Combined BSA-Seq and RNA-Seq Analyses Identify Candidate Genes Associated with Self-Incompatibility in Cabbage (Brassica oleracea var. capitata)

Cabbage (Brassica oleracea var. capitata), a member of the Brassicaceae family, is an important vegetable crop grown worldwide. Self-incompatibility (SI) in cabbage is a key trait that prevents self-fertilization and inbreeding, thereby maintaining genetic diversity within populations. Although several genes related to SI have been reported, its genetic control remains unclear. In this study, we developed an F2 population from the highly self-compatible (SC) cabbage line 87-534 and the highly self-incompatible (SI) line 01-20, both of which exhibit the S5 haplotype. The segregation analysis of the F2 population revealed the possible control of SI by a major gene with additional modifying genetic factors. Bulk segregant analysis sequencing (BSA-Seq) and RNA sequencing (RNA-Seq) were performed on SI and SC samples selected from the F2 population. BSA-Seq revealed a candidate region on chromosome 7 (C07: 7.45 Mb to 8.93 Mb), including 32 differentially expressed genes (DEGs). RNA-Seq identified a total of 2400 DEGs between the two pools, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses suggested that plant hormone biosynthesis and signaling, plant immune response were significantly enriched and may be involved in SI. The combined analysis of BSA-Seq and RNA-Seq identified six candidate genes associated with SI, and their expression was confirmed using quantitative real-time PCR (qRT-PCR). Among them, Bol023956 encodes fructokinase, Bol023986 is involved in plant defense response, Bol024018 is related to pollen development, Bol024012 encodes a transport protein for phytohormones, Bol023943 encodes chorismate mutase 3, and Bol012515 is an important regulatory gene for chloroplast synthesis. These six genes, potentially linked to SI, should be targets for further validation. These findings provide insights into the molecular mechanisms of SI in cabbage and the selection of superior cabbage varieties.