Xianhong Ge

Alien chromosome addition lines hold significant value for breeding and genetic research. However, the genetic interaction between the recipient genome(s) and the alien chromosomes remains largely unclear. Here, we analyzed the genomic composition and gene expression of 2 purple-leaved Brassica napus alien addition lines carrying chromosome B05 from B. juncea: the monosomic line ZYCB3 (MAAL, 2n = 39, AACC + 1B05) and the disomic line ZY52 (DAAL, 2n = 40, AACC + 2B05). We assembled a chromosome-level genome of the DAAL ZY52 disomic line and characterized its genomic variation and chromosome introgression patterns. In addition to chromosome B05, multiple introgressed fragments derived from the donor B. juncea line ZYJC were identified, revealing extensive genome remodeling during distant hybridization and backcross breeding. We then used multi-omics approaches to explore chromosomal interactions and the regulation of anthocyanin biosynthesis. Notably, the addition of chromosome B05 was associated with stronger repression of homoeologous genes on C-subgenome chromosomes than on A-subgenome chromosomes. In ZY52, homoeologous genes on chromosome C01 showed reduced expression, whereas in the ZYCB3 monosomic line reduced expression was observed on both C01 and C02. Comparative transcriptomic and metabolomic analyses further showed that highly expressed anthocyanin biosynthesis genes (ABGs) on chromosome B05contributed to anthocyanin accumulation and the purple-leaf phenotype in both addition lines. Overall, this study provides new insights into interchromosomal interactions, genome remodeling, and phenotypic variation in alien addition lines.

SUMMARY: Tissue‐specific anthocyanin pigmentation is observed in rapeseed ( Brassica napus L. AACC, 2 n = 38) as well as in its ancestral diploids Brassica rapa (AA, 2 n = 20) and Brassica oleracea (CC, 2 n = 18). We previously identified the MYB genes BnaPAP2.A7b and BnaPAP2.C6a as key regulators of anthocyanin biosynthesis. Here we uncover an antagonistic regulatory mechanism in leaves involving their paralog BnaPAP2.C2 . Unlike the pigmentation‐associated genes, BnaPAP2.C2 is constitutively expressed in both green and purple leaves, regardless of anthocyanin levels. Its promoter contains two enhancers (463 and 486 bp) that synergistically regulate transcription. Competitive binding studies reveal that BnaPAP2.C2, although lacking activation capacity, sequesters BnaTT8 and outcompetes BnaPAP2.A7b, thereby suppressing anthocyanin biosynthesis. Under environmental stress, elevated expression of BnaPAP2.A7b promotes anthocyanin biosynthesis, whereas BnaPAP2.C2 is downregulated. This paralog‐specific molecular antagonism provides new insight into the evolution of MYB–bHLH interaction specificity. Together, these findings uncover a novel inhibitory mechanism within the anthocyanin regulatory hierarchy of polyploid rapeseed, highlighting competitive binding as an evolutionary innovation driving functional diversification of duplicated MYB regulators.

Wallflower (Erysimum cheiri) belongs to the monogeneric Erysimeae tribe of the mustard family (Brassicaceae). It is widely cultivated as an ornamental garden plant and appreciated for its diverse flower colors. However, the absence of a high-quality genome has hampered research on wallflower genome evolution and the mechanisms underlying variations in flower color. Here, we assembled a nearly gap-free telomere-to-telomere genome of E. cheiri. The assembled genome enabled the reconstruction of genome evolution in the genus Erysimum (274 species), tracing the changes from the ancestral n = 8 genome (in E. cheiranthoides) to the derived genomes with 7 (in E. nevadense) and 6 (in E. cheiri) chromosome pairs. While the reduction from n = 8 to n = 7 was mediated by a nested chromosome fusion accompanied by inversions, the further decrease to n = 6 in E. cheiri resulted from an end-to-end translocation involving the other 2 nonhomologous chromosomes. Compared with other Brassicaceae species, E. cheiri showed a notable expansion of gene families related to secondary metabolite biosynthesis. Its flower color variation is primarily determined by the biosynthesis and accumulation of carotenoids and flavonoids. We mapped the metabolic pathways for carotenoids and flavonoids, identifying the hub genes regulating their biosynthesis. This research lays an important foundation for understanding the chromosomal and genome evolution of the Erysimeae tribe and paves the way for future investigations into genetic studies and breeding applications of E. cheiri.

Orychophragmus violaceus is an ornamental plant belonging to the Brassicaceae family, known for its profusion of white to light purple, pink, and purple flowers that bloom in early spring. However, there is a lack of reports regarding the localization of the genes responsible for flower color. The aim of this research was to locate the key genes controlling flower color variation in O. violaceus, providing loci for its genetic improvement of flower color. In this study, we constructed an F₂ mapping population using the purebred white flower mutant line OvW-1 and the purebred purple flower line OvP-37, obtained candidate regions of the Ovwf locus using BSA-seq, and then used extreme recessive white-flowered plants for fine-mapping and combined with RNA-seq to predict key genes controlling the white-flowered trait. Genetic analysis indicated that the Ovwf trait is governed by a single recessive locus, designated as without cytoplasmic inheritance. Subsequently, BSA-seq and fine-mapping of the Ovwf locus within a 1.37 Mb interval. Gene annotation revealed that this interval encompasses 76 genes, of which only two genes—OV03G032130 and OV03G032280—are potentially implicated in anthocyanin biosynthesis. Further RNA-seq analysis suggested that only OvANS (OV03G032130) was differentially expressed, which may be a critical gene influencing the white flower locus Ovwf. This is the first report of fine-mapping of the flower color locus in O. violaceus. These findings contribute valuable insights into the mechanisms underlying flower color variation in O. violaceus and present a promising target for the breeding of colorful varieties.

Summary: Matthiola incana, commonly known as stock and gillyflower, is a widely grown ornamental plant whose genome is significantly larger than that of other species in the mustard family. However, the evolutionary history behind such a large genome (~2 Gb) is still unknown. Here, we have succeeded in obtaining a high‐quality chromosome‐scale genome assembly of M. incana by integrating PacBio HiFi reads, Illumina short reads and Hi‐C data. The resulting genome consists of seven pseudochromosomes with a length of 1965 Mb and 38 245 gene models. Phylogenetic analysis indicates that M. incana and other taxa of the supertribe Hesperodae represent an early‐diverging lineage in the evolutionary history of the Brassicaceae. Through a comparative analysis, we revisited the ancestral Hesperodae karyotype (AHK, n = 7) and found several differences from the well‐established ancestral crucifer karyotype (ACK, n = 8) model, including extensive inter‐ and intra‐chromosomal rearrangements. Our results suggest that the primary reason for genome obesity in M. incana is the massive expansion of long terminal repeat retrotransposons (LTR‐RTs), particularly from the Angela, Athila and Retand families. CHG methylation modification is obviously reduced in the regions where the highest density of Copia‐type LTR‐RTs and the lowest density of Gypsy‐type LTR‐RTs overlap, corresponding to the putative centromeres. Based on insertion times and methylation profiling, recently inserted LTR‐RTs were found to have a significantly different methylation pattern compared to older ones.

Key message Brassica rapa-nigra monosomic alien addition lines (MAALs) were developed and compared with B. oleracea-nigra MAALs containing the same B-genome chromosomes. The diploid Brassica nigra (black mustard) is the donor of the B-genome for two allotetraploids: B. juncea (AABB) and B. carinata (BBCC). To dissect the B-genome of B. nigra within the A-genome background of B. rapa, the progenies of resynthesized B. juncea, successively pollinated by the parental B. rapa, were screened using cytological methods and molecular markers. Seven out of eight B. rapa-nigra MAALs (2n = 21, AA + 1B₁₋₈) were obtained, except for the AA-B6 MAAL. The additional chromosome appeared as one univalent in 86.76% of pollen mother cells and formed one trivalent with two A-genome chromosomes in 13.24% of cells. Different alien B-genome chromosomes were transmitted to progeny at varying rates, with higher transmission rates via female gametes (averaging 13.59%) than via male gametes (7.31%). These MAALs exhibited significant phenotypic variations which were either of parental origins or novel traits, and chromosomal locations of some traits from B. nigra or genetic interactions were realized from the joint results of B. rapa-nigra and B. oleracea-nigra MAALs with the same additional B-subgenome chromosomes. Comparison analyses of these two sets of MAALs provided new insights into the genetic interplay of the B-genome with A- and C-genomes in these two allotetraploids.

Distant hybridization between Brassica napus and related genera serves as an effective approach for rapeseed germplasm innovation. Isatis indigotica, a wild relative of Brassica, has emerged as a valuable genetic resource for rapeseed improvement due to its medicinal properties. This study employed anchor mapping of alien chromosomal fragment localization (AMAC) method to efficiently identify alien chromosomal fragments in the progeny derived from distant hybridization between I. indigotica and Brassica napus, ‘Songyou No. 1’. Based on the AMAC method, we developed 193,101 IP and SSR markers utilizing the I. indigotica reference genome (Woad-v1.0). Through Electronic-PCR analysis against the Brassica and I. indigotica pan-genome, 27,820 specific single-locus (SSL) IP and SSR markers were obtained. Subsequently, 205 pairs of IP primers and 50 pairs of SSR primers were synthesized randomly, among which 148 pairs of IP markers (72.20%) and 45 pairs of SSR markers (90%) were verified as SSL molecular markers for the I. indigotica genome with no amplification product in four Brassica crops. These 193 SSL markers enable precise identification of one complete I6 chromosome and three chromosomal fragments (I1:1.17 Mb, I5:2.61 Mb, I7:1.11 Mb) in ‘Songyou No. 1’. Furthermore, we traced 32 genes involved in bioactive compound biosynthesis within/near these alien segments in ‘Songyou No. 1’ and developed seven functional markers. This study not only validates the efficacy of SSL markers for detecting exogenous chromatin in intergeneric hybrids but also provides valuable insights for the precise identification and mapping of desired chromosomal fragments or genes embedded in the derivatives from distant hybridization and potential applications in marker-assisted breeding for medicinal plant via distant hybridization strategy between I. indigotica and Brassica crops.

Summary: Polyploidy plays a key role in genome evolution and crop improvement. The formation of bivalents rather than multivalents during meiosis of polyploids is essential to ensure meiotic stability and optimal fertility of the species. However, the mechanisms preventing multivalent recombination in polyploids remain obscure. We studied the role of the synaptonemal complex in polyploid meiosis by mutating the transverse filament component ZYP1 in allotetraploid Brassica napus and autotetraploid Arabidopsis. In B. napus, a mutation of all four ZYP1 copies results in multivalent pairing accompanied by pairing partner switches, nonhomologous recombination, and interlocks, leading to severe chromosome entanglement and fertility abortion. The presence of only one functional allele of ZYP1 compromises synapsis and multivalent associations occur at nonsynaptic regions. Moreover, the disruption of ZYP1 causes a complete shift from predominantly multivalent pairing to exclusively multivalent pairing in pachytene cells of synthetic autotetraploid Arabidopsis thaliana, resulting in a dramatic increase in the frequency of multivalents at metaphase I. We conclude that the ZYP1‐mediated assembly of the synaptonemal complex facilitates the pairwise homologous pairing and recombination in both allopolyploid and autopolyploid species and plays a key role in ensuring a diploid‐like bivalent formation in polyploid meiosis.