Cold tolerance in rapeseed is closely related to its growth, yield, and geographical distribution. However, the mechanisms underlying cold resistance in rapeseed remain unclear. This study aimed to explore cold resistance genes and provide new insights into the molecular mechanisms of cold resistance in rapeseed. Rapeseed M98 (cold-sensitive line) and D1 (cold-tolerant line) were used as parental lines. In their F₂ population, 30 seedlings with the lowest cold damage levels and 30 with the highest cold damage levels were selected to construct cold-tolerant and cold-sensitive pools, respectively. The two pools and parental lines were analyzed using bulk segregant sequencing (BSA-seq). The G’-value analysis indicated a single peak on Chromosome C09 as the candidate interval, which had a 2.59 Mb segment with 69 candidate genes. Combined time-course and weighted gene co-expression network analyses were performed at seven time points to reveal the genetic basis of the two-parent response to low temperatures. Twelve differentially expressed genes primarily involved in plant cold resistance were identified. Combined BSA-seq and transcriptome analysis revealed BnaC09G0354200ZS, BnaC09G0353200ZS, and BnaC09G0356600ZS as the candidate genes. Quantitative real-time PCR validation of the candidate genes was consistent with RNA-seq. This study facilitates the exploration of cold tolerance mechanisms in rapeseed.

Brassica juncea is an important oilseed and vegetable crop whose flowers are typically yellow, largely owing to carotenoid pigmentation. Here, we report a novel, heritable apricot-flowered variant designated ‘Caijie,’ from a wild B. juncea accession. Metabolomic profiling revealed that the distinctive petal coloration was primarily attributable to anthocyanin accumulation. Genetic mapping via bulked segregant analysis (BSA) mapped the apricot-flowered trait to a single dominant locus within a 9.76-Mb interval on chromosome B03. Among the 1,406 annotated genes in this region, Production of Anthocyanin Pigment 2 ( BjB03.PAP2 ), which encodes an R2R3-MYB transcription factor, emerged as the most likely candidate gene. Consistent with this, transcriptomic analysis revealed coordinated upregulation of multiple structural genes involved in the anthocyanin biosynthesis pathway in the apricot-flowered variant. Further sequence analysis revealed a (TC) _n dinucleotide repeat polymorphism in the promoter of BjB03.PAP2 , representing a structural variation that is likely responsible for enhanced transcriptional activity and subsequent anthocyanin production in petals. This study unveils a previously unrecognized genetic mechanism underlying flower color variation in B. juncea , offering new insights into the evolution of floral pigmentation and a valuable genetic resource for breeding ornamental Brassica crops.