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

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.