Integrated genome-wide domestication and association analyses reveal the complex genetic basis of parthenocarpy during cucumber domestication

TL;DR

This study explores the genetic basis of parthenocarpy in cucumbers by analyzing 236 cucumber samples and identifying key genes and loci involved in this trait.

Contribution

The study identifies 34 loci associated with parthenocarpy and validates three genes for their role in regulating this trait for the first time.

Findings

34 loci associated with parthenocarpy were identified, with 27 showing evidence of selection during domestication.

Three genes (CsACA10, CsCaM, CsERT2) were cloned and verified to regulate parthenocarpy in cucumbers.

Favorable parthenocarpic alleles accumulated in cultivated cucumbers, leading to variation among cucumber groups.

Abstract

Parthenocarpy is an important target trait for the yield and quality of fruit crops. It has been used and selected in cucumber breeding for more than a hundred years, which has led to variation in parthenocarpic ability among different cucumber groups and thus resulted in a complex genetic basis. Here, we performed deep resequencing of 236 cucumbers from six cucumber groups and investigated parthenocarpic phenotypes over three years and six seasons to explore the genetic basis of parthenocarpy in cucumber. Among the 34 loci associated with parthenocarpy identified through a genome-wide association study (GWAS), 17 (50%) were correlated with reported quantitative trait loci (QTLs), and 27 (79.4%) were selected during cucumber domestication. We found that favorable parthenocarpic alleles continuously accumulated in cultivated cucumbers, and our data pinpoint that different favorable alleles were selected in the cucumber groups, leading to variations in parthenocarpic ability among them. To validate the favorable alleles detected by GWAS, we cloned three genes, CsACA10, CsCaM, and CsERT2, and verified their roles in the regulation of parthenocarpy for the first time. Our study elucidated the genetic basis and molecular mechanism of parthenocarpy, providing important germplasms for improving parthenocarpy in cucumber breeding.

The online version contains supplementary material available at 10.1186/s43897-025-00182-y.

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