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Seed quality traits of oilseed rape, Brassica napus (B. napus), exhibit quantitative inheritance determined by its genetic makeup and the environment via the mediation of a complex genetic architecture of hundreds to thousands of genes. Thus, instead of single gene analysis, network-based systems genomics and genetics approaches that combine genotype, phenotype, and molecular phenotypes offer a promising alternative to uncover this complex genetic architecture. In the current study, systems genetics approaches were used to explore the genetic regulation of lignin traits in B. napus seeds. Four QTL (qLignin_A09_1, qLignin_A09_2, qLignin_A09_3, and qLignin_C08) distributed on two chromosomes were identified for lignin content. The qLignin_A09_2 and qLignin_C08 loci were homologous QTL from the A and C subgenomes, respectively. Genome-wide gene regulatory network analysis identified eightythree subnetworks (or modules); and three modules with 910 genes in total, were associated with lignin content, which was confirmed by network QTL analysis. eQTL (expression quantitative trait loci) analysis revealed four cis-eQTL genes including lignin and flavonoid pathway genes, cinnamoyl-CoA-reductase (CCR1), and TRANSPARENT TESTA genes TT4, TT6, TT8, as causal genes. The findings validated the power of systems genetics to identify causal regulatory networks and genes underlying complex traits. Moreover, this information may enable the research community to explore new breeding strategies, such as network selection or gene engineering, to rewire networks to develop climate resilience crops with better seed quality. [ABSTRACT FROM AUTHOR]

Summary: Camelina neglecta is a diploid species from the genus Camelina, which includes the versatile oilseed Camelina sativa. These species are closely related to Arabidopsis thaliana and the economically important Brassica crop species, making this genus a useful platform to dissect traits of agronomic importance while providing a tool to study the evolution of polyploids. A highly contiguous chromosome‐level genome sequence of C. neglecta with an N50 size of 29.1 Mb was generated utilizing Pacific Biosciences (PacBio, Menlo Park, CA) long‐read sequencing followed by chromosome conformation phasing. Comparison of the genome with that of C. sativa shows remarkable coincidence with subgenome 1 of the hexaploid, with only one major chromosomal rearrangement separating the two. Synonymous substitution rate analysis of the predicted 34 061 genes suggested subgenome 1 of C. sativa directly descended from C. neglecta around 1.2 mya. Higher functional divergence of genes in the hexaploid as evidenced by the greater number of unique orthogroups, and differential composition of resistant gene analogs, might suggest an immediate adaptation strategy after genome merger. The absence of genome bias in gene fractionation among the subgenomes of C. sativa in comparison with C. neglecta, and the complete lack of fractionation of meiosis‐specific genes attests to the neopolyploid status of C. sativa. The assembled genome will provide a tool to further study genome evolution processes in the Camelina genus and potentially allow for the identification and exploitation of novel variation for Camelina crop improvement. [ABSTRACT FROM AUTHOR]

Turnip mosaic virus (TuMV) is the major virus infecting crops of the genus Brassica worldwide. A dominant resistance gene, TuRBOlb, that confers immunity to the virus isolate UK 1 (a representative pathotype 1 isolate of TuMV) on Brassica rapa was identified in the Chinese cabbage cultivar Tropical Delight. The TuRBOlb locus was mapped to a 2.9-cM interval on B. rapa chromosome 6 (A6) that was flanked by RFLP markers pNlOlel and pW137e1. This mapping used a first backcross ([B.sub.1]) population segregating for the resistance gene at TuRB01b and sets of RFLP markers employed in previous mapping experiments in Brassica. Virus-plant interaction phenotypes were assayed in inbred progeny derived from [B.sub.1] individuals to allow different virus isolates to be tested. Comparative mapping confirmed that A6 of B. rapa was equivalent to chromosome 6 of Brassica napus (A6) and that the map position of TuRBOlb in B. rapa could be identical to that of TuRBOl in B. napus. Detailed evaluation of plant-virus interactions showed that TuRB01 and TuRB01b had indistinguishable specificities to a range of TuMV isolates. The possibility that TuRB01 and TuRB01b represent similar or identical alleles at the same A genome resistance locus suggests that B. napus acquired TuRB01 from the B. rapa gene pool. Key words: virus resistance, genetic mapping, Brassica napus, comparative genomics, Turnip mosaic virus. Le virus de la mosaique du navet (TuMV) est un virus majeur qui infecte les Brassica cultives partout dans le monde. Un gene de resistance dominant, TuRB01b, lequel confere l'immunite a l'isolat UK 1 (un isolat representatif du pathotype 1 du TuMV) chez le Brassica rapa, a ete identifie chez la variete Tropical Delight du chou chinois. Le locus TuTB01b a ete situe au sein d'un intervalle de 2,9 cM sur le chromosome 6 (A6) du B. rapa, un intervalle delimite par les marqueurs RFLP pN101e1 et pW137e1. Ce travail de cartographie a ete effectue au sein d'un premier retrocroisement ([B.sub.1]) en segregation pour le gene de resistance TuRB01b et en employant des marqueurs RFLP utilises precedemment dans des travaux de cartographie chez les Brassica. Les phenotypes d'interaction virus-plante ont ete mesures au sein de descendants fixes derives des individus [B.sub.1] pour permettre de tester differents isolats du virus. Une cartographie comparee a confirme que le chromosome A6 chez le B. rapa correspond au chromosome 6 chez le Brassica napus (A6) et que la position de TuRB01b chez le B. rapa est identique a celle de TuRB01 chez le B. napus. Une evaluation fine des interactions plante-virus a montre que les locus TuRB01 et TuRB01b presentaient des specificites identiques face a une gamme d'isolats du TuMV. La possibilite que TuRB01 et TuRB01b representent des alleles similaires ou identiques a un meme locus de resistance au sein du genome A suggere que le B. napus aurait acquis le locus TuRB01 du B. rapa. [Traduit par la Redaction] Mots-cles : resistance aux virus, cartographie genetique, Brassica napus, genomique comparee, virus de la mosaique du navet., Introduction Turnip mosaic virus (TuMV) is a member of the genus Potyvirus and possesses an exceptionally broad host range; it infects 156 plant genera representing many arable, vegetable, and ornamental [...]

The architecture of the Brassica napus genome is marked by its evolutionary origins. The genome of B. napus was formed from the hybridization of two closely related diploid Brassica species, both of which evolved from an hexaploid ancestor. The extensive whole genome duplication events in its near and distant past result in the allotetraploid genome of B. napus maintaining multiple copies of most genes, which predicts a highly complex and redundant transcriptome that can confound any expression analyses. A stringent assembly of 142 399 B. napus expressed sequence tags allowed the development of a well-differentiated set of reference transcripts, which were used as a foundation to assess the efficacy of available tools for identifying and distinguishing transcripts in B. napus; including microarray hybridization and 3' anchored sequence tag capture. Microarray platforms cannot distinguish transcripts derived from the two progenitors or close homologues, although observed differential expression appeared to be biased towards unique transcripts. The use of 3' capture enhanced the ability to unambiguously identify homologues within the B. napus transcriptome but was limited by tag length. The ability to comprehensively catalogue gene expression in polyploid species could be transformed by the application of cost-efficient next generation sequencing technologies that will capture millions of long sequence tags. Key words: polyploid, homologues, next generation sequencing, expressed sequence tags, single nucleotide polymorphism, Brassica. La structure du genome chez le Brassica napus est marquee par ses origines evolutives. Le genome du B. napus aete forme suite a l'hybridation de deux especes diploi'des de Brassica tres apparenteees, toutes deux deerivees d'ancetres hexaploldes. Ces importants eveenements de duplication survenus a l'eechelle du genome entier, tant dans un passe recent que plus ancien, font en sorte que le genome alloteetraplolde du B. napus a conserve de multiples copies de la plupart des genes. Cette situation permet de penser que le transcriptome de cette espece est a la fois complexe et redondant, ce qui peut entrainer de la confusion dans les analyses d'expression. Un assemblage rigoureux de 142 399 etiquettes de sequences exprimeees chez le B. napus a permis de developper un jeu de transcrits de reference bien differencies, lesquels ont permis de mesurer l'efficacite des outils disponibles pour l'identification et la discrimination entre transcrits chez le B. napus. Les outils examinesetaient l'hybridation sur puces a ADN et la capture d'etiquettes de sequences ancrees a l'extreemitee 3'. Les puces a ADN n'arrivent pas a distinguer les transcrits provenant des deux especes progenitrices ou d'homologues proches, bien que les cas d'expression diffeerentielle observes semblaient biaisees en faveur de transcrits uniques. L'emploi d'etiquettes capturees en 3' a permis d'ameeliorer la capacite a identifier sans ambigui'te les homologues au sein du transcriptome du B. napus, mais etait limite par la taille des etiquettes. Les nouvelles technologies de sequencjage a faible coflt permettant de geenerer des millions d'etiquettes plus longues pourraient revolutionner notre capacite; a cataloguer de maniere exhaustive l'expression geenique chez des especes polyploi'des. Mots-cles: polyploldie, homologues, sequencage de seconde generation, etiquettes de sequences exprimees, variation SNP, Brassica., [Traduit par la Redaction] Introduction The study of global gene expression analysis is a powerful tool for understanding complex biological phenomena, deciphering interacting pathways, and uncovering novel genes controlling traits [...]

Summary: Ensuring faithful homologous recombination in allopolyploids is essential to maintain optimal fertility of the species. Variation in the ability to control aberrant pairing between homoeologous chromosomes in Brassica napus has been identified. The current study exploited the extremes of such variation to identify genetic factors that differentiate newly resynthesised B. napus, which is inherently unstable, and established B. napus, which has adapted to largely control homoeologous recombination.A segregating B. napus mapping population was analysed utilising both cytogenetic observations and high‐throughput genotyping to quantify the levels of homoeologous recombination.Three quantitative trait loci (QTL) were identified that contributed to the control of homoeologous recombination in the important oilseed crop B. napus. One major QTL on BnaA9 contributed between 32 and 58% of the observed variation. This study is the first to assess homoeologous recombination and map associated QTLs resulting from deviations in normal pairing in allotetraploid B. napus.The identified QTL regions suggest candidate meiotic genes that could be manipulated in order to control this important trait and further allow the development of molecular markers to utilise this trait to exploit homoeologous recombination in a crop. See also the Commentary on this article by Sourdille & Jenczewski, 229: 3041–3043. [ABSTRACT FROM AUTHOR]

The heavy selection pressure due to intensive breeding of Brassica napus has created a narrow gene pool, limiting the ability to produce improved varieties through crosses between B. napus cultivars. One mechanism that has contributed to the adaptation of important agronomic traits in the allotetraploid B. napus has been chromosomal rearrangements resulting from homoeologous recombination between the constituent A and C diploid genomes. Determining the rate and distribution of such events in natural B. napus will assist efforts to understand and potentially manipulate this phenomenon. The Brassica high-density 60K SNP array, which provides genome-wide coverage for assessment of recombination events, was used to assay 254 individuals derived from 11 diverse cultivated spring type B. napus. These analyses identified reciprocal allele gain and loss between the A and C genomes and allowed visualization of de novo homoeologous recombination events across the B. napus genome. The events ranged from loss/gain of 0.09 Mb to entire chromosomes, with almost 5% aneuploidy observed across all gametes. There was a bias toward sub-telomeric exchanges leading to genome homogenization at chromosome termini. The A genome replaced the C genome in 66% of events, and also featured more dominantly in gain of whole chromosomes. These analyses indicate de novo homoeologous recombination is a continuous source of variation in established Brassica napus and the rate of observed events appears to vary with genetic background. The Brassica 60K SNP array will be a useful tool in further study and manipulation of this phenomenon. [ABSTRACT FROM AUTHOR]

Turnip mosaic virus (TuMV) is the major virus infecting crops of the genus Brassica worldwide. A dominant resistance gene, TuRB01b, that confers immunity to the virus isolate UK 1 (a representative pathotype 1 isolate of TuMV) on Brassica rapa was identified in the Chinese cabbage cultivar Tropical Delight. The TuRB01b locus was mapped to a 2.9-cM interval on B. rapa chromosome 6 (A6) that was flanked by RFLP markers pN101e1 and pW137e1. This mapping used a first backcross (B1) population segregating for the resistance gene at TuRB01b and sets of RFLP markers employed in previous mapping experiments in Brassica. Virus-plant interaction phenotypes were assayed in inbred progeny derived from B1 individuals to allow different virus isolates to be tested. Comparative mapping confirmed that A6 of B. rapa was equivalent to chromosome 6 of Brassica napus (A6) and that the map position of TuRB01b in B. rapa could be identical to that of TuRB01 in B. napus. Detailed evaluation of plant-virus interactions showed that TuRB01 and TuRB01b had indistinguishable specificities to a range of TuMV isolates. The possibility that TuRB01 and TuRB01b represent similar or identical alleles at the same A genome resistance locus suggests that B. napus acquired TuRB01 from the B. rapa gene pool. [ABSTRACT FROM AUTHOR]

The Brassica rapa line RLR22 was resistant to eight diverse turnip mosaic virus (TuMV) isolates. A B. rapa genetic map based on 213 marker loci segregating in 120 first back-cross (B(1)) individuals was established and aligned with the B. rapa genome reference map using some of the RFLP probes. B(1) individuals were self-pollinated to produce B(1)S(1) families. The existence of two loci controlling resistance to TuMV isolate CDN 1 was established from contrasting patterns of segregation for resistance and susceptibility in the B(1)S(1) families. The first gene, recessive TuMV resistance 01 (retr01), had a recessive allele for resistance, was located on the upper portion of chromosome R4 and was epistatic to the second gene. The second gene, Conditional TuMV resistance 01 (ConTR01), possessed a dominant allele for resistance and was located on the upper portion of chromosome R8. These genes also controlled resistance to TuMV isolate CZE 1 and might be sufficient to explain the broad-spectrum resistance of RLR22. The dominant resistance gene, ConTR01, was coincident with one of the three eukaryotic initiation factor 4E (eIF4E) loci of B. rapa and possibly one of the loci of eIF(iso)4E. The recessive resistance gene retr01 was apparently coincident with one of the three loci of eIF(iso)4E in the A genome of Brassica napus and therefore, by inference, in the B. rapa genome. This suggested a mode of action for the resistance that is based on denying the viral RNA access to the translation initiation complex of the plant host. The gene retr01 is the first reported example of a recessive resistance gene mapped in a Brassica species.