A joint effort between the crop breeding team of Drs. Xingping Zhang & Yun Deng, and the bioinformatics team of Dr. Hang He at Peking University Institute of Advanced Agricultural Sciences has achieved a major advance in cucumber genomics and mutant resources. Their study, entitled “The near-complete genome assembly of pickling cucumber and its mutation library illuminates cucumber functional genomics and genetic improvement,” was published in Molecular Plant. The work not only provides a cornerstone for cucumber functional genomics but also lays a solid foundation for developing superior cucumber cultivars.

 

 

Background
Cucumber is a globally important vegetable crop, and pickling cucumbers are widely cultivated in the Americas, Europe and Asia. However, the previously released genome of the U.S. pickling cucumber is highly fragmented, severely hampering functional-genomics research and breeding progress. The Peking University teams chose the elite Russian-type gynoecious inbred line CUK2021 and generated a near-gap-free reference genome using high-accuracy ONT ultra-long reads and Hi-C scaffolding. The resulting CUK2021 assembly spans 326.24 Mb, encompassing complete centromeres and all 13 telomeres. Benchmarking metrics — read mapping rate, genome coverage and BUSCO completeness — confirm its exceptional quality.

 

Key findings
Comparative analysis between CUK2021 and the Chinese long-cucumber v4 reference revealed extensive structural variations (inversions, translocations) and local misalignments concentrated in centromeric regions. Genes within misaligned segments are enriched for functions in homologous recombination, the citric-acid cycle, and cysteine/methionine metabolism. The study also highlights the role of transposons in gene duplication: long-terminal-repeat retrotransposons (LTR-RTs), especially Copia and Gypsy superfamilies, underwent marked expansions over the past 0.5 million years, driving gene duplication and divergence.

 

To accelerate functional-genomics studies, the researchers constructed an EMS pollen mutation library in the CUK2021 background. Phenotypic mutation rates reached 1.39 % in the M1 generation and 12 % in the M2. Valuable mutants, including strong-male, shortened-internode, sparse-spine and altered-fruit-shape lines, were identified, offering both research tools and elite germplasm for pickling-cucumber improvement. Notably, repeated EMS treatment on already mutagenized materials did not significantly increase mutation density. All genome and mutant-library sequencing data have been deposited in the National Genomics Data Center for global access.

 

Figure 1. Gap-free reference genome of cucumber and EMS-induced pollen mutant library.

 

The team further dissected a mutant (m96) displaying yellowing in young leaves and cell-death patches in mature leaves and fruits. Bulked-segregant analysis, RNA-seq and functional assays showed that the phenotype is controlled by a semi-dominant gene, and the candidate locus Csa1G074800 was identified. Silencing this gene via VIGS enhanced resistance to cucumber mosaic virus, providing preliminary confirmation of its biological role.

 

This landmark study delivers invaluable resources for cucumber genetic improvement and is expected to advance the global cucumber industry, bringing tastier and higher-quality cucumbers to consumers. Continued efforts by the research teams promise even more exciting breeding innovations in the future.

 

Author information
The work represents another major advance in cucurbit crop genomics by Peking University Institute of Advanced Agricultural Sciences, following previous achievements in watermelon T2T genomics (Molecular Plant, 2022), watermelon super-pan-genome (Nature Genetics, 2024) and watermelon mutant libraries. Yao Tian, Kui Li and Tonghui Li are co-first authors; Drs. Xingping Zhang, Yun Deng, and Hang He are co-corresponding authors. The study also benefited from guidance by Academician Xing Wang Deng and Dr. Yan Xue. Funding was provided by the Shandong Science & Technology Innovation Program, the Ningbo Science & Technology Innovation Program, the Weifang Seed Industry Innovation Team, and other agencies.

 

(From left to right: Dr. Yun Deng, Dr. Hang He, Dr. Xingping Zhang, Tonghui Li, Yao Tian, Kui Li, Zenghui Chen)