BnaGVD: A genomic variation database of rapeseed (Brassica napus)

Comprehensive Morphological and Molecular Insights into Drought Tolerance Variation at Germination Stage in Brassica napus Accessions

Drought constitutes a noteworthy abiotic stressor, detrimentally impacting seed germination, plant development, and agricultural yield. In response to the threats imposed by climate change and water paucity, this study examined the morphological divergence and genetic governance of drought resilience traits at the germination stage in 196 rapeseed (Brassica napus L.) lines under both normal (0 MPa) and drought-induced stress (-0.8 MPa) scenarios. Our study showed that the composite drought tolerance D value is a reliable index for identifying drought resilience. Through a genome-wide association study (GWAS), we uncovered 37 significant SNP loci and 136 putative genes linked to drought tolerance based on the D value. A key discovery included the gene BnaA01g29390D (BnNCED3), encoding 9-cis-epoxycarotenoid dioxygenase, which exhibited significantly heightened expression levels in drought-resistant accessions (p < 0.01), underscoring its potential as a positive drought stress regulator and a suitable candidate for genetically enhancing drought resilience. Moreover, we pinpointed four stress-reactive transcription factors (BnaA07g26740D, BnaA07g26870D, BnaA07g26910D, and BnaA07g26980D), two E3 ubiquitin-protein ligases (BnaA05g22900D and BnaC06g28950D), two enzymes (BnaA01g29390D and BnaA03g48550D), and two photosystem-associated proteins (BnaA05g22950D and BnaC06g28840D) as vital components in drought response mechanisms. The construction of a regulatory network reveals an ABA-dependent pathway (NCED3/RGLG5/IDD14) that contributes to drought tolerance in rapeseed seedlings, alongside the involvement of a drought avoidance strategy (APRR6/PHYB). The SNPs and genes unveiled in this study offer a substantial theoretical foundation for subsequent investigations targeting genetic improvement for drought resilience during seed germination in rapeseed.

Identification of lncRNAs regulating seed traits in Brassica juncea and development of a comprehensive seed omics database

Brassica juncea is a crucial oilseed crop, and its seeds possess high economic value as they are a source of edible oil. In order to understand the role of long non coding RNAs (lncRNAs) in the regulation of seed development, we carried out computational analysis using transcriptome data of developing seeds of two contrasting genotypes of B. juncea, Pusajaikisan (PJK) and Early Heera 2 (EH2). The seeds were sampled at three stages, 15, 30, and 45 days after pollination. We identified 1,539 lncRNAs, of which 809 were differentially expressed. We also carried out extensive characterization and functional analysis of seed lncRNAome. The expression patterns were analysed using k-means clustering, and the targets were analysed using pathway, transcription factor, and GO enrichment, as well as ortholog information. We shortlisted a total of 25 robust lncRNA candidates for seed size, oil content, and seed coat color. We also identified 4 lncRNAs as putative precursors of miRNAs regulating seed development. Moreover, a total of 28 miRNA-lncRNA-mRNA regulatory networks regulating seed traits were identified. We also developed a comprehensive database, (BrassIca juncea database or "BIJ" ( https://bij.cuh.ac.in/ ), which provides seed omics as well as other functional genomics and genetics data in an easily accessible form. These candidate lncRNAs are suitable for including in crop improvement programs through molecular breeding, as well as for future validations through genome editing. Together, the knowledge of these candidate lncRNAs and availability of BIJ database shall leverage the crop improvement efforts in B. juncea.

The story of a decade: Genomics, functional genomics, and molecular breeding in Brassica napus

Rapeseed (Brassica napus L.) is one of the major global sources of edible vegetable oil and is also used as a feed and pioneer crop and for sightseeing and industrial purposes. Improvements in genome sequencing and molecular marker technology have fueled a boom in functional genomic studies of major agronomic characters such as yield, quality, flowering time, and stress resistance. Moreover, introgression and pyramiding of key functional genes have greatly accelerated the genetic improvement of important traits. Here we summarize recent progress in rapeseed genomics and genetics, and we discuss effective molecular breeding strategies by exploring these findings in rapeseed. These insights will extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture throughout the world.

Functional genomics of Brassica napus: Progresses, challenges, and perspectives

Brassica napus, commonly known as rapeseed or canola, is a major oil crop contributing over 13% to the stable supply of edible vegetable oil worldwide. Identification and understanding the gene functions in the B. napus genome is crucial for genomic breeding. A group of genes controlling agronomic traits have been successfully cloned through functional genomics studies in B. napus. In this review, we present an overview of the progress made in the functional genomics of B. napus, including the availability of germplasm resources, omics databases and cloned functional genes. Based on the current progress, we also highlight the main challenges and perspectives in this field. The advances in the functional genomics of B. napus contribute to a better understanding of the genetic basis underlying the complex agronomic traits in B. napus and will expedite the breeding of high quality, high resistance and high yield in B. napus varieties.

Genotypic variation of tocopherol content in a representative genetic population and genome-wide association study on tocopherol in rapeseed (Brassica napus)

Tocopherols (Tocs) are a kind of lipid-soluble substance required for the normal physiological function of mammals, particularly their antioxidant capacity. Rapeseed (Brassica napus) oil is an important source of exogenous Tocs. However, the genotypic differences in the total Toc contents, the Toc composition in the seeds, and the molecular markers associated with the seed Toc remain largely unknown. Here, we selected 290 rapeseed accessions based on the resequencing of 991 genomes in a worldwide collection of rapeseed germplasm. The contents of the four Toc isoforms, namely, α-, β-, γ-, and δ-Tocs, were also measured. Results show that the total Toc content and the γ-/α-Toc ratio varied greatly across the accessions from 85.34 to 387.00 mg/mg and 0.65 to 5.03, respectively. Furthermore, we conducted genome-wide association studies on the Tocs, which identified 28 and 73 single nucleotide polymorphisms significantly associated with the variation of total Toc content and γ-/α-Toc ratio, respectively. Bna.C02.VTE4, a putative orthologue of Arabidopsis VITAMIN E DEFICIENT 4, was tightly associated with the γ-/α-Toc ratio. This study recommends specific genetic materials with particularly high total Toc and/or low γ-/α-Toc ratio and the molecular markers and haplotypes associated with these quality traits for rapeseed breeding.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01394-0.

Structural variations and environmental specificities of flowering time-related genes in Brassica napus

We found that the flowering time order of accessions in a genetic population considerably varied across environments, and homolog copies of essential flowering time genes played different roles in different locations. Flowering time plays a critical role in determining the life cycle length, yield, and quality of a crop. However, the allelic polymorphism of flowering time-related genes (FTRGs) in Brassica napus, an important oil crop, remains unclear. Here, we provide high-resolution graphics of FTRGs in B. napus on a pangenome-wide scale based on single nucleotide polymorphism (SNP) and structural variation (SV) analyses. A total of 1337 FTRGs in B. napus were identified by aligning their coding sequences with Arabidopsis orthologs. Overall, 46.07% of FTRGs were core genes and 53.93% were variable genes. Moreover, 1.94%, 0.74%, and 4.49% FTRGs had significant presence-frequency differences (PFDs) between the spring and semi-winter, spring and winter, and winter and semi-winter ecotypes, respectively. SNPs and SVs across 1626 accessions of 39 FTRGs underlying numerous published qualitative trait loci were analyzed. Additionally, to identify FTRGs specific to an eco-condition, genome-wide association studies (GWASs) based on SNP, presence/absence variation (PAV), and SV were performed after growing and observing the flowering time order (FTO) of plants in a collection of 292 accessions at three locations in two successive years. It was discovered that the FTO of plants in a genetic population changed a lot across various environments, and homolog copies of some key FTRGs played different roles in different locations. This study revealed the molecular basis of the genotype-by-environment (G × E) effect on flowering and recommended a pool of candidate genes specific to locations for breeding selection.

Investigation of Brassica and its relative genomes in the post-genomics era

The Brassicaceae family includes many economically important crop species, as well as cosmopolitan agricultural weed species. In addition, Arabidopsis thaliana, a member of this family, is used as a molecular model plant species. The genus Brassica is mesopolyploid, and the genus comprises comparatively recently originated tetrapolyploid species. With these characteristics, Brassicas have achieved the commonly accepted status of model organisms for genomic studies. This paper reviews the rapid research progress in the Brassicaceae family from diverse omics studies, including genomics, transcriptomics, epigenomics, and three-dimensional (3D) genomics, with a focus on cultivated crops. The morphological plasticity of Brassicaceae crops is largely due to their highly variable genomes. The origin of several important Brassicaceae crops has been established. Genes or loci domesticated or contributing to important traits are summarized. Epigenetic alterations and 3D structures have been found to play roles in subgenome dominance, either in tetraploid Brassica species or their diploid ancestors. Based on this progress, we propose future directions and prospects for the genomic investigation of Brassicaceae crops.

BRAD V3.0: an upgraded Brassicaceae database

The Brassicaceae Database (BRAD version 3.0, BRAD V3.0; http://brassicadb.cn) has evolved from the former Brassica Database (BRAD V2.0), and represents an important community portal hosting genome information for multiple Brassica and related Brassicaceae plant species. Since the last update in 2015, the complex genomes of numerous Brassicaceae species have been decoded, accompanied by many omics datasets. To provide an up-to-date service, we report here a major upgrade of the portal. The Model-View-ViewModel (MVVM) framework of BRAD has been re-engineered to enable easy and sustainable maintenance of the database. The collection of genomes has been increased to 26 species, along with optimization of the user interface. Features of the previous version have been retained, with additional new tools for exploring syntenic genes, gene expression and variation data. In the 'Syntenic Gene @ Subgenome' module, we added features to view the sequence alignment and phylogenetic relationships of syntenic genes. New modules include 'MicroSynteny' for viewing synteny of selected fragment pairs, and 'Polymorph' for retrieval of variation data. The updated BRAD provides a substantial expansion of genomic data and a comprehensive improvement of the service available to the Brassicaceae research community.

Designing Future Crops: Genomics-Assisted Breeding Comes of Age

Over the past decade, genomics-assisted breeding (GAB) has been instrumental in harnessing the potential of modern genome resources and characterizing and exploiting allelic variation for germplasm enhancement and cultivar development. Sustaining GAB in the future (GAB 2.0) will rely upon a suite of new approaches that fast-track targeted manipulation of allelic variation for creating novel diversity and facilitate their rapid and efficient incorporation in crop improvement programs. Genomic breeding strategies that optimize crop genomes with accumulation of beneficial alleles and purging of deleterious alleles will be indispensable for designing future crops. In coming decades, GAB 2.0 is expected to play a crucial role in breeding more climate-smart crop cultivars with higher nutritional value in a cost-effective and timely manner.