Search

Summary: Silique number is a crucial yield‐related trait for the genetic enhancement of rapeseed (Brassica napus L.). The intricate molecular process governing the regulation of silique number involves various factors. Despite advancements in understanding the mechanisms regulating silique number in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), the molecular processes involved in controlling silique number in rapeseed remain largely unexplored. In this review, we identify candidate genes and review the roles of genes and environmental factors in regulating rapeseed silique number. We use genetic regulatory networks for silique number in Arabidopsis and grain number in rice to uncover possible regulatory pathways and molecular mechanisms involved in regulating genes associated with rapeseed silique number. A better understanding of the genetic network regulating silique number in rapeseed will provide a theoretical basis for the genetic improvement of this trait and genetic resources for the molecular breeding of high‐yielding rapeseed. [ABSTRACT FROM AUTHOR]

Cyclin B (CYCB) is a regulatory subunit of cyclin-dependent kinase (CDK), the concentration of which fluctuates to regulate cell cycle progression. Extensive studies have been performed on cyclins in numerous species, yet the evolutionary relationships and biological functions of the CYCB family genes in Brassica napus remain unclear. In this study, we identified 299 CYCB genes in 11 B. napus accessions. Phylogenetic analysis suggests that CYCB genes could be divided into three subfamilies in angiosperms and that the CYCB3 subfamily members may be a newer group that evolved in eudicots. The expansion of BnaCYCB genes underwent segmental duplication and purifying selection in genomes, and a number of drought-responsive and light-responsive cis-elements were found in their promoter regions. Additionally, expression analysis revealed that BnaCYCBs were strongly expressed in the developing seed and silique pericarp, as confirmed by the obviously reduced seed size of the mutant cycb3;1 in Arabidopsis thaliana compared with Col-0. This study provides a comprehensive evolutionary analysis of CYCB genes as well as insight into the biological function of CYCB genes in B. napus. [ABSTRACT FROM AUTHOR]

Rapeseed (Brassica napus) is a major edible oilseed crop consumed worldwide. However, its yield is seriously affected by infection from the broad-spectrum non-obligate pathogen Sclerotinia sclerotiorum due to a lack of highly resistant germplasm. Here, we identified a Sclerotinia -resistant and light-dependent lesion mimic mutant from an ethyl methanesulfonate-mutagenized population of the rapeseed inbred Zhongshuang 11 (ZS11) named lesion mimic mutant 1 (lmm1). The phenotype of lmm1 is controlled by a single recessive gene, named LESION MIMIC MUTANT 1 (LMM1), which mapped onto chromosome C04 by bulked segregant analysis within a 2.71-Mb interval. Histochemical analysis indicated that H2O2 strongly accumulated and cell death occurred around the lesion mimic spots. Among 877 differentially expressed genes (DEGs) between ZS11 and lmm1 leaves, 188 DEGs were enriched in the defense response, including 95 DEGs involved in systemic acquired resistance, which is consistent with the higher salicylic acid levels in lmm1. Combining bulked segregant analysis and transcriptome analysis, we identified a significantly up-regulated gene, BnaC4.PR2 , which encodes β-1,3-glucanase, as the candidate gene for LMM1. Overexpression of BnaC4.PR2 may induce a reactive oxygen species burst to trigger partial cell death and systemic acquired resistance. Our study provides a new genetic resource for S. sclerotiorum resistance as well as new insights into disease resistance breeding in B. napus. [ABSTRACT FROM AUTHOR]

Hypersensitive-induced response protein (HIR) is a class of plant immune proteins that play pivotal roles in Sclerotinia sclerotiorum (Lib.) de Bary resistance. However, there has been no systematic investigation and identification of HIR genes in rapeseed (Brassica napus L.). Hence, we identified 50 BnHIR genes and classified them into four groups. Subcellular localization prediction suggested that HIR proteins are mainly localized in the mitochondria. Cis-acting elements involved in light and diverse abiotic stress were found in the promoter regions of BnHIR. The majority of BnHIR genes in Groups 1/3/4 were expressed in most examined tissues, especially in leaves and siliques pericarp, while the BnHIR genes in Group 2 were not or had low expression in all detected tissues. In the case of S. sclerotiorum inoculation, HIR genes in Groups 1/3/4 were strongly induced, especially homologous genes in Group 1, which exhibited different expression patterns. Moreover, overexpression of BnHIR2.7 in Arabidopsis thaliana illustrated its prominent resistance to S. sclerotiorum. Our study provides insight into the evolutionary relationships of the HIR family genes in B. napus and lays the foundation for their resistance to S. sclerotiorum in B. napus. [ABSTRACT FROM AUTHOR]

SUMMARY: Brassica napus is an important oil crop and an allotetraploid species. However, the detailed analysis of gene function and homoeologous gene expression in all tissues at different developmental stages was not explored. In this study, we performed a global transcriptome analysis of 24 vegetative and reproductive tissues at six developmental stages (totally 111 tissues). These samples were clustered into eight groups. The gene functions of silique pericarp were similar to roots, stems and leaves. In particular, glucosinolate metabolic process was associated with root and silique pericarp. Genes involved in protein phosphorylation were often associated with stamen, anther and the early developmental stage of seeds. Transcription factor (TF) genes were more specific than structural genes. A total of 17 100 genes that were preferentially expressed in one tissue (tissue‐preferred genes, TPGs), including 889 TFs (5.2%), were identified in the 24 tissues. Some TPGs were identified as hub genes in the co‐expression network analysis, and some TPGs in different tissues were involved in different hormone pathways. About 67.0% of the homoeologs showed balanced expression, whereas biased expression of homoeologs was associated with structural divergence. In addition, the spatiotemporal expression of homoeologs was related to the presence of transposable elements (TEs) and regulatory elements (REs); more TEs and fewer REs in the promoters resulted in divergent expression in different tissues. This study provides a valuable transcriptional map for understanding the growth and development of B. napus, for identifying important genes for future crop improvement, and for exploring gene expression patterns in the B. napus. [ABSTRACT FROM AUTHOR]

Petal size determines the value of ornamental plants, and thus their economic value. However, the molecular mechanisms controlling petal size remain unclear in most non-model species. To identify quantitative trait loci and candidate genes controlling petal size in rapeseed (Brassica napus), we performed a genome-wide association study (GWAS) using data from 588 accessions over three consecutive years. We detected 16 significant single nucleotide polymorphisms (SNPs) associated with petal size, with the most significant SNPs located on chromosomes A05 and C06. A combination of GWAS and transcriptomic sequencing based on two accessions with contrasting differences in petal size identified 52 differentially expressed genes (DEGs) that may control petal size variation in rapeseed. In particular, the rapeseed gene BnaA05.RAP2.2, homologous to Arabidopsis RAP2.2, may be critical to the negative control of petal size through the ethylene signaling pathway. In addition, a comparison of petal epidermal cells indicated that petal size differences between the two contrasting accessions were determined mainly by differences in cell number. Finally, we propose a model for the control of petal size in rapeseed through ethylene and cytokinin signaling pathways. Our results provide insights into the genetic mechanisms regulating petal size in flowering plants. [ABSTRACT FROM AUTHOR]

The genus Brassica contains several economically important crops, including rapeseed (Brassica napus, 2n = 38, AACC), the second largest source of seed oil and protein meal worldwide. However, research in rapeseed is hampered because it is complicated and time-consuming for researchers to access different types of expression data. We therefore developed the Brassica Expression Database (BrassicaEDB) for the research community. In the current BrassicaEDB, we only focused on the transcriptome level in rapeseed. We conducted RNA sequencing (RNA-Seq) of 103 tissues from rapeseed cultivar ZhongShuang11 (ZS11) at seven developmental stages (seed germination, seedling, bolting, initial flowering, full-bloom, podding, and maturation). We determined the expression patterns of 101,040 genes via FPKM analysis and displayed the results using the eFP browser. We also analyzed transcriptome data for rapeseed from 70 BioProjects in the SRA database and obtained three types of expression level data (FPKM, TPM, and read counts). We used this information to develop the BrassicaEDB, including "eFP", "Treatment", "Coexpression", and "SRA Project" modules based on gene expression profiles and "Gene Feature", "qPCR Primer", and "BLAST" modules based on gene sequences. The BrassicaEDB provides comprehensive gene expression profile information and a user-friendly visualization interface for rapeseed researchers. Using this database, researchers can quickly retrieve the expression level data for target genes in different tissues and in response to different treatments to elucidate gene functions and explore the biology of rapeseed at the transcriptome level. [ABSTRACT FROM AUTHOR]

Flowering time is a key agronomic trait, directly influencing crop yield and quality. Many flowering-time genes have been identified and characterized in the model plant Arabidopsis thaliana; however, these genes remain uncharacterized in many agronomically important Brassica crops. In this study, we identified 1064, 510, and 524 putative orthologs of A.thaliana flowering-time genes from Brassica napus, Brassica rapa, and Brassica oleracea, respectively, and found that genes involved in the aging and ambient temperature pathways were fewer than those in other flowering pathways. Flowering-time genes were distributed mostly on chromosome C03 in B. napus and B. oleracea, and on chromosome A09 in B. rapa. Calculation of non-synonymous (Ka)/synonymous substitution (Ks) ratios suggested that flowering-time genes in vernalization pathways experienced higher selection pressure than those in other pathways. Expression analysis showed that most vernalization-pathway genes were expressed in flowering organs. Approximately 40% of these genes were highly expressed in the anther, whereas flowering-time integrator genes were expressed in a highly organ-specific manner. Evolutionary selection pressures were negatively correlated with the breadth and expression levels of vernalization-pathway genes. These findings provide an integrated framework of flowering-time genes in these three Brassica crops and provide a foundation for deciphering the relationship between gene expression patterns and their evolutionary selection pressures in Brassica napus. [ABSTRACT FROM AUTHOR]

NODULE-INCEPTION-like proteins (NLPs) are conserved, plant-specific transcription factors that play crucial roles in responses to nitrogen deficiency. However, the evolutionary relationships and characteristics of NLP family genes in Brassica napus are unclear. In this study, we identified 31 NLP genes in B. napus, including 16 genes located in the A subgenome and 15 in the C subgenome. Subcellular localization predictions indicated that most BnaNLP proteins are localized to the nucleus. Phylogenetic analysis suggested that the NLP gene family could be divided into three groups and that at least three ancient copies of NLP genes existed in the ancestor of both monocots and dicots prior to their divergence. The ancestor of group III NLP genes may have experienced duplication more than once in the Brassicaceae species. Three-dimensional structural analysis suggested that 14 amino acids in BnaNLP7-1 protein are involved in DNA binding, whereas no binding sites were identified in the two RWP-RK and PB1 domains conserved in BnaNLP proteins. Expression profile analysis indicated that BnaNLP genes are expressed in most organs but tend to be highly expressed in a single organ. For example, BnaNLP6 subfamily members are primarily expressed in roots, while the four BnaNLP7 subfamily members are highly expressed in leaves. BnaNLP genes also showed different expression patterns in response to nitrogen-deficient conditions. Under nitrogen deficiency, all members of the BnaNLP1/4/5/9 subfamilies were upregulated, all BnaNLP2/6 subfamily members were downregulated, and BnaNLP7/8 subfamily members showed various expression patterns in different organs. These results provide a comprehensive evolutionary history of NLP genes in B. napus, and insight into the biological functions of BnaNLP genes in response to nitrogen deficiency. [ABSTRACT FROM AUTHOR]

Sweet potato [ Ipomoea batatas (L.) Lam.] is an important food and industrial crop. Its storage root is rich in starch, which is present in the form of granules and represents the principal storage carbohydrate in plants. Starch content is an important trait of sweet potato controlling the quality and yield of industrial products. Vacuolar invertase encoding gene Ibβfruct2 was supposed to be a key regulator of starch content in sweet potato, but its function and regulation were unclear. In this study, three Ibβfruct2 gene members were detected. Their promoters displayed differences in sequence, activity, and cis -regulatory elements and might interact with different transcription factors, indicating that the three Ibβfruct2 family members are governed by different regulatory mechanisms at the transcription level. Among them, we found that only Ibβfruct2-1 show a high expression level and promoter activity, and encodes a protein with invertase activity, and the conserved domains and three conserved motifs NDPNG, RDP, and WEC are critical to this activity. Only two and six amino acid residue variations were detected in sequences of proteins encoded by Ibβfruct2-2 and Ibβfruct2-3 , respectively, compared with Ibβfruct2-1 ; although not within key motifs, these variations affected protein structure and affinities for the catalytic substrate, resulting in functional deficiency and low activity. Heterologous expression of Ibβfruct2-1 in Arabidopsis decreased starch content but increased glucose content in leaves, indicating Ibβfruct2-1 was a negative regulator of starch content. These findings represent an important advance in understanding the regulatory and functional divergence among duplicated genes in sweet potato, and provide critical information for functional studies and utilization of these genes in genetic improvement., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Zhang, Wu, Wu, Han, Ju, Fan, Yang, Tang, Cao, Wang and Lv.)

Crop production is the primary goal of agricultural activities, which is always taken into consideration. However, global agricultural systems are coming under increasing pressure from the rising food demand of the rapidly growing world population and changing climate. To address these issues, improving high-yield and climate-resilient related-traits in crop breeding is an effective strategy. In recent years, advances in omics techniques, including genomics, transcriptomics, proteomics, and metabolomics, paved the way for accelerating plant/crop breeding to cope with the changing climate and enhance food production. Optimized omics and phenotypic plasticity platform integration, exploited by evolving machine learning algorithms will aid in the development of biological interpretations for complex crop traits. The precise and progressive assembly of desire alleles using precise genome editing approaches and enhanced breeding strategies would enable future crops to excel in combating the changing climates. Furthermore, plant breeding and genetic engineering ensures an exclusive approach to developing nutrient sufficient and climate-resilient crops, the productivity of which can sustainably and adequately meet the world's food, nutrition, and energy needs. This review provides an overview of how the integration of omics approaches could be exploited to select crop varieties with desired traits., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Mahmood, Li, Fan, Chang, Niu, Li, Qu and Lu.)

Galactinol synthase (GolS) is a key enzyme in raffinose family oligosaccharide (RFO) biosynthesis. The finding that GolS accumulates in plants exposed to abiotic stresses indicates RFOs function in environmental adaptation. However, the evolutionary relationships and biological functions of GolS family in rapeseed ( Brassica napus ) and tobacco ( Nicotiana tabacum ) remain unclear. In this study, we identified 20 BnGolS and 9 NtGolS genes. Subcellular localization predictions showed that most of the proteins are localized to the cytoplasm. Phylogenetic analysis identified a lost event of an ancient GolS copy in the Solanaceae and an ancient duplication event leading to evolution of GolS4/7 in the Brassicaceae. The three-dimensional structures of two GolS proteins were conserved, with an important DxD motif for binding to UDP-galactose (uridine diphosphate-galactose) and inositol. Expression profile analysis indicated that BnGolS and NtGolS genes were expressed in most tissues and highly expressed in one or two specific tissues. Hormone treatments strongly induced the expression of most BnGolS genes and homologous genes in the same subfamilies exhibited divergent-induced expression. Our study provides a comprehensive evolutionary analysis of GolS genes among the Brassicaceae and Solanaceae as well as an insight into the biological function of GolS genes in hormone response in plants., Competing Interests: The authors declare no conflict of interest.