Genome-wide identification and evolutionary analysis of the NRAMP gene family in the AC genomes of Brassica species.

BACKGROUND: Brassica napus, a hybrid resulting from the crossing of Brassica rapa and Brassica oleracea, is one of the most important oil crops. Despite its significance, B. napus productivity faces substantial challenges due to heavy metal stress, especially in response to cadmium (Cd), which poses a significant threat among heavy metals. Natural resistance-associated macrophage proteins (NRAMPs) play pivotal roles in Cd uptake and transport within plants. However, our understanding of the role of BnNRAMPs in B. napus is limited. Thus, this study aimed to conduct genome-wide identification and bioinformatics analysis of three Brassica species: B. napus, B. rapa, and B. oleracea. RESULTS: A total of 37 NRAMPs were identified across the three Brassica species and classified into two distinct subfamilies based on evolutionary relationships. Conservative motif analysis revealed that motif 6 and motif 8 might significantly contribute to the differentiation between subfamily I and subfamily II within Brassica species. Evolutionary analyses and chromosome mapping revealed a reduction in the NRAMP gene family during B. napus evolutionary history, resulting in the loss of an orthologous gene derived from BoNRAMP3.2. Cis-acting element analysis suggested potential regulation of the NRAMP gene family by specific plant hormones, such as abscisic acid (ABA) and methyl jasmonate (MeJA). However, gene expression pattern analyses under hormonal or stress treatments indicated limited responsiveness of the NRAMP gene family to these treatments, warranting further experimental validation. Under Cd stress in B. napus, expression pattern analysis of the NRAMP gene family revealed a decrease in the expression levels of most BnNRAMP genes with increasing Cd concentrations. Notably, BnNRAMP5.1/5.2 exhibited a unique response pattern, being stimulated at low Cd concentrations and inhibited at high Cd concentrations, suggesting potential response mechanisms distinct from those of other NRAMP genes. CONCLUSIONS: In summary, this study indicates complex molecular dynamics within the NRAMP gene family under Cd stress, suggesting potential applications in enhancing plant resilience, particularly against Cd. The findings also offer valuable insights for further understanding the functionality and regulatory mechanisms of the NRAMP gene family.

Expression in A. thaliana and cellular localization reveal involvement of BjNRAMP1 in cadmium uptake.

Although Brassica juncea has demonstrated potential as a hyperaccumulator crop, it was not entirely clear how cadmium (Cd) accumulates in plants. Here, we found that BjNRAMP1 (Natural Resistance-Associated Macrophage Protein 1) plays a crucial role in the accumulation of Cd and manganese (Mn) through its expression in yeast and Arabidopsis thaliana. The high concentration of Cd exposure could induce the expression of BjNRAMP1. The ectopic expression of BjNRAMP1 in yeast led to higher accumulation of Cd and Mn compared to the vector control. BjNARAMP1 was localized to the plasma membrane and expressed in the vascular system of roots, leaves, and flowers. The overexpression of BjNRAMP1 in A. thaliana resulted in an increased accumulation of Cd in both roots and shoots, which inhibited the normal growth of transgenic lines. Moreover, Mn uptake in roots was activated by the increase in Cd stress. Together, our results indicated that BjNRAMP1 significantly contributes to the uptake of Mn and Cd in B. juncea.

A gap-free reference genome reveals structural variations associated with flowering time in rapeseed (Brassica napus).

Allopolyploid oilseed rape (Brassica napus) is an important oil crop and vegetable. However, the latest version of its reference genome, with collapsed duplications, gaps, and other issues, prevents comprehensive genomic analysis. Herein, we report a gap-free assembly of the rapeseed cv. Xiang5A genome using a combination of ONT (Oxford Nanopore Technologies) ultra-long reads, PacBio high-fidelity reads, and Hi-C datasets. It includes gap-free assemblies of all 19 chromosomes and telomere-to-telomere assemblies of eight chromosomes. Compared with previously published genomes of B. napus, our gap-free genome, with a contig N50 length of 50.70 Mb, has complete assemblies of 9 of 19 chromosomes without manual intervention, and greatly improves contiguity and completeness, thereby representing the highest quality genome assembly to date. Our results revealed that B. napus Xiang5A underwent nearly complete triplication and allotetraploidy relative to Arabidopsis thaliana. Using the gap-free assembly, we found that 917 flowering-related genes were affected by structural variation, including BnaA03.VERNALIZATION INSENSITIVE 3 and BnaC04.HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 1. These genes may play crucial roles in regulating flowering time and facilitating the adaptation of Xiang5A in the Yangtze River Basin of China. This reference genome provides a valuable genetic resource for rapeseed functional genomic studies and breeding.

BnaC01.BIN2, a GSK3-like kinase, modulates plant height and yield potential in Brassica napus.

KEY MESSAGE: Using map-based cloning and transgenic transformation, we revealed that glycogen kinase synthase 3-like kinase, BnaC01.BIN2, modulates plant height and yield in rapeseed. The modification of plant height is one of the most important goals in rapeseed breeding. Although several genes that regulate rapeseed plant height have been identified, the genetics mechanisms underlying rapeseed plant height regulation remain poorly understood, and desirable genetic resources for rapeseed ideotype breeding are scarce. Here, we map-based cloned and functionally verified that the rapeseed semi-dominant gene, BnDF4, greatly affects rapeseed plant height. Specifically, BnDF4 encodes brassinosteroid (BR)-insensitive 2, a glycogen synthase kinase 3 primarily expressed in the lower internodes to modulate rapeseed plant height by blocking basal internode-cell elongation. Transcriptome data showed that several cell expansion-related genes involving auxin and BRs pathways were significantly downregulated in the semi-dwarf mutant. Heterozygosity in the BnDF4 allele results in small stature with no marked differences in other agronomic traits. Using BnDF4 in the heterozygous condition, the hybrid displayed strong yield heterosis through optimum intermediate plant height. Our results provide a desirable genetic resource for breeding semi-dwarf rapeseed phenotypes and support an effective strategy for breeding rapeseed hybrid varieties with strong yield heterosis.

Clinical Manifestations, Imaging Features, and Pathogenic/Prognostic Risk Factors for Temporomandibular Disorders (TMD): A Case-Control Study Based on Psychogenic Factors of Patients.

Objective: To survey the clinical manifestations and imaging features of temporomandibular disorders (TMD) and analyze the risk factors for pathogenesis/prognosis through a case-control study based on psychogenic factors of patients. Methods: According to the inclusion criteria, 200 adult patients were randomly enrolled from the maxillofacial department of our hospital from January 2020 to May 2021, including 100 patients with TMD as the study group and 100 healthy patients as the control group. The study group can be assigned into four subgroups according to their clinical manifestations: (1) articular area or/and masticatory muscle pain group, (2) mandibular movement abnormality group, (3) joint murmur group, and (4) two or more symptom groups. Based on the study of psychogenic factors of patients, the clinical manifestations and imaging features of TMD were determined, and the risk factors for pathogenesis/prognosis were analyzed. Results: The distribution of psychological status in the TMD group was higher than that in the control group (P < 0.05). The distribution of anxiety, depression, and somatic symptoms in the TMD group was significantly different from that in the control group (P < 0.05). Anxiety, depression, and somatic symptoms were the risk factors for TMD. Compared with the control group, the incidence of abnormal MRI images in patients with temporomandibular disorders was significantly different (P < 0.05). There were significant differences in psychological status (anxiety, depression, and somatic symptoms) among the three groups (P < 0.05). Anxiety, depression, and somatic symptoms were the risk factors for abnormal mandibular movement and joint tremor and murmur (P < 0.05). Somatic symptoms were the risk factors for various clinical symptoms of TMD (P < 0.05). Depression was the risk factor for pain (P < 0.05). Conclusion: In patients with TMD, MRI can early identify disc abnormalities and other related imaging features, which is helpful for more comprehensive clinical evaluation and treatment of TMD patients. There exhibits no significant difference in psychological status (anxiety, depression, and somatic symptoms) of patients with different clinical symptoms, and abnormal psychological status may be one of the risk factors leading to different clinical symptoms and development of different types of TMD patients.

Fine mapping of qDB.A03, a QTL for rapeseed branching, and identification of the candidate gene.

Increasing the yield of rapeseed is required to meet the rapidly expanding demand for both edible vegetable oil and biofuel. Branching, an important determinant of yield potential in rapeseed, is controlled by a series of quantitative trait loci (QTLs). To explore the genetic mechanism regulating the natural variation of branching, a BC1F1 population derived from a cross between dense branching 2 (dense branching line) and L72 (normal branching line) was used to map QTL conferring branching in rapeseed. A major QTL, qDB.A03, for branching-related traits was identified by the BeadChip Array assisted bulked segregation analysis method, which was subsequently validated by the classical QTL mapping approach, and fine mapped to the 256 kb region. This interval contains 56 annotated or predicted genes, 8 of which are candidates for controlling the branching trait. Comparative and expression analysis revealed four promising candidate genes for qDB.A03. Fine mapping and identification of the candidate genes for qDB.A03 represents the first step toward unraveling the genetical and molecular mechanisms controlling branching in rapeseed.