Theoretical and Applied Genetics

, Volume 130, Issue 7, pp 1531–1548 | Cite as

QTL mapping of domestication and diversifying selection related traits in round-fruited semi-wild Xishuangbanna cucumber (Cucumis sativus L. var. xishuangbannanesis)

  • Yupeng Pan
  • Shuping Qu
  • Kailiang Bo
  • Meiling Gao
  • Kristin R. Haider
  • Yiqun WengEmail author
Original Article


Key message

QTL analysis revealed 11 QTL underlying flowering time and fruit size variation in the semi-wild Xishuangbanna cucumber, of which, FT6.2 and FS5.2 played the most important roles in determining photoperiod-dependent flowering time and round-fruit shape, respectively.


Flowering time and fruit size are two important traits in domestication and diversifying selection in cucumber, but their genetic basis is not well understood. Here we reported QTL mapping results on flowering time and fruit size with F2 and F2:3 segregating populations derived from the cross between WI7200, a small fruited, early flowering primitive cultivated cucumber and WI7167, a round-fruited, later flowering semi-wild Xishuangbanna (XIS) cucumber. A linkage map with 267 microsatellite marker loci was developed with 138 F2 plants. Phenotypic data of male and female flowering time, fruit length and diameter and three other traits (mature fruit weight and number, and seedling hypocotyl length) were collected in multiple environments. Three flowering time QTL, FT1.1, FT5.1 and FT6.2 were identified, in which FT6.2 played the most important role in conferring less photoperiod sensitive early flowering during domestication whereas FT1.1 seemed more influential in regulating flowering time within the cultivated cucumber. Eight consensus fruit size QTL distributed in 7 chromosomes were detected, each of which contributed to both longitudinal and radial growth in cucumber fruit development. Among them, FS5.2 on chromosome 5 exhibited the largest effect on the determination of round fruit shape that was characteristic of the WI7167 XIS cucumber. Possible roles of these flowering time and fruit size QTL in domestication of cucumber and crop evolution of the semi-wild XIS cucumber, as well as the genetic basis of round fruit shape in cucumber are discussed.


Fruit Weight Fruit Size Fruit Length Fruit Number Hypocotyl Length 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This research is supported by the National Institute of Food and Agriculture, U.S. Department of Agriculture, under award number 2015-51181-24285. SQ’s and MG’s work was partially supported by the China Scholarship Council. Names are necessary to report factually on available data; however, the USDA neither guarantees nor warrants the standard of the product, and the use of the name by USDA implies no approval of the product to the exclusion of others that may also be suitable. USDA is an equal opportunity provider and employer.

Author contributions statement

YP and SQ performed the research, analyzed the data, and wrote a draft of the manuscript. KB, MG and KH participated in data collection. YW supervised designed the experiment, participated in data analysis. YP and YW wrote the manuscript with inputs from all co-authors. All authors reviewed and approved this submission.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflicts of interest.

Supplementary material

122_2017_2908_MOESM1_ESM.pdf (1.2 mb)
Supplementary material 1 (PDF 1229 kb)


  1. Abbo S, van-Oss RP, Gopher A, Saranga Y, Ofner I, Peleg Z (2014) Plant domestication versus crop evolution: a conceptual framework for cereals and grain legumes. Trend Plant Sci 19:351–360CrossRefGoogle Scholar
  2. Andargie M, Pasquet RS, Gowda BS et al (2014) Molecular mapping of QTLs for domestication-related traits in cowpea (V. unguiculata (L.) Walp.). Euphytica 200:401–412CrossRefGoogle Scholar
  3. Bisht IS, Bhat KV, Tanwar SPS, Bhandari DC, Joshi K, Sharma AK (2004) Distribution and genetic diversity of Cucumis sativus var. hardwickii (Royle) Alef in India. J Hortic Sci Biotechnol 79:783–791CrossRefGoogle Scholar
  4. Bo KL, Shen J, Qian CT, Song H, Chen JF (2011) Genetic analysis of the important agronomic traits on Beijingjietou × Xishuangbanna cucumber recombinant inbred lines. J Nanjing Agri Univ 34:20–24Google Scholar
  5. Bo KL, Song H, Shen J, Qicn CT, Staub JE, Simon PW, Lou QF, Chen JF (2012) Inheritance and mapping of the ore gene controlling the quantity of β-carotene in cucumber (Cucumis sativus L.) endocarp. Mol Breed 30:335–344CrossRefGoogle Scholar
  6. Bo KL, Ma Z, Chen JF, Weng Y (2015) Molecular mapping reveals structural rearrangements and quantitative trait loci underlying traits with local adaptation in semi-wild Xishuangbana cucumber (Cucumis sativus L. var. xishuangbannanesis Qi et Yuan). Theor Appl Genet 128:25–39CrossRefPubMedGoogle Scholar
  7. Bo KL, Wang H, Pan YP, Behera TK, Pandey S, Wen CL, Wang YH, Simon PW, Li YH, Chen JF, Weng Y (2016) Short Hypocotyl1 (Sh1) encodes a human SMARCA3-like chromatin remodeling factor regulating hypocotyl elongation. Plant Physiol 172:1273–1292PubMedPubMedCentralGoogle Scholar
  8. Bost B, de Vienne D, Hospital F, Moreau L, Dillmann C (2001) Genetic and nongenetic bases for the L-shaped distribution of quantitative trait loci effects. Genetics 157:1773–1787PubMedPubMedCentralGoogle Scholar
  9. Broman KW, Wu H, Sen Ś, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889–890CrossRefPubMedGoogle Scholar
  10. Burke JM, Tang S, Knapp SJ, Rieseberg LH (2002) Genetic analysis of sunflower domestication. Genetics 161:1257–1267PubMedPubMedCentralGoogle Scholar
  11. Cai H, Morishima H (2002) QTL clusters reflect character associations in wild and cultivated rice. Theor Appl Genet 104:1217–1228CrossRefPubMedGoogle Scholar
  12. Candolle AD (1959) Origin of cultivated plants. Hafner Publishing, New YorkGoogle Scholar
  13. Cavagnaro PF, Senalik DA, Yang LM, Simon PW, Harkins TT, Kodira CD, Huang SW, Weng Y (2010) Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.). BMC Genomics 11:569CrossRefPubMedPubMedCentralGoogle Scholar
  14. Cheng ZC, Gu XF, Zhang SP, Miao H, Zhang RW, Liu MM, Yang SJ (2010) QTL mapping of fruit length in cucumber. China Veg Issue 12:20–25Google Scholar
  15. de Wilde WJJ, Duyfjes BEE (2010) Cucumis sativus L. forma hardwickii (Royle) W.J. de Wilde & Duyfjes and feral forma sativus. Thai For Bull (Bot) 38:98–107Google Scholar
  16. Dijkhuizen A, Staub JE (2002) QTL conditioning yield and fruit quality traits in cucumber (Cucumis sativus L.): effects of environment and genetic background. J New Seeds 4:1–30CrossRefGoogle Scholar
  17. Doebley J, Stec A (1993) Inheritance of the morphological differences between maize and teosinte: comparison of results for two F2 populations. Genetics 134:559–570PubMedPubMedCentralGoogle Scholar
  18. Doebley J, Stec A, Wendal J, Edwards M (1990) Genetic and morphological analysis of a maize-teosinte F2 population: implications for the origin of maize. Proc Natl Acad Sci USA 87:9888–9892CrossRefPubMedPubMedCentralGoogle Scholar
  19. Doebley JF, Gaut BS, Smith BD (2006) The molecular genetics of crop domestication. Cell 127:1309–1321CrossRefPubMedGoogle Scholar
  20. Doganlar S, Frary A, Daunay M-C, Lester RN, Tanksley SD (2002) Conservation of gene function in the Solanaceae as revealed by comparative mapping of domestication traits in eggplant. Genetics 161:1713–1726PubMedPubMedCentralGoogle Scholar
  21. Dorweiler J, Stec A, Kermicle J, Doebley J (1993) Teosinte glume architecture 1: a genetic locus controlling a key step in maize evolution. Science 262:233–235CrossRefPubMedGoogle Scholar
  22. Duthie JF (1903) Flora of the Upper Gangetic Plain, and of the Adjacent Siwalik and Sub-Himalayan tracts. Superintendent of Government Printing Publication, CalcuttaCrossRefGoogle Scholar
  23. Gepts P (2004) Domestication as a long-term selection experiment (Part 2). Plant Breed Rev 24:1–44Google Scholar
  24. Grandillo S, Tanksley SD (1996) QTL analysis of horticultural traits differentiating the cultivated tomato from the closely related species Lycopersicon pimpinellifolium. Theor Appl Genet 92:935–951CrossRefPubMedGoogle Scholar
  25. Harlan J (1992) Crops and man, 2nd edn. American Society of Agronomy, MadisonGoogle Scholar
  26. Harlan JR, de Wet JMJ, Price EG (1973) Comparative evolution of cereals. Evolution 27:311–325CrossRefPubMedGoogle Scholar
  27. Kennard WC, Havey MJ (1995) Quantitative trait analysis of fruit quality in cucumber: QTL detection, confirmation, and comparison with mating design variation. Theor Appl Genet 91:53–61PubMedGoogle Scholar
  28. Koinange EMK, Singh SP, Gepts P (1996) Genetic control of the domestication syndrome in common bean. Crop Sci 36:1037–1045CrossRefGoogle Scholar
  29. Lee S-J, Oh C-S, Suh J-P, McCouch SR, Ahn SN (2005) Identification of QTLs for domestication-related and agronomic traits in an Oryza sativa × O. rufipogon BC1F7 population. Plant Breed 124:209–219CrossRefGoogle Scholar
  30. Li YH, Yang LM, Pathak M, Li DW, He XM, Weng Y (2011) Fine genetic mapping of cp: a recessive gene for compact (dwarf) plant architecture in cucumber, Cucumis sativus L. Theor Appl Genet 123:973–983CrossRefPubMedGoogle Scholar
  31. Li YH, Wen CL, Weng Y (2013) Fine mapping of the pleiotropic locus B for black spine and orange mature fruit color in cucumber identifies a 50 kb region containing a R2R3-MYB transcription factor. Theor Appl Genet 126:2187–2196CrossRefPubMedGoogle Scholar
  32. Li S, Pan YP, Wen CL, Li YH, Liu XF, Zhang XL, Behera TK, Xing GM, Weng Y (2016) Integrated analysis in bi-parental and natural populations reveals CsCLAVATA3 (CsCLV3) underlying carpel number variations in cucumber. Theor Appl Genet 129:1007–1022CrossRefPubMedGoogle Scholar
  33. Liu B, Fujita T, Yan Z-H, Sakamoto S, Xu D, Abe J (2007) QTL mapping of domestication-related traits in soybean (Glycine max). Annal Bot 100:1027–1038CrossRefGoogle Scholar
  34. Lu H, Lin T, Klein J, Wang S, Qi J, Zhou Q, Sun J, Zhang Z, Weng Y, Huang S (2014) QTL-seq identifies an early flowering QTL located near Flowering Locus T in cucumber. Theor Appl Genet 127:1491–1499CrossRefPubMedGoogle Scholar
  35. Mather K, Jinks JL (1971) Biometrical genetics. Chapman and Hall, LondonCrossRefGoogle Scholar
  36. Meyer RS, Purugganan MD (2013) Evolution of crop species: genetics of domestication and diversification. Nat Rev Genet 14:840–852CrossRefPubMedGoogle Scholar
  37. Miao H, Gu XF, Zhang SP, Zhang ZH, Huang SW, Wang Y, Cheng ZC, Zhang RW, Mu S, Li M, Zhang ZX, Fang ZY (2011) Mapping QTLs for fruit-associated traits in Cucumis sativus L. Sci Agric Sin 44:5031–5040 (in Chinese) Google Scholar
  38. Miao H, Gu XF, Zhang SP, Zhang ZH, Huang SW, Wang Y, Fang ZY (2012) Mapping QTLs for seedling-associated traits in cucumber. Acta Hortic Sin 39:879–887 (in Chinese) Google Scholar
  39. Olsen KM, Wendel JF (2013) A bountiful harvest: genomic insights into crop domestication phenotypes. Annu Rev Plant Biol 64:47–70CrossRefPubMedGoogle Scholar
  40. Pan YP, Bo KL, Cheng ZH, Weng Y (2015) The loss-of-function GLABROUS 3 mutation in cucumber is due to LTR-retrotransposon insertion in a class IV HD-ZIP transcription factor gene CsGL3 that is epistatic over CsGL1. BMC Plant Biol 15:302CrossRefPubMedPubMedCentralGoogle Scholar
  41. Pan YP, Liang XJ, Gao ML, Meng HW, Liu HQ, Weng Y, Cheng ZH (2016) Round fruit shape in WI7239 cucumber is controlled by two interacting quantitative trait loci with one encoding a tomato SUN homolog. Theor Appl Genet. doi: 10.1007/s00122-016-2836-6 Google Scholar
  42. Paran I, van der Knaap E (2007) Genetic and molecular regulation of fruit and plant domestication traits in tomato and pepper. J Exp Bot 58:3841–3852CrossRefPubMedGoogle Scholar
  43. Peng J, Ronin Y, Fahima T, Roder MS, Li Y, Nevo E, Korol A (2003) Domestication quantitative trait loci in Triticum dicoccoides, the progenitor of wheat. Proc Natl Acad Sci USA 100:2489–2494CrossRefPubMedPubMedCentralGoogle Scholar
  44. Poncet V, Lanny F, Enjalbert J, Joly H, Sarr A, Robert T (1998) Genetic analysis of the domestication syndrome in pearl millet (Pennisetum glaucum L., Poaceae): inheritance of the major characters. Heredity 81:648–658CrossRefGoogle Scholar
  45. Poncet V, Lamy F, Devos KM, Gale MD, Sarr A, Robert T (2000) Genetic control of domestication traits in pearl millet (Pennisetum glaucum). Theor Appl Genet 100:147–159CrossRefGoogle Scholar
  46. Qi CZ (1983) A new type of cucumber, Cucumis sativus L. var. xishuangbannanesis Qi et Yuan. Acta Hortic Sin 10:259–263 (in Chinese) Google Scholar
  47. Qi JJ, Liu X, Shen D, Miao H, Xie BY, Li XX, Zeng P, Wang SH, Shang Y et al (2013) A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nat Genet 45:1510–1515CrossRefPubMedGoogle Scholar
  48. Ren Y, Zhang Z, Liu J, Staub JE, Han Y, Cheng Z, Li X et al (2009) An integrated genetic and cytogenetic map of the cucumber genome. PLoS ONE 4:e5795CrossRefPubMedPubMedCentralGoogle Scholar
  49. Ross-Ibarra J (2005) Quantitative trait loci and the study of plant domestication. Genetica 123:197–204CrossRefPubMedGoogle Scholar
  50. Royle JF (1835) Illustrations of the botany of the Himalayan mountains. Wm. H. Alland and Co., LondonGoogle Scholar
  51. Sebastian P, Schaefer H, Telford IRH, Renner SS (2010) Cucumber (Cucumis sativus) and melon (C. melo) have numerous wild relatives in Asia and Australia, and the sister species of melon is from Australia. Proc Natl Acad Sci USA 107:14269–14273CrossRefPubMedPubMedCentralGoogle Scholar
  52. Shang Y, Ma YS, Zhou Y, Zhang HM, Duan LX, Chen HM et al (2014) Biosynthesis, regulation, and domestication of bitterness in cucumber. Science 346:1084–1088CrossRefPubMedGoogle Scholar
  53. Shen D (2009) Genetic diversity QTL mapping of orange flesh color of Cucumis sativus L. var. xishuangbannanesis. PhD Thesis, Chinese Academy of Agricultural Sciences, Beijing, China (in Chinese)Google Scholar
  54. Stuber CW, Moll RH, Goodman MM, Schaffer HE, Weir BS (1980) Allozyme frequency changes associated with selection for increased grain-yield in maize. Genetics 95:225–236PubMedPubMedCentralGoogle Scholar
  55. Stuber CW, Edwards MD, Wendel JF (1987) Molecular marker facilitated investigations of quantitative trait loci in maize: II. Factors influencing yield and its component traits. Crop Sci 27:639–648CrossRefGoogle Scholar
  56. Tan JY, Tao QY, Niu HH, Zhang Z, Li DD, Gong ZH, Weng Y, Li Z (2015) A novel allele of monoecious (m) locus is responsible for elongated fruit shape and perfect flowers in cucumber (Cucumis sativus L.). Theor App Genet 128:2483–2493CrossRefGoogle Scholar
  57. Wang RL, Stec A, Hey J, Lukens L, Doebley J (1999) The limits of selection during maize domestication. Nature 398:236–239CrossRefPubMedGoogle Scholar
  58. Wang H, Nussbaum-Wagler T, Li B, Zhao Q, Vigouroux Y, Faller M, Bomblies K, Lukens L, Doebley JF (2005) The origin of the naked grains of maize. Nature 436:714–719CrossRefPubMedPubMedCentralGoogle Scholar
  59. Wang M, Liu SL, Zhang SP, Miao H, Wang Y, Tian GL, Lu HW, Gu XF (2014) Quantitative trait loci associated with fruit length and stalk length in cucumber using RIL population. Act Bot Boreal Occident Sin 34:1764–1770 (in Chinese) Google Scholar
  60. Wang YH, VandenLangenberg K, Wehner TC, Kraan PAG, Suelmann J, Zheng XY, Owens K, Weng Y (2016) QTL mapping for downy mildew resistance in cucumber inbred line WI7120 (PI 330628). Theor Appl Genet 129:1493–1505CrossRefPubMedGoogle Scholar
  61. Wei QZ, Wang YZ, Qin XD, Zhang YX, Zhang ZT, Wang J, Li J, Lou QF, Chen JF (2014) An SNP-based saturated genetic map and QTL analysis of fruit-related traits in cucumber using specific-length amplified fragment (SLAF) sequencing. BMC Genomics 15:1158CrossRefPubMedPubMedCentralGoogle Scholar
  62. Weng Y, Colle M, Wang Y, Yang L, Rubinstein M, Sherman A, Ophir R, Grumet R (2015) QTL mapping in multiple populations and development stages reveals dynamic QTL for fruit size in cucumbers of different market classes. Theor Appl Genet 128:1747–1763CrossRefPubMedGoogle Scholar
  63. White S, Doebley J (1998) Of genes and genomes and the origin of maize. Trends Genet 14:327–332CrossRefPubMedGoogle Scholar
  64. Wills DM, Burke JM (2007) Quantitative trait locus analysis of the early domestication of sunflower. Genetics 176:2589–2599CrossRefPubMedPubMedCentralGoogle Scholar
  65. Xiao J, Li J, Grandillo S, Ahn SN, Yuan L, Tanksley SD et al (1998) Identification of trait-improving QTL alleles from a wild rice relative, Oryza rufipogan. Genetics 150:899–909PubMedPubMedCentralGoogle Scholar
  66. Xiong LZ, Liu KD, Dai XK, Xu CG, Zhang Q (1999) Identification of genetic factors controlling domestication-related traits of rice using an F2 population of a cross between Oryza sativa and O. rufipogan. Theor Appl Genet 98:243–251CrossRefGoogle Scholar
  67. Yang LM, Koo DH, Li Y, Zhang X, Luan F, Havey MJ, Jiang J, Weng Y (2012) Chromosome rearrangements during domestication of cucumber as revealed from high-density genetic mapping and draft genome assembly. Plant J 71:895–906CrossRefPubMedGoogle Scholar
  68. Yang LM, Li DW, Li YH, Gu XF, Huang SW, Garcia-Mas J, Weng Y (2013) A 1,681-locus consensus genetic map of cultivated cucumber including 67 NB-LRR resistance gene homolog and ten gene loci. BMC Plant Biol 13:53CrossRefPubMedPubMedCentralGoogle Scholar
  69. Yuan X, Pan J, Cai R, Guan Y, Liu L, Zhang W, Li Z, He H, Zhang C, Si L, Zhu 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
  70. Zhang SP, Miao H, Cheng ZC, Liu MM, Zhang ZH, Wang XW, Sun RF, Gu XF (2011) Genetic mapping of the fruit bitterness gene(Bt)in cucumber (Cucumis sativus L.). Acta Hort Sin 38:709–716Google Scholar
  71. Zhang J, Zhou X, Yan W, Zhang Z et al (2015) Combinations of the Ghd7, Ghd8 and Hd1 genes largely define the ecogeographical adaptation and yield potential of cultivated rice. New Phytol 208:1056–1066CrossRefPubMedGoogle Scholar
  72. Zhu W, Huang L, Chen L, Yang J, Wu J, Qu M, Yao D, Guo C, Lian H, He H, Pan J, Cai R (2016) A high-density genetic map for cucumber (Cucumis sativus L.) based on specific length amplified fragment (SLAF) sequencing and QTL analysis of fruit traits in cucumber. Front. Plant Sci 7:437Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg (outside the USA) 2017

Authors and Affiliations

  1. 1.Department of HorticultureUniversity of Wisconsin-MadisonMadisonUSA
  2. 2.Horticulture CollegeNortheast Agricultural UniversityHarbinChina
  3. 3.College of Life Science, Agriculture and ForestryQiqihar UniversityQiqiharChina
  4. 4.USDA-ARS Vegetable Crops Research Unit, Horticulture DepartmentUniversity of Wisconsin-MadisonMadisonUSA

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