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  • 1
    Online-Ressource
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    Effect of ambient temperature fluctuation on the timing of the transition to the generative stage in cauliflower
    Elsevier BV ; 2018
    In:  Environmental and Experimental Botany Vol. 155 ( 2018-11), p. 742-750
    Details
    In: Environmental and Experimental Botany, Elsevier BV, Vol. 155 ( 2018-11), p. 742-750
    Materialart: Online-Ressource
    ISSN: 0098-8472
    URL: Article
    DOI: 10.1016/j.envexpbot.2018.06.013
    RVK:
    WA 15000
    Sprache: Englisch
    Verlag: Elsevier BV
    Publikationsdatum: 2018
    ZDB Id: 1497561-0
    SSG: 12
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  • 2
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    Genome-wide analysis of coordinated transcript abundance during seed development in different Brassica rapa morphotypes
    Springer Science and Business Media LLC ; 2013
    In:  BMC Genomics Vol. 14, No. 1 ( 2013-12)
    Details
    In: BMC Genomics, Springer Science and Business Media LLC, Vol. 14, No. 1 ( 2013-12)
    Kurzfassung: Brassica seeds are important as basic units of plant growth and sources of vegetable oil. Seed development is regulated by many dynamic metabolic processes controlled by complex networks of spatially and temporally expressed genes. We conducted a global microarray gene co-expression analysis by measuring transcript abundance of developing seeds from two diverse B. rapa morphotypes: a pak choi (leafy-type) and a yellow sarson (oil-type), and two of their doubled haploid (DH) progenies, (1) to study the timing of metabolic processes in developing seeds, (2) to explore the major transcriptional differences in developing seeds of the two morphotypes, and (3) to identify the optimum stage for a genetical genomics study in B. rapa seed. Results Seed developmental stages were similar in developing seeds of pak choi and yellow sarson of B. rapa ; however, the colour of embryo and seed coat differed among these two morphotypes. In this study, most transcriptional changes occurred between 25 and 35 DAP, which shows that the timing of seed developmental processes in B. rapa is at later developmental stages than in the related species B. napus . Using a Weighted Gene Co-expression Network Analysis (WGCNA), we identified 47 “gene modules”, of which 27 showed a significant association with temporal and/or genotypic variation. An additional hierarchical cluster analysis identified broad spectra of gene expression patterns during seed development. The predominant variation in gene expression was according to developmental stages rather than morphotype differences. Since lipids are the major storage compounds of Brassica seeds, we investigated in more detail the regulation of lipid metabolism. Four co-regulated gene clusters were identified with 17 putative cis -regulatory elements predicted in their 1000 bp upstream region, either specific or common to different lipid metabolic pathways. Conclusions This is the first study of genome-wide profiling of transcript abundance during seed development in B. rapa . The identification of key physiological events, major expression patterns, and putative cis -regulatory elements provides useful information to construct gene regulatory networks in B. rapa developing seeds and provides a starting point for a genetical genomics study of seed quality traits.
    Materialart: Online-Ressource
    ISSN: 1471-2164
    URL: Article
    DOI: 10.1186/1471-2164-14-840
    Sprache: Englisch
    Verlag: Springer Science and Business Media LLC
    Publikationsdatum: 2013
    ZDB Id: 2041499-7
    SSG: 12
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  • 3
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    Interploidy Introgression Shaped Adaptation during the Origin and Domestication History of Brassica napus
    Oxford University Press (OUP) ; 2023
    In:  Molecular Biology and Evolution Vol. 40, No. 9 ( 2023-09-01)
    Details
    In: Molecular Biology and Evolution, Oxford University Press (OUP), Vol. 40, No. 9 ( 2023-09-01)
    Kurzfassung: Polyploidy is recurrent across the tree of life and known as an evolutionary driving force in plant diversification and crop domestication. How polyploid plants adapt to various habitats has been a fundamental question that remained largely unanswered. Brassica napus is a major crop cultivated worldwide, resulting from allopolyploidy between unknown accessions of diploid B. rapa and B. oleracea. Here, we used whole-genome resequencing data of accessions representing the majority of morphotypes and ecotypes from the species B. rapa, B. oleracea, and B. napus to investigate the role of polyploidy during domestication. To do so, we first reconstructed the phylogenetic history of B. napus, which supported the hypothesis that the emergence of B. napus derived from the hybridization of European turnip of B. rapa and wild B. oleracea. These analyses also showed that morphotypes of swede and Siberian kale (used as vegetable and fodder) were domesticated before rapeseed (oil crop). We next observed that frequent interploidy introgressions from sympatric diploids were prominent throughout the domestication history of B. napus. Introgressed genomic regions were shown to increase the overall genetic diversity and tend to be localized in regions of high recombination. We detected numerous candidate adaptive introgressed regions and found evidence that some of the genes in these regions contributed to phenotypic diversification and adaptation of different morphotypes. Overall, our results shed light on the origin and domestication of B. napus and demonstrate interploidy introgression as an important mechanism that fuels rapid diversification in polyploid species.
    Materialart: Online-Ressource
    ISSN: 0737-4038 , 1537-1719
    URL: Article
    DOI: 10.1093/molbev/msad199
    Sprache: Englisch
    Verlag: Oxford University Press (OUP)
    Publikationsdatum: 2023
    ZDB Id: 2024221-9
    SSG: 12
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  • 4
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    Mapping quantitative trait loci for tissue culture response in VCS3M-DH population of Brassica rapa
    Springer Science and Business Media LLC ; 2013
    In:  Plant Cell Reports Vol. 32, No. 8 ( 2013-8), p. 1251-1261
    Details
    In: Plant Cell Reports, Springer Science and Business Media LLC, Vol. 32, No. 8 ( 2013-8), p. 1251-1261
    Materialart: Online-Ressource
    ISSN: 0721-7714 , 1432-203X
    URL: Article
    DOI: 10.1007/s00299-013-1433-2
    Sprache: Englisch
    Verlag: Springer Science and Business Media LLC
    Publikationsdatum: 2013
    ZDB Id: 1462082-0
    SSG: 12
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  • 5
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    Genetic relationships within Brassica rapa as inferred from AFLP fingerprints
    Springer Science and Business Media LLC ; 2005
    In:  Theoretical and Applied Genetics Vol. 110, No. 7 ( 2005-5), p. 1301-1314
    Details
    In: Theoretical and Applied Genetics, Springer Science and Business Media LLC, Vol. 110, No. 7 ( 2005-5), p. 1301-1314
    Materialart: Online-Ressource
    ISSN: 0040-5752 , 1432-2242
    URL: Article
    DOI: 10.1007/s00122-005-1967-y
    RVK:
    WA 15000
    Sprache: Englisch
    Verlag: Springer Science and Business Media LLC
    Publikationsdatum: 2005
    ZDB Id: 1478966-8
    SSG: 12
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 6
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    Evidence for two domestication lineages supporting a middle-eastern origin for Brassica oleracea crops from diversified kale populations
    Oxford University Press (OUP) ; 2022
    In:  Horticulture Research Vol. 9 ( 2022-01-05)
    Details
    In: Horticulture Research, Oxford University Press (OUP), Vol. 9 ( 2022-01-05)
    Kurzfassung: Brassica oleracea displays enormous phenotypic variation, including vegetables like cabbage, broccoli, cauliflower, kohlrabi, kales etc. Its domestication has not been clarified, despite several genetic studies and investigations of ancient literature. We used 14 152 high-quality SNP markers for population genetic studies and species-tree estimation (treating morphotypes as “species”) using SVD-quartets coalescent-modelling of a collection of 912 globally distributed accessions representing ten morphotypes of B. oleracea, wild B. oleracea accessions and nine related C9 Brassica species. Our genealogical tree provided evidence for two domestication lineages, the “leafy head” lineage (LHL) and the “arrested inflorescence” lineage (AIL). It also showed that kales are polyphyletic with regards to B. oleracea morphotypes, which fits ancient literature describing highly diverse kale types at around 400 BC. The SVD-quartets species tree topology showed that different kale clades are sister to either the LHL or the AIL. Cabbages from the middle-east formed the first-branching cabbage-clade, supporting the hypothesis that cabbage domestication started in the middle-east, which is confirmed by archeological evidence and historic writings. We hypothesize that cabbages and cauliflowers stem from kales introduced from Western Europe to the middle-east, possibly transported with the tin-trade routes in the Bronze age, to be re-introduced later into Europe. Cauliflower is the least diverse morphotype showing strong genetic differentiation with other morphotypes except broccoli, suggesting a strong genetic bottleneck. Genetic diversity reduced from landraces to modern hybrids for almost all morphotypes. This comprehensive Brassica C-group germplasm collection provides valuable genetic resources and a sound basis for B. oleracea breeding.
    Materialart: Online-Ressource
    ISSN: 2052-7276
    URL: Article
    DOI: 10.1093/hr/uhac033
    Sprache: Englisch
    Verlag: Oxford University Press (OUP)
    Publikationsdatum: 2022
    ZDB Id: 2781828-7
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  • 7
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    Genome-wide transcriptome analysis reveals molecular pathways involved in leafy head formation of Chinese cabbage (Brassica rapa)
    Oxford University Press (OUP) ; 2019
    In:  Horticulture Research Vol. 6, No. 1 ( 2019-12)
    Details
    In: Horticulture Research, Oxford University Press (OUP), Vol. 6, No. 1 ( 2019-12)
    Kurzfassung: Chinese cabbage plants go through seedling and rosette stages before forming their leafy head. Chinese cabbage plants resemble pak-choi plants at their seedling stage, but in their rosette stage the leaves of Chinese cabbage differentiate, as they increase in size with shorter petioles. In order to understand the molecular pathways that play a role in leafy head formation, transcript abundance of young emerging leaves was profiled during development of two Chinese cabbage genotypes and a single pak-choi genotype. The two Chinese cabbages differed in many aspects, among others earliness, leaf size and shape, leaf numbers, and leafy head shape. Genome-wide transcriptome analysis clearly separated the seedling stages of all three genotypes together with the later stages from pak-choi, from the later developmental stages of both Chinese cabbages (rosette, folding, and heading). Weighted correlation network analysis and hierarchical clustering using Euclidean distances resulted in gene clusters with transcript abundance patterns distinguishing the two Chinese cabbages from pak-choi. Three clusters included genes with transcript abundance affected by both genotype and developmental stage, whereas two clusters showed only genotype effects. This included a genotype by developmental stage cluster highly enriched with the MapMan category photosynthesis, with high expression during rosette and folding in Chinese cabbages and low expression in the heading inner leaves that are not exposed to light. The other clusters contained many genes in the MapMan categories Cell, showing again differences between pak-choi and both Chinese cabbages. We discuss how this relates to the differences in leaf blade growth between Chinese cabbage and pak-choi, especially at the rosette stage. Overall, comparison of the transcriptome between leaves of two very different Chinese cabbages with pak-choi during plant development allowed the identification of specific gene categories associated with leafy head formation.
    Materialart: Online-Ressource
    ISSN: 2662-6810 , 2052-7276
    URL: Article
    DOI: 10.1038/s41438-019-0212-9
    Sprache: Englisch
    Verlag: Oxford University Press (OUP)
    Publikationsdatum: 2019
    ZDB Id: 2781828-7
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  • 8
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    Online-Ressource
    What makes turnips: anatomy, physiology and transcriptome during early stages of its hypocotyl-tuber development
    Oxford University Press (OUP) ; 2019
    In:  Horticulture Research Vol. 6, No. 1 ( 2019-12)
    Details
    In: Horticulture Research, Oxford University Press (OUP), Vol. 6, No. 1 ( 2019-12)
    Materialart: Online-Ressource
    ISSN: 2052-7276
    URL: Article
    DOI: 10.1038/s41438-019-0119-5
    Sprache: Englisch
    Verlag: Oxford University Press (OUP)
    Publikationsdatum: 2019
    ZDB Id: 2781828-7
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  • 9
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    Online-Ressource
    Validation of reference genes for real-time quantitative PCR normalisation in non-heading Chinese cabbage
    CSIRO Publishing ; 2012
    In:  Functional Plant Biology Vol. 39, No. 4 ( 2012), p. 342-
    Details
    In: Functional Plant Biology, CSIRO Publishing, Vol. 39, No. 4 ( 2012), p. 342-
    Kurzfassung: Non-heading Chinese cabbage is an important vegetable crop that includes pak choi, caixin and several Japanese vegetables like mizuna, mibuna and komatsuna. Gene expression studies are frequently used to unravel the genetics of complex traits and in such studies the proper selection of reference genes for normalisation is crucial. We assessed the expression of 13 candidate reference genes including ACTIN, ACTIN-1, ACTIN-2, GAPDH, Tub_α, CyP, EF1-α, 18S rRNA, UBQ, UBC30, PPR, PP2A and MDH. Their expression stabilities were analysed using two programs, geNorm and NormFinder, in 20 different samples that represent four strategic groups. Results showed that no single gene was uniformly expressed in all tested samples. ACTIN and CyP are proposed as good reference genes when studying developmental stages. CyP, Tub_α and UBC30 are good reference genes when studying different tissues (from flowering to seed set). CyP and Tub_α are the most stable reference genes under biotic stress treatments using the fungi Peronospora parasitica and Alternaria brassicicola. UBC30, EF1-α and ACTIN are recommended for normalisation in abiotic stress studies, including hormone, salt, drought, cold and heath treatments. Moreover, at least five reference genes (ACTIN, CyP, UBC30, EF1-α and UBQ) are required for accurate qRT–PCR data normalisation when studying gene expression across all tested samples.
    Materialart: Online-Ressource
    ISSN: 1445-4408
    URL: Article
    DOI: 10.1071/FP11246
    Sprache: Englisch
    Verlag: CSIRO Publishing
    Publikationsdatum: 2012
    SSG: 12
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  • 10
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    Design of a Brassica rapa core collection for association mapping studiesThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.
    Canadian Science Publishing ; 2010
    In:  Genome Vol. 53, No. 11 ( 2010-11), p. 884-898
    Details
    In: Genome, Canadian Science Publishing, Vol. 53, No. 11 ( 2010-11), p. 884-898
    Kurzfassung: A Brassica rapa collection of 239 accessions, based on two core collections representing different morphotypes from different geographical origins, is presented and its use for association mapping is illustrated for flowering time. We analyzed phenotypic variation of leaf and seed pod traits, plant architecture, and flowering time using data collected from three field experiments and evaluated the genetic diversity with a set of SSR markers. The Wageningen University and Research Centre (WUR) and the Vavilov Research Institute of Plant Industry (VIR) core collections had similar representations of most morphotypes, as illustrated by the phenotypic and genetic variation within these groups. The analysis of population structure revealed five subgroups in the collection, whereas previous studies of the WUR core collection indicated four subgroups; the fifth group identified consisted mainly of oil accessions from the VIR core collection, winter oils from Pakistan, and a number of other types. A very small group of summer oils is described, that is not related to other oil accessions. A candidate gene approach was chosen for association mapping of flowering time with a BrFLC1 biallelic CAPS marker and a BrFLC2 multiallelic SSR marker. The two markers were significantly associated with flowering time, but their effects were confined to certain morphotypes and (or) alleles. Based on these results, we discuss the optimal design for an association mapping population and the need to fix the heterogeneous accessions to facilitate phenotyping and genotyping.
    Materialart: Online-Ressource
    ISSN: 0831-2796 , 1480-3321
    URL: Article
    DOI: 10.1139/G10-082
    Sprache: Englisch
    Verlag: Canadian Science Publishing
    Publikationsdatum: 2010
    ZDB Id: 2020635-5
    SSG: 12
    Standort Signatur Einschränkungen Verfügbarkeit
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