Assembly and comparison of two closely related Brassica napus genomes

Brassica Panache: A multi-species graph pangenome representing presence absence variation across forty-one Brassica genomes

Brassicas are an economically important crop species that provide a source of healthy oil and vegetables. With the rising population and the impact of climate change on agriculture, there is an increasing need to improve agronomically important traits of crops such as Brassica. The genomes of plant species have significant sequence presence absence variation (PAV), which is a source of genetic variation that can be used for crop improvement, and this species variation can be captured through the construction of pangenomes. Graph pangenomes are a recent reference format that represent the genomic variation with a species or population as alternate paths in a sequence graph. Graph pangenomes contain information on alignment, PAV, and annotation. Here we present the first multi-species graph pangenome for Brassica visualized with pangenome analyzer with chromosomal exploration (Panache).

Genome-Wide Identification of the CAT Genes and Molecular Characterization of Their Transcriptional Responses to Various Nutrient Stresses in Allotetraploid Rapeseed

Brassica napus is an important oil crop in China and has a great demand for nitrogen nutrients. Cationic amino acid transporters (CAT) play a key role in amino acid absorption and transport in plants. However, the CATs family has not been reported in B. napus so far. In this study, genome-wide analysis identified 22 CAT members in the B. napus genome. Based on phylogenetic and synteny analysis, BnaCATs were classified into four groups (Group I-Group IV). The members in the same subgroups showed similar physiochemical characteristics and intron/exon and motif patterns. By evaluating cis-elements in the promoter regions, we identified some cis-elements related to hormones, stress and plant development. Darwin's evolutionary analysis indicated that BnaCATs might have experienced strong purifying selection pressure. The BnaCAT family may have undergone gene expansion; the chromosomal location of BnaCATs indicated that whole-genome replication or segmental replication may play a major driving role. Differential expression patterns of BnaCATs under nitrate limitation, phosphate shortage, potassium shortage, cadmium toxicity, ammonium excess and salt stress conditions indicated that they were responsive to different nutrient stresses. In summary, these findings provide a comprehensive survey of the BnaCAT family and lay a foundation for the further functional analysis of family members.

A stepwise guide for pangenome development in crop plants: an alfalfa (Medicago sativa) case study

BACKGROUND

The concept of pangenomics and the importance of structural variants is gaining recognition within the plant genomics community. Due to advancements in sequencing and computational technology, it has become feasible to sequence the entire genome of numerous individuals of a single species at a reasonable cost. Pangenomes have been constructed for many major diploid crops, including rice, maize, soybean, sorghum, pearl millet, peas, sunflower, grapes, and mustards. However, pangenomes for polyploid species are relatively scarce and are available in only few crops including wheat, cotton, rapeseed, and potatoes.

MAIN BODY

In this review, we explore the various methods used in crop pangenome development, discussing the challenges and implications of these techniques based on insights from published pangenome studies. We offer a systematic guide and discuss the tools available for constructing a pangenome and conducting downstream analyses. Alfalfa, a highly heterozygous, cross pollinated and autotetraploid forage crop species, is used as an example to discuss the concerns and challenges offered by polyploid crop species. We conducted a comparative analysis using linear and graph-based methods by constructing an alfalfa graph pangenome using three publicly available genome assemblies. To illustrate the intricacies captured by pangenome graphs for a complex crop genome, we used five different gene sequences and aligned them against the three graph-based pangenomes. The comparison of the three graph pangenome methods reveals notable variations in the genomic variation captured by each pipeline.

CONCLUSION

Pangenome resources are proving invaluable by offering insights into core and dispensable genes, novel gene discovery, and genome-wide patterns of variation. Developing user-friendly online portals for linear pangenome visualization has made these resources accessible to the broader scientific and breeding community. However, challenges remain with graph-based pangenomes including compatibility with other tools, extraction of sequence for regions of interest, and visualization of genetic variation captured in pangenome graphs. These issues necessitate further refinement of tools and pipelines to effectively address the complexities of polyploid, highly heterozygous, and cross-pollinated species.

Allelic Variation of BnaFTA2 and BnaFTC6 Is Associated With Flowering Time and Seasonal Crop Type in Rapeseed (Brassica napus L.)

Different ecological types of rapeseed (Brassica napus L.), including winter, spring, and semi-winter cultivars, exhibit varying flowering times and cannot be planted in the same cultivation areas. FLOWERING LOCUS T (FT) plays a key role in regulating flowering. In allotetraploid B. napus six copies of FT (BnaFT) have been reported. However, there is uncertainty about how the translated products of each paralog, as well as cis-allelic variations at each locus, contribute functionally to flowering time and define specific crop types. In this study, we confirm that BnaFT exhibit distinct expression patterns in different crop types of rapeseed. Using the CRISPR/Cas9 gene editing system, we provide functional evidence that the mutants between Bnaft paralogues affects the regulation of flowering time. Furthermore, we identify a new haplotype of BnaFT.A2 that is associated with early flowering time, although this appears necessary but not sufficient to confer a spring type phenotype. Three haplotypes of BnaFT.C6 were further identified and associated with both flowering time and crop types. We speculate that variations in both BnaFT.A2 and BnaFT.C6 may have undergone diversifying selection during the divergence of seasonal crop types in rapeseed.

Identification and expression profiling of GAPDH family genes involved in response to Sclerotinia sclerotiorum infection and phytohormones in Brassica napus

Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a crucial enzyme in glycolysis, an essential metabolic pathway for carbohydrate metabolism across all living organisms. Recent research indicates that phosphorylating GAPDH exhibits various moonlighting functions, contributing to plant growth and development, autophagy, drought tolerance, salt tolerance, and bacterial/viral diseases resistance. However, in rapeseed (Brassica napus), the role of GAPDHs in plant immune responses to fungal pathogens remains unexplored. In this study, 28 genes encoding GAPDH proteins were revealed in B. napus and classified into three distinct subclasses based on their protein structural and phylogenetic relationships. Whole-genome duplication plays a major role in the evolution of BnaGAPDHs. Synteny analyses revealed orthologous relationships, identifying 23, 26, and 26 BnaGAPDH genes with counterparts in Arabidopsis, Brassica rapa, and Brassica oleracea, respectively. The promoter regions of 12 BnaGAPDHs uncovered a spectrum of responsive elements to biotic and abiotic stresses, indicating their crucial role in plant stress resistance. Transcriptome analysis characterized the expression profiles of different BnaGAPDH genes during Sclerotinia sclerotiorum infection and hormonal treatment. Notably, BnaGAPDH17, BnaGAPDH20, BnaGAPDH21, and BnaGAPDH22 exhibited sensitivity to S. sclerotiorum infection, oxalic acid, hormone signals. Intriguingly, under standard physiological conditions, BnaGAPDH17, BnaGAPDH20, and BnaGAPDH22 are primarily localized in the cytoplasm and plasma membrane, with BnaGAPDH21 also detectable in the nucleus. Furthermore, the nuclear translocation of BnaGAPDH20 was observed under H2O2 treatment and S. sclerotiorum infection. These findings might provide a theoretical foundation for elucidating the functions of phosphorylating GAPDH.

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.

Lipid Metabolism and Improvement in Oilseed Crops: Recent Advances in Multi-Omics Studies

Oilseed crops are rich in plant lipids that not only provide essential fatty acids for the human diet but also play important roles as major sources of biofuels and indispensable raw materials for the chemical industry. The regulation of lipid metabolism genes is a major factor affecting oil production. In this review, we systematically summarize the metabolic pathways related to lipid production and storage in plants and highlight key research advances in characterizing the genes and regulatory factors influencing lipid anabolic metabolism. In addition, we integrate the latest results from multi-omics studies on lipid metabolism to provide a reference to better understand the molecular mechanisms underlying oil anabolism in oilseed crops.

The high-quality sequencing of the Brassica rapa 'XiangQingCai' genome and exploration of genome evolution and genes related to volatile aroma

'Vanilla' (XQC, brassica variety chinensis) is an important vegetable crop in the Brassica family, named for its strong volatile fragrance. In this study, we report the high-quality chromosome-level genome sequence of XQC. The assembled genome length was determined as 466.11 Mb, with an N50 scaffold of 46.20 Mb. A total of 59.50% repetitive sequences were detected in the XQC genome, including 47 570 genes. Among all examined Brassicaceae species, XQC had the closest relationship with B. rapa QGC ('QingGengCai') and B. rapa Pakchoi. Two whole-genome duplication (WGD) events and one recent whole-genome triplication (WGT) event occurred in the XQC genome in addition to an ancient WGT event. The recent WGT was observed to occur during 21.59-24.40 Mya (after evolution rate corrections). Our findings indicate that XQC experienced gene losses and chromosome rearrangements during the genome evolution of XQC. The results of the integrated genomic and transcriptomic analyses revealed critical genes involved in the terpenoid biosynthesis pathway and terpene synthase (TPS) family genes. In summary, we determined a chromosome-level genome of B. rapa XQC and identified the key candidate genes involved in volatile fragrance synthesis. This work can act as a basis for the comparative and functional genomic analysis and molecular breeding of B. rapa in the future.

Genome composition in Brassica interspecific hybrids affects chromosome inheritance and viability of progeny

Interspecific hybridization is widespread in nature and can result in the formation of new hybrid species as well as the transfer of traits between species. However, the fate of newly formed hybrid lineages is relatively understudied. We undertook pairwise crossing between multiple genotypes of three Brassica allotetraploid species Brassica juncea (2n = AABB), Brassica carinata (2n = BBCC), and Brassica napus (2n = AACC) to generate AABC, BBAC, and CCAB interspecific hybrids and investigated chromosome inheritance and fertility in these hybrids and their self-pollinated progeny. Surprisingly, despite the presence of a complete diploid genome in all hybrids, hybrid fertility was very low. AABC and BBAC first generation (F1) hybrids both averaged ~16% pollen viability compared to 3.5% in CCAB hybrids: most CCAB hybrid flowers were male-sterile. AABC and CCAB F1 hybrid plants averaged 5.5 and 0.5 seeds per plant, respectively, and BBAC F1 hybrids ~56 seeds/plant. In the second generation (S1), all confirmed self-pollinated progeny resulting from CCAB hybrids were sterile, producing no self-pollinated seeds. Three AABC S1 hybrids putatively resulting from unreduced gametes produced 3, 14, and 182 seeds each, while other AABC S1 hybrids averaged 1.5 seeds/plant (0-8). BBAC S1 hybrids averaged 44 seeds/plant (range 0-403). We also observed strong bias towards retention rather than loss of the haploid genomes, suggesting that the subgenomes in the Brassica allotetraploids are already highly interdependent, such that loss of one subgenome is detrimental to fertility and viability. Our results suggest that relationships between subgenomes determine hybridization outcomes in these species.

Genetic factors inherited from both diploid parents interact to affect genome stability and fertility in resynthesized allotetraploid Brassica napus

Established allopolyploids are known to be genomically stable and fertile. However, in contrast, most newly resynthesized allopolyploids are infertile and meiotically unstable. Identifying the genetic factors responsible for genome stability in newly formed allopolyploid is key to understanding how 2 genomes come together to form a species. One hypothesis is that established allopolyploids may have inherited specific alleles from their diploid progenitors which conferred meiotic stability. Resynthesized Brassica napus lines are often unstable and infertile, unlike B. napus cultivars. We tested this hypothesis by characterizing 41 resynthesized B. napus lines produced by crosses between 8 Brassica rapa and 8 Brassica oleracea lines for copy number variation resulting from nonhomologous recombination events and fertility. We resequenced 8 B. rapa and 5 B. oleracea parent accessions and analyzed 19 resynthesized lines for allelic variation in a list of meiosis gene homologs. SNP genotyping was performed using the Illumina Infinium Brassica 60K array for 3 individuals per line. Self-pollinated seed set and genome stability (number of copy number variants) were significantly affected by the interaction between both B. rapa and B. oleracea parental genotypes. We identified 13 putative meiosis gene candidates which were significantly associated with frequency of copy number variants and which contained putatively harmful mutations in meiosis gene haplotypes for further investigation. Our results support the hypothesis that allelic variants inherited from parental genotypes affect genome stability and fertility in resynthesized rapeseed.

A High-Continuity Genome Assembly of Chinese Flowering Cabbage (Brassica rapa var. parachinensis) Provides New Insights into Brassica Genome Structure Evolution

Chinese flowering cabbage (Brassica rapa var. parachinensis) is a popular and widely cultivated leaf vegetable crop in Asia. Here, we performed a high quality de novo assembly of the 384 Mb genome of 10 chromosomes of a typical cultivar of Chinese flowering cabbage with an integrated approach using PacBio, Illumina, and Hi-C technology. We modeled 47,598 protein-coding genes in this analysis and annotated 52% (205.9/384) of its genome as repetitive sequences including 17% in DNA transposons and 22% in long terminal retrotransposons (LTRs). Phylogenetic analysis reveals the genome of the Chinese flowering cabbage has a closer evolutionary relationship with the AA diploid progenitor of the allotetraploid species, Brassica juncea. Comparative genomic analysis of Brassica species with different subgenome types (A, B and C) reveals that the pericentromeric regions on chromosome 5 and 6 of the AA genome have been significantly expanded compared to the orthologous genomic regions in the BB and CC genomes, largely driven by LTR-retrotransposon amplification. Furthermore, we identified a large number of structural variations (SVs) within the B. rapa lines that could impact coding genes, suggesting the functional significance of SVs on Brassica genome evolution. Overall, our high-quality genome assembly of the Chinese flowering cabbage provides a valuable genetic resource for deciphering the genome evolution of Brassica species and it can potentially serve as the reference genome guiding the molecular breeding practice of B. rapa crops.

Key Advances in the New Era of Genomics-Assisted Disease Resistance Improvement of Brassica Species

Disease resistance improvement remains a major focus in breeding programs as diseases continue to devastate Brassica production systems due to intensive cultivation and climate change. Genomics has paved the way to understand the complex genomes of Brassicas, which has been pivotal in the dissection of the genetic underpinnings of agronomic traits driving the development of superior cultivars. The new era of genomics-assisted disease resistance breeding has been marked by the development of high-quality genome references, accelerating the identification of disease resistance genes controlling both qualitative (major) gene and quantitative resistance. This facilitates the development of molecular markers for marker assisted selection and enables genome editing approaches for targeted gene manipulation to enhance the genetic value of disease resistance traits. This review summarizes the key advances in the development of genomic resources for Brassica species, focusing on improved genome references, based on long-read sequencing technologies and pangenome assemblies. This is further supported by the advances in pathogen genomics, which have resulted in the discovery of pathogenicity factors, complementing the mining of disease resistance genes in the host. Recognizing the co-evolutionary arms race between the host and pathogen, it is critical to identify novel resistance genes using crop wild relatives and synthetic cultivars or through genetic manipulation via genome-editing to sustain the development of superior cultivars. Integrating these key advances with new breeding techniques and improved phenotyping using advanced data analysis platforms will make disease resistance improvement in Brassica species more efficient and responsive to current and future demands.

Genome-wide exploration of the GDSL-type esterase/lipase gene family in rapeseed reveals several BnGELP proteins active during early seedling development

The Gly-Asp-Ser-Leu (GDSL)-type esterase/lipase proteins (GELP) are one of the most important families of lipolytic enzymes and play prominent roles in seed germination and early seedling establishment through mobilizing the lipids stored in seeds. However, there are no comprehensive studies systematically investigating the GELP gene family in Brassica napus (BnGELP), and their biological significance to these physiological processes are far from understood. In the present study, a total of 240 BnGELP genes were identified in B. napus cultivar "Zhongshuang 11" (ZS11), which is nearly 2.3-fold more GELP genes than in Arabidopsis thaliana. The BnGELP genes clustered into 5 clades based on phylogenetic analysis. Ten BnGELPs were identified through zymogram analysis of esterase activity followed by mass spectrometry, among which five clustered into the clade 5. Gene and protein architecture, gene expression, and cis-element analyses of BnGELP genes in clade 5 suggested that they may play different roles in different tissues and in response to different abiotic stresses. BnGELP99 and BnGELP159 were slightly induced by cold, which may be attributed to two low-temperature responsive cis-acting regulatory elements present in their promoters. An increased activity of esterase isozymes by cold was also observed, which may reflect other cold inducible esterases/lipases in addition to the ten identified BnGELPs. This study provides a systemic view of the BnGELP gene family and offers a strategy for researchers to identify candidate esterase/lipase genes responsible for lipid mobilization during seed germination and early seedling establishment.

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.

The giant diploid faba genome unlocks variation in a global protein crop

Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of biodiversity1. However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value2. Faba bean (Vicia faba L.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13 Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the improvement of sustainable protein production across the Mediterranean, subtropical and northern temperate agroecological zones.

GROP: A genomic information repository for oilplants

Biomass energy is an essential component of the agriculture economy and represents an important and particularly significant renewable energy source in the fight against fossil fuel depletion and global warming. The recognition that many plants naturally synthesize hydrocarbons makes these oil plants indispensable resources for biomass energy, and the advancement of next-generation sequencing technology in recent years has now made available mountains of data on plants that synthesize oil. We have utilized a combination of bioinformatic protocols to acquire key information from this massive amount of genomic data and to assemble it into an oil plant genomic information repository, built through website technology, including Django, Bootstrap, and echarts, to create the Genomic Information Repository for Oil Plants (GROP) portal (http://grop.site/) for genomics research on oil plants. The current version of GROP integrates the coding sequences, protein sequences, genome structure, functional annotation information, and other information from 18 species, 22 genome assemblies, and 46 transcriptomes. GROP also provides BLAST, genome browser, functional enrichment, and search tools. The integration of the massive amounts of oil plant genomic data with key bioinformatics tools in a database with a user-friendly interface allows GROP to serve as a central information repository to facilitate studies on oil plants by researchers worldwide.

Characterization of Cry2 genes (CRY2a and CRY2b) of B. napus and comparative analysis of BnCRY1 and BnCRY2a in regulating seedling photomorphogenesis

Cryptochrome 2 (CRY2) perceives blue/UV-A light and regulates photomorphogenesis in plants. However, besides Arabidopsis, CRY2 has been functionally characterized only in native species of japonica rice and tomato. In the present study, the BnCRY2a, generating a relatively longer cDNA and harboring an intron in its 5'UTR, has been characterized in detail. Western blot analysis revealed that BnCRY2a is light labile and degraded rapidly by 26S proteasome when seedlings are irradiated with blue light. For functional analysis, BnCRY2a was over-expressed in Brassica juncea, a related species more amenable to transformation. The BnCRY2a over-expression (BnCRY2a^OE) transgenics developed short hypocotyl and expanded cotyledons, accumulated more anthocyanin in light-grown seedlings, and displayed early flowering on maturity. Early flowering in BnCRY2a^OE transgenics was coupled with the up-regulation of many flowering-related genes such as FT. The present study also highlights the differential light sensitivity of cry1 and cry2 in controlling hypocotyl elongation growth in Brassica. BnCRY2a^OE seedlings developed much shorter hypocotyl under the low-intensity of blue light, while BnCRY1^OE seedling hypocotyls were shorter under the high-intensity blue light, compared to untransformed seedlings.

Oil plant genomes: current state of the science

Vegetable oils are an indispensable nutritional component of the human diet as well as important raw materials for a variety of industrial applications such as pharmaceuticals, cosmetics, oleochemicals, and biofuels. Oil plant genomes are highly diverse, and their genetic variation leads to a diversity in oil biosynthesis and accumulation along with agronomic traits. This review discusses plant oil biosynthetic pathways, current state of genome assembly, polyploidy and asymmetric evolution of genomes of oil plants and their wild relatives, and research progress of pan-genomics in oil plants. The availability of complete high-resolution genomes and pan-genomes has enabled the identification of structural variations in the genomes that are associated with the diversity of agronomic and environment fitness traits. These and future genomes also provide powerful tools to understand crop evolution and to harvest the rich natural variations to improve oil crops for enhanced productivity, oil quality, and adaptability to changing environments.

Allele segregation analysis of F1 hybrids between independent Brassica allohexaploid lineages

In the Brassica genus, we find both diploid species (one genome) and allotetraploid species (two different genomes) but no naturally occurring hexaploid species (three different genomes, AABBCC). Although hexaploids can be produced via human intervention, these neo-polyploids have quite unstable genomes and usually suffer from severe genome reshuffling. Whether these genome rearrangements continue in later generations and whether genomic arrangements follow similar, reproducible patterns between different lineages is still unknown. We crossed Brassica hexaploids resulting from different species combinations to produce five F₁ hybrids and analyzed the karyotypes of the parents and the F₁ hybrids, as well as allele segregation in a resulting test-cross population via molecular karyotyping using SNP array genotyping. Although some genomic regions were found to be more likely to be duplicated, deleted, or rearranged, a consensus pattern was not shared between genotypes. Brassica hexaploids had a high tolerance for fixed structural rearrangements, but which rearrangements occur and become fixed over many generations does not seem to show either strong reproducibility or to indicate selection for stability. On average, we observed 10 de novo chromosome rearrangements contributed almost equally from both parents to the F₁ hybrids. At the same time, the F₁ hybrid meiosis produced on average 8.6 new rearrangements. Hence, the increased heterozygosity in the F₁ hybrid did not significantly improve genome stability in our hexaploid hybrids and might have had the opposite effect. However, hybridization between lineages was readily achieved and may be exploited for future genetics and breeding purposes.

Construction of a Quantitative Genomic Map, Identification and Expression Analysis of Candidate Genes for Agronomic and Disease-Related Traits in Brassica napus

Rapeseed is the second most important oil crop in the world. Improving seed yield and seed oil content are the two main highlights of the research. Unfortunately, rapeseed development is frequently affected by different diseases. Extensive research has been made through many years to develop elite cultivars with high oil, high yield, and/or disease resistance. Quantitative trait locus (QTL) analysis has been one of the most important strategies in the genetic deciphering of agronomic characteristics. To comprehend the distribution of these QTLs and to uncover the key regions that could simultaneously control multiple traits, 4,555 QTLs that have been identified during the last 25 years were aligned in one unique map, and a quantitative genomic map which involved 128 traits from 79 populations developed in 12 countries was constructed. The present study revealed 517 regions of overlapping QTLs which harbored 2,744 candidate genes and might affect multiple traits, simultaneously. They could be selected to customize super-rapeseed cultivars. The gene ontology and the interaction network of those candidates revealed genes that highly interacted with the other genes and might have a strong influence on them. The expression and structure of these candidate genes were compared in eight rapeseed accessions and revealed genes of similar structures which were expressed differently. The present study enriches our knowledge of rapeseed genome characteristics and diversity, and it also provided indications for rapeseed molecular breeding improvement in the future.

Genome-Wide Identification and Expression Analysis of SNARE Genes in Brassica napus

SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) are central components that drive membrane fusion events during exocytosis and endocytosis and play important roles in different biological processes of plants. In this study, we identified 237 genes encoding SNARE family proteins in B. napus in silico at the whole-genome level. Phylogenetic analysis showed that BnaSNAREs could be classified into five groups (Q (a-, b-, c-, bc-) and R) like other plant SNAREs and clustered into twenty-five subclades. The gene structure and protein domain of each subclade were found to be highly conserved. In many subclades, BnaSNAREs are significantly expanded compared with the orthologous genes in Arabidopsis thaliana. BnaSNARE genes are expressed differentially in the leaves and roots of B. napus. RNA-seq data and RT-qPCR proved that some of the BnaSNAREs are involved in the plant response to S. sclerotiorum infection as well as treatments with toxin oxalic acid (OA) (a virulence factor often secreted by S. sclerotiorum) or abscisic acid (ABA), methyl jasmonate (MeJA), and salicylic acid (SA), which individually promote resistance to S. sclerotiorum. Moreover, the interacted proteins of BnaSNAREs contain some defense response-related proteins, which increases the evidence that BnaSNAREs are involved in plant immunity. We also found the co-expression of BnaSYP121/2s, BnaSNAPs, and BnaVAMP722/3s in B. napus due to S. sclerotiorum infection as well as the probable interaction among them.

Pangenomics in crop improvement-from coding structural variations to finding regulatory variants with pangenome graphs

Since the first reported crop pangenome in 2014, advances in high-throughput and cost-effective DNA sequencing technologies facilitated multiple such studies including the pangenomes of oilseed rape (Brassica napus L.), soybean [Glycine max (L.) Merr.], rice (Oryza sativa L.), wheat (Triticum aestivum L.), and barley (Hordeum vulgare L.). Compared with single-reference genomes, pangenomes provide a more accurate representation of the genetic variation present in a species. By combining the genomic data of multiple accessions, pangenomes allow for the detection and annotation of complex DNA polymorphisms such as structural variations (SVs), one of the major determinants of genetic diversity within a species. In this review we summarize the current literature on crop pangenomics, focusing on their application to find candidate SVs involved in traits of agronomic interest. We then highlight the potential of pangenomes in the discovery and functional characterization of noncoding regulatory sequences and their variations. We conclude with a summary and outlook on innovative data structures representing the complete content of plant pangenomes including annotations of coding and noncoding elements and outcomes of transcriptomic and epigenomic experiments.

Quantitative Trait Locus Mapping for Resistance Against Pyrenopeziza brassicae Derived From a Brassica napus Secondary Gene Pool

Use of host resistance is the most economical and environmentally safe way to control light leaf spot disease of oilseed rape (Brassica napus). The causal organism of light leaf spot, Pyrenopeziza brassicae, is one of the most economically damaging pathogens of oilseed rape in the United Kingdom and it is considered to have a high potential to evolve due to its mixed reproduction system and airborne ascospores. This necessitates diverse sources of host resistance, which are inadequate at present to minimize yield losses caused by this disease. To address this, we screened a doubled haploid (DH) population of oilseed rape, derived from a secondary gene pool (ancestral genomes) of B. napus for the introgression of resistance against P. brassicae. DH lines were phenotyped using controlled-environment and glasshouse experiments with P. brassicae populations obtained from three different geographic locations in the United Kingdom. Selected DH lines with different levels of resistance were further studied in a controlled-environment experiment using both visual (scanning electron microscope - SEM) and molecular (quantitative PCR) assessment methods to understand the mode/s of host resistance. There was a clear phenotypic variation for resistance against P. brassicae in this DH population. Quantitative trait locus (QTL) analysis identified four QTLs with moderate to large effects, which were located on linkage groups C1, C6, and C9. Of these, the QTL on the linkage group C1 appeared to have a major effect on limiting P. brassicae asexual sporulation. Study of the sub-cuticular growth phase of P. brassicae using qPCR and SEM showed that the pathogen was able to infect and colonise both resistant and susceptible Q DH lines and control B. napus cultivars. However, the rate of increase of pathogen biomass was significantly smaller in resistant lines, suggesting that the resistance segregating in this DH population limits colonisation/sporulation by the pathogen rather than eliminating the pathogen. Resistance QTLs identified in this study provide a useful resource for breeding cultivar resistance for effective control of light leaf spot and form a starting point for functional identification of the genes controlling resistance against P. brassicae that can contribute to our knowledge on mechanisms of partial resistance of crops against pathogens.

Searching for Homologous Genes Using Daisychain

Genome assemblies have become a standard tool of genomics research and are relatively inexpensive to produce due to falling sequencing costs. For many species, there are now several reference-grade genome assemblies. However, comparing different assemblies or the same or related individuals is not an easy task, especially with different levels of quality of assembly and annotation. Tools are needed to visualise related genes with different IDs across genome assemblies. Here, we present a workflow to search and visualise related genes using Daisychain, a web-based tool aimed at researchers who wish to compare genes between assemblies.

Making a Pangenome Using the Iterative Mapping Approach

Pangenomes have replaced single reference genomes as genetic references, as they contain a better scope of the diversity found in a single species. This protocol outlines the iterative mapping approach in constructing a pangenome, including how to check the raw data, align the data to a reference, how to assemble the data, and how to remove potential contaminants from the final assembly.

Dissection of Quantitative Blackleg Resistance Reveals Novel Variants of Resistance Gene Rlm9 in Elite Brassica napus

Blackleg is one of the major fungal diseases in oilseed rape/canola worldwide. Most commercial cultivars carry R gene-mediated qualitative resistances that confer a high level of race-specific protection against Leptosphaeria maculans, the causal fungus of blackleg disease. However, monogenic resistances of this kind can potentially be rapidly overcome by mutations in the pathogen's avirulence genes. To counteract pathogen adaptation in this evolutionary arms race, there is a tremendous demand for quantitative background resistance to enhance durability and efficacy of blackleg resistance in oilseed rape. In this study, we characterized genomic regions contributing to quantitative L. maculans resistance by genome-wide association studies in a multiparental mapping population derived from six parental elite varieties exhibiting quantitative resistance, which were all crossed to one common susceptible parental elite variety. Resistance was screened using a fungal isolate with no corresponding avirulence (AvrLm) to major R genes present in the parents of the mapping population. Genome-wide association studies revealed eight significantly associated quantitative trait loci (QTL) on chromosomes A07 and A09, with small effects explaining 3-6% of the phenotypic variance. Unexpectedly, the qualitative blackleg resistance gene Rlm9 was found to be located within a resistance-associated haploblock on chromosome A07. Furthermore, long-range sequence data spanning this haploblock revealed high levels of single-nucleotide and structural variants within the Rlm9 coding sequence among the parents of the mapping population. The results suggest that novel variants of Rlm9 could play a previously unknown role in expression of quantitative disease resistance in oilseed rape.

Current status of structural variation studies in plants

Structural variations (SVs) including gene presence/absence variations and copy number variations are a common feature of genomes in plants and, together with single nucleotide polymorphisms and epigenetic differences, are responsible for the heritable phenotypic diversity observed within and between species. Understanding the contribution of SVs to plant phenotypic variation is important for plant breeders to assist in producing improved varieties. The low resolution of early genetic technologies and inefficient methods have previously limited our understanding of SVs in plants. However, with the rapid expansion in genomic technologies, it is possible to assess SVs with an ever-greater resolution and accuracy. Here, we review the current status of SV studies in plants, examine the roles that SVs play in phenotypic traits, compare current technologies and assess future challenges for SV studies.

Genome-scale identification of plant defensin (PDF) family genes and molecular characterization of their responses to diverse nutrient stresses in allotetraploid rapeseed

Plant defensins (PDFs), short peptides with strong antibacterial activity, play important roles in plant growth, development, and stress resistance. However, there are few systematic analyses on PDFs in Brassica napus. Here, bioinformatics methods were used to identify genome-wide PDFs in Brassica napus, and systematically analyze physicochemical properties, expansion pattern, phylogeny, and expression profiling of BnaPDFs under diverse nutrient stresses. A total of 37 full-length PDF homologs, divided into two subgroups (PDF1s and PDF2s), were identified in the rapeseed genome. A total of two distinct clades were identified in the BnaPDF phylogeny. Clade specific conserved motifs were identified within each clade respectively. Most BnaPDFs were proved to undergo powerful purified selection. The PDF members had enriched cis-elements related to growth and development, hormone response, environmental stress response in their promoter regions. GO annotations indicate that the functional pathways of BnaPDFs are mainly involved in cells killing and plant defense responses. In addition, bna-miRNA164 and bna-miRNA172 respectively regulate the expression of their targets BnaA2.PDF2.5 and BnaC7.PDF2.6. The expression patterns of BnaPDFs were analyzed in different tissues. BnaPDF1.2bs was mainly expressed in the roots, whereas BnaPDF2.2s and BnaPDF2.3s were both expressed in stamen, pericarp, silique, and stem. However, the other BnaPDF members showed low expression levels in various tissues. Differential expression of BnaPDFs under nitrate limitation, ammonium excess, phosphorus starvation, potassium deficiency, cadmium toxicity, and salt stress indicated that they might participate in different nutrient stress resistance. The genome-wide identification and characterization of BnaPDFs will enrich understanding of their molecular characteristics and provide elite gene resources for genetic improvement of rapeseed resistance to nutrient stresses.

The Bnapus50K array: a quick and versatile genotyping tool for Brassica napus genomic breeding and research

Rapeseed is a globally cultivated commercial crop, primarily grown for its oil. High-density single nucleotide polymorphism (SNP) arrays are widely used as a standard genotyping tool for rapeseed research, including for gene mapping, genome-wide association studies, germplasm resource analysis, and cluster analysis. Although considerable rapeseed genome sequencing data have been released, DNA arrays are still an attractive choice for providing additional genetic data in an era of high-throughput whole-genome sequencing. Here, we integrated re-sequencing DNA array data (32,216, 304 SNPs) from 505 inbred rapeseed lines, allowing us to develop a sensitive and efficient genotyping DNA array, Bnapus50K, with a more consistent genetic and physical distribution of probes. A total of 42,090 high-quality probes were filtered and synthesized, with an average distance between adjacent SNPs of 8 kb. To improve the practical application potential of this array in rapeseed breeding, we also added 1,618 functional probes related to important agronomic traits such as oil content, disease resistance, male sterility, and flowering time. The additional probes also included those specifically for detecting genetically modified material. These probes show a good detection efficiency and are therefore useful for gene mapping, along with crop variety improvement and identification. The novel Bnapus50K DNA array developed in this study could prove to be a quick and versatile genotyping tool for B. napus genomic breeding and research.

Genomic identification of nitrogen assimilation-related genes and transcriptional characterization of their responses to nitrogen in allotetraploid rapeseed

BACKGROUND

Nitrogen (N) is an essential macronutrient to maintain plant growth and development. Plants absorb nitrate-N or ammonium-N in the environment and undergo reduction reactions catalyzed by nitrate reductase (NR), nitrite reductase (NIR), glutamine synthetase (GS), and glutamine oxoglutarate aminotransferase (GOGAT) within plants.

METHODS AND RESULTS

A total of 42 N assimilation-related genes (NAG) members were identified in rapeseed. Darwin's evolutionary pressure analysis showed that rapeseed NAGs underwent purification selection. Cis-element analysis revealed differences in the transcriptional regulation of NAGs between Arabidopsis and rapeseed. Expression analyses revealed that NRs were expressed mainly in old leaves, NIRs were expressed mainly in old leaves and lower stem peels, while the expression situation between different subfamilies of GSs and GOGATs was more complicated.

CONCLUSIONS

Differential expression of NAGs suggested that they might be involved in abiotic stresses. The above results greatly enriched our understanding of NAGs' molecular characteristics and provided central gene resources for NAGs-mediated NUE improvement in rapeseed.

Both overlapping and independent loci underlie seed number per pod and seed weight in Brassica napus by comparative quantitative trait loci analysis

Seed number per pod (SNPP) and seed weight (SW) are two components of seed yield in rapeseed (Brassica napus). Here, a natural population of rapeseed was employed for genome-wide association analysis for SNPP and SW across multi-years. A total of 101 and 77 SNPs significantly associated with SNPP and SW with the phenotypic variances (R2) ranging from 1.35 to 29.47% and from 0.78 to 34.58%, respectively. And 43 and 33 homologs of known genes from model plants were located in the 65 and 49 haplotype blocks (HBs) for SNPP and SW, respectively. Notably, we found 5 overlapping loci and 3 sets of loci with collinearity for both SNPP and SW, of which 4 overlapping loci harbored the haplotypes with the same direction of genetic effects on SNPP and SW, indicating high possibility to simultaneously improve SNPP and SW in rapeseed. Our findings revealed both overlapping and independent loci controlling seed number per pod and seed weight in rapeseed.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01232-1.

Stable, fertile lines produced by hybridization between allotetraploids Brassica juncea (AABB) and Brassica carinata (BBCC) have merged the A and C genomes

Many flowering plant taxa contain allopolyploids that share one or more genomes in common. In the Brassica genus, crop species Brassica juncea and Brassica carinata share the B genome, with 2n = AABB and 2n = BBCC genome complements, respectively. Hybridization results in 2n = BBAC hybrids, but the fate of these hybrids over generations of self-pollination has never been reported. We produced and characterized B. juncea × B. carinata (2n = BBAC) interspecific hybrids over six generations of self-pollination under selection for high fertility using a combination of genotyping, fertility phenotyping, and cytogenetics techniques. Meiotic pairing behaviour improved from 68% bivalents in the F₁ to 98% in the S₅ /S₆ generations, and initially low hybrid fertility also increased to parent species levels. The S₅ /S₆ hybrids contained an intact B genome (16 chromosomes) plus a new, stable A/C genome (18-20 chromosomes) resulting from recombination and restructuring of A and C-genome chromosomes. Our results provide the first experimental evidence that two genomes can come together to form a new, restructured genome in hybridization events between two allotetraploid species that share a common genome. This mechanism should be considered in interpreting phylogenies in taxa with multiple allopolyploid species.

Assembly of the non-heading pak choi genome and comparison with the genomes of heading Chinese cabbage and the oilseed yellow sarson

Brassica rapa displays a wide range of morphological diversity which is exploited for a variety of food crops. Here we present a high-quality genome assembly for pak choi (Brassica rapa L. subsp. chinensis), an important non-heading leafy vegetable, and comparison with the genomes of heading type Chinese cabbage and the oilseed form, yellow sarson. Gene presence-absence variation (PAV) and genomic structural variations (SV) were identified, together with single nucleotide polymorphisms (SNPs). The structure and expression of genes for leaf morphology and flowering were compared between the three morphotypes revealing candidate genes for these traits in B. rapa. The pak choi genome assembly and its comparison with other B. rapa genome assemblies provides a valuable resource for the genetic improvement of this important vegetable crop and as a model to understand the diversity of morphological variation across Brassica species.

Sclerotinia Stem Rot Resistance in Rapeseed: Recent Progress and Future Prospects

Sclerotinia stem rot (SSR) of rapeseed (Brassica napus), caused by the soil-borne fungus Sclerotinia sclerotiorum, is one of the main diseases seriously affecting the yield and oil quality of infected rapeseed crops. The complexity of the inheritance of resistance and of the interaction mechanisms between rapeseed and S. sclerotiorum limits resistance gene identification and molecular breeding. In this review, the latest progress of research into resistance to SSR in B. napus is summarized from the following three directions: the pathogenesis mechanisms of S. sclerotiorum, the resistance mechanisms of B. napus toward S. sclerotiorum, and rapeseed breeding for resistance to SSR. This review aims to provide a theoretical basis and useful reference for analyzing the mechanism of the interaction between B. napus and S. sclerotiorum, searching for gene loci associated with the resistance response, and for achieving disease-resistance genetic manipulation and molecular design breeding in rapeseed.

Comparison and evolutionary analysis of Brassica nucleotide binding site leucine rich repeat (NLR) genes and importance for disease resistance breeding

The Brassica genus contains many agriculturally significant oilseed and vegetable crops, however the crop yield is threatened by a range of fungal and bacterial pathogens. Nucleotide Binding Site Leucine Rich Repeat (NLR) genes play important roles in plant innate immunity. The evolution of NLR genes is influenced by genomic processes and pathogen selection. At the whole genome level, whole genome duplications (WGDs) generate abundant gene copies, most of which are lost during genome fractionation. At sub-genomic levels, some retained copies undergo duplication forming clusters which facilitate rapid evolution through recombination. The number, distribution and genetic variations of the NLR genes vary among Brassica species and within populations suggesting differential selection pressure exerted by pathogen populations throughout the evolutionary history. A study of the evolution of disease resistance genes in agriculturally important plants such as Brassicas helps gain insights into their function and inform the identification of resistance genes for breeding of resistant lines.

A high-quality Brassica napus genome reveals expansion of transposable elements, subgenome evolution and disease resistance

Rapeseed (Brassica napus L.) is a recent allotetraploid crop, which is well known for its high oil production. Here, we report a high-quality genome assembly of a typical semi-winter rapeseed cultivar, 'Zhongshuang11' (hereafter 'ZS11'), using a combination of single-molecule sequencing and chromosome conformation capture (Hi-C) techniques. Most of the high-confidence sequences (93.1%) were anchored to the individual chromosomes with a total of 19 centromeres identified, matching the exact chromosome count of B. napus. The repeat sequences in the A and C subgenomes in B. napus expanded significantly from 500 000 years ago, especially over the last 100 000 years. These young and recently amplified LTR-RTs showed dispersed chromosomal distribution but significantly preferentially clustered into centromeric regions. We exhaustively annotated the nucleotide-binding leucine-rich repeat (NLR) gene repertoire, yielding a total of 597 NLR genes in B. napus genome and 17.4% of which are paired (head-to-head arrangement). Based on the resequencing data of 991 B. napus accessions, we have identified 18 759 245 single nucleotide polymorphisms (SNPs) and detected a large number of genomic regions under selective sweep among the three major ecotype groups (winter, semi-winter and spring) in B. napus. We found 49 NLR genes and five NLR gene pairs colocated in selective sweep regions with different ecotypes, suggesting a rapid diversification of NLR genes during the domestication of B. napus. The high quality of our B. napus 'ZS11' genome assembly could serve as an important resource for the study of rapeseed genomics and reveal the genetic variations associated with important agronomic traits.

Characterization and fine mapping of a new dwarf mutant in Brassica napus

BACKGROUND

Plant height is an important plant characteristic closely related to yield performance of many crops. Reasonable reduction of plant height of crops is beneficial for improving yield and enhancing lodging resistance.

RESULTS

In the present study, we described the Brassica napus dwarf mutant bnd2 that was isolated using ethyl methanesulfonate (EMS) mutagenesis. Compared to wild type (WT), bnd2 exhibited reduced height and shorter hypocotyl and petiole leaves. By crossing the bnd2 mutant with the WT strain, we found that the ratio of the mutant to the WT in the F₂ population was close to 1:3, indicating that bnd2 is a recessive mutation of a single locus. Following bulked segregant analysis (BSA) by resequencing, BND2 was found to be located in the 13.77-18.08 Mb interval of chromosome A08, with a length of 4.31 Mb. After fine mapping with single nucleotide polymorphism (SNP) and insertion/deletion (InDel) markers, the gene was narrowed to a 140-Kb interval ranging from 15.62 Mb to 15.76 Mb. According to reference genome annotation, there were 27 genes in the interval, of which BnaA08g20960D had an SNP type variation in the intron between the mutant and its parent, which may be the candidate gene corresponding to BND2. The hybrid line derived from a cross between the mutant bnd2 and the commercial cultivar L329 had similar plant height but higher grain yield compared to the commercial cultivar, suggesting that the allele bnd2 is beneficial for hybrid breeding of lodging resistant and high yield rapeseed.

CONCLUSION

In this study, we identified a novel dwarf mutant of rapeseed with a new locus, which may be useful for functional analyses of genetic mechanisms of plant architecture and grain yield in rapeseed.

Genomics Armed With Diversity Leads the Way in Brassica Improvement in a Changing Global Environment

Meeting the needs of a growing world population in the face of imminent climate change is a challenge; breeding of vegetable and oilseed Brassica crops is part of the race in meeting these demands. Available genetic diversity constituting the foundation of breeding is essential in plant improvement. Elite varieties, land races, and crop wild species are important resources of useful variation and are available from existing genepools or genebanks. Conservation of diversity in genepools, genebanks, and even the wild is crucial in preventing the loss of variation for future breeding efforts. In addition, the identification of suitable parental lines and alleles is critical in ensuring the development of resilient Brassica crops. During the past two decades, an increasing number of high-quality nuclear and organellar Brassica genomes have been assembled. Whole-genome re-sequencing and the development of pan-genomes are overcoming the limitations of the single reference genome and provide the basis for further exploration. Genomic and complementary omic tools such as microarrays, transcriptomics, epigenetics, and reverse genetics facilitate the study of crop evolution, breeding histories, and the discovery of loci associated with highly sought-after agronomic traits. Furthermore, in genomic selection, predicted breeding values based on phenotype and genome-wide marker scores allow the preselection of promising genotypes, enhancing genetic gains and substantially quickening the breeding cycle. It is clear that genomics, armed with diversity, is set to lead the way in Brassica improvement; however, a multidisciplinary plant breeding approach that includes phenotype = genotype × environment × management interaction will ultimately ensure the selection of resilient Brassica varieties ready for climate change.

Legume Pangenome Construction Using an Iterative Mapping and Assembly Approach

A pangenome is a collection of genomic sequences found in the entire species rather than a single individual. It allows for comprehensive, species-wide characterization of genetic variations and mining of variable genes which may play important roles in phenotypes of interest. Recent advances in sequencing technologies have facilitated draft genome sequence construction and have made pangenome constructions feasible. Here, we present a reference genome-based iterative mapping and assembly method to construct a pangenome for a legume species.

Fine Mapping of a Locus Underlying the Ectopic Blade-Like Outgrowths on Leaf and Screening Its Candidate Genes in Rapeseed (Brassica napus L.)

Leaf is an important organ for higher plants, and the shape of it is one of the crucial traits of crops. In this study, we investigated a unique aberrant leaf morphology trait in a mutational rapeseed material, which displayed ectopic blade-like outgrowths on the adaxial side of leaf. The abnormal line 132000B-3 was crossed with the normal line 827-3. Based on the F_{2 : 3} family, we constructed two DNA pools (normal pool and abnormal pool) by the bulked segregant analysis (BSA) method and performed whole genome re-sequencing (WGR), obtaining the single-nucleotide polymorphism (SNP) and insertion/deletion (InDel) data. The SNP-index method was used to calculate the Δ(SNP/InDel-index), and then an association region was identified on chromosome A10 with a length of 5.5 Mbp, harboring 1048 genes totally. Subsequently, the fine mapping was conducted by using the penta-primer amplification refractory mutation system (PARMS), and the associated region was narrowed down to a 35.1-kbp segment, containing only seven genes. These seven genes were then analyzed according to their annotations and finally, BnA10g0422620 and BnA10g0422610, orthologs of LATE MERISTEM IDENTITY1 (LMI1) gene from Arabidopsis and REDUCED COMPLEXITY (RCO) gene from its relative Cardamine hirsuta, respectively, were identified as the candidate genes responding to this blade-like outgrowth trait in rapeseed. This study provides a novel perspective into the leaf formation in Brassica plants.

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

Rapeseed (Brassica napus L.) is a typical polyploid crop and one of the most important oilseed crops worldwide. With the rapid progress on high-throughput sequencing technologies and the reduction of sequencing cost, large-scale genomic data of a specific crop have become available. However, raw sequence data are mostly deposited in the sequence read archive of the National Center of Biotechnology Information (NCBI) and the European Nucleotide Archive (ENA), which is freely accessible to all researchers. Extensive tools for practical purposes should be developed to efficiently utilize these large raw data. Here, we report a web-based rapeseed genomic variation database (BnaGVD, http://rapeseed.biocloud.net/home) from which genomic variations, such as single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) across a world-wide collection of rapeseed accessions, can be referred. The current release of the BnaGVD contains 34,591,899 high-quality SNPs and 12,281,923 high-quality InDels and provides search tools to retrieve genomic variations and gene annotations across 1,007 accessions of worldwide rapeseed germplasm. We implement a variety of built-in tools (e.g., BnaGWAS, BnaPCA, and BnaStructure) to help users perform in-depth analyses. We recommend this web resource for accelerating studies on the functional genomics and screening of molecular markers for rapeseed breeding.

Sorghum Pan-Genome Explores the Functional Utility for Genomic-Assisted Breeding to Accelerate the Genetic Gain

Sorghum (Sorghum bicolor L.) is a staple food crops in the arid and rainfed production ecologies. Sorghum plays a critical role in resilient farming and is projected as a smart crop to overcome the food and nutritional insecurity in the developing world. The development and characterisation of the sorghum pan-genome will provide insight into genome diversity and functionality, supporting sorghum improvement. We built a sorghum pan-genome using reference genomes as well as 354 genetically diverse sorghum accessions belonging to different races. We explored the structural and functional characteristics of the pan-genome and explain its utility in supporting genetic gain. The newly-developed pan-genome has a total of 35,719 genes, a core genome of 16,821 genes and an average of 32,795 genes in each cultivar. The variable genes are enriched with environment responsive genes and classify the sorghum accessions according to their race. We show that 53% of genes display presence-absence variation, and some of these variable genes are predicted to be functionally associated with drought adaptation traits. Using more than two million SNPs from the pan-genome, association analysis identified 398 SNPs significantly associated with important agronomic traits, of which, 92 were in genes. Drought gene expression analysis identified 1,788 genes that are functionally linked to different conditions, of which 79 were absent from the reference genome assembly. This study provides comprehensive genomic diversity resources in sorghum which can be used in genome assisted crop improvement.

Current Status of the Disease-Resistant Gene(s)/QTLs, and Strategies for Improvement in Brassica juncea

Brassica juncea is a major oilseed crop in tropical and subtropical countries, especially in south-east Asia like India, China, Bangladesh, and Pakistan. The widespread cultivation of genetically similar varieties tends to attract fungal pathogens which cause heavy yield losses in the absence of resistant sources. The conventional disease management techniques are often expensive, have limited efficacy, and cause additional harm to the environment. A substantial approach is to identify and use of resistance sources within the Brassica hosts and other non-hosts to ensure sustainable oilseed crop production. In the present review, we discuss six major fungal pathogens of B. juncea: Sclerotinia stem rot (Sclerotinia sclerotiorum), Alternaria blight (Alternaria brassicae), White rust (Albugo candida), Downy mildew (Hyaloperonospora parasitica), Powdery mildew (Erysiphe cruciferarum), and Blackleg (Leptoshaeria maculans). From discussing studies on pathogen prevalence in B. juncea, the review then focuses on highlighting the resistance sources and quantitative trait loci/gene identified so far from Brassicaceae and non-filial sources against these fungal pathogens. The problems in the identification of resistance sources for B. juncea concerning genome complexity in host subpopulation and pathotypes were addressed. Emphasis has been laid on more elaborate and coordinated research to identify and deploy R genes, robust techniques, and research materials. Examples of fully characterized genes conferring resistance have been discussed that can be transformed into B. juncea using advanced genomics tools. Lastly, effective strategies for B. juncea improvement through introgression of novel R genes, development of pre-breeding resistant lines, characterization of pathotypes, and defense-related secondary metabolites have been provided suggesting the plan for the development of resistant B. juncea.

Recent Findings Unravel Genes and Genetic Factors Underlying Leptosphaeria maculans Resistance in Brassica napus and Its Relatives

Among the Brassica oilseeds, canola (Brassica napus) is the most economically significant globally. However, its production can be limited by blackleg disease, caused by the fungal pathogen Lepstosphaeria maculans. The deployment of resistance genes has been implemented as one of the key strategies to manage the disease. Genetic resistance against blackleg comes in two forms: qualitative resistance, controlled by a single, major resistance gene (R gene), and quantitative resistance (QR), controlled by numerous, small effect loci. R-gene-mediated blackleg resistance has been extensively studied, wherein several genomic regions harbouring R genes against L. maculans have been identified and three of these genes were cloned. These studies advance our understanding of the mechanism of R gene and pathogen avirulence (Avr) gene interaction. Notably, these studies revealed a more complex interaction than originally thought. Advances in genomics help unravel these complexities, providing insights into the genes and genetic factors towards improving blackleg resistance. Here, we aim to discuss the existing R-gene-mediated resistance, make a summary of candidate R genes against the disease, and emphasise the role of players involved in the pathogenicity and resistance. The comprehensive result will allow breeders to improve resistance to L. maculans, thereby increasing yield.

How Population Structure Impacts Genomic Selection Accuracy in Cross-Validation: Implications for Practical Breeding

Over the last two decades, the application of genomic selection has been extensively studied in various crop species, and it has become a common practice to report prediction accuracies using cross validation. However, genomic prediction accuracies obtained from random cross validation can be strongly inflated due to population or family structure, a characteristic shared by many breeding populations. An understanding of the effect of population and family structure on prediction accuracy is essential for the successful application of genomic selection in plant breeding programs. The objective of this study was to make this effect and its implications for practical breeding programs comprehensible for breeders and scientists with a limited background in quantitative genetics and genomic selection theory. We, therefore, compared genomic prediction accuracies obtained from different random cross validation approaches and within-family prediction in three different prediction scenarios. We used a highly structured population of 940 Brassica napus hybrids coming from 46 testcross families and two subpopulations. Our demonstrations show how genomic prediction accuracies obtained from among-family predictions in random cross validation and within-family predictions capture different measures of prediction accuracy. While among-family prediction accuracy measures prediction accuracy of both the parent average component and the Mendelian sampling term, within-family prediction only measures how accurately the Mendelian sampling term can be predicted. With this paper we aim to foster a critical approach to different measures of genomic prediction accuracy and a careful analysis of values observed in genomic selection experiments and reported in literature.

Long-read assembly of the Brassica napus reference genome Darmor-bzh

BACKGROUND

The combination of long reads and long-range information to produce genome assemblies is now accepted as a common standard. This strategy not only allows access to the gene catalogue of a given species but also reveals the architecture and organization of chromosomes, including complex regions such as telomeres and centromeres. The Brassica genus is not exempt, and many assemblies based on long reads are now available. The reference genome for Brassica napus, Darmor-bzh, which was published in 2014, was produced using short reads and its contiguity was extremely low compared with current assemblies of the Brassica genus.

FINDINGS

Herein, we report the new long-read assembly of Darmor-bzh genome (Brassica napus) generated by combining long-read sequencing data and optical and genetic maps. Using the PromethION device and 6 flowcells, we generated ∼16 million long reads representing 93× coverage and, more importantly, 6× with reads longer than 100 kb. This ultralong-read dataset allows us to generate one of the most contiguous and complete assemblies of a Brassica genome to date (contig N50 > 10 Mb). In addition, we exploited all the advantages of the nanopore technology to detect modified bases and sequence transcriptomic data using direct RNA to annotate the genome and focus on resistance genes.

CONCLUSION

Using these cutting-edge technologies, and in particular by relying on all the advantages of the nanopore technology, we provide the most contiguous Brassica napus assembly, a resource that will be valuable to the Brassica community for crop improvement and will facilitate the rapid selection of agronomically important traits.

Linkage mapping and QTL analysis of flowering time using ddRAD sequencing with genotype error correction in Brassica napus

BACKGROUND

Brassica napus is an important oilseed crop cultivated worldwide. During domestication and breeding of B. napus, flowering time has been a target of selection because of its substantial impact on yield. Here we use double digest restriction-site associated DNA sequencing (ddRAD) to investigate the genetic basis of flowering in B. napus. An F2 mapping population was derived from a cross between an early-flowering spring type and a late-flowering winter type.

RESULTS

Flowering time in the mapping population differed by up to 25 days between individuals. High genotype error rates persisted after initial quality controls, as suggested by a genotype discordance of ~ 12% between biological sequencing replicates. After genotype error correction, a linkage map spanning 3981.31 cM and compromising 14,630 single nucleotide polymorphisms (SNPs) was constructed. A quantitative trait locus (QTL) on chromosome C2 was detected, covering eight flowering time genes including FLC.

CONCLUSIONS

These findings demonstrate the effectiveness of the ddRAD approach to sample the B. napus genome. Our results also suggest that ddRAD genotype error rates can be higher than expected in F2 populations. Quality filtering and genotype correction and imputation can substantially reduce these error rates and allow effective linkage mapping and QTL analysis.