Validation of an updated Associative Transcriptomics platform for the polyploid crop species Brassica napus by dissection of the genetic architecture of erucic acid and tocopherol isoform variation in seeds

Deciphering the heterogeneous glucosinolates composition in leaves and seeds: strategies for developing Brassica napus genotypes with low seed glucosinolates content but high leaf glucosinolates content

Rapeseed cakes with low glucosinolates content (GC) possess high feeding value. However, the pursuit of low-GC seeds has inadvertently resulted in a reduction of GC in leaves, making plants more susceptible to stress and lowering their nutritional quality. Therefore, it is imperative to disrupt the tight association between GC in these two tissues and ultimately develop genotypes with low-GC seeds but high-GC leaves. The distinct mechanisms underlying glucosinolate (GSL) synthesis in these two tissues remain unclear. Here, we discovered that aliphatic and aromatic GSLs, rather than indole GSLs, contribute to the positive correlation between GC in seeds and leaves. We performed selective-sweep analyses and identified the genomic footprints left after decades of intense selection for low-GC seeds. By conducting genome-wide association studies and analyzing differentially expressed genes in high- and low-GC seeds and leaves, we compiled lists of distinct genes involved in GSL synthesis in leaves and seeds separately. In particular, BnMYB28 plays a key role in regulating GC in both seeds and leaves. Selection and manipulation of BnaC09.MYB28 would affect GC in both tissues. However, downregulation of BnaA02.MYB28 and/or BnaC02.MYB28 would likely reduce GC in seeds without causing a concurrent reduction in GC in leaves.

Evolving best practices for transcriptome-wide association studies accelerate discovery of gene-phenotype links

Transcriptome-wide association studies (TWAS) complement genome-wide association studies (GWAS) by using gene expression data to link specific genes to phenotypes. This review examines 37 TWAS studies across eight plant species, evaluating the impact of methodological choices on outcomes using maize and soybean datasets. Large sample sizes and synchronized sample collection for gene expression measurement appear to significantly increase power for discovering gene-phenotype linkages, while matching tissue, stage, and environment may matter much less than previously believed, making it feasible to reuse large and well-collected expression datasets across multiple studies. The development of statistical approaches and computational tools specifically optimized for plant TWAS data will ultimately be needed, but further potential remains to adapt advances developed in GWAS to TWAS contexts.

Increasing oil content in Brassica oilseed species

Brassica oilseed species are the third most important in the world, providing approximately 15 % of the total vegetable oils. Three species (Brassica rapa, B. juncea, B. napus) dominate with B. napus being the most common in Canada, China and Europe. Originally, B. napus was a crop producing seed with high erucic acid content, which still persists today, to some extent, and is used for industrial purposes. In contrast, cultivars which produce seed used for food and feed are low erucic acid cultivars which also have reduced glucosinolate content. Because of the limit to agricultural land, recent efforts have been made to increase productivity of oil crops, including Brassica oilseed species. In this article, we have detailed research in this regard. We have covered modern genetic, genomic and metabolic control analysis approaches to identifying potential targets for the manipulation of seed oil content. Details of work on the use of quantitative trait loci, genome-wide association and comparative functional genomics to highlight factors influencing seed oil accumulation are given and functional proteins which can affect this process are discussed. In summary, a wide variety of inputs are proving useful for the improvement of Brassica oilseed species, as major sources of global vegetable oil.

Primary multistep phosphorelay activation comprises both cytokinin and abiotic stress responses: insights from comparative analysis of Brassica type-A response regulators

Multistep phosphorelay (MSP) signaling integrates hormonal and environmental signals to control both plant development and adaptive responses. Type-A RESPONSE REGULATOR (RRA) genes, the downstream members of the MSP cascade and cytokinin primary response genes, are thought to mediate primarily the negative feedback regulation of (cytokinin-induced) MSP signaling. However, transcriptional data also suggest the involvement of RRA genes in stress-related responses. By employing evolutionary conservation with the well-characterized Arabidopsis thaliana RRA genes, we identified five and 38 novel putative RRA genes in Brassica oleracea and Brassica napus, respectively. Our phylogenetic analysis suggests the existence of gene-specific selective pressure, maintaining the homologs of ARR3, ARR6, and ARR16 as singletons during the evolution of Brassicaceae. We categorized RRA genes based on the kinetics of their cytokinin-mediated up-regulation and observed both similarities and specificities in this type of response across Brassicaceae species. Using bioinformatic analysis and experimental data demonstrating the cytokinin and abiotic stress responsiveness of the A. thaliana-derived TCSv2 reporter, we unveil the mechanistic conservation of cytokinin- and stress-mediated up-regulation of RRA genes in B. rapa and B. napus. Notably, we identify partial cytokinin dependency of cold stress-induced RRA transcription, thus further demonstrating the role of cytokinin signaling in crop adaptive responses.

Adaptation to reductions in chilling availability using variation in PLANT HOMOLOGOUS TO PARAFIBROMIN in Brassica napus

Winter annual crops are sown in late summer or autumn and require chilling to promote flowering the following spring. Floral initiation begins in autumn and winter, and in winter oilseed rape (OSR), continued chilling during flower development is necessary for high yield potential. This can be a problem in areas where chilling is not guaranteed, or as a result of changing climates. Here, we used chilling disruption and low chilling to identify loci with the potential to increase chilling efficiency in winter OSR. We report that time to flowering and yield potential under low chill conditions are affected by variation at the PLANT HOMOLOGOUS TO PARAFIBROMIN gene, a component of the plant PAF1c complex. We show that increases in winter chilling given to developing flowers can improve seed yields and that loss of function of BnaPHP.A05 leads to early flowering in B. rapa and B. napus and an increase in seed set where chilling is limited. Because PHP is known to specifically target the FLOWERING LOCUS C (FLC) gene in Arabidopsis, we propose that variation at PHP is useful for breeding modifications to chilling responses in polyploid crops with multiple copies of the FLC gene.

Identification of transcription factor BnHDG4-A08 as a novel candidate associated with the accumulation of oleic, linoleic, linolenic, and erucic acid in Brassica napus

KEY MESSAGE

We screened 47 significantly associated haplotype blocks for oleic, linoleic, linolenic, and erucic acid, with 17 blocks influencing multiple traits. A novel candidate of transcription factor BnHDG4 A08 influencing oleic, linoleic, linolenic, and erucic acid was identified, by a joint strategy of haplotype-based genome-wide association study, genomic resequencing, gene cloning, and co-expression network Fatty acid (FA) composition determines the quality and economic value of rapeseed oil (Brassica napus). However, the molecular network of FAs is unclear. In the current study, multi-strategies of haplotype-based genome-wide association study (GWAS), genomic resequencing, gene cloning, and co-expression network were joint to reveal novel genetic factors influencing FA accumulation in rapeseed. We identified 47 significantly associated haplotype blocks for oleic, linoleic, linolenic, and erucic acid, with 17 blocks influencing multiple traits, using a haplotype-based GWAS with phenotype data from 203 Chinese semi-winter accessions. A total of 61 rapeseed orthologs involved in acyl-lipid metabolism, carbohydrate metabolism, or photosynthesis were identified in these 17 blocks. Among these genes, BnHDG4-A08, encoding a class IV homeodomain leucine-zipper transcription factor, exhibited two single-nucleotide polymorphisms (SNPs) in the exon and intron, with significant associations with oleic, linoleic, linolenic, and erucic acid. Gene cloning further validated two SNPs in the exon of BnHDG4-A08 in a population with 75 accessions, leading to two amino acid changes (T372A and P366L) and significant variation of oleic, linoleic, linolenic, and erucic acid. A competitive allele-specific PCR (KASP) marker based on the SNPs was successfully developed and validated. Moreover, 98 genes exhibiting direct interconnections and high weight values with BnHDG4-A08 were identified through co-expression network analysis using transcriptome data from 13 accessions. Our study identified a novel FA candidate of transcription factor BnHDG4-A08 influencing oleic, linoleic, linolenic, and erucic acid. This gene provides a potential promising gene resource for the novel mechanistic understanding of transcription factors regulating FA accumulation.

Transcriptome-referenced association study provides insights into the regulation of oil and fatty acid biosynthesis in Torreya grandis kernel

INTRODUCTION

Torreya grandis is a gymnosperm belonging to Taxodiaceae. As an economically important tree, its kernels are edible and rich in oil with high unsaturated fatty acids, such as sciadonic acid. However, the kernels from different T. grandis landraces exhibit fatty acid and oil content variations.

OBJECTIVES

As a gymnosperm, does T. grandis have special regulation mechanisms for oil biosynthesis? The aim of this study was to dissect the genetic architecture of fatty acid and oil content and the underlying mechanism in T. grandis.

METHODS

We constructed a high integrity reference sequence of expressed regions of the genome in T. grandis and performed transcriptome-referenced association study (TRAS) for 10 fatty acid and oil traits of kernels in the 170 diverse T. grandis landraces. To confirm the TRAS result, we performed functional validation and molecular biology experiments for oil significantly associated genes.

RESULTS

We identified 41 SNPs from 34 transcripts significantly associated with 7 traits by TRAS (-log10 (P) greater than 6.0). Results showed that LOB domain-containing protein 40 (LBD40) and surfeit locus protein 1 (SURF1) may be indirectly involved in the regulation of oil and sciadonic acid biosynthesis, respectively. Moreover, overexpression of TgLBD40 significantly increased seed oil content. The nonsynonymous variant in the TgLBD40 coding region discovered by TRAS could alter the oil content in plants. Pearson's correlation analysis and dual-luciferase assay indicated that TgLBD40 positively enhanced oil accumulation by affecting oil biosynthesis pathway genes, such as TgDGAT1.

CONCLUSION

Our study provides new insights into the genetic basis of oil biosynthesis in T. grandis and demonstrates that integrating RNA sequencing and TRAS is a powerful strategy to perform association study independent of a reference genome for dissecting important traits in T. grandis.

A complex receptor locus confers responsiveness to necrosis and ethylene-inducing like peptides in Brassica napus

Brassica crops are susceptible to diseases which can be mitigated by breeding for resistance. MAMPs (microbe-associated molecular patterns) are conserved molecules of pathogens that elicit host defences known as pattern-triggered immunity (PTI). Necrosis and Ethylene-inducing peptide 1-like proteins (NLPs) are MAMPs found in a wide range of phytopathogens. We studied the response to BcNEP2, a representative NLP from Botrytis cinerea, and showed that it contributes to disease resistance in Brassica napus. To map regions conferring NLP response, we used the production of reactive oxygen species (ROS) induced during PTI across a population of diverse B. napus accessions for associative transcriptomics (AT), and bulk segregant analysis (BSA) on DNA pools created from a cross of NLP-responsive and non-responsive lines. In silico mapping with AT identified two peaks for NLP responsiveness on chromosomes A04 and C05 whereas the BSA identified one peak on A04. BSA delimited the region for NLP-responsiveness to 3 Mbp, containing ~245 genes on the Darmor-bzh reference genome and four co-segregating KASP markers were identified. The same pipeline with the ZS11 genome confirmed the highest-associated region on chromosome A04. Comparative BLAST analysis revealed unannotated clusters of receptor-like protein (RLP) homologues on ZS11 chromosome A04. However, no specific RLP homologue conferring NLP response could be identified. Our results also suggest that BR-SIGNALLING KINASE1 may be involved with modulating the NLP response. Overall, we demonstrate that responsiveness to NLP contributes to disease resistance in B. napus and define the associated genomic location. These results can have practical application in crop improvement.

Genomic and transcriptome analyses reveal potential contributors to erucic acid biosynthesis in seeds of rapeseed (Brassica napus)

KEY MESSAGE

Through comprehensive genomic and transcriptomic analyses, we identified a set of 23 genes that act up- or downstream of erucic acid content (EAC) production in rapeseed seeds. We selected example genes to showcase the distribution of single nucleotide polymorphisms, haplotypes associated with EAC phenotypes, and the creation of molecular markers differentiating low EAC and high EAC genotypes. Erucic acid content (EAC) is a crucial trait in rapeseed, with low LEAC oil recognized for its health benefits and high EA oil holding industrial value. Despite its significance, the genomic consequences of intensive LEAC-cultivar selection and the genetic basis underlying EA regulation remain largely unexplored. To address this knowledge gap, we conducted selective signal analyses, genome-wide association studies (GWAS), and transcriptome analyses. Our investigation unveiled the genetic footprints resulting from LEAC selection in germplasm populations, drawing attention to specific loci that contribute to enriching diversity. By integrating GWAS and transcriptome analyses, we identified a set of 23 genes that play a significant role in determining EAC in seeds or are downstream consequences of EA-level alterations. These genes have emerged as promising candidates for elucidating the potential mechanisms governing EAC in rapeseed. To exemplify the findings, we selected specific genes to demonstrate the distribution of single nucleotide polymorphisms and haplotypes associated with different EAC phenotypes. Additionally, we showcased to develop molecular markers distinguishing between LEAC and high EAC genotypes.

Pathogen lifestyle determines host genetic signature of quantitative disease resistance loci in oilseed rape (Brassica napus)

KEY MESSAGE

Using associative transcriptomics, our study identifies genes conferring resistance to four diverse fungal pathogens in crops, emphasizing key genetic determinants of multi-pathogen resistance. Crops are affected by several pathogens, but these are rarely studied in parallel to identify common and unique genetic factors controlling diseases. Broad-spectrum quantitative disease resistance (QDR) is desirable for crop breeding as it confers resistance to several pathogen species. Here, we use associative transcriptomics (AT) to identify candidate gene loci associated with Brassica napus constitutive QDR to four contrasting fungal pathogens: Alternaria brassicicola, Botrytis cinerea, Pyrenopeziza brassicae, and Verticillium longisporum. We did not identify any shared loci associated with broad-spectrum QDR to fungal pathogens with contrasting lifestyles. Instead, we observed QDR dependent on the lifestyle of the pathogen-hemibiotrophic and necrotrophic pathogens had distinct QDR responses and associated loci, including some loci associated with early immunity. Furthermore, we identify a genomic deletion associated with resistance to V. longisporum and potentially broad-spectrum QDR. This is the first time AT has been used for several pathosystems simultaneously to identify host genetic loci involved in broad-spectrum QDR. We highlight constitutive expressed candidate loci for broad-spectrum QDR with no antagonistic effects on susceptibility to the other pathogens studies as candidates for crop breeding. In conclusion, this study represents an advancement in our understanding of broad-spectrum QDR in B. napus and is a significant resource for the scientific community.

Transcriptome-wide association study coupled with eQTL analysis reveals the genetic connection between gene expression and flowering time in Arabidopsis

Genome-wide association study (GWAS) has improved our understanding of complex traits, but challenges exist in distinguishing causation versus association caused by linkage disequilibrium. Instead, transcriptome-wide association studies (TWAS) detect direct associations between expression levels and phenotypic variations, providing an opportunity to better prioritize candidate genes. To assess the feasibility of TWAS, we investigated the association between transcriptomes, genomes, and various traits in Arabidopsis, including flowering time. The associated genes formerly known to regulate growth allometry or metabolite production were first identified by TWAS. Next, for flowering time, six TWAS-newly identified genes were functionally validated. Analysis of the expression quantitative trait locus (eQTL) further revealed a trans-regulatory hotspot affecting the expression of several TWAS-identified genes. The hotspot covers the FRIGIDA (FRI) gene body, which possesses multiple haplotypes differentially affecting the expression of downstream genes, such as FLOWERING LOCUS C (FLC) and SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1). We also revealed multiple independent paths towards the loss of function of FRI in natural accessions. Altogether, this study demonstrates the potential of combining TWAS with eQTL analysis to identify important regulatory modules of FRI-FLC-SOC1 for quantitative traits in natural populations.

The current scenario and future perspectives of transgenic oilseed mustard by CRISPR-Cas9

PURPOSE

Production of a designer crop having added attributes is the primary goal of all plant biotechnologists. Specifically, development of a crop with a simple biotechnological approach and at a rapid pace is most desirable. Genetic engineering enables us to displace genes among species. The newly incorporated foreign gene(s) in the host genome can create a new trait(s) by regulating the genotypes and/or phenotypes. The advent of the CRISPR-Cas9 tools has enabled the modification of a plant genome easily by introducing mutation or replacing genomic fragment. Oilseed mustard varieties (e.g., Brassica juncea, Brassica nigra, Brassica napus, and Brassica carinata) are one such plants, which have been transformed with different genes isolated from the wide range of species. Current reports proved that the yield and value of oilseed mustard has been tremendously improved by the introduction of stably inherited new traits such as insect and herbicide resistance. However, the genetic transformation of oilseed mustard remains incompetent due to lack of potential plant transformation systems. To solve numerous complications involved in genetically modified oilseed mustard crop varieties regeneration procedures, scientific research is being conducted to rectify the unwanted complications. Thus, this study provides a broader overview of the present status of new traits introduced in each mentioned varieties of oilseed mustard plant by different genetical engineering tools, especially CRISPR-Cas9, which will be useful to improve the transformation system of oilseed mustard crop plants.

METHODS

This review presents recent improvements made in oilseed mustard genetic engineering methodologies by using CRISPR-Cas9 tools, present status of new traits introduced in oilseed mustard plant varieties.

RESULTS

The review highlighted that the transgenic oilseed mustard production is a challenging process and the transgenic varieties of oilseed mustard provide a powerful tool for enhanced mustard yield. Over expression studies and silencing of desired genes provide functional importance of genes involved in mustard growth and development under different biotic and abiotic stress conditions. Thus, it can be expected that in near future CRISPR can contribute enormously in improving the mustard plant's architecture and develop stress resilient oilseed mustard plant species.

Interploidy Introgression Shaped Adaptation during the Origin and Domestication History of Brassica napus

Polyploidy is recurrent across the tree of life and known as an evolutionary driving force in plant diversification and crop domestication. How polyploid plants adapt to various habitats has been a fundamental question that remained largely unanswered. Brassica napus is a major crop cultivated worldwide, resulting from allopolyploidy between unknown accessions of diploid B. rapa and B. oleracea. Here, we used whole-genome resequencing data of accessions representing the majority of morphotypes and ecotypes from the species B. rapa, B. oleracea, and B. napus to investigate the role of polyploidy during domestication. To do so, we first reconstructed the phylogenetic history of B. napus, which supported the hypothesis that the emergence of B. napus derived from the hybridization of European turnip of B. rapa and wild B. oleracea. These analyses also showed that morphotypes of swede and Siberian kale (used as vegetable and fodder) were domesticated before rapeseed (oil crop). We next observed that frequent interploidy introgressions from sympatric diploids were prominent throughout the domestication history of B. napus. Introgressed genomic regions were shown to increase the overall genetic diversity and tend to be localized in regions of high recombination. We detected numerous candidate adaptive introgressed regions and found evidence that some of the genes in these regions contributed to phenotypic diversification and adaptation of different morphotypes. Overall, our results shed light on the origin and domestication of B. napus and demonstrate interploidy introgression as an important mechanism that fuels rapid diversification in polyploid species.

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.

Novel gene loci associated with susceptibility or cryptic quantitative resistance to Pyrenopeziza brassicae in Brassica napus

Quantitative disease resistance (QDR) controls the association of the light leaf spot pathogen with Brassica napus; four QDR loci that were in linkage disequilibrium and eight gene expression markers were identified. Quantitative disease resistance (QDR) can provide durable control of pathogens in crops in contrast to resistance (R) gene-mediated resistance which can break down due to pathogen evolution. QDR is therefore a desirable trait in crop improvement, but little is known about the causative genes, and so it is difficult to incorporate into breeding programmes. Light leaf spot, caused by Pyrenopeziza brassicae, is an important disease of oilseed rape (canola, Brassica napus). To identify new QDR gene loci, we used a high-throughput screening pathosystem with P. brassicae on 195 lines of B. napus combined with an association transcriptomics platform. We show that all resistance against P. brassicae was associated with QDR and not R gene-mediated. We used genome-wide association analysis with an improved B. napus population structure to reveal four gene loci significantly (P = 0.0001) associated with QDR in regions showing linkage disequilibrium. On chromosome A09, enhanced resistance was associated with heterozygosity for a cytochrome P450 gene co-localising with a previously described locus for seed glucosinolate content. In addition, eight significant gene expression markers with a false discovery rate of 0.001 were associated with QDR against P. brassicae. For seven of these, expression was positively correlated with resistance, whereas for one, a HXXXD-type acyl-transferase, negative correlation indicated a potential susceptibility gene. The study identifies novel QDR loci for susceptibility and resistance, including novel cryptic QDR genes associated with heterozygosity, that will inform future crop improvement.

Uncovering Trait Associations Resulting in Maximal Seed Yield in Winter and Spring Oilseed Rape

Seed yield is a complex trait for many crop species including oilseed rape (OSR) (Brassica napus), the second most important oilseed crop worldwide. Studies have focused on the contribution of distinct factors in seed yield such as environmental cues, agronomical practices, growth conditions, or specific phenotypic traits at the whole plant level, such as number of pods in a plant. However, how female reproductive traits contribute to whole plant level traits, and hence to seed yield, has been largely ignored. Here, we describe the combined contribution of 33 phenotypic traits within a B. napus diversity set population and their trade-offs at the whole plant and organ level, along with their interaction with plant level traits. Our results revealed that both Winter OSR (WOSR) and Spring OSR (SOSR); the two more economically important OSR groups in terms of oil production; share a common dominant reproductive strategy for seed yield. In this strategy, the main inflorescence is the principal source of seed yield, producing a good number of ovules, a large number of long pods with a concomitantly high number of seeds per pod. Moreover, we observed that WOSR opted for additional reproductive strategies than SOSR, presenting more plasticity to maximise seed yield. Overall, we conclude that OSR adopts a key strategy to ensure maximal seed yield and propose an ideal ideotype highlighting crucial phenotypic traits that could be potential targets for breeding.

Distribution of MITE family Monkey King in rapeseed (Brassica napus L) and its influence on gene expression

Miniature inverted-repeat transposable elements (MITEs) are a group of class II transposable elements. The MITE Monkey King (MK) was first discovered upstream of BnFLC.A10. In this study, genome resequencing of four selected B. napus accessions, revealed more than 4000 distributed copies of MKs constituting ~2.4 Mb of the B. napus genomic sequence and caused 677 polymorphisms among the four accessions. MK -polymorphism-related markers across 128 natural and 58 synthetic accessions revealed more polymorphic MKs in natural than synthetic accessions. Ten MK -induced indels significantly affected the expression levels of the nearest gene based on RNAseq analysis, six of these effects were subsequently confirmed using qRT-PCR. Decreased expression pattern of MK -derived miRNA-bna-miR6031 was also observed under various stress treatments. Further research focused on the MITE families should promote not only our understanding of gene regulatory networks but also inform crop improvement efforts.

A 598-bp InDel Variation in the Promoter Region of Bna.SOC1.A05 Is Predominantly Present in Winter Type Rapeseeds

During rapeseed domestication and breeding, genetic diversity allowed to adapt it to different eco-geographical regions and to shape its useful traits. Structural variations (SVs), including presence/absence variations (PAVs), are thought to play a major role in the genetic diversity and phenotypic plasticity of rapeseed. In this study, we detected a 598-bp PAV within the promoter region of an Arabidopsis ortholog of a major flowering time gene and a downstream target of FLC, SOC1, which is one of the first genes that are upregulated in rapeseed during vernalization. Further analysis showed that the insertion is present predominantly in winter types while absent in spring types. The 589-bp sequence is present only in the A sub-genome indicating that it originated from Brassica rapa. Since the genomic region around Bna.SOC1.A05 showed a strong reduction in nucleotide diversity, the insertion might represent a larger selected sweep for rapeseed adaptation. Cis-element analysis showed that the insertion contains an ACGTG box, which is the strongest binding motif for the HY5 transcription factor in Arabidopsis. In addition, expression analyses showed that mRNA levels of Bna.SOC1.A05 were lower in accessions carrying the insertion compared to the ones that had no insertion.

Total FLC transcript dynamics from divergent paralogue expression explains flowering diversity in Brassica napus

Flowering time is a key adaptive and agronomic trait. In Arabidopsis, natural variation in expression levels of the floral repressor FLOWERING LOCUS C (FLC) leads to differences in vernalization. In Brassica napus there are nine copies of FLC. Here, we study how these multiple FLC paralogues determine vernalization requirement as a system. We collected transcriptome time series for Brassica napus spring, winter, semi-winter, and Siberian kale crop types. Modelling was used to link FLC expression dynamics to floral response following vernalization. We show that relaxed selection pressure has allowed expression of FLC paralogues to diverge, resulting in variation of FLC expression during cold treatment between paralogues and accessions. We find that total FLC expression dynamics best explains differences in cold requirement between cultivars, rather than expression of specific FLC paralogues. The combination of multiple FLC paralogues with different expression dynamics leads to rich behaviour in response to cold and a wide range of vernalization requirements in B. napus. We find evidence for different strategies to determine the response to cold in existing winter rapeseed accessions.

Two Brassica napus cultivars differ in gene expression, but not in their response to submergence

Heavy rainfall causes flooding of natural ecosystems as well as farmland, negatively affecting plant performance. While the responses of the wild model organism Arabidopsis thaliana to such stress conditions is well understood, little is known about the responses of its relative, the important oil crop plant Brassica napus. For the first time, we analyzed the molecular response of Brassica napus seedlings to full submergence in a natural light-dark cycle. We used two cultivars in this study, a European hybrid cultivar and an Asian flood-tolerant cultivar. Despite their genomic differences, those genotypes showed no major differences in their responses to submergence. The molecular responses to submergence included the induction of defense- and hormone-related pathways and the repression of biosynthetic processes. Furthermore, RNAseq revealed a strong carbohydrate-starvation response under submergence in daylight, which corresponded with a fast depletion of sugars. Consequently, both B. napus cultivars exhibited a strong growth repression under water, but there was no indication of a low-oxygen response. The ability of the European hybrid cultivar to form a short-lived leaf gas film neither increased underwater net photosynthesis, underwater dark respiration nor growth during submergence. Due to the high sensitivity of both cultivars, the analysis of other cultivars or related species with higher submergence tolerance is required in order to improve flood tolerance of this crop species. One major target could be the improvement of underwater photosynthesis efficiency in order to enhance submergence survival.

Combining quantitative trait locus and co-expression analysis allowed identification of new candidates for oil accumulation in rapeseed

In crops there are quantitative trait loci (QTLs) in which some of the causal quantitative trait genes (QTGs) have not been functionally characterized even in the model plant Arabidopsis. We propose an approach to delineate QTGs in rapeseed by coordinating expression of genes located within QTLs and known orthologs related to traits from Arabidopsis. Using this method in developing siliques 15 d after pollination in 71 lines of rapeseed, we established an acyl-lipid metabolism co-expression network with 21 modules composed of 270 known acyl-lipid genes and 3503 new genes. The core module harbored 76 known genes involved in fatty acid and triacylglycerol biosynthesis and 671 new genes involved in sucrose transport, carbon metabolism, amino acid metabolism, seed storage protein processes, seed maturation, and phytohormone metabolism. Moreover, the core module closely associated with the modules of photosynthesis and carbon metabolism. From the co-expression network, we selected 12 hub genes to identify their putative Arabidopsis orthologs. These putative orthologs were functionally analysed using Arabidopsis knockout and overexpression lines. Four knockout mutants exhibited lower seed oil content, while the seed oil content in 10 overexpression lines was significantly increased. Therefore, combining gene co-expression network analysis and QTL mapping, this study provides new insights into the detection of QTGs and into acyl-lipid metabolism in rapeseed.

Using single-plant-omics in the field to link maize genes to functions and phenotypes

Most of our current knowledge on plant molecular biology is based on experiments in controlled laboratory environments. However, translating this knowledge from the laboratory to the field is often not straightforward, in part because field growth conditions are very different from laboratory conditions. Here, we test a new experimental design to unravel the molecular wiring of plants and study gene-phenotype relationships directly in the field. We molecularly profiled a set of individual maize plants of the same inbred background grown in the same field and used the resulting data to predict the phenotypes of individual plants and the function of maize genes. We show that the field transcriptomes of individual plants contain as much information on maize gene function as traditional laboratory-generated transcriptomes of pooled plant samples subject to controlled perturbations. Moreover, we show that field-generated transcriptome and metabolome data can be used to quantitatively predict individual plant phenotypes. Our results show that profiling individual plants in the field is a promising experimental design that could help narrow the lab-field gap.

Insights on SNP types, detection methods and their utilization in Brassica species: Recent progress and future perspectives

The genus Brassica, family Brassicaceae (Cruciferae), comprises many important species of oil crops, vegetables and medicinal plants including B. rapa, B. oleracea, B. nigra, B. napus, B. juncea, B. carinata. Genomic researches in Brassica species is constrained by polyploidization, mainly due to its complicated genomic structure. However, rapid development of methods for detecting single nucleotide polymorphisms (SNP), such as next generation sequencing and SNP microarray, has accelerated release of reference Brassica species genomes as well as discovery of large numbers and genome-wide SNPs, thus intensifying forward genetics in this genus. In this review, we summarize biological characteristics, classification and various methods for detecting SNPs, focusing on high-throughput techniques. Moreover, we describe the pivotal roles of SNPs in genetic diversity, linkage map construction and QTL mapping, comparative genomics, linkage disequilibrium and genome-wide association studies. These insights are expected to deepen our understanding and guide further advancements in Brassica species research.

Comprehensive Transcriptomic Analysis for Developing Seeds of a Synthetic Brassica Hexaploid

Polyploidization is a universal phenomenon in plants and plays a crucial role in evolution. In this study, the transcriptomes of developing seeds of a synthetic Brassica hexaploid and its parents (B. rapa and B. carinata) were analyzed to find the gene expression changes in hexaploid seeds. There were 3166 and 3893 DEGs between the Brassica hexaploid and its parents at the full-size stage and mature stage, respectively, most of which were upregulated in hexaploid seeds compared to its parents. At the mature stage, the hexaploid seeds showed a greater difference from its parents. These DEGs had a wide range of functions, which may account for the physiological and morphological differences between the Brassica hexaploid and its parents. The KEGG pathway analysis revealed that hexaploid seeds had higher levels of expression of genes involved in metabolic pathways, RNA transport and biosynthesis of secondary metabolites, and the expression levels in the photosynthesis-related pathways were significantly higher than those in B. rapa. Transgressive expression was the main non-additive expression pattern of the Brassica hexaploid. The gene expression difference between the Brassica hexaploid and its paternal parent was more significant than that with its maternal parent, which may be due in part to the cytoplasmic and maternal effects. Moreover, transcription factor genes, such as G2-like, MYB and mTERF, were highly expressed in hexaploid seeds, possibly promoting their resistance to stress. Our results may provide valuable insights into the adaptation mechanisms of polyploid plants.

Association Mapping of Seed Quality Traits Under Varying Conditions of Nitrogen Application in Brassica juncea L. Czern & Coss

Indian mustard (Brassica juncea) is a major source of vegetable oil in the Indian subcontinent. The seed cake left after the oil extraction is used as livestock feed. We examined the genetic architecture of oil, protein, and glucosinolates by conducting a genome-wide association study (GWAS), using an association panel comprising 92 diverse genotypes. We conducted trait phenotyping over 2 years at two levels of nitrogen (N) application. Genotyping by sequencing was used to identify 66,835 loci, covering 18 chromosomes. Genetic diversity and phenotypic variations were high for the studied traits. Trait performances were stable when averaged over years and N levels. However, individual performances differed. General and mixed linear models were used to estimate the association between the SNP markers and the seed quality traits. Population structure, principal components (PCs) analysis, and discriminant analysis of principal components (DAPCs) were included as covariates to overcome the bias due to the population stratification. We identified 16, 23, and 27 loci associated with oil, protein, and glucosinolates, respectively. We also established LD patterns and haplotype structures for the candidate genes. The average block sizes were larger on A-genome chromosomes as compared to the B- genome chromosomes. Genetic associations differed over N levels. However, meta-analysis of GWAS datasets not only improved the power to recognize associations but also helped to identify common SNPs for oil and protein contents. Annotation of the genomic region around the identified SNPs led to the prediction of 21 orthologs of the functional candidate genes related to the biosynthesis of oil, protein, and glucosinolates. Notable among these are: LACS5 (A09), FAD6 (B05), ASN1 (A06), GTR2 (A06), CYP81G1 (B06), and MYB44 (B06). The identified loci will be very useful for marker-aided breeding for seed quality modifications in B. juncea.

Validation of an Associative Transcriptomics platform in the polyploid crop species Brassica juncea by dissection of the genetic architecture of agronomic and quality traits

The development of more productive crops will be key to addressing the challenges that climate change, population growth and diminishing resources pose to global food security. Advanced 'omics techniques can help to accelerate breeding by facilitating the identification of genetic markers for use in marker-assisted selection. Here, we present the validation of a new Associative Transcriptomics platform in the important oilseed crop Brassica juncea. To develop this platform, we established a pan-transcriptome reference for B. juncea, to which we mapped transcriptome data from a diverse panel of B. juncea accessions. From this panel, we identified 355 050 single nucleotide polymorphism variants and quantified the abundance of 93 963 transcripts. Subsequent association analysis of functional genotypes against a number of important agronomic and quality traits revealed a promising candidate gene for seed weight, BjA.TTL, as well as additional markers linked to seed colour and vitamin E content. The establishment of the first full-scale Associative Transcriptomics platform for B. juncea enables rapid progress to be made towards an understanding of the genetic architecture of trait variation in this important species, and provides an exemplar for other crops.

A Brassica napus Reductase Gene Dissected by Associative Transcriptomics Enhances Plant Adaption to Freezing Stress

Cold treatment (vernalization) is required for winter crops such as rapeseed (Brassica napus L.). However, excessive exposure to low temperature (LT) in winter is also a stress for the semi-winter, early-flowering rapeseed varieties widely cultivated in China. Photosynthetic efficiency is one of the key determinants, and thus a good indicator for LT tolerance in plants. So far, the genetic basis underlying photosynthetic efficiency is poorly understood in rapeseed. Here the current study used Associative Transcriptomics to identify genetic loci controlling photosynthetic gas exchange parameters in a diversity panel comprising 123 accessions. A total of 201 significant Single Nucleotide Polymorphisms (SNPs) and 147 Gene Expression Markers (GEMs) were detected, leading to the identification of 22 candidate genes. Of these, Cab026133.1, an ortholog of the Arabidopsis gene AT2G29300.2 encoding a tropinone reductase (BnTR1), was further confirmed to be closely linked to transpiration rate. Ectopic expressing BnTR1 in Arabidopsis plants significantly increased the transpiration rate and enhanced LT tolerance under freezing conditions. Also, a much higher level of alkaloids content was observed in the transgenic Arabidopsis plants, which could help protect against LT stress. Together, the current study showed that AT is an effective approach for dissecting LT tolerance trait in rapeseed and that BnTR1 is a good target gene for the genetic improvement of LT tolerance in plant.

The impact of reducing fatty acid desaturation on the composition and thermal stability of rapeseed oil

Oilseed rape (Brassica napus) is the third largest source of vegetable oil globally. In addition to food uses, there are industrial applications that exploit the ability of the species to accumulate the very-long-chain fatty acid (VLCFA) erucic acid in its seed oil, controlled by orthologues of FATTY ACID ELONGASE 1 (Bna.FAE1.A8 and Bna.FAE1.C3). The proportion of polyunsaturated fatty acids (PUFAs) in rapeseed oil is predicted to affect its thermal stability and is controlled by orthologues of FATTY ACID DESATURASE 2, particularly Bna.FAD2.C5. Our aim was to develop rapeseed lines combining high erucic and low PUFA characters and to assess the impact on thermal stability of the oil they produce. The new type of rapeseed oil (high erucic low polyunsaturate; HELP) contained a substantially greater proportion of erucic acid (54%) compared with high erucic rapeseed oil (46%). Although the total VLCFA content was greater in oil from HELP lines (64%) than from high erucic rapeseed (57%), analysis of triacylglycerol composition showed negligible incorporation of VLCFAs into the sn-2 position. Rancimat analysis showed that the thermal stability of rapeseed oil was improved greatly as a consequence of reduction of PUFA content, from 3.8 and 4.2 h in conventional low erucic and high erucic rapeseed oils, respectively, to 11.3 and 16.4 h in high oleic low PUFA (HOLP) and HELP oils, respectively. Our results demonstrate that engineering of the lipid biosynthetic pathway of rapeseed, using traditional approaches, enables the production of renewable industrial oils with novel composition and properties.

Integration of metabolome and transcriptome reveals flavonoid accumulation in the intergeneric hybrid between Brassica rapa and Raphanus sativus

Brassica rapa and Raphanus sativus are two important edible vegetables that contain numerous nutritional ingredients. However, the agronomic traits and nutritional components of the intergeneric hybrid of B. rapa and R. sativus remain poorly understood. In this study, we used a stably inherited intergeneric hybrid of B. rapa and R. sativus as a model to study its metabolome and transcriptome profiles. Morphological and cytological analysis showed the intergeneric hybrid had the expected chromosome number and normal meiosis behavior. Moreover, the metabolome analysis showed multiple important secondary metabolites, including flavonoids and glucosinolates, were significantly upregulated in the hybrid. Furthermore, transcriptome data revealed that the expression level of the important genes involved in phenylpropanoid and flavonoid pathways was significantly upregulated in the hybrid. Ultimately, our data indicate the intergeneric hybrid will be a valuable bioengineering resource and promise to become a new-type hybrid vegetable with great medicinal value in future.

Assembly and characterisation of a unique onion diversity set identifies resistance to Fusarium basal rot and improved seedling vigour

KEY MESSAGE

A unique, global onion diversity set was assembled, genotyped and phenotyped for beneficial traits. Accessions with strong basal rot resistance and increased seedling vigour were identified along with associated markers. Conserving biodiversity is critical for safeguarding future crop production. Onion (Allium cepa L.) is a globally important crop with a very large (16 Gb per 1C) genome which has not been sequenced. While onions are self-fertile, they suffer from severe inbreeding depression and as such are highly heterozygous as a result of out-crossing. Bulb formation is driven by daylength, and accessions are adapted to the local photoperiod. Onion seed is often directly sown in the field, and hence seedling establishment is a critical trait for production. Furthermore, onion yield losses regularly occur worldwide due to Fusarium basal rot caused by Fusarium oxysporum f. sp. cepae. A globally relevant onion diversity set, consisting of 10 half-sib families for each of 95 accessions, was assembled and genotyping carried out using 892 SNP markers. A moderate level of heterozygosity (30-35%) was observed, reflecting the outbreeding nature of the crop. Using inferred phylogenies, population structure and principal component analyses, most accessions grouped according to local daylength. A high level of intra-accession diversity was observed, but this was less than inter-accession diversity. Accessions with strong basal rot resistance and increased seedling vigour were identified along with associated markers, confirming the utility of the diversity set for discovering beneficial traits. The onion diversity set and associated trait data therefore provide a valuable resource for future germplasm selection and onion breeding.

Vitamin E in Plants: Biosynthesis, Transport, and Function

Vitamin E, which includes both tocopherols and tocotrienols, comprises lipid-soluble antioxidants that modulate lipid peroxidation. Recently, significant advances have been made in our understanding of vitamin E biosynthesis, transport, and function. The phytyl moiety from chlorophyll degradation is used for tocopherol biosynthesis. An α-tocopherol-binding protein (TBP) has been identified in tomato (SlTBP) serving in intraorganellar vitamin E transport in plants. Moreover, α-tocopherol not only scavenges free radicals through flip-flop movements in the lipid bilayer, but may also contribute to fine-tuning the transmission of specific signals outside chloroplasts. Vitamin E, and α-tocopherol in particular, appear to be essential for plant development and help to provide the most suitable response to a number of environmental stresses.

The vernalisation regulator FLOWERING LOCUS C is differentially expressed in biennial and annual Brassica napus

Plants in temperate areas evolved vernalisation requirement to avoid pre-winter flowering. In Brassicaceae, a period of extended cold reduces the expression of the flowering inhibitor FLOWERING LOCUS C (FLC) and paves the way for the expression of downstream flowering regulators. As with all polyploid species of the Brassicaceae, the model allotetraploid Brassica napus (rapeseed, canola) is highly duplicated and carries 9 annotated copies of Bna.FLC. To investigate whether these multiple homeologs and paralogs have retained their original function in vernalisation or undergone subfunctionalisation, we compared the expression patterns of all 9 copies between vernalisation-dependent (biennial, winter type) and vernalisation-independent (annual, spring type) accessions, using RT-qPCR with copy-specific primers and RNAseq data from a diversity set. Our results show that only 3 copies – Bna.FLC.A03b, Bna.FLC.A10 and to some extent Bna.FLC.C02 – are differentially expressed between the two growth types, showing that expression of the other 6 copies does not correlate with growth type. One of those 6 copies, Bna.FLC.C03b, was not expressed at all, indicating a pseudogene, while three further copies, Bna.FLC.C03a and Bna.FLC.C09ab, did not respond to cold treatment. Sequence variation at the COOLAIR binding site of Bna.FLC.A10 was found to explain most of the variation in gene expression. However, we also found that Bna.FLC.A10 expression is not fully predictive of growth type.

Genetic architecture of glucosinolate variation in Brassica napus

The diverse biological activities of glucosinolate (GSL) hydrolysis products play significant biological and economical roles in the defense system and nutritional qualities of Brassica napus (oilseed rape). Yet, genomic-based study of the B. napus GSL regulatory mechanisms are scarce due to the complexity of working with polyploid species. To address these challenges, we used transcriptome-based GWAS approach, Associative Transcriptomics (AT), across a diversity panel of 288 B. napus genotypes to uncover the underlying genetic basis controlling quantitative variation of GSLs in B. napus vegetative tissues. Single nucleotide polymorphism (SNP) markers and gene expression markers (GEMs) associations identify orthologues of MYB28/HAG1 (AT5G61420), specifically the copies on chromosome A9 and C2, to be the key regulators of aliphatic GSL variation in leaves. We show that the positive correlation observed between aliphatic GSLs in seed and leaf is due to the amount synthesized, as controlled by Bna.HAG1.A9 and Bna.HAG1.C2, rather than by variation in the transport processes. In addition, AT and differential expression analysis in root tissues implicate an orthologue of MYB29/HAG3 (AT5G07690), Bna.HAG3.A3, as controlling root aromatic GSL variation. Based on the root expression data we also propose Bna.MAM3.A3 to have a role in controlling phenylalanine chain elongation for aromatic GSL biosynthesis. This work uncovers a regulator of homophenylalanine-derived aromatic GSLs and implicates the shared biosynthetic pathways between aliphatic and aromatic GSLs.

Data in support of genetic architecture of glucosinolate variations in Brassica napus

The transcriptome-based GWAS approach, Associative Transcriptomics (AT), which was employed to uncover the genetic basis controlling quantitative variation of glucosinolates in Brassica napus vegetative tissues is described. This article includes the phenotypic data of leaf and root glucosinolate (GSL) profiles across a diversity panel of 288 B. napus genotypes, as well as information on population structure and levels of GSLs grouped by crop types. Moreover, data on genetic associations of single nucleotide polymorphism (SNP) markers and gene expression markers (GEMs) for the major GSL types are presented in detail, while Manhattan plots and QQ plots for the associations of individual GSLs are also included. Root genetic association are supported by differential expression analysis generated from root RNA-seq. For further interpretation and details, please see the related research article entitled 'Genetic architecture of glucosinolate variation in Brassica napus' (Kittipol et al., 2019).

Analysing the genetic architecture of clubroot resistance variation in Brassica napus by associative transcriptomics

Clubroot is a destructive soil-borne pathogen of Brassicaceae that causes significant recurrent reductions in yield of cruciferous crops. Although there is some resistance in oilseed rape (a crop type of the species Brassica napus), the genetic basis of that resistance is poorly understood. In this study, we used an associative transcriptomics approach to elucidate the genetic basis of resistance to clubroot pathotype ECD 17/31/31 across a genetic diversity panel of 245 accessions of B. napus. A single nucleotide polymorphism (SNP) association analysis was performed with 256,397 SNPs distributed across the genome of B. napus and combined with transcript abundance data of 53,889 coding DNA sequence (CDS) gene models. The SNP association analysis identified two major loci (on chromosomes A2 and A3) controlling resistance and seven minor loci. Within these were a total of 86 SNP markers. Altogether, 392 genes were found in these regions. Another 21 genes were implicated as potentially involved in resistance using gene expression marker (GEM) analysis. After GO enrichment analysis and InterPro functional analysis of the identified genes, 82 candidate genes were identified as having roles in clubroot resistance. These results provide useful information for marker-assisted breeding which could lead to acceleration of pyramiding of multiple clubroot resistance genes in new varieties.

Transcriptome and organellar sequencing highlights the complex origin and diversification of allotetraploid Brassica napus

Brassica napus, an allotetraploid crop, is hypothesized to be a hybrid from unknown varieties of Brassica rapa and Brassica oleracea. Despite the economic importance of B. napus, much is unresolved regarding its phylogenomic relationships, genetic structure, and diversification. Here we conduct a comprehensive study among diverse accessions from 183 B. napus (including rapeseed, rutabaga, and Siberian kale), 112 B. rapa, and 62 B. oleracea and its wild relatives. Using RNA-seq of B. napus accessions, we define the genetic diversity and sub-genome variance of six genetic clusters. Nuclear and organellar phylogenies for B. napus and its progenitors reveal varying patterns of inheritance and post-formation introgression. We discern regions with signatures of selective sweeps and detect 8,187 differentially expressed genes with implications for B. napus diversification. This study highlights the complex origin and evolution of B. napus providing insights that can further facilitate B. napus breeding and germplasm preservation.

Whole-Genome Resequencing of a Worldwide Collection of Rapeseed Accessions Reveals the Genetic Basis of Ecotype Divergence

Rapeseed (Brassica napus), an important oilseed crop, has adapted to diverse climate zones and latitudes by forming three main ecotype groups, namely winter, semi-winter, and spring types. However, genetic variations underlying the divergence of these ecotypes are largely unknown. Here, we report the global pattern of genetic polymorphisms in rapeseed determined by resequencing a worldwide collection of 991 germplasm accessions. A total of 5.56 and 5.53 million single-nucleotide polymorphisms (SNPs) as well as 1.86 and 1.92 million InDels were identified by mapping reads to the reference genomes of "Darmor-bzh" and "Tapidor," respectively. We generated a map of allelic drift paths that shows splits and mixtures of the main populations, and revealed an asymmetric evolution of the two subgenomes of B. napus by calculating the genetic diversity and linkage disequilibrium parameters. Selective-sweep analysis revealed genetic changes in genes orthologous to those regulating various aspects of plant development and response to stresses. A genome-wide association study identified SNPs in the promoter regions of FLOWERING LOCUS T and FLOWERING LOCUS C orthologs that corresponded to the different rapeseed ecotype groups. Our study provides important insights into the genomic footprints of rapeseed evolution and flowering-time divergence among three ecotype groups, and will facilitate screening of molecular markers for accelerating rapeseed breeding.

Species-Wide Variation in Shoot Nitrate Concentration, and Genetic Loci Controlling Nitrate, Phosphorus and Potassium Accumulation in Brassica napus L

Large nitrogen, phosphorus and potassium fertilizer inputs are used in many crop systems. Identifying genetic loci controlling nutrient accumulation may be useful in crop breeding strategies to increase fertilizer use efficiency and reduce financial and environmental costs. Here, variation in leaf nitrate concentration across a diversity population of 383 genotypes of Brassica napus was characterized. Genetic loci controlling variation in leaf nitrate, phosphorus and potassium concentration were then identified through Associative Transcriptomics using single nucleotide polymorphism (SNP) markers and gene expression markers (GEMs). Leaf nitrate concentration varied over 8-fold across the diversity population. A total of 455 SNP markers were associated with leaf nitrate concentration after false-discovery-rate (FDR) correction. In linkage disequilibrium of highly associated markers are a number of known nitrate transporters and sensors, including a gene thought to mediate expression of the major nitrate transporter NRT1.1. Several genes influencing root and root-hair development co-localize with chromosomal regions associated with leaf P concentration. Orthologs of three ABC-transporters involved in suberin synthesis in roots also co-localize with association peaks for both leaf nitrate and phosphorus. Allelic variation at nearby, highly associated SNPs confers large variation in leaf nitrate and phosphorus concentration. A total of five GEMs associated with leaf K concentration after FDR correction including a GEM that corresponds to an auxin-response family protein. Candidate loci, genes and favorable alleles identified here may prove useful in marker-assisted selection strategies to improve fertilizer use efficiency in B. napus.

Dissecting the complex regulation of lodging resistance in Brassica napus

Lodging continues to be a major cause of yield loss in important crop species such as Brassica napus. Understanding the genetic regulation of lodging resistance is therefore of key interest to breeders worldwide. Current strategies aimed at minimising lodging risk involve the incorporation of dwarfing genes or the application of plant growth regulators. However, despite these efforts, lodging continues to be a persistent problem and it is therefore of high interest that novel, complimentary strategies for lodging control are implemented. One approach would be to focus on understanding the genetic properties underlying stem mechanical strength. With this in mind, we screened a training genetic diversity panel of B. napus accession for variation in stem mechanical strength and related traits. Using Associative Transcriptomics, we identified molecular markers for a suite of valuable traits. Using an independent test genetic diversity panel, we show that the methods employed are robust for identification of predictive markers. Furthermore, based on conserved synteny with Arabidopsis thaliana, we are able to provide a biological context to the marker associations detected and provide evidence for a role in pectin methylesterification in contributing to stem mechanical strength in Brassicaceae.

Identification of Candidate Genes for Calcium and Magnesium Accumulation in Brassica napus L. by Association Genetics

Calcium (Ca) and magnesium (Mg) are essential plant nutrients and vital for human and animal nutrition. Biofortification of crops has previously been suggested to alleviate widespread human Ca and Mg deficiencies. In this study, new candidate genes influencing the leaf accumulation of Ca and Mg were identified in young Brassica napus plants using associative transcriptomics of ionomics datasets. A total of 247 and 166 SNP markers were associated with leaf Ca and Mg concentration, respectively, after false discovery rate correction and removal of SNPs with low second allele frequency. Gene expression markers at similar positions were also associated with leaf Ca and Mg concentration, including loci on chromosomes A10 and C2, within which lie previously identified transporter genes ACA8 and MGT7. Further candidate genes were selected from seven loci and the mineral composition of whole Arabidopsis thaliana shoots were characterized from lines mutated in orthologous genes. Four and two mutant lines had reduced shoot Ca and Mg concentration, respectively, compared to wild type plants. Three of these mutations were found to have tissue specific effects; notably reduced silique Ca in all three such mutant lines. This knowledge could be applied in targeted breeding, with the possibility of increasing Ca and Mg in plant tissue for improving human and livestock nutrition.