Brassica Species Research Articles

Genome-wide identification and expression analysis of the anthocyanin-related genes during seed coat development in six Brassica species

Yellow seed is one favorite trait for the breeding of Brassica oilseed crops, but the performance of seed coat color is very complicated due to the involvement of various pigments. The change of seed coat color of Brassica crops is related to the specific synthesis and accumulation of anthocyanin, and the expression level of structural genes in anthocyanin synthesis pathway is specifically regulated by transcription factors. Despite some previous reports on the regulations of seed coat color from linkage marker development, gene fine-mapping and multi-omics association analysis, the trait of Brassica crops is affected by the evolutionary events such as genome triploidization, the regulatory mechanism is still largely unknown. In this study, we identified genes related to anthocyanin synthesis in six Brassica crops in U-triangle at the genome-wide level and performed collinearity analysis. A total of 1119 anthocyanin-related genes were identified, the collinear relationship of anthocyanin-related genes on subgenomic chromosomes was the best in B. napus (AACC) and the worst in B. carinata (BBCC). The comparisons of gene expressions for anthocyanin metabolic pathways in seed coats during seed development revealed differences in its metabolism among these species. Interestingly, the R2R3-MYB transcription factors MYB5 and TT2 were differentially expressed at all eight stages of seed coat development, indicating that they might be the key genes that caused the variation of the seed coat color. The expression curve and trend analyses of the seed coat development period showed that the main reason for the unexpressed copies of MYB5 and TT2 was likely gene silencing caused by gene structural variation. These results were valuable for the genetic improvement of Brassica seed coat color, and also provided new insights into gene multicopy evolution in Brassica polyploids.

Indexing Resilience to Heat and Drought Stress in the Wild Relatives of Rapeseed-Mustard.

Wild species are weedy relatives and progenitors of cultivated crops, usually maintained in their centres of origin. They are rich sources of diversity as they possess many agriculturally important traits. In this study, we analysed 25 wild species and 5 U triangle species of Brassica for their potential tolerance against heat and drought stress during germination and in order to examine the early seedling stage. We identified the germplasms based on the mean membership function value (MFV), which was calculated from the tolerance index of shoot length, root length, and biochemical analysis. The study revealed that B. napus (GSC-6) could withstand high temperatures and drought. Other genotypes that were tolerant to the impact of heat stress were B. tournefortii (RBT 2002), D. gomez-campoi, B. tournefortii (Rawa), L. sativum, and B. carinata (PC-6). C. sativa resisted drought but did not perform well when subjected to high temperatures. Tolerance to drought was observed in B. fruticulosa (Spain), B. tournefortii (RBT 2003), C. bursa-pastoris (late), D. muralis, C. abyssinica (EC694145), C. abyssinica (EC400058) and B. juncea (Pusa Jaikisan). This investigation contributes to germplasm characterization and the identification of the potential source of abiotic stress tolerance in the Brassica breeding programme. These identified genotypes can be potential sources for transferring the gene(s)/genomic regions that determine tolerance to the elite cultivars.

Resynthesized Rapeseed (Brassica napus): Breeding and Genomics

Resynthesized rapeseed lines (2n = 4x = 38, AACC), which recreate the historical hybridization between progenitor species Brassica rapa (2n = 2x = 20, AA) and B. oleracea (2n = 2x = 18, CC) to produce Brassica napus (2n = 4x = 38, AACC), have been an important research subject for many years. These lines not only comprise useful genetic resources in rapeseed breeding for the introgression of genetic diversity and many agronomically important traits, but have also increased our understanding of how meiosis evolved in polyploid plants. In this review, we discuss and summarize how these lines have been produced via interspecific crosses over several decades and the resulting fertility and agronomically useful traits in this germplasm, as well as meiotic instability issues in these hybrids, and the putative role of meiosis genes, gene expression and other gene regulatory networks in the stabilization of meiosis. Finally, we discuss the direct use of resynthesized and semi-resynthesized Brassica napus for hybrid breeding as well as for the study of other unexplored agronomic traits of interest for the improvement of elite rapeseed cultivars.

Comparative phylogenomic insights of KCS and ELO gene families in Brassica species indicate their role in seed development and stress responsiveness

Very long-chain fatty acids (VLCFAs) possess more than twenty carbon atoms and are the major components of seed storage oil, wax, and lipids. FAE (Fatty Acid Elongation) like genes take part in the biosynthesis of VLCFAs, growth regulation, and stress responses, and are further comprised of KCS (Ketoacyl-CoA synthase) and ELO (Elongation Defective Elongase) sub-gene families. The comparative genome-wide analysis and mode of evolution of KCS and ELO gene families have not been investigated in tetraploid Brassica carinata and its diploid progenitors. In this study, 53 KCS genes were identified in B. carinata compared to 32 and 33 KCS genes in B. nigra and B. oleracea respectively, which suggests that polyploidization might has impacted the fatty acid elongation process during Brassica evolution. Polyploidization has also increased the number of ELO genes in B. carinata (17) over its progenitors B. nigra (7) and B. oleracea (6). Based on comparative phylogenetics, KCS, and ELO proteins can be classified into eight and four major groups, respectively. The approximate date of divergence for duplicated KCS and ELO genes varied from 0.03 to 3.20 million years ago (MYA). Gene structure analysis indicated that the maximum number of genes were intron-less and remained conserved during evolution. The neutral type of selection seemed to be predominant in both KCS and ELO genes evolution. String-based protein-protein interaction analysis suggested that bZIP53, a transcription factor might be involved in the activation of transcription of ELO/KCS genes. The presence of biotic and abiotic stress-related cis-regulatory elements in the promoter region suggests that both KCS and ELO genes might also play their role in stress tolerance. The expression analysis of both gene family members reflect their preferential seed-specific expression, especially during the mature embryo development stage. Furthermore, some KCS and ELO genes were found to be specifically expressed under heat stress, phosphorus starvation, and Xanthomonas campestris infection. The current study provides a basis to understand the evolution of both KCS and ELO genes in fatty acid elongation and their role in stress tolerance.

The Effect of Water Stress on the Glucosinolate Content and Profile: A Comparative Study on Roots and Leaves of Brassica oleracea L. Crops

Drought is one of the major challenges of global crop production, and its severity is increasing because of climate change. This abiotic stress is an important target for Brassica species, which are generally grown in arid and semi-arid climates. This study was conducted to investigate the effects of water deficit on a set of accessions belonging to the Brassica core collection of the EU H2020 BRESOV project, represented by Brassica oleracea L. crops and Brassica oleracea complex species (n = 9). In particular, the variation in the amount and profile of the glucosinolates (GLSs) compounds was analyzed on the root and the leaf tissues. The plant morphometric traits and GLSs amount and profile were detected for the plants grown in cold greenhouse in Catania (Sicily) during the autumn–winter season for ten weeks. The results showed a wide qualitative and quantitative variation among the Brassica accessions. The GLSs profile varied qualitatively and quantitively among both genotypes and portions of the plants (hypogenous-root and epigeous-leaf). Plants grown under drought stress, for the last two weeks of the growing cycle under consideration, showed a higher amount of GLS in their leaves (190.1 ± 8.9 µmol. g−1 d.w.) compared to their roots (17.3 ± 1.9 µmol. g−1 d.w.). Under water stress conditions, the highest increase in the glucosinolate amount was detected in broccoli (the accession BR1) with 85.4% and in cauliflower (the accession CV1) with 72.8% in the roots and leaves, respectively. Positive correlations were found between the major leaf and root GLSs identified. The selection of chemotypes allows for an important time reduction during the breeding programs after crossing accessions with the specific profiles of glucosinolates.

Whole-Genome Comparison Reveals Structural Variations behind Heading Leaf Trait in Brassica oleracea

Brassica oleracea displays remarkable morphological variations. It intrigued researchers to study the underlying cause of the enormous diversification of this organism. However, genomic variations in complex heading traits are less known in B. oleracea. Herein, we performed a comparative population genomics analysis to explore structural variations (SVs) responsible for heading trait formation in B. oleracea. Synteny analysis showed that chromosomes C1 and C2 of B. oleracea (CC) shared strong collinearity with A01 and A02 of B. rapa (AA), respectively. Two historical events, whole genome triplication (WGT) of Brassica species and differentiation time between AA and CC genomes, were observed clearly by phylogenetic and Ks analysis. By comparing heading and non-heading populations of B. oleracea genomes, we found extensive SVs during the diversification of the B. oleracea genome. We identified 1205 SVs that have an impact on 545 genes and might be associated with the heading trait of cabbage. Overlapping the genes affected by SVs and the differentially expressed genes identified by RNA-seq analysis, we identified six vital candidate genes that may be related to heading trait formation in cabbage. Further, qRT-PCR experiments also verified that six genes were differentially expressed between heading leaves and non-heading leaves, respectively. Collectively, we used available genomes to conduct a comparison population genome analysis and identify candidate genes for the heading trait of cabbage, which provides insight into the underlying reason for heading trait formation in B. oleracea.

Genetic Components of Self-Incompatibility in Brassica Vegetables

Brassica vegetables are very important to human beings. Self-incompatibility (SI) is a common phenomenon in Brassica. Breeding by SI lines is an important way to utilize heterosis of Brassica vegetables. It is believed that the SI inheritance in Brassica species is controlled by three linkage genes on the S-locus, including SRK (S-locus receptor kinase), SCR (S-locus cystine-rich protein)/SP11 (S-locus protein 11), and SLG (S-locus glycoprotein). SRK is the female determinant and SCR/SP11 is the pollen S gene. The expression of SLG is necessary for SRK, and it enhances the SRK-mediated SI reaction. In addition to these three S-locus genes, some other functional molecules also have significant regulatory effects on SI, such as ARC1 (arm repeat containing 1), MLPK (M-locus protein kinase), Exo70A1 (exocyst compounds), THLl/THL2 (thioredoxin H-like), MOD (aquaporin), SLR (S-locus-related glycoprotein), BPCI (pollen calcium-binding protein I), etc. SI is also associated with the dominant/recessive relationship between S alleles. Here, the genetic elements and molecular mechanisms of SI, mainly in Brassica vegetables, are reviewed.

Genome wide identification and expression profiling of Early responsive to dehydration 6 (ERD6)-like gene family in chickpea (Cicer arietinum L.)

Early responsive to dehydration 6 (ERD6)-like is one of the least studied subfamily in plants. Initial evidences based on couple of genes suggest that members of this family are tonoplastic and export glucose to cytosol from tonoplast. However, no information is available on ERD6-like genes in agricultural crops except limited information on Brassica species. In this study, we identified 8, 12, 6 and 7 ERD6-like genes, respectively in Cicer arietinum, Arachis hypogea, Oryza sativa and Glycine max. These and A. thaliana genes were divided into five subgroups based on phylogenetic analysis of proteins. C. arietinum genes were characterized in detail and new nomenclature to these genes was proposed to overcome ambiguities in names of genes. Intron/exon numbers did not vary much among the genes, however, gene/mRNA/coding region/ untranslated regions and proteins showed considerable length variations. Though isoforms were reported for two genes, isoforms of only CaERD6-like 6.3 could be confirmed experimentally. While motifs and transmembrane domains varied among the ERD6-like proteins, all belonged to glucose transport subfamily suggesting those to be glucose transporters. Transcription of genes varied among four chickpea organs with higher expression in some organs and lower in others. Under cold-stress, three genes over-expressed in leaves and roots whereas four genes down-regulated in leaves and two in roots. This is the first report on genome wide identification of ERD6-like genes in four crops of agricultural importance and detailed characterization and expression analysis in chickpea organs under normal growth conditions and cold-stress.

Identification and determination of Phenolic compounds in Brassica L. (Brassicaceae) species grow in Iraq

The present search content identification Phenolic compounds and determination type of compound, concentration and its percentage by high performance liquid chromatochraphy (HPLC) and compared chemical compounds for species that identified seven phenolic compounds for nine species Brassica L.(Brassicaceae) collected from mid and north of Iraq, five species wild B.campestris, B.deflexa, B. juncea, B. nigra and B. tournifortii and four species cultivated B.olearaceae var. botrytis, B.olearaceae var. capitata, B.olearaceae var. gongyloides and B.rapa and determined concentration and percentage by HPLC. These compound are Cinnamic acid, ferulic acid, isorhamentin, kaempferol, P-coumaric acid, quercetein and Sinapic acid and variance compounds between species in study .
 The study showed that the phenolic compound (Cinnamic acid) was the high concentrate 121.86 mg/ ml in the species B.tournifortii and the percentage were 11.89% and low concentrate 10.32 mg ml in the species B.olearaceae var. gongyloides and the percentage were 3.71 % while the p-coumaric acid was the highest concentrate 186.41 mg/ ml in the species B.juncea and the proportions were 15.35% and the lowest concentrate 6.25 mg/ ml and the percentage were 2.24 % in B.olearaceae var. gongyloides, which shows the existence of variety in the phenolic content between the species under study.

Genome-wide analysis of Catalase gene family reveal insights into abiotic stress response mechanism in Brassica juncea and B. rapa.

Environmental stresses affect the yield and productivity of Brassica crops. Catalases are important antioxidant enzymes involved in reducing excess hydrogen peroxide produced by environmental stresses. In the present study, nine and seven CAT family members in two oilseed Brassica species (B. juncea and B. rapa) were identified with complete characterization based on gene and protein structure. Phylogenetic classification categorized CAT proteins into three classes and differentiated the monocot and dicot-specific CAT proteins. Further, the gene and protein characterizations revealed a high degree of conservation across the CAT family members. Differences were observed in the CAT-HEME binding affinity in CAT1, CAT2, and CAT3 isozymes, which could suggest their differential enzyme activities in different conditions. Furthermore, protein-protein interaction with other antioxidant proteins suggested their coordinated role in ROS scavenging mechanisms. Notably, the differential gene expression of BjuCATs and BraCATs and CAT enzyme activities suggested their crucial roles in major abiotic stresses faced by Brassica species. Promoter analysis in BjuCATs and BraCATs suggested the presence of abiotic-stress responsive cis-regulatory elements. Gene regulatory network analysis suggested miRNA and TF mediated stress response in BjuCATs and BraCATs. CAT family screening and characterization in Brassica sp. has established a basic ground for further functional validation in abiotic and heavy-metal stresses which can help in developing stress tolerant crops.

A near-complete genome assembly of Brassica rapa provides new insights into the evolution of centromeres.

Brassica rapa comprises many important cultivated vegetables and oil crops. However, Chiifu v3.0, the current B. rapa reference genome, still contains hundredsof gaps. Here, we presented a near-complete genome assembly of B. rapa Chiifu v4.0, which was 424.59 Mb with only two gaps, using Oxford Nanopore Technology (ONT) ultralong-read sequencing and Hi-C technologies. The new assembly contains 12 contigs, with a contig N50 of 38.26 Mb. Eight of the ten chromosomes were entirely reconstructed in a single contig from telomere to telomere. We found that the centromeres were mainly invaded by ALE and CRM long terminal repeats (LTRs). Moreover, there is a high divergence of centromere length and sequence among B. rapa genomes. We further found that centromeres are enriched for Copia invaded at 0.14 MYA on average, while pericentromeres are enriched for Gypsy LTRs invaded at 0.51 MYA on average. These results indicated the different invasion mechanisms of LTRs between the two structures. In addition, a novel repetitive sequence PCR630 was identified in the pericentromeres of B. rapa. Overall, the near-complete genome assembly, B. rapa Chiifu v4.0, offers valuable tools for genomic and genetic studies of Brassica species and provides new insights into the evolution of centromeres.

Can relative sensitivity of cover crop species to chloroacetamide and pyrazole herbicides be exploited to design interseeding mixtures?

AbstractDrill-interseeding cover crops into standing corn (V3 to V5 growth stage) provides opportunities for increasing functional diversity in cropping systems by facilitating use of cover crop mixtures that include grass, legume, and brassica species. Designing herbicide-based weed control programs that negotiate tradeoffs between crop protection and environmental goals when interseeding mixtures remains a major challenge. The objective of this study was to use greenhouse-based dose-response assays to describe the relative sensitivity of 12 cover crop species that differ in traits, including taxonomic group and seed mass, to chloroacetamide (acetochlor, dimethenamid, S-metolachlor; Group 15 herbicides as categorized by the Weed Science Society of America) and pyrazole (pyroxasulfone; Group 15) herbicides. Nonlinear models were fit, and effective doses were estimated (ED50) to compare relative sensitivities of cover crop species to each herbicide. Brassica species (winter canola, Dwarf Essex rape, daikon radish) were less sensitive than small-seeded legumes (medium red clover, crimson clover) and grasses (annual ryegrass) in response to each chloroacetamide, but similar in response to pyroxasulfone. Austrian winter pea, a large-seeded legume, was less sensitive to each herbicide compared to other legumes (crimson clover, medium red clover, hairy vetch). Cereal rye and triticale were less sensitive to dimethenamid, S-metolachlor, and pyroxasulfone compared to annual ryegrass, but similar sensitivities were observed for acetochlor. These results suggest that relative differences in sensitivity to chloroacetamide and pyrazole herbicides could be exploited when designing cover crop mixtures for interseeding. It is imperative, however, to use these findings in conjunction with field-based observations of cover crop injury potential in interseeded systems.

Hypersensitive-like response in Brassica plants is specifically induced by molecules from egg-associated secretions of cabbage white butterflies

Plants perceive and respond to herbivore insect eggs. Upon egg deposition on leaves, a strong hypersensitive response (HR)-like cell death can be activated leading to egg desiccation and/or dropping. In Brassica spp., including many crops, the HR-like mechanism against eggs of cabbage white butterflies (Pieris spp.) is poorly understood. Using two Brassica species, the crop B. rapa and its wild relative B. nigra, we studied the cellular and molecular plant response to Pieris brassicae eggs and characterized potential insect egg-associated molecular patterns (EAMPs) inducing HR-like cell death. We found that eggs of P. brassicae induced typical hallmarks of early immune responses, such as callose deposition, production of reactive oxygen species and cell death in B. nigra and B. rapa leaf tissue, also in plants that did not express HR-like cell death. However, elevated levels of ethylene production and upregulation of salicylic acid-responsive genes were only detected in a B. nigra accession expressing HR-like cell death. Eggs and egg wash from P. brassicae contains compounds that induced such responses, but the eggs of the generalist moth Mamestra brassicae did not. Furthermore, wash made from hatched Pieris eggs, egg glue, and accessory reproductive glands (ARG) that produce this glue, induced HR-like cell death, whereas washes from unfertilized eggs dissected from the ovaries or removal of the glue from eggs resulted in no or a reduced response. This suggests that there is one or multiple egg associated molecular pattern (EAMP) located in the egg glue a that teresponse in B. nigra is specific to Pieris species. Lastly, our results indicate that the EAMP is neither lipidic nor proteinaceous. Our study expands the knowledge on the mechanism of Brassica-Pieris-egg interaction and is a step closer toward identification of EAMPs in Pieris egg glue and corresponding receptor(s) in Brassica.

Genome-Wide Association Study of Glucosinolate Metabolites (mGWAS) in Brassica napus L.

Glucosinolates (GSLs) are secondary plant metabolites that are enriched in rapeseed and related Brassica species, and they play important roles in defense due to their anti-nutritive and toxic properties. Here, we conducted a genome-wide association study of six glucosinolate metabolites (mGWAS) in rapeseed, including three aliphatic glucosinolates (m145 gluconapin, m150 glucobrassicanapin and m151 progoitrin), one aromatic glucosinolate (m157 gluconasturtiin) and two indole glucosinolates (m165 indolylmethyl glucosinolate and m172 4-hydroxyglucobrassicin), respectively. We identified 113 candidate intervals significantly associated with these six glucosinolate metabolites. In the genomic regions linked to the mGWAS peaks, 187 candidate genes involved in glucosinolate biosynthesis (e.g., BnaMAM1, BnaGGP1, BnaSUR1 and BnaMYB51) and novel genes (e.g., BnaMYB44, BnaERF025, BnaE2FC, BnaNAC102 and BnaDREB1D) were predicted based on the mGWAS, combined with analysis of differentially expressed genes. Our results provide insight into the genetic basis of glucosinolate biosynthesis in rapeseed and should facilitate marker-based breeding for improved seed quality in Brassica species.

Novel resistances provide new avenues to manage Alternaria leaf spot (Alternaria brassicae) in canola (Brassica napus), mustard (B. juncea) and other Brassicaceae crops.

Alternaria leaf spot (Alternaria brassicae) can be a devastating disease in canola (Brassica napus) and mustard (B. juncea) but there are no highly effective host resistances available. Screening of 150 diverse Brassicaceae varieties under glasshouse conditions highlighted important novel resistances, in particular, Camelina sativa 4076 and Diplotaxis erucoides Wasabi Rocket with complete resistance across disease assessment parameters [leaf incidence (%LDI), severity (%LAD), consequent defoliation (%LCI)]. Next most resistant were C. sativa CSA (%LDI 0.6; %LAD 0.4), 4144 (%LDI 1.2; %LAD 0.5), 405 (%LDI 1.7; %LAD 0.7), C. sativa 3274 (%LDI 2.5; %LAD 0.8), Carrichtera annua CAN3 (%LDI 7.7; %LAD 4.0) and Sisymbrium irio London Rocket (%LDI 2.1; %LAD 0.8), all with %LCI values of 0. Other genotypes showing high level resistance included S. erysimoides SER 4 (%LDI 11.8; %LAD 5.6; %LCI 0), D. cardaminoides wild rocket (%LDI 15.5; %LAD 7.2; %LCI 0), and showing moderate resistance were Brassica carinata ML-EM-1 (Rungwe), B. insularis Moris, B. napus ZY006, B. oxyrrhina BOX1, B. oleracea var. capitata Sugarloaf, B. tournefortii CN01-104-2 and Sinapis alba Concerta with %LDI 21.6-29.8, %LAD 12.8-21.0 and %LCI 0-5.7. In particular, B. napus ZY006 for canola and B. oleracea var. capitata cv. Sugarloaf can now be directly utilized, i.e., without crossing impairment, for Brassica species and vegetable breeding programs, respectively. While all B. juncea genotypes were susceptible, there were some less susceptible varieties from India in comparison with genotypes from Australia or China. The most susceptible test genotype was Rapistrum sativus (%LDI 89.4; %LAD 83.9; %LCI 71.0), highlighting the value of the resistances identified. These findings not only highlight a range of novel resistances against A. brassicae for canola/mustard and other diverse Brassicaceae breeding programs to develop resistant commercial varieties, but also emphasize highly susceptible varieties to avoid in both breeding programs and commercial situations conducive to Alternaria leaf spot.

Decoding allelic diversity, transcript variants and transcriptional complexity of CENH3 gene in Brassica oleracea var. botrytis.

Histone proteins play a critical role in the primary organization of nucleosomes, which is the fundamental unit of chromatin. Among the fivetypes of the histones, histone H3 has multiple variants, and the number differs among thespecies. Amongst histone H3 variants, centromeric histone H3 (CENH3) is crucial for centromere identification and proper chromosomal segregation during cell division. In the present study, we have identified 17 putative histone H3 genes of Brassica oleracea. Furthermore, we have done a detailed characterization of the CENH3 gene of B. oleracea. We showed that a single CENH3 gene exhibits allelic diversity with at least two alleles and alternative splicing pattern. Also, we have identified a CENH3 gene-specific co-dominant cleaved amplified polymorphic sequence marker SNP34(A/C) to distinguish CENH3 alleles and follow their expression in leaf and flower tissues. The gene structure analysis of theCENH3 gene revealed the conserved 5'-CAGCAG-3' sequence at the intron 3-exon 4 junction in B. oleracea, which serves as an alternative splicing site with one-codon (alanine) addition/deletion. However, this one-codon alternative splicing feature is not conserved in the CENH3 genes of wild allied Brassica species. Our finding suggests that transcriptional complexity and alternative splicing might play a key role in the transcriptional regulation and function of the CENH3 gene in B. oleracea. Altogether, data generated from the present study can serve as a primary information resource and can be used to engineer CENH3 gene towards developing haploid inducer lines in B. oleracea.

Unraveling Large and Polyploidy Genome of the Crucifer Orychophragmus violaceus in China, a Potential Oil Crop.

The genus Orychophragmus in the Brassicaceae family includes the types with 2n = 20, 22, 24, and 48. The species O. violaceus (L.) O. E. Schulz has 2n = 24 and is widely cultivated as an ornamental plant in China. This review summarizes the research progress of its genome structure and evolution in the context of cytogenetics and genome sequencing. This species has a large genome size of ~1 Gb and longer chromosomes than those of Brassica species, which is attributable to the burst of TE insertions. Even more, one tetraploidization event from about 600-800 million years ago is elucidated to occur during its genome evolution, which is consistent with the polyploidy nature of its genome revealed by the meiotic pairing patterns. Its chromosomes are still characterized by a larger size and deeper staining than those from Brassica species in their intergeneric hybrids, which is likely related to their inherent differences between genome structures and cytology. Its genome is dissected by the development of additional alien lines, and some traits are located on individual chromosomes. Due to the abundant dihydroxy fatty acids in its seed oil with superior lubricant properties and wide environmental adaptations, this plant promises to be utilized as one new oil crop in the future.

Genome-wide association and RNA-seq analyses identify loci for pod orientation in rapeseed (Brassica napus).

Spatial distribution and orientation of pods on the main raceme (stem) and branches could affect rapeseed yield. However, genomic regions underlying the pod orientation were not described in Brassica species. Here, we determined the extent of genetic variation in pod orientation, described as the angles of pedicel on raceme (APR) and angles of the pod on pedicel (APP) among 136 rapeseed accessions grown across three environments of the upper, middle and lower Yangtze River in China. The APR ranged from 59° to 109°, while the APP varied from 142° to 178°. Statistical analysis showed that phenotypic variation was due to genotypic (G) and environmental (E) effects. Using the genome-wide association analysis (GWAS) approach, two QTLs for APR (qBnAPR.A02 and qBnAPR.C02) and two for APP (qBnAPP.A05 and qBnAPP.C05), having minor to moderate allelic effects (4.30% to 19.47%) were identified. RNA-seq analysis revealed 606 differentially expressed genes (DEGs) in two rapeseed accessions representing the extreme phenotypes for pod orientation and different alleles at the QTLs of APR. Three DEGs (BnLAZY4.A02, BnSAUR32.A02, and BnSAUR32.C02) were identified as the most likely candidates responsible for variation in pod orientation (APR). This study elucidates the genomic regions and putative candidate genes underlying pod orientation in B. napus.

Genetic Diversity Analysis of Non-Heading Chinese Cabbage of Resistance to Clubroot Disease Based on SNP Molecular Markers

Clubroot disease is a kind of soil-borne disease that seriously infects Brassica species. In this study, we collected 121 varieties of non-heading Chinese cabbages. In order to better understand the genetic variation and to screen suitable clubroot disease-resistant parental material, we re-sequenced them to examine the population genetic structure, population genetic diversity, population differentiation index, and selective sweep based on SNPs. The mapping rate with the reference genome was high, and data quality analysis revealed that the sequencing quality was good. The annotated data indicated that intronic and intergenic areas held the majority of SNPs and indels. Four subgroups of 121 non-heading Chinese cabbages were identified using principal component analysis, phylogenetic tree, and genetic structure analysis. An examination of genetic diversity revealed that while selfing may happen in subgroups C and D, heterozygosity may exist in subgroups A and B. In subgroup B, self-fertilization is not possible. There was a moderate degree of genetic differentiation between subgroups B and C (Fst = 0.0744347). For genes in certain sweep regions, we also ran GO enrichment and KEGG enrichment analysis. Two disease resistance-related genes, BraA01g042910.3.5C and BraA06g019360.3.5C, were examined. These findings will serve as a theoretical foundation for developing novel, clubroot disease-resistant types of non-heading Chinese cabbages.

Variation in glucosinolates and the formation of functional degradation products in two Brassica species during spontaneous fermentation

Vegetables from the Brassica species are excellent sources of glucosinolates (GLSs), the precursors of health-promoting isothiocyanates (ITCs). Fermentation enhances the biotransformation of GLSs into potential bioactive ITCs. To explore the biotransformation of GLSs during Brassica fermentation, the changes in GLSs during the fermentation of two Brassica species (i.e., cauliflower and broccoli); the formation of corresponding breakdown products; and the shifts in physicochemical parameters, bacterial communities, and myrosinase activities involved in GLSs degradation were systematically investigated. Nine aliphatic, three indolic, and two benzenic GLSs were identified in fermented cauliflower (FC) and fermented broccoli (FB). Aliphatic glucoiberin and glucoraphanin were the major forms of GLS in FC and FB, respectively; indolic glucobrassicin was also abundant in both FC and FB. The total GLS content decreased by 85.29% and 65.48% after 3 d of fermentation in FC and FB, respectively. After 2 d of fermentation, a significant increase in bioactive GLS degradation products (P < 0.05), including sulforaphane (SFN), iberin (IBN), 3,3-diindolylmethane (DIM), and ascorbigen (ARG), was observed in FC and FB compared to in fresh cauliflower and broccoli. Moreover, variations in pH value and titratable acidity in FC and FB correlated with Brassica fermentation and were accomplished by lactic acid bacteria, including Weissella, Lactobacillus-related genera, Leuconostoc, Lactococcus, and Streptococcus. These changes may enhance the biotransformation of GSLs to ITCs. Overall, our results indicate fermentation leads to the degradation of GLSs and the accumulation of functional degradation products in FC and FB.