Alloplasmic lines, in which the nuclear genome is combined with wild cytoplasm, are often characterized by cytoplasmic male sterility (CMS), regardless of whether it was derived from sexual or somatic hybridization with wild relatives. In this study, we sequenced and analyzed the mitochondrial genomes of five such alloplasmic lines in Brassica juncea. The assembled and annotated mitochondrial genomes of the five alloplasmic lines were found to have virtually identical gene contents. They preserved most of the ancestral mitochondrial segments, and the same candidate male sterility gene (orf108) was found harbored in mitotype-specific sequences. We also detected promiscuous sequences of chloroplast origin that were conserved among plants of the Brassicaceae, and found the RNA editing profiles to vary across the five mitochondrial genomes. On the basis of our characterization of the genetic nature of five alloplasmic mitochondrial genomes, we speculated that the putative candidate male sterility gene orf108 may not be responsible for the CMS observed in Brassica oxyrrhina and Diplotaxis catholica. Furthermore, we propose the potential coincidence of CMS in alloplasmic lines. Our findings lay the foundation for further elucidation of male sterility gene.

Most flowering plants have evolved a self-incompatibility (SI) system to maintain genetic diversity by preventing self-pollination. The Brassica 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 S haplotype, named BrS-325, was identified in a pak choi line ‘325’, which was responsible for the completely self-compatible phenotype. To obtain the entire S 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 B. rapa. S locus comparative analysis showed that the closest relatives to BrS-325 was BrS-60, and high sequence polymorphism existed in the S locus. Meanwhile, two duplicated SRKs (BrSRK-325a and BrSRK-325b) were distributed in the BrS-325 locus with opposite transcription directions. BrSRK-325b and BrSCR-325 were expressed normally at the transcriptional level. The multiple sequence alignment of SCRs and SRKs in class II S 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 S haplotype BrS-325 in B. rapa. The complete SC phenotype of ‘325’ showed the potential for practical breeding application value in B. rapa.

Bolting time is a pivotal agronomic trait that determines the yield and commercial quality of Brassica rapa ssp. chinensis var. utilis. To investigate the molecular basis of early bolting, an early-bolting line ‘m662’ and a late-bolting line ‘t151’ were used in this study. Phenotypic evaluation combined with shoot apical meristem (SAM) observation showed that 10 days of low-temperature vernalization markedly accelerated bolting in ‘t151’. Subsequently, SAM samples from ‘m662’, non-vernalized ‘t151’, and 10-day vernalized ‘V10-t151’ were collected at five developmental stages (7, 10, 13, 16, and 19 d after transplanting) for transcriptome sequencing. Weighted gene co-expression network analysis revealed that key module genes related to gibberellin signaling were specifically enriched in ‘m662’ before bolting, whereas those in the middle and late bolting stages were enriched in hormone response, cell cycle regulation, and floral organ development. In ‘t151’, hub genes detected at 7–13 d included three paralogs of the floral integrator gene SOC1 and BraA06.FPF1. BrSOC1 (BraA03g024230.4C) was significantly upregulated in response to vernalization. DEGs identified during the late developmental stage (16–19 d) included genes involved in transmembrane transport processes, flower development, reproductive shoot system development. Expression analysis across the three materials showed that vernalization accelerated bolting in ‘t151’ by repressing BrFLC expression and promoting BrSOC1 expression. This study elucidates the dynamic transcriptomic network underlying early bolting in non-heading Chinese cabbage, providing key functional genes and mechanistic insights for bolting regulation and molecular breeding.