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Genetic diversity and population structure of core watermelon (Citrullus lanatus) genotypes using DArTseq-based SNPs

Yang, Xingping; Ren, Runsheng; Ray, Rumiana; Xu, Jinhua; Li, Pingfang; Zhang, Man; Liu, Guang; Yao, Xiefeng; Kilian, Andrzej


Xingping Yang

Runsheng Ren

Professor of Plant Pathology

Jinhua Xu

Pingfang Li

Man Zhang

Guang Liu

Xiefeng Yao

Andrzej Kilian


Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai var. lanatus] is an economically important vegetable belonging to the Cucurbitaceae family. Genotypes that exhibit agronomically important traits are selected for the development of elite cultivars. Understanding the genetic diversity and the genotype population structure based on molecular markers at the genome level can speed up the utilization of diverse genetic resources for varietal improvement. In the present study, we carried out an analysis of genetic diversity based on 3882 SNP markers across 37 core watermelon genotypes, including the most widely used watermelon varieties and wild watermelon. Based on the SNP genotyping data of the 37 watermelon genotypes screened, gene diversity and polymorphism information content values across chromosomes varied between 0.03–0.5 and 0.02–0.38, with averages of 0.14 and 0.13, respectively. The two wild watermelon genotypes were distinct from cultivated varieties and the remaining 35 cultivated genotypes were differentiated into three major clusters: 20 genotypes were grouped in cluster I; 11 genotypes were grouped in cluster II; three advanced breeding lines of yellow fruit flesh and genotype SW043 were grouped in cluster III. The results from neighbour-joining dendrogram, principal coordinate analysis and STRUCTURE analysis approaches were consistent, and the grouping of genotypes was generally in agreement with their origins. Here we reveal the genetic relationships among the core watermelon genotypes maintained at the Jiangsu Academy of Agricultural Sciences, China. The molecular and phenotypic characterization of the existing core watermelon genotypes, together with specific agronomic characteristics, can be utilized by researchers and breeders for future watermelon improvement.


Yang, X., Ren, R., Ray, R., Xu, J., Li, P., Zhang, M., …Kilian, A. (2016). Genetic diversity and population structure of core watermelon (Citrullus lanatus) genotypes using DArTseq-based SNPs. Plant Genetic Resources, 14(3),

Journal Article Type Article
Acceptance Date Nov 27, 2015
Online Publication Date Jan 21, 2016
Publication Date Sep 30, 2016
Deposit Date Jul 3, 2017
Publicly Available Date Jul 3, 2017
Journal Plant Genetic Resources
Print ISSN 1479-2621
Electronic ISSN 1479-2621
Publisher Cambridge University Press
Peer Reviewed Peer Reviewed
Volume 14
Issue 3
Keywords core genotypes; genetic diversity; molecular markers; SNPs; watermelon
Public URL
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