Theoretical and Applied Genetics

, Volume 119, Issue 4, pp 621–634 | Cite as

Comparative analysis of marker-assisted and phenotypic selection for yield components in cucumber

Original Paper


Theoretical studies suggest that marker-assisted selection (MAS) has case-specific advantages over phenotypic selection (PHE) for selection of quantitative traits. However, few studies have been conducted that empirically compare these selection methods in the context of a plant breeding program. For direct comparison of the effectiveness of MAS and PHE, four cucumber (Cucumis sativus L.; 2n = 2x = 14) inbred lines were intermated and then maternal bulks were used to create four base populations for recurrent mass selection. Each of these populations then underwent three cycles of PHE (open-field evaluations), MAS (genotyping at 18 marker loci), and random mating without selection. Both MAS and PHE were practiced for yield indirectly by selecting for four yield-component traits that are quantitatively inherited with 2–6 quantitative trait loci per trait. These traits were multiple lateral branching, gynoecious sex expression (gynoecy), earliness, and fruit length to diameter ratio. Both MAS and PHE were useful for multi-trait improvement, but their effectiveness depended upon the traits and populations under selection. Both MAS and PHE provided improvements in all traits under selection in at least one population, except for earliness, which did not respond to MAS. The populations with maternal parents that were inferior for a trait responded favorably to both MAS and PHE, while those with maternal parents of superior trait values either did not change or decreased during selection. Generally, PHE was most effective for gynoecy, earliness, and fruit length to diameter ratio, while MAS was most effective for multiple lateral branching and provided the only increase in yield (fruit per plant).

Supplementary material

122_2009_1072_MOESM1_ESM.pdf (49 kb)
Supplementary Table (PDF 50KB)


  1. Bernardo R (2002) Breeding for quantitative traits in plants, 1st edn. Stemma Press, WoodburyGoogle Scholar
  2. Bernardo R, Charcosset A (2006) Usefulness of gene information in marker-assisted recurrent selection: a simulation appraisal. Crop Sci 46:614–621CrossRefGoogle Scholar
  3. Bernardo R, Yu J (2007) Prospects for genomewide selection for quantitative traits in maize. Crop Sci 47:1082–1090CrossRefGoogle Scholar
  4. Bohn M, Groh S, Khairallah MM, Hoisington DA, Utz HF, Melchinger AE (2001) Re-evaluation of the prospects of marker-assisted selection for improving insect resistance against Diatraea spp in tropical maize by cross validation and independent validation. Theor Appl Genet 103:1059–1067CrossRefGoogle Scholar
  5. Casler MD (1999) Phenotypic recurrent selection methodology for reducing fiber concentration in smooth bromegrass. Crop Sci 39:381–390Google Scholar
  6. Collard BCY, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Phil Trans R Soc B 363:557–572PubMedCrossRefGoogle Scholar
  7. Collard BCY, Jahufer MZZ, Brouwer JB, Pang ECK (2005) An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: The basic concepts. Euphytica 142:169–196CrossRefGoogle Scholar
  8. Cramer CS, Wehner TC (1998) Fruit yield and yield component means and correlations of four slicing cucumber populations improved through six to ten cycles of recurrent selection. J Am Soc Hort Sci 123:388–395Google Scholar
  9. Cramer CS, Wehner TC (1999) Little heterosis for yield and yield components in hybrids of six cucumber inbreds. Euphytica 110:99–108CrossRefGoogle Scholar
  10. Cramer CS, Wehner TC (2000a) Path analysis of the correlation between fruit number and plant traits of cucumber populations. HortScience 35:708–711Google Scholar
  11. Cramer CS, Wehner TC (2000b) Fruit yield and yield component correlations of four pickling cucumber populations. Cucurbit Genet Coop Rpt 23:12–15Google Scholar
  12. Davies J, Berzonsky WA, Leach GD (2006) A comparison of marker-assisted and phenotypic selection for high grain protein content in spring wheat. Euphytica 152:117–134CrossRefGoogle Scholar
  13. de Oliveira EJ, Alzate-Marin AL, Borem A, Fagundes SD, de Barros EG, Moreira MA (2005) Molecular marker-assisted selection for development of common bean lines resistant to angular leaf spot. Plant Breed 124:572–575CrossRefGoogle Scholar
  14. Eathington SR, Dudley JW, Rufener GK (1997) Usefulness of marker-QTL associations in early generation selection. Crop Sci 37:1686–1693Google Scholar
  15. Edwards MD, Page NJ (1994) Evaluation of marker-assisted selection through computer simulation. Theor Appl Genet 88:376–382CrossRefGoogle Scholar
  16. Fan Z, Robbins MD, Staub JE (2006) Population development by phenotypic selection with subsequent marker-assisted selection for line extraction in cucumber (Cucumis sativus L.). Theor Appl Genet 112:843–855PubMedCrossRefGoogle Scholar
  17. Fazio G (2001) Comparative study of marker-assisted and phenotypic selecton and genetic analysis of yield components in cucumber. PhD dissertation, University of Wisconsin MadisonGoogle Scholar
  18. Fazio G, Chung SM, Staub JE (2003a) Comparative analysis of response to phenotypic and marker-assisted selection for multiple lateral branching in cucumber (Cucumis sativus L.). Theor Appl Genet 107:875–883PubMedCrossRefGoogle Scholar
  19. Fazio G, Staub JE, Stevens MR (2003b) Genetic mapping and QTL analysis of horticultural traits in cucumber (Cucumis sativus L.) using recombinant inbred lines. Theor Appl Genet 107:864–874PubMedCrossRefGoogle Scholar
  20. Flint-Garcia SA, Darrah LL, McMullen MD, Hibbard BE (2003) Phenotypic versus marker-assisted selection for stalk strength and second-generation European corn borer resistance in maize. Theor Appl Genet 107:1331–1336PubMedCrossRefGoogle Scholar
  21. Francia E, Tacconi G, Crosatti C, Barabaschi D, Bulgarelli D, Dall’Aglio E, Vale G (2005) Marker assisted selection in crop plants. Plant Cell Tissue Organ Cult 82:317–342CrossRefGoogle Scholar
  22. Fredrick LR, Staub JE (1989) Combining ability analyses of fruit yield and quality in near-homozygous lines derived from cucumber. J Am Soc Hort Sci 114:332–338Google Scholar
  23. Gimelfarb A, Lande R (1994a) Simulation of marker assisted selection for nonadditive traits. Genet Res 64:127–136PubMedCrossRefGoogle Scholar
  24. Gimelfarb A, Lande R (1994b) Simulation of marker assisted selection in hybrid populations. Genet Res 63:39–47PubMedGoogle Scholar
  25. Gupta PK, Roy JK, Prasad M (2001) Single nucleotide polymorphisms: a new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on their use in plants. Curr Sci 80:524–535Google Scholar
  26. Hoeck JA, Fehr WR, Shoemaker RC, Welke GA, Johnson SL, Cianzio SR (2003) Molecular marker analysis of seed size in soybean. Crop Sci 43:68–74CrossRefGoogle Scholar
  27. Huang S, Du Y, Wang X, Gu X, Xie B, Zhang Z, Wang J, Li R, Li S, Ren Y, Wang J, Yang H, Jin W, Fei Z, Kilian A, Staub JE, van der Vossen E, Li G (2008) The cucumber genome initiative—an international effort to unlock the genetic potential of an orphan crop using novel genomic technology. In: Abstracts of the plant and animal genomes XVI conference, San Diego, California, 12–16 January 2008Google Scholar
  28. Kuchel H, Fox R, Reinheimer J, Mosionek L, Willey N, Bariana H, Jefferies S (2007) The successful application of a marker-assisted wheat breeding strategy. Mol Breed 20:295–308CrossRefGoogle Scholar
  29. Kupper RS, Staub JE (1988) Combining ability between lines of Cucumis sativus L. and Cucumis sativus var. hardwickii (R.) Alef. Euphytica 38:197–210CrossRefGoogle Scholar
  30. Lande R, Thompson R (1990) Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics 124:743–756PubMedGoogle Scholar
  31. Lower RL, Edwards MD (1986) Cucumber breeding. In: Bassett MJ (ed) Breeding vegetable crops. AVI, Westport, pp 173–207Google Scholar
  32. Mohring S, Salamini F, Schneider K (2004) Multiplexed, linkage group-specific SNP marker sets for rapid genetic mapping and fingerprinting of sugar beet (Beta vulgaris L.). Mol Breed 14:475–488CrossRefGoogle Scholar
  33. Moreau L, Charcosset A, Gallais A (2004) Experimental evaluation of several cycles of marker-assisted selection in maize. Euphytica 137:111–118CrossRefGoogle Scholar
  34. Nam YW, Lee JR, Song KH, Lee MK, Robbins MD, Chung SM, Staub JE, Zhang HB (2005) Construction of two BAC libraries from cucumber (Cucumis sativus L.) and identification of clones linked to yield component quantitative trait loci. Theor Appl Genet 111:150–161PubMedCrossRefGoogle Scholar
  35. Nijs APMD, Visser DL (1980) Induction of male flowering in gynoecious cucumbers (Cucumis sativus L.) by silver ions. Euphytica 29:273–280CrossRefGoogle Scholar
  36. Polashock JJ, Vorsa N (2002) Development of SCAR markers for DNA fingerprinting and germplasm analysis of American cranberry. J Am Soc Hort Sci 127:677–684Google Scholar
  37. Robbins MD (2006) Molecular marker development, QTL pyramiding, and comparative analysis of phenotypic and marker-assisted selection in cucumber. Dissertation, University of Wisconsin MadisonGoogle Scholar
  38. Robbins MD, Staub JE (2004) Strategies for selection of multiple, quantitatively inherited yield components in cucumber. In: Lebeda A, Paris HS (eds) Progress in cucurbit genetics and breeding research. proceedings of Cucurbitaceae 2004, the 8th EUCARPIA meeting on cucurbit genetics and breeding. Palacky University, Olomouc, pp 401–408Google Scholar
  39. Robbins MD, Staub JE, Fazio G (2002) Deployment of molecular markers for multi-trait selection in cucumber. In: Cucurbitaceae 2002. American Society of Horticultural Science Press, Alexandria, pp 41–47Google Scholar
  40. Romagosa I, Han F, Ullrich SE, Hayes PM, Wesenberg DM (1999) Verification of yield QTL through realized molecular marker-assisted selection responses in a barley cross. Mol Breed 5:143–152CrossRefGoogle Scholar
  41. SAS (2003) SAS software, Version 9.1 for Windows. Copyright© 2002–2003 by SAS Institute Inc., Cary, NCGoogle Scholar
  42. Schneider KA, Brothers ME, Kelly JD (1997) Marker-assisted selection to improve drought resistance in common bean. Crop Sci 37:51–60CrossRefGoogle Scholar
  43. Serquen FC, Bacher J, Staub JE (1997a) Genetic analysis of yield components in cucumber at low plant density. J Am Soc Hort Sci 122:522–528Google Scholar
  44. Serquen FC, Bacher J, Staub JE (1997b) Mapping and QTL analysis of horticultural traits in a narrow cross in cucumber (Cucumis sativus L.) using random-amplified polymorphic DNA markers. Mol Breed 3:257–268CrossRefGoogle Scholar
  45. Shetty NV, Wehner TC (2002) Screening the cucumber germplasm collection for fruit yield and quality. Crop Sci 42:2174–2183CrossRefGoogle Scholar
  46. Staub JE, Crubaugh LK (2001) Cucumber inbred line USDA 6632E. Cucurbit Genet Coop Rpt 24:6–7Google Scholar
  47. Staub JE, Knerr LD, Hopen HJ (1992) Plant density and herbicides affect cucumber productivity. J Am Soc Hort Sci 117:48–53Google Scholar
  48. Staub JE, Crubaugh LK, Fazio G (2002) Cucumber recombinant inbred lines. Cucurbit Genet Coop Rpt 25:1–2Google Scholar
  49. Staub JE, Robbins MD, Chung S, López-Sesé AI (2004) Molecular methodologies for improved genetic diversity assessment in cucumber and melon. Acta Hort 637:41–47Google Scholar
  50. Steele RGD, Torrie JH, Dickey DA (1996) Principles and procedure in statistics, 3rd edn. McGraw-Hill, New YorkGoogle Scholar
  51. Steele KA, Price AH, Shashidhar HE, Witcombe JR (2006) Marker-assisted selection to introgress rice QTLs controlling root traits into an Indian upland rice variety. Theor Appl Genet 112:208–222PubMedCrossRefGoogle Scholar
  52. Stromberg LD, Dudley JW, Rufener GK (1994) Comparing conventional early generation selection with molecular marker assisted selection in maize. Crop Sci 34:1221–1225CrossRefGoogle Scholar
  53. Tang SX, Kishore VK, Knapp SJ (2003) PCR-multiplexes for a genome-wide framework of simple sequence repeat marker loci in cultivated sunflower. Theor Appl Genet 107:6–19PubMedGoogle Scholar
  54. Van Berloo R, Stam P (1999) Comparison between marker-assisted selection and phenotypical selection in a set of Arabidopsis thaliana recombinant inbred lines. Theor Appl Genet 98:113–118CrossRefGoogle Scholar
  55. van Berloo R, Stam P (2001) Simultaneous marker-assisted selection for multiple traits in autogamous crops. Theor Appl Genet 102:1107–1112CrossRefGoogle Scholar
  56. Wehner TC (1989) Breeding for improved yield in cucumber. Plant Breed Rev 6:323–359Google Scholar
  57. Wehner TC, Lower RL, Staub JE, Tolla GE (1989) Convergent-divergent selection for cucumber fruit yield. HortScience 24:667–669Google Scholar
  58. Willcox MC, Khairallah MM, Bergvinson D, Crossa J, Deutsch JA, Edmeades GO, Gonalez-de-Leon D, Jiang C, Jewell DC, Mihm JA, Williams WP, Hoisington D (2002) Selection for resistance to southwestern corn borer using marker-assisted and conventional backcrossing. Crop Sci 42:1516–1528Google Scholar
  59. Xu YB, Crouch JH (2008) Marker-assisted selection in plant breeding: from publications to practice. Crop Sci 48:391–407CrossRefGoogle Scholar
  60. Yousef GG, Juvik JA (2001) Comparison of phenotypic and marker-assisted selection for quantitative traits in sweet corn. Crop Sci 41:645–655CrossRefGoogle Scholar
  61. Yu K, Park SJ, Poysa V (2000) Marker-assisted selection of common beans for resistance to common bacterial blight: efficacy and economics. Plant Breed 119:411–415CrossRefGoogle Scholar
  62. Zhang W, Smith C (1992) Computer simulation of marker-assisted selection utilizing linkage disequilibrium. Theor Appl Genet 83:813–820Google Scholar
  63. Zhang C, Tar’an B, Warkentin T, Tullu A, Bett KE, Vandenberg B, Somers DJ (2006) Selection for lodging resistance in early generations of field pea by molecular markers. Crop Sci 46:321–329CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  1. 1.Vegetable Crops Research Unit, Department of HorticultureUSDA ARS, University of Wisconsin MadisonMadisonUSA
  2. 2.OARDC, The Ohio State UniversityWoosterUSA
  3. 3.Forage and Range Research Laboratory, USDA-ARSLoganUSA

Personalised recommendations