Evidence map›Paper›PMID 42481758›Full record

ArticleNature genetics2026

Pangenome-resolved structural variation drives adaptation and trait evolution in cucumber.

Jiantao Guan, Xiangsheng Li, Han Miao, Xuemei Yan, Xiaoping Liu, Xingfang Gu, Richard G F Visser, Yuling Bai, Sanwen Huang, Zhonghua Zhang and 2 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature genetics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Structural Variation and Its Roles in Plant Genomes.Plants (Basel, Switzerland) · 2026
    Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

12 authors.

Jiantao Guan *State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.ORCID http://orcid.org/0000-0003-1607-009X
Xiangsheng Li *State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
Han Miao *State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
Xuemei Yan *State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
Xiaoping LiuState Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
Xingfang GuState Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
Richard G F VisserPlant Breeding, Wageningen University and Research, Wageningen, the Netherlands.ORCID http://orcid.org/0000-0002-0213-4016
Yuling BaiPlant Breeding, Wageningen University and Research, Wageningen, the Netherlands.
Sanwen HuangNational Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.ORCID http://orcid.org/0000-0002-8547-5309
Zhonghua ZhangEngineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, China. zhangzhonghua@qau.edu.cn.ORCID http://orcid.org/0000-0002-1034-227X
Shaoyun DongState Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China. dongshaoyun@caas.cn.ORCID http://orcid.org/0000-0002-8035-8656
Shengping ZhangState Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China. zhangshengping@caas.cn.ORCID http://orcid.org/0000-0001-9056-3381

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Cucumber (Cucumis sativus L.) is a global vegetable crop and powerful model for sex determination, fruit development and vascular biology. We present high-quality genome assemblies for 125 cultivated and wild accessions, capturing worldwide genetic diversity. Syntenic gene family analysis characterized 37,897 gene families and revealed haplotype diversity shaped by geographic expansion. Comparative analyses uncovered copy-number variations linked to local adaptation, including a CsFT tandem duplication promoting early flowering at higher latitudes. This resource reduces reference bias, enabling the annotation of resistance loci and the discovery of CsCcu, a nucleotide-binding leucine-rich repeat-type R gene conferring scab resistance. We cataloged 135,597 structural variations and quantified their regulatory effects, with ~30% driving trait diversification among geographic groups. Integrating structural variations into genome-wide association studies identified 172 quantitative trait loci for 38 agronomic traits, including a rare long terminal repeat insertion regulating fruit length via CsSPL1. Our findings provide a genomic toolkit for cucumber evolution research and precision breeding.

Indexed as

Adaptation, PhysiologicalCucumis sativusEvolution, MolecularGenome, PlantChromosome MappingDNA Copy Number VariationsGenetic VariationGenome-Wide Association StudyHaplotypesPhenotypeQuantitative Trait Loci

Identifiers

PMID42481758
PMCPMC13447089

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.