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Construction of a high-density DArTseq SNP-based genetic map and identification of genomic regions with segregation distortion in a genetic population derived from a cross between feral and cultivated-type watermelon

Molecular Genetics and Genomics volume 290, pages 1457–1470 (2015)Cite this article

Abstract

Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] is an economically important vegetable crop grown extensively worldwide. To facilitate the identification of agronomically important traits and provide new information for genetic and genomic research on this species, a high-density genetic linkage map of watermelon was constructed using an F2 population derived from a cross between elite watermelon cultivar K3 and wild watermelon germplasm PI 189225. Based on a sliding window approach, a total of 1,161 bin markers representing 3,465 SNP markers were mapped onto 11 linkage groups corresponding to the chromosome pair number of watermelon. The total length of the genetic map is 1,099.2 cM, with an average distance between bins of 1.0 cM. The number of markers in each chromosome varies from 62 in chromosome 07 to 160 in chromosome 05. The length of individual chromosomes ranged between 61.8 cM for chromosome 07 and 140.2 cM for chromosome 05. A total of 616 SNP bin markers showed significant (P < 0.05) segregation distortion across all 11 chromosomes, and 513 (83.3 %) of these distorted loci showed distortion in favor of the elite watermelon cultivar K3 allele and 103 were skewed toward PI 189225. The number of SNPs and InDels per Mb varied considerably across the segregation distorted regions (SDRs) on each chromosome, and a mixture of dense and sparse SNPs and InDel SDRs coexisted on some chromosomes suggesting that SDRs were randomly distributed throughout the genome. Recombination rates varied greatly among each chromosome, from 2.0 to 4.2 centimorgans per megabase (cM/Mb). An inconsistency was found between the genetic and physical positions on the map for a segment on chromosome 11. The high-density genetic map described in the present study will facilitate fine mapping of quantitative trait loci, the identification of candidate genes, map-based cloning, as well as marker-assisted selection (MAS) in watermelon breeding programs.

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Acknowledgments

The authors wish to thank Damian Jaccoud and Haitao Xiang for providing the SNP data and answering questions about data analysis. This research was supported by Grants from the China Postdoctoral Science Foundation (2013M541624), Jiangsu Province Postdoctoral Science Foundation (1301068B) and the Jiangsu Provincial Major Support Program for Agriculture (BE2012323).

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Affiliations

  1. Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing, 210014, China

    Runsheng Ren, Pingfang Li, Jinhua Xu, Man Zhang, Guang Liu, Xiefeng Yao & Xingping Yang

  2. Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK

    Runsheng Ren & Rumiana Ray

  3. DArT P/L, PO Box 7141, Yarralumla, Canberra, ACT, 2600, Australia

    Andrzej Kilian

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  1. Runsheng Ren
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  2. Rumiana Ray
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  3. Pingfang Li
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  4. Jinhua Xu
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  5. Man Zhang
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  6. Guang Liu
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  7. Xiefeng Yao
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Correspondence to Xingping Yang.

Additional information

Communicated by S. Hohmann.

Electronic supplementary material

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Supplementary Table 1. The number of SNP in each bin marker (XLS) (XLSX 32 kb)

438_2015_997_MOESM2_ESM.xlsx

Supplementary Table 2. Bin markers used to construct the genetic map of watermelon. Their chromosome, bin position, genetic distance, marker name, bin marker start, bin marker end and bin marker length are listed.(XLS) (XLSX 58 kb)

Supplementary Table 3. The genetic map of K3 × PI 189225 144 individuals F2 population.(XLS) (XLSX 42 kb)

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Ren, R., Ray, R., Li, P. et al. Construction of a high-density DArTseq SNP-based genetic map and identification of genomic regions with segregation distortion in a genetic population derived from a cross between feral and cultivated-type watermelon. Mol Genet Genomics 290, 1457–1470 (2015). https://doi.org/10.1007/s00438-015-0997-7

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  • DOI: https://doi.org/10.1007/s00438-015-0997-7

Keywords

  • Watermelon
  • Linkage map
  • SNP
  • High density
  • DArTseq