Genetic mapping and development of molecular markers for a candidate gene locus controlling rind color in watermelon

  • Bingbing Li
  • Shengjie Zhao
  • Junling Dou
  • Aslam Ali
  • Haileslassie Gebremeskel
  • Lei Gao
  • Nan He
  • Xuqiang LuEmail author
  • Wenge Liu
Original Article


Key message

ClCG08G017810 (ClCGMenG) encoding a 2-phytyl-1,4-beta-naphthoquinone methyltransferase protein is associated with formation of dark green versus light green rind color in watermelon.


Rind color is an important agronomic trait in watermelon [Citrullus lanatus (Thunb.) Matsum. and Nakai], but the underlying molecular mechanism for this trait is not fully known. In the present study, we identified a single locus on chromosome 8 accounting for watermelon rind color (dark green vs. light green). Genetic analysis of F1, F2, and BC1 populations derived from two parental lines (9904 with dark green rind and Handel with light green rind) revealed that the watermelon rind color (dark green vs. light green) is controlled by a single locus, and dark green is dominant to light green rind. Initial mapping revealed a region of interest spanning 2.07 Mb on chromosome 8. Genetic mapping with CAPS and SNP markers narrowed down the candidate region to 31.4 kb. Gene annotation of the corresponding region in the reference genome revealed the ClCG08G017810 gene sequence encoding the 2-phytyl-1,4-beta-naphthoquinone methyltransferase protein. The sequence alignment of the candidate gene with the two parental lines suggested a nonsynonymous SNP mutation in the coding region of ClCG08G017810, converting an arginine (R) to glycine (G). The SNP might be associated with rind color of 103 watermelon germplasm lines investigated in this study. The qRT-PCR analysis revealed higher expression of ClCG08G017810 in dark green rind than in light green rind. Therefore, ClCG08G017810 is a candidate gene associated with watermelon rind color. The present study facilitates marker-assisted selection useful for the development of cultivars with desirable rind color.



This research was supported by National Key R&D Program of China (2018YFD0100704), the Agricultural Science and Technology Innovation Program (CAAS-ASTIP-2018-ZFRI), the China Agriculture Research System (CARS-25-03), the National Nature Science Foundation of China (31672178 and 31471893) and Central Public-interest Scientific Institution Basal Research Fund (Nos. 1616032017209 and 1610192016209).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standard

The experiments in this study comply with the current laws of China.

Supplementary material

122_2019_3384_MOESM1_ESM.tif (793 kb)
Supplementary Fig. 1 Genotype identification of rind color in 103 watermelon germplasm resources. (XLSX 13 kb)
122_2019_3384_MOESM2_ESM.tif (2.3 mb)
Supplementary Fig. 2 The 5′ upstream region sequence of ClCG08G017810 in 9904 and Handel. (XLSX 13 kb)
122_2019_3384_MOESM3_ESM.xlsx (13 kb)
Supplementary Table 1 The segregation ratio of rind color among different populations. (XLSX 13 kb)
122_2019_3384_MOESM4_ESM.xlsx (9 kb)
Supplementary Table 2 The information of the CAPS and SNP markers on chromosome 8 used for the polymorphic analysis. (XLSX 9 kb)
122_2019_3384_MOESM5_ESM.xlsx (62 kb)
Supplementary Table 3 The primer information for the sequence and expression analysis of the candidate genes. (XLSX 62 kb)
122_2019_3384_MOESM6_ESM.xlsx (10 kb)
Supplementary Table 4 Genotype identification of rind color in F2 population and 103 watermelon germplasm resources. (XLSX 9 kb)


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Copyright information

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

Authors and Affiliations

  • Bingbing Li
    • 1
  • Shengjie Zhao
    • 1
  • Junling Dou
    • 1
  • Aslam Ali
    • 1
  • Haileslassie Gebremeskel
    • 1
  • Lei Gao
    • 1
  • Nan He
    • 1
  • Xuqiang Lu
    • 1
    Email author
  • Wenge Liu
    • 1
  1. 1.Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural SciencesZhengzhouChina

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