Jianli Liang

Chinese cabbage forms a leafy head as its main edible organ, a process involving extensive morphological and transcriptional changes. Here, we employed ATAC-seq to profile a time-series chromatin accessibility landscape across key developmental stages of leaf heading. This analysis revealed highly dynamic, stage-specific chromatin accessible regions accompanied by distinct transcription factors activities. Genes associated with adaxial-abaxial polarity and hormone signaling displayed dynamic accessibility patterns, suggesting their critical roles in head formation. BrKAN2 emerged as a key candidate regulator. Mutant analysis in Chinese cabbage and overexpression in Arabidopsis significantly altered leaf morphology and dorsoventral polarity. Population genetic analysis further indicated strong selection on BrKAN2 in heading Brassica rapa . Integration of DAP-seq and ATAC-seq identified BrKAN2.1 target genes enriched in organ development and hormone-related pathways, which were validated by VIGS and EMSA. Auxin responsiveness assays underscored the importance of auxin signaling in heading. Collectively, these findings uncover a dynamic chromatin landscape underlying leaf heading and establish BrKAN2 as a central regulatory factor, offering new insights for genetic improvement of Chinese cabbage.

Ethiopian mustard (Brassica carinata A. Braun) is one of the Brassica leafy vegetables and oilseed crops, which can withstand adverse environmental conditions. This study was conducted to characterize and evaluate the leaf attributes of 313 Ethiopian mustard accessions grown in the greenhouse and field in 2018/19 in Beijing, China. Data on 18 different leaf morphological attributes were collected based on the IBPGR for Brassica and Raphanus descriptor format and Fiji Image J. The collected data were subjected to descriptive statistics using JMP version 14 software. Results indicate that the majority of the accessions had serrated leaf margin, intermediate juvenile development, rounded apex leaf shape, absence of leaf pubescence, number of lobes > 5 and had intermediate number of leaves per plant with frequencies of 101, 213, 223, 244, 183 and 289, respectively. The accessions had also white midrib color, light green leaf color, purple petiole color, purple stem color and purple apex leaf color pigments with frequencies of 168, 165, 104, 113 and 122, respectively. Significant differences were observed among the accessions for leaf size attributes (p < 0.001) indicating their potential as leafy vegetables. Furthermore, there were significant accession × environment effects for the laminal length, total leaf length, leaf area, leaf weight and petiole length. Notably, 71% of the accessions had an average of 81 days flowering time. The multivariate cluster and principal component analyses divided the 313 accessions into eight groups with distinctive information; consisting of 81, 37, 79, 38, 14, 11, 6 and 47 accessions. Thus, this study provides important information about Ethiopian mustard germplasms that is vital for further advancement and genetic improvement of the crop.

High-throughput Chromatin Conformation Capture (Hi-C) technologies can be used to investigate the three-dimensional genomic structure of plants. However, the practical utility of these technologies is impeded by significant background noise, hindering their capability in detecting fine 3D genomic structures. In this study, we optimized the Bridge Linker Hi-C technology (BL-Hi-C) to comprehensively investigate the 3D chromatin landscape of Brassica rapa and Brassica oleracea. The Bouquet configuration of both B. rapa and B. oleracea was elucidated through the construction of a 3D genome simulation. The optimized BL-Hi-C exhibited lower background noise compared to conventional Hi-C methods. Taking this advantage, we used BL-Hi-C to identify FLC gene loops in Arabidopsis, B. rapa, and B. oleracea. We observed that gene loops of FLC2 exhibited conservation across Arabidopsis, B. rapa, and B. oleracea. While gene loops of syntenic FLCs exhibited conservation across B. rapa and B. oleracea, variations in gene loops were evident among multiple paralogs FLCs within the same species. Collectively, our findings highlight the high sensitivity of optimized BL-Hi-C as a powerful tool for investigating the fine 3D genomic organization.

The species Brassica rapa includes enormous leafy vegetables with extreme leaf morphological diversity. Leaf traits such as size, shape, weight, and ratio of the leaf blade to the petiole contribute to yield, appearance, and desirability to consumers. These leaf-related traits are controlled by quantitative trait loci (QTLs). The construction of high-density bin maps using low-coverage sequencing is a powerful method for QTL fine-mapping and gene identification. In this study, we performed whole-genome re-sequencing of Wutacai ‘Zhongbaye’ and Chinese cabbage ‘HN53’ and 150 F₂ individuals to construct a high-density bin map for QTL mapping of 11 leaf-related traits. The parental lines and F₂ population were re-sequenced at 10x and 1x coverage, respectively. A map containing 565 bin markers was constructed based on parental single-nucleotide polymorphisms and a modified sliding window approach. The total map length was 944.6 cM and the average distance of the bins was 1.65 cM. In total, 60 significant QTLs controlling 11 leaf-related traits were detected. We further identified candidate genes responsible for these complex leaf-related traits. These findings suggest that this cost-effective bin-mapping approach is capable of rapid identification of QTLs and candidate genes, and will thus facilitate the dissection of the underlying molecular basis of leaf morphological variations and accelerate the improvement of B. rapa vegetable breeding.

Doubled haploid (DH) technology based on in vivo haploid induction (HI), which is used to obtain true-breeding lines within a single generation, is a technique that significantly increases modern crop-breeding efficiency. Recently, dicot Arabidopsis thaliana lines containing mutations in DMP8/9 were used as haploid inducer lines, but the use of this new HI mechanism is limited in Brassicaceae species, which include many important vegetable, oil, and fodder crops. Here, we investigated the phylogenetic distribution of the DMP8 and DMP9 homologous genes from 26 sequenced Brassicaceae species. We found that DMP8 only exists in the tribe Arabideae, while multiple copies of the DMP9 gene are presenting in all the investigated Brassicaceae species. The syntenic DMP9 genes were divided into two groups derived from the S genomic block and R genomic block, respectively. We further investigated the duplication, structure variations, and expression of the DMP9 genes in Brassica species that had undergone an extra whole-genome triplication. Our results revealed that DMP9 was lost in the most fractionated (MF2) subgenome, and the retained DMP9s in the least fractionated (LF) subgenome and medium fractionated (MF1) subgenome showed diversified expression patterns, indicating their functional diversification. Our results will be useful for obtaining the target DMP genes for the establishing of HI lines in Brassicaceae crops.

Flowering time is important for Brassica rapa vegetables because premature bolting before harvest can lower yield and quality. FLOWERING LOCUS C (FLC) acts as a key repressor of flowering. In this study, we identified a nonsynonymous mutation at the 58th nucleotide of exon1 in BrFLC1 (named as Pe1+58 (A/C)) by screening resequencing data of 199 B. rapa accessions and verified this mutation as being related to flowering time variation. Strong linkage inheritance was detected between this locus and a previously reported splicing site mutation at intron 6 of BrFLC1 (Pi6+1 (G/A)), showing as co-occurrence of BrFLC1Pe1+58(A) and BrFLC1Pi6+1(G), named as haplotype H1: AG, or co-occurrence of BrFLC1Pe1+58(C) and BrFLC1Pi6+1(A), named as haplotype H2: CA. The frequency distribution of BrFLC1 haplotypes skewed to the haplotype H1 in turnip, broccoletto, mizuna, komatsuna, and taicai, while it was skewed to the haplotype H2 in caixin, pak choi, zicaitai, and wutacai. The frequencies of the two haplotypes were comparable in Chinese cabbage. This indicated that BrFLC1 haplotypes were related to B. rapa intraspecific diversification. Further analysis of a Chinese cabbage collection revealed that accessions from the spring ecotype preferred to keep H1: AG and almost all accessions from the summer ecotype were H2: CA. The early flowering haplotype of BrFLC1 was purified in summer Chinese cabbage, indicating that BrFLC1 had been strongly selected during genetic improvement of summer Chinese cabbages. A significant difference in flowering time of F₂ individuals with the homologous BrFLC1Pi6+1(G) allele but different BrFLC1Pe1+58 (A/C) alleles, indicated that this locus had independent genetic effects on flowering time. The newly identified allelic diversity of BrFLC1 can be used for breeding of resistance to premature bolting in B. rapa vegetables.

Energy and food source crop demand claims to be vulnerable to climate change impacts. The new and orphan crops, which in the past have received only limited research attention but are sustainable to environmental systems, are needed. In this review, we summarize the available literature about Ethiopian mustard as an alternative energy source and its sustainable economic importance as a new promising Brassicacea crop for new opportunities in the face of producing sustainable environment and energy development. Ethiopian mustard has many advantages and can be adopted to replace crops that are susceptible to adverse environmental conditions. Ethiopian mustard is becoming a new promising Brassicaceae crop with the current global energy demand increases. However, researchers have only focused on energy source production which has resulted in developing high erucic acid varieties. This results partly in limited studies on developing Ethiopian mustard edible oil varieties. The adoption and scaling-up of this promising crop as an oilseed crop in developing countries and Mediterranean conditions can sustain the impact of climate change with the demand for food and energy debate concepts. Indeed, further agronomic, quality and genomic studies on oilseed nutritional traits for efficient breeding and utilization are needed.