Non-vernalization requirement in Chinese kale caused by loss of BoFLC and low expressions of its paralogs

A graph-based pan-genome of Brassica oleracea provides new insights into its domestication and morphotype diversification

The domestication of Brassica oleracea has resulted in diverse morphological types with distinct patterns of organ development. Here we report a graph-based pan-genome of B. oleracea constructed from high-quality genome assemblies of different morphotypes. The pan-genome harbors over 200 structural variant hotspot regions enriched in auxin- and flowering-related genes. Population genomic analyses revealed that early domestication of B. oleracea focused on leaf or stem development. Gene flows resulting from agricultural practices and variety improvement were detected among different morphotypes. Selective-sweep and pan-genome analyses identified an auxin-responsive small auxin up-regulated RNA gene and a CLAVATA3/ESR-RELATED family gene as crucial players in leaf-stem differentiation during the early stage of B. oleracea domestication and the BoKAN1 gene as instrumental in shaping the leafy heads of cabbage and Brussels sprouts. Our pan-genome and functional analyses further revealed that variations in the BoFLC2 gene play key roles in the divergence of vernalization and flowering characteristics among different morphotypes, and variations in the first intron of BoFLC3 are involved in fine-tuning the flowering process in cauliflower. This study provides a comprehensive understanding of the pan-genome of B. oleracea and sheds light on the domestication and differential organ development of this globally important crop species.

Upregulation of tandem duplicated BoFLC1 genes is associated with the non-flowering trait in Brassica oleracea var. capitata

Tandem duplicated BoFLC1 genes (BoFLC1a and BoFLC1b), which were identified as the candidate causal genes for the non-flowering trait in the cabbage mutant 'nfc', were upregulated during winter in 'nfc'. The non-flowering natural cabbage mutant 'nfc' was discovered from the breeding line 'T15' with normal flowering characteristics. In this study, we investigated the molecular basis underlying the non-flowering trait of 'nfc'. First, 'nfc' was induced to flower using the grafting floral induction method, and three F₂ populations were generated. The flowering phenotype of each F₂ population was widely distributed with non-flowering individuals appearing in two populations. QTL-seq analysis detected a genomic region associated with flowering date at approximately 51 Mb on chromosome 9 in two of the three F₂ populations. Subsequent validation and fine mapping of the candidate genomic region using QTL analysis identified the quantitative trait loci (QTL) at 50,177,696-51,474,818 bp on chromosome 9 covering 241 genes. Additionally, RNA-seq analysis in leaves and shoot apices of 'nfc' and 'T15' plants identified 19 and 15 differentially expressed genes related to flowering time, respectively. Based on these results, we identified tandem duplicated BoFLC1 genes, which are homologs of the floral repressor FLOWERING LOCUS C, as the candidate genes responsible for the non-flowering trait of 'nfc'. We designated the tandem duplicated BoFLC1 genes as BoFLC1a and BoFLC1b. Expression analysis revealed that the expression levels of BoFLC1a and BoFLC1b were downregulated during winter in 'T15' but were upregulated and maintained during winter in 'nfc'. Additionally, the expression level of the floral integrator BoFT was upregulated in the spring in 'T15' but hardly upregulated in 'nfc'. These results suggest that the upregulated levels of BoFLC1a and BoFLC1b contributed to the non-flowering trait of 'nfc'.

Identification and characterization analysis of candidate genes controlling mushroom leaf development in Chinese kale by BSA-seq

Mushroom leaves (MLs) are malformed leaves that develop from the leaf veins in some of Chinese kale genotypes. To study the genetic model and molecular mechanism of ML development in Chinese kale, the F2 segregation population was constructed by two inbred lines, genotype Boc52 with ML and genotype Boc55 with normal leaves (NL). In the present study, we have identified for the first time that the development of mushroom leaves may be affected by the change of adaxial-abaxial polarity of leaves. Examination of the phenotypes of F1 and F2 segregation populations suggested that ML development is controlled by two dominant major genes inherited independently. BSA-seq analysis showed that a major quantitative trait locus (QTL) qML4.1 that controls ML development is located within 7.4 Mb on chromosome kC4. The candidate region was further narrowed to 255 kb by linkage analysis combined with insertion/deletion (InDel) markers, and 37 genes were predicted in this region. According to the expression and annotation analysis, a B3 domain-containing transcription factor NGA1-like gene, BocNGA1, was identified as a key candidate gene for controlling ML development in Chinese kale. Fifteen single nucleotide polymorphisms (SNPs) were found in coding sequences and 21 SNPs and 3 InDels found in the promoter sequences of BocNGA1 from the genotype Boc52 with ML. The expression levels of BocNGA1 in ML genotypes are significantly lower than in the NL genotypes, which suggests that BocNGA1 may act as a negative regulator for ML genesis in Chinese kale. This study provides a new foundation for Chinese kale breeding and for the study of the molecular mechanism of plant leaf differentiation.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01364-6.