Integrating BSA-Seq, QTL Mapping, and RNA-Seq to Identify Candidate Genes for Hollow Heart in Cucumber Fruits

Cucumber (Cucumis sativus L.) is a globally significant vegetable crop, and its fruit quality remains a major focus of research. The hollow-heart trait, characterized by internal cracks or cavities, severely compromises both the commercial value and edible quality of cucumber fruit. In this study, a six-generation segregating population (P1, P2, F1, F2, BC1P1, BC1P2) was developed from the parental lines “JZ6-1-2” and “D0432-3-4”. BSA-seq was employed to map candidate genomic regions associated with the hollow-heart trait to chromosomes 2, 3, and 7. Subsequently, a major QTL for the trait was delineated on chromosome 7, spanning a region containing 98 genes. Comparative RNA-seq between the parental lines identified 2141 differentially expressed genes. The integration of QTL mapping and RNA-seq data revealed 11 candidate genes residing within the key QTL interval. Through further validation via qRT-PCR, gene sequence comparison, and gene annotation, Csa7G039280 was identified as a promising candidate gene regulating hollow-heart formation, potentially via the lignin biosynthesis pathway. The identification of these candidate regions and genes provides critical information for molecular breeding aimed at developing non-hollow-heart cucumber varieties, thereby enhancing the understanding of the genetic regulatory mechanisms underlying this economically important trait.