Theoretical and Applied Genetics

, Volume 131, Issue 4, pp 947–958 | Cite as

Genetic mapping reveals a candidate gene (ClFS1) for fruit shape in watermelon (Citrullus lanatus L.)

  • Junling Dou
  • Shengjie Zhao
  • Xuqiang Lu
  • Nan He
  • Lei Zhang
  • Aslam Ali
  • Hanhui Kuang
  • Wenge Liu
Original Article


Key message

A 159 bp deletion in ClFS1 gene encoding IQD protein is responsible for fruit shape in watermelon.


Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] is known for its rich diversity in fruit size and shape. Fruit shape has been one of the major objectives of watermelon breeding. However, the candidate genes and the underlying genetic mechanism for such an important trait in watermelon are unknown. In this study, we identified a locus on chromosome 3 of watermelon genome controlling fruit shape. Segregation analysis in F2 and BC1 populations derived from a cross between two inbred lines “Duan125” (elongate fruit) and “Zhengzhouzigua” (spherical fruit) suggests that fruit shape of watermelon is controlled by a single locus and elongate fruit (OO) is incompletely dominant to spherical fruit (oo) with the heterozygote (Oo) being oval fruit. GWAS profiles among 315 accessions identified a major locus designated on watermelon chromosome 3, which was confirmed by BSA-seq mapping in the F2 population. The candidate gene was mapped to a region 46 kb on chromosome 3. There were only four genes present in the corresponding region in the reference genome. Four candidate genes were sequenced in this region, revealing that the CDS of Cla011257 had a 159 bp deletion which resulted in the omission of 53 amino acids in elongate watermelon. An indel marker was derived from the 159 bp deletion to test the F2 population and 105 watermelon accessions. The results showed that Cla011257 cosegregated with watermelon fruit shape. In addition, the Cla011257 expression was the highest at ovary formation stage. The predicted protein of the Cla011257 gene fitted in IQD protein family which was reported to have association with cell arrays and Ca2+-CaM signaling modules. Clear understanding of the genes facilitating the fruit shape along with marker association selection will be an effective way to develop new cultivars.



This work was supported by the Agricultural Science and Technology Innovation Program (ASTIP) (CAAS-ASTIP-2017-ZFRI), the China Agriculture Research System (CARS-25-03), and the Central Public-interest Scientific Institution Basal Research Fund, China (1610192016301 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_2018_3050_MOESM1_ESM.xlsx (68 kb)
Supplementary material 1 (XLSX 68 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Junling Dou
    • 1
    • 2
  • Shengjie Zhao
    • 1
  • Xuqiang Lu
    • 1
  • Nan He
    • 1
  • Lei Zhang
    • 2
  • Aslam Ali
    • 1
  • Hanhui Kuang
    • 2
  • Wenge Liu
    • 1
  1. 1.Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
  2. 2.College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina

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