A comprehensive analysis of two Chinese cucumber genomes and a mutant population as resources for precision breeding

Abstract

Cucumis sativus L., commonly known as cucumber, is an important vegetable crop worldwide, with China as the largest producer, particularly of the North and South China types. While extensive genomic research has focused on the North China type, especially the Chinese Long 9930, studies on the South China type remain limited. In this study, we assembled high-quality genomes of two widely cultivated and representative parent varieties: S36 (North China type) and H19 (South China type), and conducted mutagenesis analyses. Comparative genome analysis revealed a large number of structural variants between two North China types and two South China types, with many of the affected genes showing strong homology to known functional loci, potentially contributing to phenotypic divergence. We also constructed an EMS mutant library through the mutagenesis of S36 and identified a gene that encodes chlorophyll oxidase, demonstrating the method’s effectiveness for rapid gene discovery. In conclusion, this study provides valuable insights into the classification and evolution of cucumber, highlighting the promising potential of forward genetic approaches in cucumber breeding.

Acknowledgments

The research was supported by the State Key Laboratory of Vegetable Biobreeding (SKLVB202506 to X.L.), the National Key Research and Development Program of China (2023YFF1000100 to T.L.), the Tianjin Major Project for Seed Industry (23ZXZYSN00010), the 111 Project (B17043 to T.L.), and the Construction of Beijing Science and Technology Innovation and Service Capacity in Top Subjects (CEFF-PXM2019_014207_000032 to T.L.).

Author Contributions

H.H. and T.L. conceived and designed the study. H.H., J.W., W.K., W.M., L.Z., Y.L., and J.L. planted and prepared the materials. J.H. performed the bioinformatics analysis. J.W. and X.L. designed and performed molecular experiments. J.H and J.W. wrote the manuscript. T.L., H.H., and X.L. edited and improved the manuscript. All authors approved the final manuscript.

Data availability

The original sequencing data for genome assembly and annotation as well as the sequencing data from mutants and bulked pools for BSA analysis have been deposited in the BIG Submission Portal (https://ngdc.cncb.ac.cn/) under BioProject accession number PRJCA038364. The assembled genomes S36 and H19 were deposited in the Genome Warehouse (GWH) database of the Big Data Center (https://bigd.big.ac.cn/gwh/) under the accession number GWHGDGZ00000000.1 and GWHGDGY00000000.1, respectively.

Conflicts of interest statement

The authors declare no competing interest.

Supplementary material

Supplementary material is available at Horticulture Research online.

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