Genetic and Molecular Characterization of a Self-Compatible Brassica rapa Line Possessing a New Class II S Haplotype

Most flowering plants have evolved a self-incompatibility (SI) system to maintain genetic diversity by preventing self-pollination. The species possesses sporophytic self-incompatibility (SSI), which is controlled by the pollen- and stigma-determinant factors SP11/SCR and SRK. However, the mysterious molecular mechanism of SI remains largely unknown. Here, a new class II haplotype, named , was identified in a pak choi line '325', which was responsible for the completely self-compatible phenotype. To obtain the entire locus sequences, a complete pak choi genome was gained through Nanopore sequencing and de novo assembly, which provided a good reference genome for breeding and molecular research in . locus comparative analysis showed that the closest relatives to was , and high sequence polymorphism existed in the locus. Meanwhile, two duplicated ( and ) were distributed in the locus with opposite transcription directions. and were expressed normally at the transcriptional level. The multiple sequence alignment of SCRs and SRKs in class II haplotypes showed that a number of amino acid variations were present in the contact regions (CR II and CR III) of BrSCR-325 and the hypervariable regions (HV I and HV II) of BrSRK-325s, which may influence the binding and interaction between the ligand and the receptor. Thus, these results suggested that amino acid variations in contact sites may lead to the SI destruction of a new class II haplotype in . The complete SC phenotype of '325' showed the potential for practical breeding application value in .