The progress of intersubgenomic heterosis studies in Brassica napus

The new nomenclature of Brassica has been suggested in a previous study by same authours where the symbols of Ar, Aj and An represented the A genome in the Brassica rapa, Brassica juncea and Brassica napus, Bb, Bj and Bc for the B genome of Brassica nigra (black mustard), B. juncea and Brassica carinata, Co, Cn and Cc for the C genome of Brassica oleracea, B. napus and B. carinata. Numerous efforts have focused on exploring novel B. napus (AnAnCnCn) breeding stocks by the hybridization between Brassica species. Thereafter, most interspecific hybrids in Brassicas could be considered as intersubgenomic hybrids. In this review, examples are shown from recent studies on the method for construction of new-typed B. napus with genome composition of ArArCcCc and ArArCnCn, the meiosis and embryo sac development of new-typed B. napus, the appearance of intersubgenomic (AnArCnCc and ArAnCnCn) heterosis and the mechanism for production of intersubgenomic heterosis were described

Genomic evidence for genes encoding leucine-rich repeat receptors linked to resistance against the eukaryotic extra- and intracellular Brassica napus pathogens Leptosphaeria maculans and Plasmodiophora brassicae

© 2018 Stotz et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Genes coding for nucleotide-binding leucine-rich repeat (LRR) receptors (NLRs) control resistance against intracellular (cell-penetrating) pathogens. However, evidence for a role of genes coding for proteins with LRR domains in resistance against extracellular (apoplastic) fungal pathogens is limited. Here, the distribution of genes coding for proteins with eLRR domains but lacking kinase domains was determined for the Brassica napus genome. Predictions of signal peptide and transmembrane regions divided these genes into 184 coding for receptor-like proteins (RLPs) and 121 coding for secreted proteins (SPs). Together with previously annotated NLRs, a total of 720 LRR genes were found. Leptosphaeria maculans-induced expression during a compatible interaction with cultivar Topas differed between RLP, SP and NLR gene families; NLR genes were induced relatively late, during the necrotrophic phase of pathogen colonization. Seven RLP, one SP and two NLR genes were found in Rlm1 and Rlm3/Rlm4/Rlm7/Rlm9 loci for resistance against L. maculans on chromosome A07 of B. napus. One NLR gene at the Rlm9 locus was positively selected, as was the RLP gene on chromosome A10 with LepR3 and Rlm2 alleles conferring resistance against L. maculans races with corresponding effectors AvrLm1 and AvrLm2, respectively. Known loci for resistance against L. maculans (extracellular hemi-biotrophic fungus), Sclerotinia sclerotiorum (necrotrophic fungus) and Plasmodiophora brassicae (intracellular, obligate biotrophic protist) were examined for presence of RLPs, SPs and NLRs in these regions. Whereas loci for resistance against P. brassicae were enriched for NLRs, no such signature was observed for the other pathogens. These findings demonstrate involvement of (i) NLR genes in resistance against the intracellular pathogen P. brassicae and a putative NLR gene in Rlm9-mediated resistance against the extracellular pathogen L. maculans.Peer reviewe

Increased regeneration efficiency of _Brassica napus_ L. cultivars Star, Westar and Cyclone from hypocotyle and cotyledonary explants

The comparative organogenesis of _Brassica napus_ L cultivars Cyclone, Star and Westar was studied. The cotyledonary explants gave a higher response to all the combinations of 0.5 mg/L 2,4-D and BAP (0.5, 1.0,1.5 and 2.0 mg/L} used for optimizing the conditions for callus induction. The best mean weight and mean length of callus was obtained at 0.5 mg/L 2,4-D and 1.5mg/L BAP for Star cotyledonary explants. For the complete plant regeneration the new method of exposing the explants culture to Growth regulator free medium was performed. The method was applicable to both hypocotyl and cotyledonary explants. The Shoot Induction Frequency for hypocotyl (6-34%) in the three cultivars is higher than the cotyledonary explants (3-23%). The method is speedy and almost all of the shoots and some unshooted calli (78%) form roots on the same media without prior transfer to rooting medium

Surviving a Genome Collision: Genomic Signatures of Allopolyploidization in the Recent Crop Species

Polyploidization has played a major role in crop plant evolution, leading to advantageous traits that have been selected by humans. Here, we describe restructuring patterns in the genome of Brassica napus L., a recent allopolyploid species. Widespread segmental deletions, duplications, and homeologous chromosome exchanges were identified in diverse genome sequences from 32 natural and 20 synthetic accessions, indicating that homeologous exchanges are a major driver of postpolyploidization genome diversification. Breakpoints of genomic rearrangements are rich in microsatellite sequences that are known to interact with the meiotic recombination machinery. In both synthetic and natural B. napus, a subgenome bias was observed toward exchanges replacing larger chromosome segments from the C-subgenome by their smaller, homeologous A-subgenome segments, driving postpolyploidization genome size reduction. Selection in natural B. napus favored segmental deletions involving genes associated with immunity, reproduction, and adaptation. Deletions affecting mismatch repair system genes, which are assumed to control homeologous recombination, were also found to be under selection. Structural exchanges between homeologous subgenomes appear to be a major source of novel genetic diversity in de novo allopolyploids. Documenting the consequences of genomic collision by genomic resequencing gives insights into the adaptive processes accompanying allopolyploidization

Molecular studies of Arabidopsis and Brassica with focus on resistance to Leptosphaeria maculans

Blackleg caused by Leptosphaeria maculans is a widespread fungal disease on B~assica napus (oilseed rape). In contrast, Arabidopsis thaliana and B. nigra are in general highly resistant. This study presents results from genomic interaction between the A. thaliana and B. napus genome with focus on L. maculans resistance. Identification and partial characterization of A. thaliana resistance in accessions, L. maculans susceptible mutants, and signaling pathways were also performed. Finally, a resistance gene to L. maculans from B. nigra was cloned and transferred to B. napus. Chromosome counts and RFLP analyses of A. thaliana DNA content in A. thaliana (+) B. napus back-crossed progeny were performed. The results showed that in BC,, originating from symmetric hybrids, the frequency of retained A. thaliana loci was reduced to 42%. The average chromosome number decreased from 48 in BC1 to 39 in BC2. These results can be compared with the asymmetric hybrid derived BC,, that had 16% loci present and an average chromosome number of 38. Clearly, symmetric hybrid offspring retained most DNA as complete chromosomes whereas asymmetric hybrid offspring contained mostly DNA fragments. Pathogen screening of the hybrid offspring revealed both cotyledon and adult leaf resistance to L. maculans. The adult leaf resistance was localized to chromosome 3 from A. thaliana, on two areas on each side of the centromere. A. thaliana resistance was examined in 171 accessions from 27 countries. Only four accessions displayed any susceptibility. To further explore the underlying causes of the resistance, a set of L. maculans disease susceptible mutants (lms) were isolated. Two of the mutants, lmsl and lms5 have been mapped to chromosome 2 and 1, respectively. The resistance was further analyzed with respect to defense signaling and effector molecules. The results indicated that resistance in A . thaliana against L . maculans depended on camalexin and is independent on salicylic acid, jasmonic acid or ethylene response. In contrast, lmsl produced wild type level of camalexin and higher expression levels than wild type of P R l , and PDFl.2. The results suggest the possibility of at least two independent resistance factors in A. thaliana. A gene conferring resistance to L. maculans, L m l , was cloned from B. nigra. Sequence analysis revealed a novel protein with two putative trans-membrane motifs and homology to the nin protein of Lotus japonicus and to A. thaliana sequences of unknown function. The knowledge gained in A. thaliana and from Lml will promote a further understanding of the mechanisms underlying resistance to L. macula

Origins of the amphiploid species Brassica napus L. investigated by chloroplast and nuclear molecular markers

Background: The amphiploid species Brassica napus (oilseed rape, Canola) is a globally important oil crop yielding food, biofuels and industrial compounds such as lubricants and surfactants. Identification of the likely ancestors of each of the two genomes (designated A and C) found in B. napus would facilitate incorporation of novel alleles from the wider Brassica genepool in oilseed rape crop genetic improvement programmes. Knowledge of the closest extant relatives of the genotypes involved in the initial formation of B. napus would also allow further investigation of the genetic factors required for the formation of a stable amphiploid and permit the more efficient creation of fully fertile re-synthesised B. napus. We have used a combination of chloroplast and nuclear genetic markers to investigate the closest extant relatives of the original maternal progenitors of B. napus. This was based on a comprehensive sampling of the relevant genepools, including 83 accessions of A genome B. rapa L. (both wild and cultivated types), 94 accessions of B. napus and 181 accessions of C genome wild and cultivated B. oleracea L. and related species. Results: Three chloroplast haplotypes occurred in B. napus. The most prevalent haplotype (found in 79% of accessions) was not present within the C genome accessions but was found at low frequencies in B. rapa. Chloroplast haplotypes characteristic of B. napus were found in a small number of wild and weedy B. rapa populations, and also in two accessions of cultivated B. rapa 'brocoletto'. Whilst introgression of the B. napus chloroplast type in the wild and weedy B. rapa populations has been proposed by other studies, the presence of this haplotype within the two brocoletto accessions is unexplained. Conclusions: The distribution of chloroplast haplotypes eliminates any of the C genome species as being the maternal ancestor of the majority of the B. napus accessions. The presence of multiple chloroplast haplotypes in B. napus and B. rapa accessions was not correlated with nuclear genetic diversity as determined by AFLPs, indicating that such accessions do not represent recent hybrids. Whilst some chloroplast diversity observed within B. napus can be explained by introgression from inter-specific crosses made during crop improvement programmes, there is evidence that the original hybridisation event resulting in to B. napus occurred on more than one occasion, and involved different maternal genotypes

The CACTA transposon Bot1 played a major role in Brassica genome divergence and gene proliferation

We isolated and characterized a Brassica C genome-specific CACTA element, which was designated Bot1 (Brassica oleracea transposon 1). After analysing phylogenetic relationships, copy numbers and sequence similarity of Bot1 and Bot1 analogues in B. oleracea (C genome) versus Brassica rapa (A genome), we concluded that Bot1 has encountered several rounds of amplification in the oleracea genome only, and has played a major role in the recent rapa and oleracea genome divergence. We performed in silico analyses of the genomic organization and internal structure of Bot1, and established which segment of Bot1 is C-genome specific. Our work reports a fully characterized Brassica repetitive sequence that can distinguish the Brassica A and C chromosomes in the allotetraploid Brassica napus, by fluorescent in situ hybridization. We demonstrated that Bot1 carries a host S locus-associated SLL3 gene copy. We speculate that Bot1 was involved in the proliferation of SLL3 around the Brassica genome. The present study reinforces the assumption that transposons are a major driver of genome and gene evolution in higher plants

Host pathogen interactions in relation to management of light leaf spot disease (caused by Pyrenopeziza brassicae) on Brassica species

Light leaf spot, caused by Pyrenopeziza brassicae, is currently the most damaging disease problem in oilseed rape in the UK. According to recent survey data, the severity of epidemics has increased progressively across the UK, with current yield losses of up to £160M per annum in England and more severe epidemics in Scotland. Light leaf spot is a polycyclic disease with primary inoculum consisting of air-borne ascospores produced on diseased debris from the previous cropping season. Splash-dispersed conidia produced on diseased leaves are the main component of the secondary inoculum. P. brassicae is also able to infect and cause considerable yield losses on vegetable brassicas, especially Brussels sprouts. There may be spread of light leaf spot among different brassica species. Since they have a wide host range, Pyrenopeziza brassicae populations are likely to have considerable genetic diversity and there is evidence suggesting population variations between different regions, which need further study. Available disease-management tools are not sufficient to provide adequate control of the disease. There is a need to identify new sources of resistance, which can be integrated with fungicide applications to achieve sustainable management of light leaf spot. Several major resistance genes and quantitative trait loci have been identified in previous studies, but rapid improvements in the understanding of molecular mechanisms underpinning B. napus – P. brassicae interactions can be expected through exploitation of novel genetic and genomic information for brassicas and extracellular fungal pathogens.Peer reviewe

Evaluation of the risks of contaminating low erucic acid rapeseed with high erucic rapeseed and identification of mitigation strategies

High erucic acid rapeseed (HEAR) oil is under increasing demand for various industrial applications. However, many growers are concerned that if they grow the crop, they will not be able to revert to other rapeseed varieties in the future due to the risk of erucic acid (EA) contamination of the harvested seed and inability to maintain acceptable erucic acid thresholds. This review considered published literature and, using the same criteria as that used to contain transgenic crops, aimed to identify the key risks of erucic acid contamination, broadly prioritise them and identify pragmatic mitigation options. Oilseed rape has a number of traits that increase the risk of low erucic acid rapeseed (LEAR) crops being contaminated with EA from HEAR varieties. The quantity of seed produced and the potential for seed dormancy coupled with partial autogamy (self-fertilisation) facilitate the establishment and persistence of volunteer and feral populations. The large quantities of pollen produced when the crop is in flower mean there is also a high potential for cross-pollination. Self-sown volunteer plants represent the highest potential contamination risk, followed by the presence of arable weeds (e.g., wild mustard) whose seeds are also high in EA. Other risks arise from the cross-pollination of compatible wild relatives and the mixing of seed prior to sowing. It is important that both HEAR and LEAR varieties are appropriately managed since risks and their potential for mitigation arise throughout the entire LEAR crop production process. The length of rotation, type of tillage, cultivar choice, buffer zones, effective weed management and basic machinery hygiene are all factors that can reduce the risk of erucic acid contamination of LEAR crops and maintain the required thresholds.Peer reviewedFinal Published versio