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This study evaluated the genotyping by sequencing (GBS) protocol for fingerprinting Brassica rapa, and the data derived were more reliable than the re-sequencing data of B. rapa. Of the 10 enzyme solutions used to analyze the numbers of genotypes and single-nucleotide polymorphisms (SNPs) in B. rapa, five solutions showed better results, namely, A (HaeIII, 450-500 bp), E (RsaI+HaeIII, 500-550 bp), F (RsaI+HaeIII, 500-600 bp), G(RsaI+HaeIII, 'All' fragment), and J (RsaI+EcaRV-HF ([R]), 'All' fragment). The five enzyme solutions showed less than 40% similarity in different individuals from various samples, and 90% similarity between two individuals from one sample. The E enzyme solution was the most suitable for fingerprinting B. rapa, revealing well-distributed SNPs in the whole genome. Of the 82 highly inbred lines and 18 [F.sub.1] lines of B. rapa sequenced by GBS in the E enzyme solution, known parents of 10 [F.sub.1] lines were verified, and male parents were discovered for 8 [F.sub.1] lines that had only known female parents. This study provides a valuable method for screening parents for [F.sub.1] lines in B. rapa for the efficient evaluation of GBS with varied library construction strategies. Key wards: Brassica rapa, genotyping by sequencing, single-nucleotide polymorphisms, fingerprinting, [F.sub.1] lines, applied breeding. Cette etude a cherche a evaluer le potentiel du protocole de genotypage par sequencage (GBS) pour dresser des empreintes genetiques chez le Brassica rapa. Les donnees obtenues se sont averees plus fiables que celles derivees du re-sequencage de B. rapa. Des dix protocoles enzymatiques employes pour analyser le nombre de genotypes et de polymorphismes mono-nucleotidiques (SNP), cinq ont montre de meilleurs resultats: les protocoles A(HaeIII, 450-500 pb), E (RsaI + HaeIII, 500-550 pb), F (RsaI + HaeIII, 500-600 pb), G (RsaI + HaeIII, [much less than] Tous [much greater than]les fragments) et J (RsaI + EcoRV-HF*, [much less than] Tous [much greater than]les fragments). Les cinq protocoles enzymatiques offraient moins de 40 % de simi-larite entre individus differents et plus de 90 % de similarite entre deux individus de la meme accession. Le proto-cole E s'est avere le meilleur pour produire des empreintes genetiques chez le B. rapa, produisant des SNP bien distribues sur l'ensemble du genome. Les auteurs ont analyse 82 lignees hautement fixees et 18 [F.sub.1] du B. rapa au moyen du GBS avec le protocole E. Ils ont pu confirmer les parents connus pour 10 [F.sub.1] et les parents males ont ete identifies pour 8 [F.sub.1] dont seul le parent femelle etait connu. Cette etude fournit, au terme d'une evaluation effi-ciente de plusieurs protocoles de preparation de librairies GBS, une methode utile pour identifier les parents de [F.sub.1] chez le B. rapa dans le contexte de l'amelioration genetique. [Traduit par la Redaction] Mots-cles: Brassica rapa, genotypage par sequen^age, polymorphismes mono-nucleotidiques, [F.sub.1], selection appliquee., Introduction In the past, reference genome sequences of many crops have provided a mass of information for understanding acrop's genomic variation and genome evolution. Owing to the genome-wide abundance of [...]

Abstract: R2R3-MYB transcription factors (TFs) have been shown to play important roles in plants, including in development and in various stress conditions. Phylogenetic analysis showed the presence of 249 R2R3-MYB [...]

Genetic diversity was studied in a collection of 61 accessions of Brassica rapa, which were mostly oil-type turnip rapes but also included two oil-type subsp. dichotoma and five subsp. trilocularis accessions, as well as three leaf-type subspecies (subsp. japonica, pekinensis, and chinensis) and five turnip cultivars (subsp. rapa). Two-hundred and nine SNP markers, which had been discovered by amplicon resequencing, were used to genotype 893 plants from the B. rapa collection using Illumina BeadXpress. There was great variation in the diversity indices between accessions. With STRUCTURE analysis, the plant collection could be divided into three groups that seemed to correspond to morphotype and flowering habit but not to geography. According to AMOVA analysis, 65% of the variation was due to variation within accessions, 25% among accessions, and 10% among groups. A smaller subset of the plant collection, 12 accessions, was also studied with 5727 GBS-SNPs. Diversity indices obtained with GBS-SNPs correlated well with those obtained with Illumina BeadXpress SNPs. The developed SNP markers have already been used and will be used in future plant breeding programs as well as in mapping and diversity studies. Keywords: Brassica rapa, SNP, genetic diversity, GBS, STRUCTURE. La diversite genetique a ete etudiee au sein d'une collection de 61 accessions du Brassica rapa, laquelle comprenait principalement des navettes oleagineuses, deux accessions oleagineuses de la subsp. dichotoma et cinq accessions appartenant a la subsp. trilocularis, ainsi que trois sous-especes a feuilles (subsp. japonica pekinensis et chinensis) et cinq cultivars de navet (subsp. rapa). Deux cents neuf marqueurs SNP, decouverts par sequen^age d'amplicons, ont ete employes pour genotyper 893 plantes de cette collection de B. rapa a l'aide d'un appareil Illumina BeadXpress. Une grande variation a ete observee pour les indices de diversite entre accessions. Au moyen d'une analyse STRUCTURE, la collection a ete divisee en trois groupes correspondant au type morphologique et au mode de floraison, mais non ti l'origine geographique. Suite a une analyse AMOVA, il a ete observe que 65% de la variation existait au sein des accessions, 25% entre les accessions et 10% entre les groupes. Un plus petit sous-ensemble de la collection compose de 12 accessions a egalement ete caracterise au moyen de 5727 marqueurs GBS-SNP. Les indices de diversite obtenus a l'aide des GBS-SNP concordaient bien avec ceux obtenus au moyen des SNP Illumina BeadXpress. Les marqueurs SNP ainsi mis au point ont deja ete employes et le seront encore dans de futurs travaux en selection de meme que dans le cadre d'etudes de cartographie et de diversite genetiques. [Traduit par la Redaction] Mots-cles : Brassica rapa, SNP, diversite genetique, GBS, STRUCTURE., Introduction Brassica rapa L. (2n = 20, AA, haploid genome size 485 Mb) is an obligate out-crossing crucifer grown worldwide. The species is morphologically very variable and contains a large [...]

Association mapping has been used increasingly in natural populations with rich genetic diversity to detect DNA-based markers that are associated with important agronomic traits. Brassica napus is an important oil crop with limited genetic diversity. 'New-type' B. napus that is introgressed with subgenomic components from related species has been developed to broaden the genetic basis of 'traditional' B. napus. In this study, new-type B. napus lines and a collection of traditional B. napus varieties from different countries were used as two different populations to evaluate seed oil content and to determine the efficacy of association mapping by comparison with previous study of linkage mapping. Relatively rich genetic diversity, but a higher level of linkage disequilibrium was observed in the new-type B. napus as compared with the traditional B. napus. Similarly, a larger variation in oil content and a greater number of associated markers were detected in the population of new-type B. napus. Meanwhile, more than half of the genetic loci, to which the associated markers corresponded, were located within the quantitative trait loci intervals identified previously in linkage mapping experiments, which demonstrated the power of association mapping in B. napus. Key words: Brassica napus, genetic diversity, seed oil content, quantitative trait loci (QTL), association mapping. Resume : L'analyse d'association est de plus en plus utiliseee au sein de populations naturelles riches en diversite genetique pour deetecter des marqueurs genetiques qui sont associes a des caracteres agronomiques. Le Brassica napus est une culture oleagineuse importante qui presente une diversite genetique restreinte. Des B. napus de << type nouveau >>, obtenus par introgression de composantes sub-genomiques provenant d'especes apparentees, ont ete developpees pour elargir l'assise genetique des B. napus << traditionnels >>. Dans ce travail, des lignees du B. napus de << type nouveau >> ainsi qu'une collection de cultivars du B. napus de type << traditionnel >> provenant de divers pays ont ete employees pour former deux populations au sein desquelles la teneur en huile des graines a ete mesuree et l'efficacite des analyses d'association a ete comparee aux etudes anterieures fondees sur des cartes de liaison genetique. Une diversite; genetique relativement elevee et un plus grand desequilibre de liaison ont ete observes au sein des B. napus de type << nouveau >> par rapport au type << traditionnel >>. Pareillement, une plus grande variation pour la teneur en huile et un plus grand nombre de marqueurs associes ont ete detectes chez les B. napus de type << nouveau >>. Plus de la moitie des locus genetiques auxquels correspondaient les marqueurs associees etaient situees au sein d'intervalles QTL identifies lors d'experiences anterieures, ce qui demontre la puissance des analyses d'association chez le B. napus. Mots-cles : Brassica napus, diversite; genetique, teneur en huile dans les graines, locus de caractere quantitatif (QTL), analyse d'association., [Traduit par la Redaction] Introduction Mapping of quantitative trait loci (QTL) has proven to be a reliable way to dissect complex traits that are controlled by multiple genes (Salvi and [...]

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 [...]

Quantitative traits, such as size and weight in animals and seed yield in plants, are distributed normally, even within a population of genetically identical individuals. For example, in plants, various factors, such as local soil quality, microclimate, and sowing depth, affect growth differences among individual plants of isogenic populations. Besides these physical factors, also epigenetic components contribute to differences in growth and yield. The network that regulates crop yield is still not well understood. Although this network is expected to have epigenetic elements, it is completely unclear whether it would be possible to shape the epigenome to increase crop yield. Here we show that energy use efficiency is an important factor in determining seed yield in canola (Brassica napus) and that it can be selected artificially through an epigenetic feature. From an isogenic canola population of which the individual plants and their self-fertilized progenies were recursively selected for respiration intensity, populations with distinct physiological and agronomical characteristics could be generated. These populations were found to be genetically identical, but epigenetically different. Furthermore, both the DNA methylation patterns as well as the agronomical and physiological characteristics of the selected lines were heritable. Hybrids derived from parent lines selected for high energy use efficiencies had a 5% yield increase on top of heterosis. Our results demonstrate that artificial selection allows the increase of the yield potential by selecting populations with particular epigenomic states. Brassica napus/epigenome doi/10.1073/pnas.0908755106

Yield is the most important and complex trait for the genetic improvement of crops. Although much research into the genetic basis of yield and yield-associated traits has been reported, in each such experiment the genetic architecture and determinants of yield have remained ambiguous. One of the most intractable problems is the interaction between genes and the environment. We identified 85 quantitative trait loci (QTL) for seed yield along with 785 QTL for eight yield-associated traits, from 10 natural environments and two related populations of rapeseed. A trait-by-trait meta-analysis revealed 401 consensus QTL, of which 82.5% were clustered and integrated into 111 pleiotropic unique QTL by metaanalysis, 47 of which were relevant for seed yield. The complexity of the genetic architecture of yield was demonstrated, illustrating the pleiotropy, synthesis, variability, and plasticity of yield QTL. The idea of estimating indicator QTL for yield QTL and identifying potential candidate genes for yield provides an advance in methodology for complex traits. DOI: 10.1534/genetics.109.101642

The two genomes (A and C) of the allopolyploid Brassica napus have been clearly distinguished using genomic in situ hybridization (GISH) despite the fact that the two extant diploids, B. rapa (A, n = 10) and B. oleracea (C, n = 9), representing the progenitor genomes, are closely related. Using DNA from B. oleracea as the probe, with B. rapa DNA and the intergenic spacer of the B. oleracea 45S rDNA as the block, hybridization occurred on 9 of the 19 chromosome pairs along the majority of their length. The pattern of hybridization confirms that the two genomes have remained distinct in B. napus line DH 12075, with no significant genome homogenization and no large-scale translocations between the genomes. Fluorescence in situ hybridization (FISH)--with 45S rDNA and a BAC that hybridizes to the pericentromeric heterochromatin of several chromosomes--followed by GISH allowed identification of six chromosomes and also three chromosome groups. Our procedure was used on the B. napus cultivar Westar, which has an interstitial reciprocal translocation. Two translocated segments were detected in pollen mother cells at the pachytene stage of meiosis. Using B. oleracea chromosome-specific BACs as FISH probes followed by GISH, the chromosomes involved were confirmed to be A7 and C6.

Abstract: The spectrum of resistance to isolates of Leptosphaeria maculans and the map location of a new blackleg resistance gene found in the canola cultivar Brassica napus 'Surpass 400' are [...]

Abstract: Oilseed rape (Brassica napus) in Australia and China have similar origins, with introductions from Europe, Canada, and Japan in the mid 20th century, and there has been some interchange [...]

Abstract: The yellow seed coat trait in No. 2127-17, a resynthesized purely yellow Brassica napus line, is controlled by a single partially dominant gene, Y. A double-haploid population derived from [...]

Abstract: A linear mitochondrial plasmid is present in some varieties of rapeseed. To elucidate its origin and transmission the author investigated types of mitochondrial genome and the presence of plasmid [...]

Abstract: In an earlier study, the progenies of intergeneric hybrids Brassica napus (2n = 38) x Orychophragmus violaceus (2n = 24) were investigated in successive generations ([F.sub.1]-[F.sub.4]) for the cytological [...]

Chromosomal rearrangements can be triggered by recombination between distinct but related regions. Brassica napus (AACC; 2n = 38) is a recent allopolyploid species whose progenitor genomes are widely replicated. In this article, we analyze the extent to which chromosomal rearrangements originate from homeologous recombination during meiosis of haploid B. napus (n = 19) by genotyping progenies of haploid X euploid B. napus with molecular markers. Our study focuses on three pairs of homeologous regions selected for their differing levels of divergence (N1/N11, N3/N13, and N9/N18). We show that a high number of chromosomal rearrangements occur during meiosis of B. napus haploid and are transmitted by first division restitution (FDR)-like unreduced gametes to their progeny; half of the progeny of Darmor-bzh haploids display duplications and/or losses in the chromosomal regions being studied. We demonstrate that half of these rearrangements are due to recombination between regions of primary homeology, which represents a 10- to 100-fold increase compared to the frequency of homeologous recombination measured in euploid lines. Some of the other rearrangements certainly result from recombination between paralogous regions because we observed an average of one to two autosyndetic A-A and/or C-C bivalents at metaphase I of the B. napus haploid. These results are discussed in the context of genome evolution of B. napus.

Abstract: Quantitative trait loci (QTLs) contributing to yellow seed colour and acid detergent fibre (ADF) were localized and compared in 3 mapping populations developed from 2 crosses (designated 'YE1' and [...]

In allopolyploid species, fair meiosis could be challenged by homeologous chromosome pairing and is usually achieved by the action of homeologous pairing suppressor genes. Oilseed rape (Brassica napus) haploids (AC, n = 19) represent an attractive model for studying the mechanisms used by allopolyploids to ensure the diploid-like meiotic pairing pattern. In oilseed rape haploids, homeologous chromosome pairing at metaphase I was found to be genetically based and controlled by a major gene, PrBn, segregating in a background of polygenic variation. In this study, we have mapped PrBn within a 10-cM interval on the C genome linkage group DY15 and shown that PrBn displays incomplete penetrance or variable expressivity. We have identified three to six minor QTL/BTL that have slight additive effects on the amount of pairing at metaphase I but do not interact with PrBn. We have also detected a number of other loci that interact epistatically, notably with PrBn. Our results support the idea that, as in other polyploid species, metaphase I homeologous pairing in oilseed rape haploids is controlled by an integrated system of several genes, which function in a complex manner.

Polyploidization is a widespread process that results in the merger of two or more genomes in a common nucleus. To investigate modifications of gene expression occurring during allopolyploid formation, the Brassica napus allotetraploid model was chosen. Large-scale analyses of the proteome were conducted on two organs, the stem and root, so that > 1600 polypeptides were screened. Comparative proteomics of synthetic B. napus and its homozygous diploid progenitors B. rapa and B. oleracea showed that very few proteins disappeared or appeared in the amphiploids (< 1%), but a strikingly high number (25-38%) of polypeptides displayed quantitative nonadditive pattern. Nonstochastic gene expression repatterning was found since 99% of the detected variations were reproducible in four independently created amphiploids. More than 60% of proteins displayed a nonadditive pattern closer to the paternal parent B. rapa. Interspecific hybridization triggered the majority of the deviations (89%), whereas very few variations (~3%) were associated with genome doubling and more significant alterations arose from selfing (~9%). Some nonadditive proteins behaved similarly in both organs, while others exhibited contrasted behavior, showing rapid organ-specific regulation. B. napus formation was therefore correlated with immediate and directed nonadditive changes in gene expression, suggesting that the early steps of allopolyploidization repatterning are controlled by nonstochastic mechanisms.

The LmR1 locus, which controls seedling resistance to the blackleg fungus Leptosphaeria maculans in the Brassica napus cultivar Shiralee, was positioned on linkage group N7. Fine genetic mapping in a population of 2500 backcross lines identified three molecular markers that cosegregated with LmR1. Additional linkage mapping in a second population colocalized a seedling resistance gene, ChnR1, from the cultivar Cresor to the same genetic interval on N7 as LmR1. Both genes were located in a region that showed extensive inter- and intragenomic duplications as well as intrachromosomal tandem duplications. The tandem duplications seem to have occurred in the Brassica lineage before the divergence of B. rapa and B. oleracea but after the separation of Brassica and Arabidopsis from a common ancestor. Microsynteny was found between the region on N7 carrying the resistance gene and the end of Arabidopsis chromosome 1, interrupted by a single inversion close to the resistance locus. The collinear region in Arabidopsis was assayed for the presence of possible candidate genes for blackleg resistance. These data provided novel insights into the genomic structure and evolution of plant resistance loci and an evaluation of the candidate gene approach using comparative mapping with a model organism.

Genetic maps of Brassica napus were constructed from four segregating populations of doubled haploid lines. Each mapping population had the same male parent and used the same set of RFLP probes, facilitating the construction of a consensus map. Chromosomal rearrangements were identified in each population by molecular marker analysis and were classified as de novo homeologous nonreciprocal transpositions (HNRTs), preexisting HNRTs, and homeologous reciprocal transpositions (HRTs). Ninety-nine de novo HNRTs were identified by the presence of a few lines having duplication of a chromosomal region and loss of the corresponding homeologous region. These de novo HNRTs were more prevalent in one population that had a resynthesized B. napus as a parent. Preexisting HNRTs were identified by fragment duplication or fragment loss in many DH lines due to the segregation of HNRTs preexisting in one of the parents. Nine preexisting HNRTs were identified in the three populations involving natural B. napus parents, which likely originated from previous homeologous exchanges. The male parent had a previously described HRT between N7 and N16, which segregated in each population. These data suggest that chromosomal rearrangements caused by homeologous recombination are widespread in B. napus. The effects of these rearrangements on allelic and phenotypic diversity are discussed.