Chromosome rearrangements during domestication of cucumber as revealed by high-density genetic mapping and draft genome assembly

Authors

  • Luming Yang,

    1. Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
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    • These authors contributed equally to this work.

  • Dal-Hoe Koo,

    1. Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
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    • These authors contributed equally to this work.

  • Yuhong Li,

    1. Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
    2. Horticulture College, Northwest A&F University, Yangling, 712100, China
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  • Xuejiao Zhang,

    1. Horticulture College, Northeast Agricultural University, Harbin, 150030, China
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  • Feishi Luan,

    1. Horticulture College, Northeast Agricultural University, Harbin, 150030, China
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  • Michael J. Havey,

    1. Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
    2. United States Department of Agriculture – Agricultural Research Service, Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
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  • Jiming Jiang,

    1. Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
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  • Yiqun Weng

    Corresponding author
    1. Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
    2. United States Department of Agriculture – Agricultural Research Service, Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
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(e-mail weng4@wisc.edu)

Summary

Cucumber, Cucumis sativus L. is the only taxon with 2n = 2= 14 chromosomes in the genus Cucumis. It consists of two cross-compatible botanical varieties: the cultivated C. sativus var. sativus and the wild C. sativus var. hardwickii. There is no consensus on the evolutionary relationship between the two taxa. Whole-genome sequencing of the cucumber genome provides a new opportunity to advance our understanding of chromosome evolution and the domestication history of cucumber. In this study, a high-density genetic map for cultivated cucumber was developed that contained 735 marker loci in seven linkage groups spanning 707.8 cM. Integration of genetic and physical maps resulted in a chromosome-level draft genome assembly comprising 193 Mbp, or 53% of the 367 Mbp cucumber genome. Strategically selected markers from the genetic map and draft genome assembly were employed to screen for fosmid clones for use as probes in comparative fluorescence in situ hybridization analysis of pachytene chromosomes to investigate genetic differentiation between wild and cultivated cucumbers. Significant differences in the amount and distribution of heterochromatins, as well as chromosomal rearrangements, were uncovered between the two taxa. In particular, six inversions, five paracentric and one pericentric, were revealed in chromosomes 4, 5 and 7. Comparison of the order of fosmid loci on chromosome 7 of cultivated and wild cucumbers, and the syntenic melon chromosome I suggested that the paracentric inversion in this chromosome occurred during domestication of cucumber. The results support the sub-species status of these two cucumber taxa, and suggest that C. sativus var. hardwickii is the progenitor of cultivated cucumber.

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