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Integrating BSA-Seq, QTL Mapping, and RNA-Seq to Identify Candidate Genes for Hollow Heart in Cucumber Fruits
Mengyao Kong1, Chenran Gu1, Xiaoyue Li1
1Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China.
Plants (Basel, Switzerland)
|May 13, 2026
Summary
Researchers identified a key gene, Csa7G039280, in cucumber (Cucumis sativus L.) linked to the hollow-heart trait. This finding aids in developing cucumber varieties with improved fruit quality through molecular breeding.
Area of Science:
- Plant Genetics
- Agricultural Science
- Molecular Biology
Background:
- Cucumber (Cucumis sativus L.) fruit quality is crucial for commercial value.
- The hollow-heart trait, marked by internal cracks, significantly reduces cucumber marketability and edibility.
Purpose of the Study:
- To identify genetic factors controlling the hollow-heart trait in cucumber.
- To pinpoint candidate genes for molecular breeding of non-hollow-heart cucumber varieties.
Main Methods:
- Developed a six-generation segregating population from distinct parental lines.
- Employed Bulked Segregant Analysis sequencing (BSA-seq) for quantitative trait loci (QTL) mapping.
- Utilized comparative RNA sequencing (RNA-seq) and quantitative real-time PCR (qRT-PCR) for gene validation.
Main Results:
- Mapped candidate genomic regions for the hollow-heart trait to chromosomes 2, 3, and 7.
- Delineated a major QTL on chromosome 7 containing 98 genes.
- Identified 11 candidate genes within the QTL interval, with Csa7G039280 highlighted as a promising candidate potentially involved in lignin biosynthesis.
Conclusions:
- Csa7G039280 is a strong candidate gene regulating the hollow-heart trait in cucumber.
- Understanding these genetic mechanisms facilitates breeding for improved cucumber fruit quality.
