5.6 cM. The location of F and de was defined by genetic linkage and quantitative trait locus (QTL) analysis to be associated with SSR loci CSWCT28 and CSWCTT14 at 5.0 cM and 0.8 cM, respectively. RIL-based QTL analysis of the number of lateral branches in three environments revealed four location-independent factors that cumulatively explained 42% of the observed phenotypic variation. QTLs conditioning lateral branching (mlb1.1), fruit length/diameter ratio (ldr1.2) and sex expression (sex1.2) were associated with de. Sex expression was influenced by three genomic regions corresponding to F and de both on linkage Group 1, and a third locus (sex6.1) on linkage Group 6. QTLs conditioning the number of fruit per plant (fpl1.2), the number of lateral branches (mlb1.4) and fruit length/diameter ratio (ldr1.3) were associated with ll. The potential value of these marker-trait associations (i.e., yield components) for plant improvement is portended by the relatively high LOD scores (2.6 to 13.0) and associated R2 values (1.5% to 32.4%) that are affiliated with comparatively few genetic factors (perhaps 3 to 10).

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

Fig. 1.


  1. Austin DF, Lee M (1996) Comparative mapping in F2:3 and F6:7 generations of quantitative trait loci for grain yield and yield components in maize. Theor Appl Genet 92:817–826

  2. Basten CJ, Wang S, Weir BS, Zeng ZB (2001) QTL Cartographer version 1.21 for Windows Release 1.21. Department of Statistics, North Carolina State University, Raleigh, North Carolina

  3. Beavis WD (1998) QTL analyses: power, precision, and accuracy. In: Paterson AH (ed) Molecular dissection of complex traits. CRC Press, Boca Raton, pp 145–162

  4. Beyer EMJ (1976) Silver ion: a potent anti-ethylene agent in cucumber and tomato. HortScience 11:195–196

  5. Bradeen JM, Staub JE, Wye C, Antonise R, Peleman J (2001) Towards an expanded and integrated linkage map of cucumber (Cucumis sativus L.). Genome 44:111–119

  6. Burr B, Burr FA, Thompson KH, Albertson MC, Stuber CW (1988) Gene mapping with recombinant inbreds in maize. Genetics 118:519–526

  7. Cantliffe DJ (1981) Alteration of sex expression in cucumber due to changes in temperature, light intensity, and photoperiod. J Am Soc Hort Sci 106:133–136

  8. Cargill G (1962) Studies of factors affecting the yield and quality of cucumbers. I. Fruit length and fruit setting. Acta Agric Sand 12:355–362

  9. Carrillo JM, Rousset M, Qualset CO, Kasarda DD (1990) Use of recombinant inbred lines of wheat for study of associations of high-molecular-weight glutenin subunit alleles to quantitative traits. 1. Grain yield and quality prediction tests. Theor Appl Genet 79:321–330

  10. Cowen NM (1988) The use of replicated progenies in marker-based mapping of QTLs. Theor Appl Genet 75:857–862

  11. Cramer CS, Wehner TC (2000) Path analysis of the correlation between fruit number and plant traits of cucumber populations. HortScience 35:708–711

  12. Danin Poleg Y, Reis N, Baudracco Arnas S, Pitrat M, Staub JE, Oliver M, Arus P, de Vicente CM, Katzir N (2000) Simple sequence repeats in Cucumis mapping and map merging. Genome 43:963–974

  13. Danin Poleg Y, Reis N, Tzuri G, Katzir N (2001) Development and characterization of microsatellite markers in Cucumis. Theor Appl Genet 102:61–72

  14. Dijkhuizen, A, Staub JE (2003) Effects of environment and genetic background on QTLs conditioning yield and fruit quality traits in cucumber (Cucumis sativus L.). J New Seeds (in press)

  15. Fazio G (2001) Comparative study of marker-assisted and phenotypic selection and genetic analysis of yield components in cucumber. Dissertation, University of Wisconsin-Madison

  16. Fazio G, Staub JE (2000) Method for the development and characterization of microsatellite markers in cucumber. Cucurbit Genet Coop Rep 23:4–7

  17. Fazio G, Staub JE (2003) Comparative analysis of response to phenotypic and marker-assisted selection for multiple lateral branching in cucumber (Cucumis sativus L.). Theor Appl Genet DOI 10.1007/s00122-003-1313-1

  18. Fazio G, Staub JE, Chung SM (2002) Development and characterization of PCR markers in cucumber (Cucumis sativus L.). J Am Soc Hort Sci 127:545–557

  19. Fuller GL, Leopold CA (1977) The role of nucleic acid synthesis in cucumber fruit set. J Am Soc Hort Sci 102:384–388

  20. Fulton TM, Beckbunn T, Emmatty D, Eshed Y, Lopez J, Petiard V, Uhlig J, Zamir D, Tanksley SD (1997) QTL analysis of an advanced backcross of Lycopersicon peruvianum to the cultivated tomato and comparisons with QTLs found in other wild species. Theor Appl Genet 95:881–894

  21. Goldman IL, Paran I, Zamir D (1995) Quantitative trait locus analysis of a recombinant inbred line population derived from the Lycopersicon esculentum × Lycopersicon cheesmanii cross. Theor Appl Genet 90:925–932

  22. Horejsi T, Box JM, Staub JE (1999) Efficiency of randomly amplified polymorphic DNA to sequence-characterized amplified-region marker conversion and their comparative polymerase chain reaction sensitivity in cucumber. J Am Soc Hort Sci 124:128–135

  23. Horejsi T, Staub JE, Thomas C (2000) Linkage of random amplified polymorphic DNA markers to downy mildew resistance in cucumber (Cucumis sativus L.). Euphytica 115:105–113

  24. Katzir N, Danin Poleg Y, Tzuri G, Karchi Z, Lavi U, Cregan PB (1996) Length polymorphism and homologies of microsatellites in several Cucurbitaceae species. Theor Appl Genet 93:1282–1290

  25. Kennard WC, Poetter K, Dijkhuizen A, Meglic V, Staub JE, Havey MJ (1994) Linkages among RFLP, RAPD, isozyme, disease-resistance, and morphological markers in narrow and wide crosses of cucumber. Theor Appl Genet 89:42–48

  26. King GJ, Lynn JR, Dover CJ, Evans KM (2001) Resolution of quantitative trait loci for mechanical measures accounting for genetic variation in fruit texture of apple (Malus pumila Mill.). Theor Appl Genet 4:1227–1235

  27. Knapp SJ, Bridges WC (1990) Using molecular markers to estimate quantitative trait locus parameters power and genetic variances for unreplicated and replicated progeny. Genetics 126:769–777

  28. Knerr LD, Staub JE (1992) Inheritance and linkage relationships of isozyme loci in cucumber (Cucumis sativus L.). Theor Appl Genet 84:217–224

  29. Littell RC, Milliken GA, Stroup WW, Wolfinger RD (1996) SAS system for mixed models. SAS Istitute Inc., Cary, North Carolina

  30. Lower RL, Nijs TPM (1979) Effect of plant-type genes on growth and sex expression of pickling cucumbers. HortScience 14:435

  31. Lower RL, Edwards MD (1986) Cucumber breeding, In: Bassett MJ (ed) Breeding vegetable crops. AVI Pub. Co, Westport, Connecticut

  32. Mansur LM, Orf JH, Chase K, Jarvik T, Cregan PB, Lark KG (1996) Genetic mapping of agronomic traits using recombinant inbred lines of soybean. Crop Sci 36:1327–1336

  33. Marquez-Cedillo LA, Hayes PM, Jones BL, Kleinhofs A, Legge WG, Rossnagel BG, Sato K, Ullrich E, Wesenberg DM (2000) QTL analysis of malting quality in barley based on the doubled-haploid progeny of two elite North American varieties representing different germplasm groups. Theor Appl Genet 101:173–184

  34. Meglic V, Staub JE (1996) Inheritance and linkage relationships of isozyme and morphological loci in cucumber (Cucumis sativus L.). Theor Appl Genet 92:865–872

  35. Melchinger AE, Utz HF, Schon CC (1998) Quantitative trait locus (QTL) mapping using different testers and independent population samples in maize reveals low power of QTL detection and large bias in estimates of QTL effects. Genetics 149:383–403

  36. Paran I, Goldman IL, Zamir D (1997) QTL analysis of morphological traits in a tomato recombinant inbred line population. Genome 40:242–248

  37. Paran I, Goldman IL, Tanksley SD, Zamir D (1995) Recombinant inbred lines for genetic mapping in tomato. Theor Appl Genet 90:542–548

  38. Paterson AH, Damon S, Hewitt JD, Zamir D, Rabinowitch HD, Lincoln SE, Lander ES, Tanksley SD (1991) Mendelian factors underlying quantitative traits in tomato: comparison across species, generations, and environments. Genetics 127:181–197

  39. Peterson CE (1960) A gynoecious inbred line of cucumber. Michigan Agric Exp Station Quart Bull 43:40–42

  40. Peterson CE (1978) Plant introductions in the improvement of vegetable cultivars. HortScience 10:575–579

  41. Pierce LK, Whener TC (1990) Review of genes and linkage groups in cucumber. HortScience 25:605–615

  42. Reiter RS, Williams JKG, Feldman KA, Rafalski A, Tingey SV, Scolnik PA (1992) Global and local genome mapping in Arabidopsis thaliana by using recombinant inbred lines and random amplified polymorphic DNAs. Proc Natl Acad Sci USA 89:1477–1481

  43. Romagosa I, Han F, Ullrich SE, Hayes PM, Wesenberg DM (1999) Verification of yield QTLs through realized molecular marker-assisted selection responses in a barley cross. Mol Breed 5:143–152

  44. Saliba-Colombani V, Causse M, Langlois D, Philouze J, Buret M (2001) Genetic analysis of organoleptic quality in fresh market tomato. 1. Mapping QTLs for physical and chemical traits. Theor Appl Genet 102:259–272

  45. Serquen FC, Staub JE (1996) Environment can affect the placement of discrete traits on genetic maps: the case of sex expression in cucumber. Cucurbit Genet Coop Rep 19:10–12

  46. Serquen FC, Bacher J, Staub JE (1997a) Mapping and QTL analysis of horticultural traits in a narrow cross in cucumber (Cucumis sativus L.) using random-amplified polymorphic DNA markers. Mol Breed 3:257–268

  47. Serquen FC, Bacher J, Staub JE (1997b) Genetic analysis of yield components in cucumber at low plant density. J Am Soc Hort Sci 122:522–528

  48. Simpson SP (1989) Detection of linkage between quantitative trait loci and restriction fragment length polymorphisms using inbred lines. Theor Appl Genet 77:815–819

  49. Staub JE (1999) Intellectual property rights, genetic markers, and hybrid seed production. J New Seeds 1:39–64

  50. Staub JE, Meglic V (1993) Molecular genetic markers and their legal relevance for cultivar discrimination: a case study in cucumber. HortTechnology 3:291–300

  51. Staub JE, Peterson CE, Crubaugh LK, Palmer MJ (1992) Cucumber population WI 6383 and derived inbreds WI 5098 and WI 5551. HortScience 27:1340–1341

  52. Staub JE, Bacher J, Crubaugh L (1995) Problems associated with the selection of determinate cucumber (Cucumis sativus L.) plant types in a multiple lateral background. Cucurbit Genet Coop Rep 18:7–9

  53. Staub JE, Serquen FC, Gupta M (1996a) Genetic markers, map construction, and their application in plant breeding. HortScience 31:729–741

  54. Staub JE, Gabert A, Wehner TC (1996b) Plant variety protection – a consideration of genetic relationships. HortScience 31:1086–1091

  55. Tang D, Wu W, Li W, Lu H, Worland AJ (2000) Mapping of QTLs conferring resistance to bacterial leaf streak in rice. Theor Appl Genet 101:286–291

  56. Tanksley SD (1993) Mapping polygenes. Annu Rev Genet 27:205–233

  57. University of Arkansas-Fayetteville (1993) H-19 Cucumber Plant Variety Protection Certificate USA 1993

  58. USDA-NASS (1999) Statistical Bullettin 946c

  59. Utz HF, Melchinger AE, Schon CC (2000) Bias and sampling error of the estimated proportion of genotypic variance explained by quantitative trait loci determined from experimental data in maize using cross validation and validation with independent samples. Genetics 154:1839–1849

  60. Van Ooijen JW, Voorrips RE (2001) Joinmap Version 3.0, Software for the calculation of genetic linkage maps Release 3.0. Plant Research International, Wageningen, The Netherlands

  61. Voorrips RE (2001) MapChart Version 2.0: Windows software for the graphical presentation of linkage maps and QTLs. Release 2.0. Plant Research International, Wageningen, The Netherlands

  62. Walters SA, Shetty NV, Wehner TC (2001) Segregation and linkage of several genes in cucumber. J Am Soc Hort Sci 126:442–450

  63. Wehner TC (1989) Breeding for improved yield in cucumber. Plant Breed Rev 6:323–359

  64. Wehner TC, Staub JE, Peterson CE (1987) Inheritance of little-leaf and multi-branched plant habit in cucumber. Cucurbit Genet Coop Rep 10:33–34

  65. Yousef GG, Juvik JA (2001) Comparison of phenotypic and marker-assisted selection for quantitative traits in sweet corn. Crop Sci 41:645–655

  66. Zhang Q, Gabert AC, Baggett JR (1992) Parents and mating systems affect the transfer of gynoecious flowering to Chinese monoecious cucumbers. J Am Soc Hort Sci 117:515–517

Download references


This research was partially supported by grant No. IS-2708-96 from the U.S.-Israel Binational Agricultural Research and Development (BARD) Fund.

Author information

Correspondence to J. E. Staub.

Additional information

Communicated by H.C. Becker

Mention of trade name, proprietary product, or specific equipment does not constitute a guarantee or warranty by the USDA and does not imply its approval to the exclusion of other products that may be suitable

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Fazio, G., Staub, J.E. & Stevens, M.R. Genetic mapping and QTL analysis of horticultural traits in cucumber (Cucumis sativus L.) using recombinant inbred lines. Theor Appl Genet 107, 864–874 (2003). https://doi.org/10.1007/s00122-003-1277-1

Download citation


  • Linkage Analysis
  • Yield Components
  • Linkage Map
  • Composite Interval Mapping
  • Pleiotropic Effects