Theoretical and Applied Genetics

, Volume 132, Issue 5, pp 1505–1521 | Cite as

Identification of quantitative trait loci governing subgynoecy in cucumber

  • Khin Thanda Win
  • Chunying Zhang
  • Renato Rodrigues Silva
  • Jeong Hwan Lee
  • Young-Cheon Kim
  • Sanghyeob LeeEmail author
Original Article


Key message

QTL-seq analysis identified three major QTLs conferring subgynoecy in cucumbers. Furthermore, sequence and expression analyses predicted candidate genes controlling subgynoecy.


The cucumber (Cucumis sativus L.) is a typical monoecious having individual male and female flowers, and sex differentiation is an important developmental process that directly affects its fruit yield. Subgynoecy represents a sex form with a high degree of femaleness and would have alternative use as gynoecy under limited resource conditions. Recently, many studies have been reported that QTL-seq, which integrates the advantages of bulked segregant analysis and high-throughput whole-genome resequencing, can be a rapid and cost-effective way of mapping QTLs. Segregation analysis in the F2 and BC1 populations derived from a cross between subgynoecious LOSUAS and monoecious BMB suggested the quantitative nature of subgynoecy in cucumbers. Both genome-wide SNP profiling of subgynoecious and monoecious bulks constructed from F2 and BC1 plants consistently identified three significant genomic regions, one on chromosome 3 (sg3.1) and another two on short and long arms of chromosome 1 (sg1.1 and sg1.2). Classical QTL analysis using the F2 confirmed sg3.1 (R2 = 42%), sg1.1 (R2 = 29%) and sg1.2 (R2 = 18%) as major QTLs. These results revealed the unique genetic inheritance of subgynoecious line LOSUAS through two distinct major QTLs, sg3.1 and sg1.1, which mainly increase degree of femaleness, while another QTL, sg1.2, contributes to decrease it. This study demonstrated that QTL-seq allows rapid and powerful detection of QTLs using preliminary generation mapping populations such as F2 or BC1 population and further that the identified QTLs could be useful for molecular breeding of cucumber lines with high yield potential.



We would like to thank Prof. Ki Whan Song for supplying cucumber inbred lines and Dr. Yong Suk Jung for his contribution in managing the data analysis.

Author Contribution statement

SL and KTW designed the research. KTW and CYZ developed the plant materials and performed field work and genetic analysis. KTW conducted the sequence data analysis and wrote the manuscript. RRS conducted statistical analysis. JHL, YK and CYZ conducted RNA expression-level analysis. All authors reviewed and approved this submission.


This work was supported by the Next-Generation BioGreen 21 Program (Plant Molecular Breeding Center No. PJ01329601) of Rural Development Administration, Republic of Korea.

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.

Supplementary material

122_2019_3295_MOESM1_ESM.docx (7.5 mb)
Supplementary material 1 (DOCX 7695 kb)


  1. Abe A, Kosugi S, Yoshida K, Natsume S, Takagi H, Kanzaki H, Matsumura H, Yoshida K, Mitsuoka C, Tamiru M (2012) Genome sequencing reveals agronomically important loci in rice using MutMap. Nat Biotechnol 30:174–178CrossRefGoogle Scholar
  2. Asghar H, Wazir FK, Suleman A (1990) Influence of growth promoting hormones on the growth, sex expression and production of Cucumis sativus. Sarhad J Agric 6(6):563–569Google Scholar
  3. Bai Y, Pavan S, Zheng Z, Zappel NF, Reinstadler A, Lotti C, Giovanni C, Ricciardi L, Lindhout P et al (2008) Naturally occurring broad-spectrum powdery mildew resistance in a Central American tomato accession is caused by loss of Mlo function. Mol Plant-Microbe Interact 21:30–39CrossRefGoogle Scholar
  4. Bu F, Chen H, Shi Q, Zhou Q, Gao D, Zhang Z, Huang S (2015) A major quantitative trait locus conferring subgynoecy in cucumber. Theor Appl Genet 129:97–104CrossRefGoogle Scholar
  5. Bukovac MJ, Wittwer SH (1961) Gibberellins modification of flower sex expression in Cucumis sativus L. Adv Chem Ser Gibberellins 28:80–88CrossRefGoogle Scholar
  6. Chandler JW (2011) The hormonal regulation of flower development. J Plant Growth Regul 30:242–254CrossRefGoogle Scholar
  7. Chen H, Tian Y, Lu X, Liu X (2011) The inheritance of two novel subgynoecious genes in cucumber (Cucumis sativus L.). Sci Hortic 127:464–467CrossRefGoogle Scholar
  8. Das S, Upadhyaya H, Bajaj D et al (2015) Deploying QTL-seq for rapid delineation of a potential candidate gene underlying major trait-associated QTL in chickpea. DNA Res 22:193–203CrossRefGoogle Scholar
  9. Dorca-Fornell C, Gregis V, Grandi V, Coupland G, Colombo L, Kater MM (2011) The Arabidopsis SOC1-like genes AGL42, AGL71 and AGL72 promote flowering in the shoot apical and axillary meristems. Plant J 67:1006–1017CrossRefGoogle Scholar
  10. Fazio G, Staub J, Stevens M (2003) Genetic mapping and QTL analysis of horticultural traits in cucumber (Cucumis sativus L.) using recombinant inbred lines. Theor Appl Genet 107:864–874CrossRefGoogle Scholar
  11. Galun E (1962) Study of the inheritance of sex expression in the cucumber. The interaction of major genes with modifying genetic and non-genetic factors. Genetica 32:134–163CrossRefGoogle Scholar
  12. Gerashchenkov GA, Rozhnova NA (2013) The involvement of phytohormones in the plant sex regulation. Russ J Plant Physiol 60:597–610CrossRefGoogle Scholar
  13. Golenberg EM, West NW (2013) Hormonal interactions and gene regulation can link monoecy and environmental plasticity to the evolution of dioecy in plants. Am J Bot 100:1022–1037CrossRefGoogle Scholar
  14. Goto N, Pharis RP (1999) Role of gibberellin in the development of floral organs of the gibberellin-deficient mutant, ga1-1, of Arabidopsis thaliana. Can J Bot 77:944–954Google Scholar
  15. Guo D, Zhang J, Wang X, Han X, Wei B, Wang J, Li B, Yu H, Huang Q, Gu H, Qu LJ, Qin G (2015) The WRKY transcription factor WRKY71/EXB1 control shoot branching by transcriptionally regulating RAX genes in Arabidopsis. Plant Cell 27:3112–3127CrossRefGoogle Scholar
  16. Han J, Murray JE, Yu QY, Moore PH, Ming R (2014) The effects of gibberellic acid on sex expression and secondary sexual characteristics in papaya. HortScience 49:378–383CrossRefGoogle Scholar
  17. Hidayatullah AB, Bano A, Khokhar KM (2009) Sex expression and level of phytohormones in monoecious cucumber as affected by plant growth regulators. Sarhad J Agric 25:173–177Google Scholar
  18. Hisano H, Sakamoto K, Takagi H, Terauchi R, Sato K (2017) Exome QTL-seq maps monogenic locus and QTLs in barley. BMC Genom 18:125. CrossRefGoogle Scholar
  19. Huang S, Li R, Zhang Z, Li L, Gu X, Fan W, Lucas WJ, Wang X, Xie B, Ni P (2009) The genome of the cucumber, Cucumis sativus L. Nat Genet 41:1275–1281CrossRefGoogle Scholar
  20. Illa-Berenguer E, Van Houten J, Huang Z, Van der Knaap E (2015) Rapid and reliable identification of tomato fruit weight and locule number loci by QTL-seq. Theor Appl Genet 128:1329–1342CrossRefGoogle Scholar
  21. Jacobsen SE, Olszewski NE (1991) Characterization of the arrest in anther development associated with gibberellin deficiency of the gib-1 mutant of tomato. Plant Physiol 97:409–414CrossRefGoogle Scholar
  22. Kamachi S, Sekimoto H, Kondo N, Sakai S (1997) Cloning of a cDNA for a 1-aminocyclopropane-1-carboxylate synthase that is expressed during development of female flowers at the apices of Cucumis sativus L. Plant Cell Physiol 38:1197–1206CrossRefGoogle Scholar
  23. Kamachi S, Mizusawa H, Matsuura S, Sakai S (2000) Expression of two 1-aminocyclopropane-1-carboxylate synthase genes, CSACS1 and CS-ACS2, correlated with sex phenotypes in cucumber plants (Cucumis sativus L.). Plant Biothnol 17:69–74Google Scholar
  24. Knopf RR, Trebitsh T (2006) The female-specific Cs-ACS1G gene of cucumber. A case of gene duplication and recombination between the non-sex-specific 1-aminocyclopropane-1-carboxylate synthase gene and a branched-chain amino acid transaminase gene. Plant Cell Physiol 47:1217–1228CrossRefGoogle Scholar
  25. Korzeniewska A, Galecka T, Niemirowicz-Szczytt K (2000) Ethephon treatment on a monoecious cucumber accession for hybrid seed production, 510th edn. International Society for Horticultural Science (ISHS), Leuven, pp 269–272Google Scholar
  26. Kubicki B (1969) Investigations on sex determination in cucumber (Cucumis sativus L.). Genet Pol 10:5–143Google Scholar
  27. Kubicki B (1974) New sex types in cucumber and their uses in breeding work. In: Able ST (ed), XIX international horticultural congress 1974 September 11–18 Warszawa, pp 475–485Google Scholar
  28. Lander ES, Green P (1987) Construction of multilocus genetic linkage maps in humans. Proc Natl Sci USA 84:2363–2367CrossRefGoogle Scholar
  29. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359CrossRefGoogle Scholar
  30. Lee J, Lee I (2010) Regulation and function of SOC1, a flowering pathway integrator. J Exp Bot 61:2247–2254CrossRefGoogle Scholar
  31. Li H, Durbin R (2009) Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics 25:1754–1760CrossRefGoogle Scholar
  32. Li Z, Pan J, Guan Y, Tao Q, He H, Si L, Cai R (2008) Development and fine mapping of three co-dominant SCAR markers linked to the M/m gene in the cucumber plant (Cucumis sativus L.). Theor Appl Genet 117:1253–1260CrossRefGoogle Scholar
  33. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup (2009a) The sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25:2078–2079CrossRefGoogle Scholar
  34. Li Z, Huang S, Liu S, Pan J, Zhang Z, Tao Q, Shi Q, Jia Z, Zhang W, Chen H (2009b) Molecular isolation of the M gene suggests that a conserved-residue conversion induces the formation of bisexual flowers in cucumber plants. Genetics 182:1381–1385CrossRefGoogle Scholar
  35. Liu S, Xu L, Jia Z, Xu Y, Yang Q, Fei Z, Lu X, Chen H, Huang S (2008) Genetic association of ETHYLENE-INSENSITIVE3-like sequence with the sex-determining M locus in cucumber (Cucumis sativus L.). Theor Appl Genet 117:927–933CrossRefGoogle Scholar
  36. Liu C, Xi W, Shen L, Tan C, Yu H (2009) Regulation of floral patterning by flowering time genes. Dev Cell 16:711–722CrossRefGoogle Scholar
  37. Lu H, Lin T, Klein J, Wang S, Qi J, Zhou Q et al (2014) QTL-seq identifies an early flowering QTL located near FLOWERING LOCUS T in cucumber. Theor Appl Genet 127:1491–1499. CrossRefGoogle Scholar
  38. Malepszy S, Niemirowicz-Szczytt K (1991) Sex determination in cucumber (Cucumis sativus L.) as a model system for molecular biology. Plant Sci 80:39–47CrossRefGoogle Scholar
  39. Megharaj KC, Ajjappalavar PS, Revanappa Manjunathagowda DC, Bommesh JC (2017) Sex manipulation in cucurbitaceous vegetables. Int J Curr Microbiol App Sci 6(9):1839–1851CrossRefGoogle Scholar
  40. Mibus H, Tatlioglu T (2004) Molecular characterization and isolation of the F/f gene for femaleness in cucumber (Cucumis sativus L.). Theor Appl Genet 109:1669–1676CrossRefGoogle Scholar
  41. Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 88:9828–9832CrossRefGoogle Scholar
  42. Migocka M, Papierniak A (2011) Identification of suitable reference genes for studying gene expression in cucumber plants subjected to abiotic stress and growth regulators. Mol Breed 28(3):343–357CrossRefGoogle Scholar
  43. Nelson JC (1997) QGene: software for marker-based genomic analysis and breeding. Mol Breed 3:239–245CrossRefGoogle Scholar
  44. Niwa M, Daimon Y, Kurotani K, Higo A, Pruneda-Paz JL, Breton G, Mitsuda N, Kay SA, Ohme-Takagi M, Endo M, Araki T (2013) BRANCHED1 interacts with FLOWERING LOCUS T to repress the floral transition of the axillary meristems in Arabidopsis. Plant Cell 25:1228–1242CrossRefGoogle Scholar
  45. Perl-Treves R (1999) Male to female conversion along the cucumber shoot: approaches to studying sex genes and floral development in Cucumis sativus. Bios Scientific Publishers, Oxford, pp 189–215Google Scholar
  46. Peterson CE, Anhder LD (1960) Induction of staminate flower in gynoecious cucumber with GA3. Science 131:1673–1674CrossRefGoogle Scholar
  47. Pike LM, Peterson CE (1969) Gibberellin A4/A7 for induction of staminate flowers on the gynoecious cucumber (Cucumis sativus L.). Euphytica 18:106–109Google Scholar
  48. Ren Y, Zhang Z, Liu J et al (2009) An integrated genetic and cytogenetic map of the cucumber genome. PLoS ONE 4:e5795CrossRefGoogle Scholar
  49. Rudich J, Halevy AH (1974) Involvement of abscissic acid in the regulation of sex expression in cucumber. Plant Cell Physiol 15:635–642CrossRefGoogle Scholar
  50. Rudich J, Halevy AH, Kedar N (1972) The level of phytohormones in monoecious and gynoecious cucumbers as affected by photoperiod and ethephon. Plant Physiol 50:585–590CrossRefGoogle Scholar
  51. Sabbagh E, Sabbagh SK, Panjehkeh N, Bolok-Yazdi HR (2018) Jasmonic acid induced systemic resistance in infected cucumber by pythium aphanidermatum. Tarim Bilimleri Dergisi J Agric Sci 24:143–152CrossRefGoogle Scholar
  52. Salvi S, Tuberosa R (2005) To clone or not to clone plant QTLs: present and future challenges. Trends Plant Sci 10:297–304CrossRefGoogle Scholar
  53. Seale M, Bennett T, Leyser O (2017) BRC1 expression regulates bud activation potential but is not necessary or sufficient for bud growth inhibition in Arabidopsis. Development 144:1661–1673CrossRefGoogle Scholar
  54. Shiber A, Gaur R, Rimon-Knopf R, Zelcer A, Trebitsh T, Pitrat M (2008) The origin and mode of function of the female locus in cucumber. Cucurbitaceae 2008:263–270Google Scholar
  55. Shifriss O (1961) Sex control in cucumbers. J Hered 52:5–12CrossRefGoogle Scholar
  56. Singh VK, Khan AW, Jaganathan D, Thudi M, Roorkiwal M, Takagi H, Garg V, Kumar V, Chitikineni A, Gaur PM et al (2016) QTL-seq for rapid identification of candidate genes for 100-seed weight and root/total plant dry weight ratio under rainfed conditions in chickpea. Plant Biotechnol J 14:2110–2119CrossRefGoogle Scholar
  57. Srivastava R, Upadhyaya HD, Kumar R, Daware A, Basu U, Shimray W et al (2017) A multiple QTL-Seq strategy delineates potential genomic loci governing flowering time in chickpea. Front Plant Sci 8:1105. CrossRefGoogle Scholar
  58. Sun TP (2008) Gibberellin metabolism, perception and signaling pathways in Arabidopsis. In: Rockville MD (ed), The Arabidopsis Book. American Society of Plant Biologists, Rockville. Google Scholar
  59. Takagi H, Abe A, Yoshida K, Kosugi S, Natsume S, Mitsuoka C, Uemura A, Utsushi H, Tamiru M, Takuno S (2013) QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J 74:174–183CrossRefGoogle Scholar
  60. Takahashi H, Jaffe M (1983) Further studies of auxin and ACC induced feminization in the cucumber plant using ethylene inhibitors. Phyton 44:81–86Google Scholar
  61. Trebitsh T, Rudich J, Riov J (1987) Auxin, biosynthesis of ethylene and sex expression in cucumber (Cucumis sativus). Plant Growth Regul 5:105–113CrossRefGoogle Scholar
  62. Trebitsh T, Staub JE, O’Neill SD (1997) Identification of a 1-aminocyclopropane- 1-carboxylic acid synthase gene linked to the female (F) locus that enhances female sex expression in cucumber. Plant Physiol 113:987–995CrossRefGoogle Scholar
  63. Wang SH, Sui XL, Hu LP, Sun JL, Wei YX, Zhang ZX (2010) Effects of exogenous abscisic acid pre-treatment of cucumber (Cucumis sativus) seeds on seedling growth and water-stress tolerance. N Z J Crop Hort Sci 38:7–18CrossRefGoogle Scholar
  64. Wang H, Cheng H, Wang W et al (2016) Identification of BnaYUCCA6 as a candidate gene for branch angle in Brassica napus by QTL-seq. Sci Rep 6:38493CrossRefGoogle Scholar
  65. Wei QZ, Fu WY, Wang YZ, Qin XD, Wang J, Li J, Lou QF, Chen KF (2016) Rapid identification of fruit length loci in cucumber (Cucumis sativus L.) using next-generation sequencing (NGS)-based QTL analysis. Sci Rep 6:27496CrossRefGoogle Scholar
  66. Win KT, Zhang C, Song K, Lee JH, Lee S (2015) Development and characterization of a co-dominant molecular marker via sequence analysis of a genomic region containing the Female (F) locus in cucumber (Cucumis sativus L.). Mol Breed 35:229CrossRefGoogle Scholar
  67. Wu T, Qin Z, Feng Z, Zhou X, Xin M, Du Y (2012) Functional analysis of the promoter of a female specific cucumber CsACS1G gene. Plant Mol Biol Rep 30:235–241. CrossRefGoogle Scholar
  68. Yamasaki S, Fujii N, Matsuura S, Mizusawa H, Takahashi H (2001) The M locus and ethylene-controlled sex determination in andromonoecious cucumber plants. Plant Cell Physiol 42:608–619CrossRefGoogle Scholar
  69. Yamasaki S, Fujii N, Takahashi H (2003) Characterization of ethylene effects on sex determination in cucumber plants. Sex Plant Reprod 16:103–111CrossRefGoogle Scholar
  70. Yamasaki S, Fujii N, Takahashi H (2005) Hormonal regulation of sex expression in plants. Vitam Horm 72:79–110CrossRefGoogle Scholar
  71. Yin TJ, Quinn JA (1995) Tests of a mechanistic model of one hormone regulating both sexes in Cucumis sativus (Cucurbitaceae). Am J Bot 82:1537–1546CrossRefGoogle Scholar
  72. Yuan X, Pan J, Cai R, Guan Y, Liu L, Zhang W, Li Z, He H, Zhang C, Si L (2008) Genetic mapping and QTL analysis of fruit and flower related traits in cucumber (Cucumis sativus L.) using recombinant inbred lines. Euphytica 164:473–491CrossRefGoogle Scholar
  73. Zhang WW, Pan JS, He HL, Zhang C, Li Z, Zhao JL, Yuan XJ, Zhu LH, Huang SW, Cai R (2012) Construction of a high density integrated genetic map for cucumber (Cucumis sativus L.). Theor Appl Genet 124:249–259CrossRefGoogle Scholar
  74. Zhang Y, Zhang X, Liu B, Wang W, Liu X, Chen C, Liu X, Yang S, Ren H (2014) A GAMYB homologue CsGAMYB1 regulates sex expression of cucumber via an ethylene-independent pathway. J Exp Bot 65:3201–3213CrossRefGoogle Scholar

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© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Plant Genomics Laboratory, Department of Plant Biotechnology, College of Life SciencesSejong UniversitySeoulRepublic of Korea
  2. 2.Institute of Mathematics and StatisticsFederal University of GoiásGoiâniaBrazil
  3. 3.Division of Life SciencesChonbuk National UniversityJeonjuRepublic of Korea
  4. 4.Plant Engineering Research InstituteSejong UniversitySeoulRepublic of Korea

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