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Boideau F, Richard G, Coriton O, Huteau V, Belser C, Deniot G, Eber F, Falentin C, Ferreira de Carvalho J, Gilet M, Lodé-Taburel M, Maillet L, Morice J, Trotoux G, Aury JM, Chèvre AM, Rousseau-Gueutin M. Epigenomic and structural events preclude recombination in Brassica napus. New Phytol 2022; 234:545-559. [PMID: 35092024 DOI: 10.1111/nph.18004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/15/2022] [Indexed: 06/14/2023]
Abstract
Meiotic recombination is a major evolutionary process generating genetic diversity at each generation in sexual organisms. However, this process is highly regulated, with the majority of crossovers lying in the distal chromosomal regions that harbor low DNA methylation levels. Even in these regions, some islands without recombination remain, for which we investigated the underlying causes. Genetic maps were established in two Brassica napus hybrids to detect the presence of such large nonrecombinant islands. The role played by DNA methylation and structural variations in this local absence of recombination was determined by performing bisulfite sequencing and whole genome comparisons. Inferred structural variations were validated using either optical mapping or oligo fluorescence in situ hybridization. Hypermethylated or inverted regions between Brassica genomes were associated with the absence of recombination. Pairwise comparisons of nine B. napus genome assemblies revealed that such inversions occur frequently and may contain key agronomic genes such as resistance to biotic stresses. We conclude that such islands without recombination can have different origins, such as DNA methylation or structural variations in B. napus. It is thus essential to take into account these features in breeding programs as they may hamper the efficient combination of favorable alleles in elite varieties.
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Affiliation(s)
- Franz Boideau
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | - Gautier Richard
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | - Olivier Coriton
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | - Virginie Huteau
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | - Caroline Belser
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
| | - Gwenaelle Deniot
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | - Frédérique Eber
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | - Cyril Falentin
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | | | - Marie Gilet
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | | | - Loeiz Maillet
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | - Jérôme Morice
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | - Gwenn Trotoux
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
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Boideau F, Pelé A, Tanguy C, Trotoux G, Eber F, Maillet L, Gilet M, Lodé-Taburel M, Huteau V, Morice J, Coriton O, Falentin C, Delourme R, Rousseau-Gueutin M, Chèvre AM. A Modified Meiotic Recombination in Brassica napus Largely Improves Its Breeding Efficiency. Biology (Basel) 2021; 10:biology10080771. [PMID: 34440003 PMCID: PMC8389541 DOI: 10.3390/biology10080771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/10/2021] [Accepted: 08/10/2021] [Indexed: 01/31/2023]
Abstract
Simple Summary The selection of varieties more resilient to disease and climate change requires generating new genetic diversity for breeding. The main mechanism for reshuffling genetic information is through the recombination of chromosomes during meiosis. We showed in oilseed rape (Brassica napus, AACC, 2n = 4x = 38), which is a natural hybrid formed from a cross between turnip (B. rapa, AA, 2n = 2x = 20) and cabbage (B. oleracea, CC, 2n = 2x = 18), that there is significantly more crossovers occurring along the entire A chromosomes in allotriploid AAC (crossbetween B. napus and B. rapa) than in diploid AA or allotetraploid AACC hybrids. We demonstrated that these allotriploid AAC hybrids are highly efficient to introduce new variability within oilseed rape varieties, notably by enabling the introduction of small genomic regions carrying genes controlling agronomically interesting traits. Abstract Meiotic recombination is the main tool used by breeders to generate biodiversity, allowing genetic reshuffling at each generation. It enables the accumulation of favorable alleles while purging deleterious mutations. However, this mechanism is highly regulated with the formation of one to rarely more than three crossovers, which are not randomly distributed. In this study, we showed that it is possible to modify these controls in oilseed rape (Brassica napus, AACC, 2n = 4x = 38) and that it is linked to AAC allotriploidy and not to polyploidy per se. To that purpose, we compared the frequency and the distribution of crossovers along A chromosomes from hybrids carrying exactly the same A nucleotide sequence, but presenting three different ploidy levels: AA, AAC and AACC. Genetic maps established with 202 SNPs anchored on reference genomes revealed that the crossover rate is 3.6-fold higher in the AAC allotriploid hybrids compared to AA and AACC hybrids. Using a higher SNP density, we demonstrated that smaller and numerous introgressions of B. rapa were present in AAC hybrids compared to AACC allotetraploid hybrids, with 7.6 Mb vs. 16.9 Mb on average and 21 B. rapa regions per plant vs. nine regions, respectively. Therefore, this boost of recombination is highly efficient to reduce the size of QTL carried in cold regions of the oilseed rape genome, as exemplified here for a QTL conferring blackleg resistance.
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Affiliation(s)
- Franz Boideau
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Alexandre Pelé
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, 61-614 Poznan, Poland
| | - Coleen Tanguy
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Gwenn Trotoux
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Frédérique Eber
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Loeiz Maillet
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Marie Gilet
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Maryse Lodé-Taburel
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Virginie Huteau
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Jérôme Morice
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Olivier Coriton
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Cyril Falentin
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Régine Delourme
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Mathieu Rousseau-Gueutin
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Anne-Marie Chèvre
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
- Correspondence: ; Tel.: +33-2-23-48-51-31
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Istace B, Belser C, Falentin C, Labadie K, Boideau F, Deniot G, Maillet L, Cruaud C, Bertrand L, Chèvre AM, Wincker P, Rousseau-Gueutin M, Aury JM. Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case. Biology (Basel) 2021; 10:732. [PMID: 34439964 PMCID: PMC8389630 DOI: 10.3390/biology10080732] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 11/29/2022]
Abstract
With the rise of long-read sequencers and long-range technologies, delivering high-quality plant genome assemblies is no longer reserved to large consortia. Not only sequencing techniques, but also computer algorithms have reached a point where the reconstruction of assemblies at the chromosome scale is now feasible at the laboratory scale. Current technologies, in particular long-range technologies, are numerous, and selecting the most promising one for the genome of interest is crucial to obtain optimal results. In this study, we resequenced the genome of the yellow sarson, Brassica rapa cv. Z1, using the Oxford Nanopore PromethION sequencer and assembled the sequenced data using current assemblers. To reconstruct complete chromosomes, we used and compared three long-range scaffolding techniques, optical mapping, Omni-C, and Pore-C sequencing libraries, commercialized by Bionano Genomics, Dovetail Genomics, and Oxford Nanopore Technologies, respectively, or a combination of the three, in order to evaluate the capability of each technology.
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Affiliation(s)
- Benjamin Istace
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057 Evry, France; (B.I.); (C.B.); (L.B.); (P.W.)
| | - Caroline Belser
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057 Evry, France; (B.I.); (C.B.); (L.B.); (P.W.)
| | - Cyril Falentin
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France; (C.F.); (F.B.); (G.D.); (L.M.); (A.-M.C.); (M.R.-G.)
| | - Karine Labadie
- Genoscope, Institut François Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057 Evry, France; (K.L.); (C.C.)
| | - Franz Boideau
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France; (C.F.); (F.B.); (G.D.); (L.M.); (A.-M.C.); (M.R.-G.)
| | - Gwenaëlle Deniot
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France; (C.F.); (F.B.); (G.D.); (L.M.); (A.-M.C.); (M.R.-G.)
| | - Loeiz Maillet
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France; (C.F.); (F.B.); (G.D.); (L.M.); (A.-M.C.); (M.R.-G.)
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057 Evry, France; (K.L.); (C.C.)
| | - Laurie Bertrand
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057 Evry, France; (B.I.); (C.B.); (L.B.); (P.W.)
| | - Anne-Marie Chèvre
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France; (C.F.); (F.B.); (G.D.); (L.M.); (A.-M.C.); (M.R.-G.)
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057 Evry, France; (B.I.); (C.B.); (L.B.); (P.W.)
| | - Mathieu Rousseau-Gueutin
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France; (C.F.); (F.B.); (G.D.); (L.M.); (A.-M.C.); (M.R.-G.)
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057 Evry, France; (B.I.); (C.B.); (L.B.); (P.W.)
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Ferreira de Carvalho J, Stoeckel S, Eber F, Lodé-Taburel M, Gilet MM, Trotoux G, Morice J, Falentin C, Chèvre AM, Rousseau-Gueutin M. Untangling structural factors driving genome stabilization in nascent Brassica napus allopolyploids. New Phytol 2021; 230:2072-2084. [PMID: 33638877 DOI: 10.1111/nph.17308] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 02/22/2021] [Indexed: 05/28/2023]
Abstract
Allopolyploids have globally higher fitness than their diploid progenitors; however, by comparison, most resynthesized allopolyploids have poor fertility and highly unstable genome. Elucidating the evolutionary processes promoting genome stabilization and fertility is thus essential to comprehend allopolyploid success. Using the Brassica model, we mimicked the speciation process of a nascent allopolyploid species by resynthesizing allotetraploid Brassica napus and systematically selecting for euploid individuals over eight generations in four independent allopolyploidization events with contrasted genetic backgrounds, cytoplasmic donors, and polyploid formation type. We evaluated the evolution of meiotic behavior and fertility and identified rearrangements in S1 to S9 lineages to explore the positive consequences of euploid selection on B. napus genome stability. Recurrent selection of euploid plants for eight generations drastically reduced the percentage of aneuploid progenies as early as the fourth generation, concomitantly with a decrease in number of newly fixed homoeologous rearrangements. The consequences of homoeologous rearrangements on meiotic behavior and seed number depended strongly on the genetic background and cytoplasm donor. The combined use of both self-fertilization and recurrent euploid selection allowed identification of genomic regions associated with fertility and meiotic behavior, providing complementary evidence to explain B. napus speciation success.
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Affiliation(s)
| | - Solenn Stoeckel
- IGEPP, INRAE, Institut Agro, Université de Rennes, Le Rheu, 35650, France
| | - Frédérique Eber
- IGEPP, INRAE, Institut Agro, Université de Rennes, Le Rheu, 35650, France
| | | | | | - Gwenn Trotoux
- IGEPP, INRAE, Institut Agro, Université de Rennes, Le Rheu, 35650, France
| | - Jérôme Morice
- IGEPP, INRAE, Institut Agro, Université de Rennes, Le Rheu, 35650, France
| | - Cyril Falentin
- IGEPP, INRAE, Institut Agro, Université de Rennes, Le Rheu, 35650, France
| | - Anne-Marie Chèvre
- IGEPP, INRAE, Institut Agro, Université de Rennes, Le Rheu, 35650, France
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Rousseau-Gueutin M, Belser C, Da Silva C, Richard G, Istace B, Cruaud C, Falentin C, Boideau F, Boutte J, Delourme R, Deniot G, Engelen S, de Carvalho JF, Lemainque A, Maillet L, Morice J, Wincker P, Denoeud F, Chèvre AM, Aury JM. Long-read assembly of the Brassica napus reference genome Darmor-bzh. Gigascience 2020; 9:giaa137. [PMID: 33319912 PMCID: PMC7736779 DOI: 10.1093/gigascience/giaa137] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/18/2020] [Accepted: 11/09/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The combination of long reads and long-range information to produce genome assemblies is now accepted as a common standard. This strategy not only allows access to the gene catalogue of a given species but also reveals the architecture and organization of chromosomes, including complex regions such as telomeres and centromeres. The Brassica genus is not exempt, and many assemblies based on long reads are now available. The reference genome for Brassica napus, Darmor-bzh, which was published in 2014, was produced using short reads and its contiguity was extremely low compared with current assemblies of the Brassica genus. FINDINGS Herein, we report the new long-read assembly of Darmor-bzh genome (Brassica napus) generated by combining long-read sequencing data and optical and genetic maps. Using the PromethION device and 6 flowcells, we generated ∼16 million long reads representing 93× coverage and, more importantly, 6× with reads longer than 100 kb. This ultralong-read dataset allows us to generate one of the most contiguous and complete assemblies of a Brassica genome to date (contig N50 > 10 Mb). In addition, we exploited all the advantages of the nanopore technology to detect modified bases and sequence transcriptomic data using direct RNA to annotate the genome and focus on resistance genes. CONCLUSION Using these cutting-edge technologies, and in particular by relying on all the advantages of the nanopore technology, we provide the most contiguous Brassica napus assembly, a resource that will be valuable to the Brassica community for crop improvement and will facilitate the rapid selection of agronomically important traits.
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Affiliation(s)
| | - Caroline Belser
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Gautier Richard
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France
| | - Benjamin Istace
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Cyril Falentin
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France
| | - Franz Boideau
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France
| | - Julien Boutte
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France
| | - Regine Delourme
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France
| | - Gwenaëlle Deniot
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France
| | - Stefan Engelen
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | | | - Arnaud Lemainque
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Loeiz Maillet
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France
| | - Jérôme Morice
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | - France Denoeud
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Anne-Marie Chèvre
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
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Boutte J, Maillet L, Chaussepied T, Letort S, Aury JM, Belser C, Boideau F, Brunet A, Coriton O, Deniot G, Falentin C, Huteau V, Lodé-Taburel M, Morice J, Trotoux G, Chèvre AM, Rousseau-Gueutin M, Ferreira de Carvalho J. Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in Brassica rapa. Front Plant Sci 2020; 11:577536. [PMID: 33281844 PMCID: PMC7689015 DOI: 10.3389/fpls.2020.577536] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/24/2020] [Indexed: 05/07/2023]
Abstract
Traditionally, reference genomes in crop species rely on the assembly of one accession, thus occulting most of intraspecific diversity. However, rearrangements, gene duplications, and transposable element content may have a large impact on the genomic structure, which could generate new phenotypic traits. Comparing two Brassica rapa genomes recently sequenced and assembled using long-read technology and optical mapping, we investigated structural variants and repetitive content between the two accessions and genome size variation among a core collection. We explored the structural consequences of the presence of large repeated sequences in B. rapa 'Z1' genome vs. the B. rapa 'Chiifu' genome, using comparative genomics and cytogenetic approaches. First, we showed that large genomic variants on chromosomes A05, A06, A09, and A10 are due to large insertions and inversions when comparing B. rapa 'Z1' and B. rapa 'Chiifu' at the origin of important length differences in some chromosomes. For instance, lengths of 'Z1' and 'Chiifu' A06 chromosomes were estimated in silico to be 55 and 29 Mb, respectively. To validate these observations, we compared using fluorescent in situ hybridization (FISH) the two A06 chromosomes present in an F1 hybrid produced by crossing these two varieties. We confirmed a length difference of 17.6% between the A06 chromosomes of 'Z1' compared to 'Chiifu.' Alternatively, using a copy number variation approach, we were able to quantify the presence of a higher number of rDNA and gypsy elements in 'Z1' genome compared to 'Chiifu' on different chromosomes including A06. Using flow cytometry, the total genome size of 12 Brassica accessions corresponding to a B. rapa available core collection was estimated and revealed a genome size variation of up to 16% between these accessions as well as some shared inversions. This study revealed the contribution of long-read sequencing of new accessions belonging to different cultigroups of B. rapa and highlighted the potential impact of differential insertion of repeat elements and inversions of large genomic regions in genome size intraspecific variability.
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Affiliation(s)
- Julien Boutte
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, France
- *Correspondence: Julien Boutte,
| | - Loeiz Maillet
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, France
| | | | | | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut de biologie François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Caroline Belser
- Génomique Métabolique, Genoscope, Institut de biologie François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Franz Boideau
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, France
| | - Anael Brunet
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, France
| | | | | | - Cyril Falentin
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, France
| | | | | | - Jérôme Morice
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, France
| | - Gwenn Trotoux
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, France
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7
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Ferreira de Carvalho J, Lucas J, Deniot G, Falentin C, Filangi O, Gilet M, Legeai F, Lode M, Morice J, Trotoux G, Aury JM, Barbe V, Keller J, Snowdon R, He Z, Denoeud F, Wincker P, Bancroft I, Chèvre AM, Rousseau-Gueutin M. Cytonuclear interactions remain stable during allopolyploid evolution despite repeated whole-genome duplications in Brassica. Plant J 2019; 98:434-447. [PMID: 30604905 DOI: 10.1111/tpj.14228] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 12/14/2018] [Accepted: 01/02/2019] [Indexed: 06/09/2023]
Abstract
Several plastid macromolecular protein complexes are encoded by both nuclear and plastid genes. Therefore, cytonuclear interactions are held in place to prevent genomic conflicts that may lead to incompatibilities. Allopolyploidy resulting from hybridization and genome doubling of two divergent species can disrupt these fine-tuned interactions, as newly formed allopolyploid species confront biparental nuclear chromosomes with a uniparentally inherited plastid genome. To avoid any deleterious effects of unequal genome inheritance, preferential transcription of the plastid donor over the other donor has been hypothesized to occur in allopolyploids. We used Brassica as a model to study the effects of paleopolyploidy in diploid parental species, as well as the effects of recent and ancient allopolyploidy in Brassica napus, on genes implicated in plastid protein complexes. We first identified redundant nuclear copies involved in those complexes. Compared with cytosolic protein complexes and with genome-wide retention rates, genes involved in plastid protein complexes show a higher retention of genes in duplicated and triplicated copies. Those redundant copies are functional and are undergoing strong purifying selection. We then compared transcription patterns and sequences of those redundant gene copies between resynthesized allopolyploids and their diploid parents. The neopolyploids showed no biased subgenome expression or maternal homogenization via gene conversion, despite the presence of some non-synonymous substitutions between plastid genomes of parental progenitors. Instead, subgenome dominance was observed regardless of the maternal progenitor. Our results provide new insights on the evolution of plastid protein complexes that could be tested and generalized in other allopolyploid species.
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Affiliation(s)
| | - Jérémy Lucas
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Gwenaëlle Deniot
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Cyril Falentin
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Olivier Filangi
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Marie Gilet
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Fabrice Legeai
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Maryse Lode
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Jérôme Morice
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Gwenn Trotoux
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique, Genoscope, Institut de biologie François-Jacob, Evry, 91057, France
| | - Valérie Barbe
- Commissariat à l'Energie Atomique, Genoscope, Institut de biologie François-Jacob, Evry, 91057, France
| | - Jean Keller
- UMR CNRS 6553 ECOBIO, OSUR, Université de Rennes 1, Rennes, 35042, France
| | - Rod Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, Giessen, 35392, Germany
| | - Zhesi He
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - France Denoeud
- Commissariat à l'Energie Atomique, Genoscope, Institut de biologie François-Jacob, Evry, 91057, France
- UMR CNRS 8030, Evry, CP5706, France
- Université d'Evry-Val-d'Essonne, Université Paris-Saclay, Evry, 91000, France
| | - Patrick Wincker
- Commissariat à l'Energie Atomique, Genoscope, Institut de biologie François-Jacob, Evry, 91057, France
- UMR CNRS 8030, Evry, CP5706, France
- Université d'Evry-Val-d'Essonne, Université Paris-Saclay, Evry, 91000, France
| | - Ian Bancroft
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Anne-Marie Chèvre
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
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Belser C, Istace B, Denis E, Dubarry M, Baurens FC, Falentin C, Genete M, Berrabah W, Chèvre AM, Delourme R, Deniot G, Denoeud F, Duffé P, Engelen S, Lemainque A, Manzanares-Dauleux M, Martin G, Morice J, Noel B, Vekemans X, D'Hont A, Rousseau-Gueutin M, Barbe V, Cruaud C, Wincker P, Aury JM. Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps. Nat Plants 2018; 4:879-887. [PMID: 30390080 DOI: 10.1038/s41477-018-0289-4] [Citation(s) in RCA: 208] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 09/24/2018] [Indexed: 05/19/2023]
Abstract
Plant genomes are often characterized by a high level of repetitiveness and polyploid nature. Consequently, creating genome assemblies for plant genomes is challenging. The introduction of short-read technologies 10 years ago substantially increased the number of available plant genomes. Generally, these assemblies are incomplete and fragmented, and only a few are at the chromosome scale. Recently, Pacific Biosciences and Oxford Nanopore sequencing technologies were commercialized that can sequence long DNA fragments (kilobases to megabase) and, using efficient algorithms, provide high-quality assemblies in terms of contiguity and completeness of repetitive regions1-4. However, even though genome assemblies based on long reads exhibit high contig N50s (>1 Mb), these methods are still insufficient to decipher genome organization at the chromosome level. Here, we describe a strategy based on long reads (MinION or PromethION sequencers) and optical maps (Saphyr system) that can produce chromosome-level assemblies and demonstrate applicability by generating high-quality genome sequences for two new dicotyledon morphotypes, Brassica rapa Z1 (yellow sarson) and Brassica oleracea HDEM (broccoli), and one new monocotyledon, Musa schizocarpa (banana). All three assemblies show contig N50s of >5 Mb and contain scaffolds that represent entire chromosomes or chromosome arms.
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Affiliation(s)
- Caroline Belser
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Benjamin Istace
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Erwan Denis
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Marion Dubarry
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Franc-Christophe Baurens
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Cyril Falentin
- IGEPP, INRA, Agrocampus Ouest, Université Rennes 1, BP35327, Le Rheu, France
| | - Mathieu Genete
- Université Lille, CNRS, UMR 8198-Evo-Eco-Paleo, Lille, France
| | - Wahiba Berrabah
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Anne-Marie Chèvre
- IGEPP, INRA, Agrocampus Ouest, Université Rennes 1, BP35327, Le Rheu, France
| | - Régine Delourme
- IGEPP, INRA, Agrocampus Ouest, Université Rennes 1, BP35327, Le Rheu, France
| | - Gwenaëlle Deniot
- IGEPP, INRA, Agrocampus Ouest, Université Rennes 1, BP35327, Le Rheu, France
| | - France Denoeud
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, Evry, France
| | - Philippe Duffé
- IGEPP, INRA, Agrocampus Ouest, Université Rennes 1, BP35327, Le Rheu, France
| | - Stefan Engelen
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Arnaud Lemainque
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | | | - Guillaume Martin
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Jérôme Morice
- IGEPP, INRA, Agrocampus Ouest, Université Rennes 1, BP35327, Le Rheu, France
| | - Benjamin Noel
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Xavier Vekemans
- Université Lille, CNRS, UMR 8198-Evo-Eco-Paleo, Lille, France
| | - Angélique D'Hont
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | | | - Valérie Barbe
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Corinne Cruaud
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, Evry, France
| | - Jean-Marc Aury
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France.
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Kumar V, Paillard S, Fopa-Fomeju B, Falentin C, Deniot G, Baron C, Vallée P, Manzanares-Dauleux MJ, Delourme R. Multi-year linkage and association mapping confirm the high number of genomic regions involved in oilseed rape quantitative resistance to blackleg. Theor Appl Genet 2018; 131:1627-1643. [PMID: 29728747 DOI: 10.1007/s00122-018-3103-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/20/2018] [Indexed: 05/02/2023]
Abstract
A repertoire of the genomic regions involved in quantitative resistance to Leptosphaeria maculans in winter oilseed rape was established from combined linkage-based QTL and genome-wide association (GWA) mapping. Linkage-based mapping of quantitative trait loci (QTL) and genome-wide association studies are complementary approaches for deciphering the genomic architecture of complex agronomical traits. In oilseed rape, quantitative resistance to blackleg disease, caused by L. maculans, is highly polygenic and is greatly influenced by the environment. In this study, we took advantage of multi-year data available on three segregating populations derived from the resistant cv Darmor and multi-year data available on oilseed rape panels to obtain a wide overview of the genomic regions involved in quantitative resistance to this pathogen in oilseed rape. Sixteen QTL regions were common to at least two biparental populations, of which nine were the same as previously detected regions in a multi-parental design derived from different resistant parents. Eight regions were significantly associated with quantitative resistance, of which five on A06, A08, A09, C01 and C04 were located within QTL support intervals. Homoeologous Brassica napus genes were found in eight homoeologous QTL regions, which corresponded to 657 pairs of homoeologous genes. Potential candidate genes underlying this quantitative resistance were identified. Genomic predictions and breeding are also discussed, taking into account the highly polygenic nature of this resistance.
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Affiliation(s)
- Vinod Kumar
- IGEPP, AGROCAMPUS OUEST, INRA, Univ Rennes, 35650, Le Rheu, France
| | - Sophie Paillard
- IGEPP, AGROCAMPUS OUEST, INRA, Univ Rennes, 35650, Le Rheu, France
| | | | - Cyril Falentin
- IGEPP, AGROCAMPUS OUEST, INRA, Univ Rennes, 35650, Le Rheu, France
| | - Gwenaëlle Deniot
- IGEPP, AGROCAMPUS OUEST, INRA, Univ Rennes, 35650, Le Rheu, France
| | - Cécile Baron
- IGEPP, AGROCAMPUS OUEST, INRA, Univ Rennes, 35650, Le Rheu, France
| | - Patrick Vallée
- IGEPP, AGROCAMPUS OUEST, INRA, Univ Rennes, 35650, Le Rheu, France
| | | | - Régine Delourme
- IGEPP, AGROCAMPUS OUEST, INRA, Univ Rennes, 35650, Le Rheu, France.
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10
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Pelé A, Trotoux G, Eber F, Lodé M, Gilet M, Deniot G, Falentin C, Nègre S, Morice J, Rousseau-Gueutin M, Chèvre AM. The poor lonesome A subgenome of Brassica napus var. Darmor (AACC) may not survive without its mate. New Phytol 2017; 213:1886-1897. [PMID: 27575298 DOI: 10.1111/nph.14147] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/12/2016] [Indexed: 06/06/2023]
Abstract
Constitutive genomes of allopolyploid species evolve throughout their life span. However, the consequences of long-term alterations on the interdependency between each original genome have not been established. Here, we attempted an approach corresponding to subgenome extraction from a previously sequenced natural allotetraploid, offering a unique opportunity to evaluate plant viability and structural evolution of one of its diploid components. We employed two different strategies to extract the diploid AA component of the Brassica napus variety 'Darmor' (AACC, 2n = 4x = 38) and we assessed the genomic structure of the latest AA plants obtained (after four to five rounds of selection), using a 60K single nucleotide polymorphism Illumina array. Only one strategy was successful and the diploid AA plants that were structurally characterized presented a lower proportion of the B. napus A subgenome extracted than expected. In addition, our analyses revealed that some genes lost in a polyploid context appeared to be compensated for plant survival, either by conservation of genomic regions from B. rapa, used in the initial cross, or by some introgressions from the B. napus C subgenome. We conclude that as little as c. 7500 yr of coevolution could lead to subgenome interdependency in the allotetraploid B. napus as a result of structural modifications.
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Affiliation(s)
- Alexandre Pelé
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | - Gwenn Trotoux
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | - Frédérique Eber
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | - Maryse Lodé
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | - Marie Gilet
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | - Gwenaelle Deniot
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | - Cyril Falentin
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | - Sylvie Nègre
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | - Jérôme Morice
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | | | - Anne-Marie Chèvre
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
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11
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Fopa Fomeju B, Falentin C, Lassalle G, Manzanares-Dauleux MJ, Delourme R. Comparative genomic analysis of duplicated homoeologous regions involved in the resistance of Brassica napus to stem canker. Front Plant Sci 2015; 6:772. [PMID: 26442081 PMCID: PMC4585320 DOI: 10.3389/fpls.2015.00772] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 09/08/2015] [Indexed: 05/18/2023]
Abstract
All crop species are current or ancient polyploids. Following whole genome duplication, structural and functional modifications result in differential gene content or regulation in the duplicated regions, which can play a fundamental role in the diversification of genes underlying complex traits. We have investigated this issue in Brassica napus, a species with a highly duplicated genome, with the aim of studying the structural and functional organization of duplicated regions involved in quantitative resistance to stem canker, a disease caused by the fungal pathogen Leptosphaeria maculans. Genome-wide association analysis on two oilseed rape panels confirmed that duplicated regions of ancestral blocks E, J, R, U, and W were involved in resistance to stem canker. The structural analysis of the duplicated genomic regions showed a higher gene density on the A genome than on the C genome and a better collinearity between homoeologous regions than paralogous regions, as overall in the whole B. napus genome. The three ancestral sub-genomes were involved in the resistance to stem canker and the fractionation profile of the duplicated regions corresponded to what was expected from results on the B. napus progenitors. About 60% of the genes identified in these duplicated regions were single-copy genes while less than 5% were retained in all the duplicated copies of a given ancestral block. Genes retained in several copies were mainly involved in response to stress, signaling, or transcription regulation. Genes with resistance-associated markers were mainly retained in more than two copies. These results suggested that some genes underlying quantitative resistance to stem canker might be duplicated genes. Genes with a hydrolase activity that were retained in one copy or R-like genes might also account for resistance in some regions. Further analyses need to be conducted to indicate to what extent duplicated genes contribute to the expression of the resistance phenotype.
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Affiliation(s)
| | - Cyril Falentin
- Institut National de la Recherche Agronomique, UMR1349 IGEPPLe Rheu, France
| | - Gilles Lassalle
- Institut National de la Recherche Agronomique, UMR1349 IGEPPLe Rheu, France
| | | | - Régine Delourme
- Institut National de la Recherche Agronomique, UMR1349 IGEPPLe Rheu, France
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12
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Chalhoub B, Denoeud F, Liu S, Parkin IAP, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B, Corréa M, Da Silva C, Just J, Falentin C, Koh CS, Le Clainche I, Bernard M, Bento P, Noel B, Labadie K, Alberti A, Charles M, Arnaud D, Guo H, Daviaud C, Alamery S, Jabbari K, Zhao M, Edger PP, Chelaifa H, Tack D, Lassalle G, Mestiri I, Schnel N, Le Paslier MC, Fan G, Renault V, Bayer PE, Golicz AA, Manoli S, Lee TH, Thi VHD, Chalabi S, Hu Q, Fan C, Tollenaere R, Lu Y, Battail C, Shen J, Sidebottom CHD, Wang X, Canaguier A, Chauveau A, Bérard A, Deniot G, Guan M, Liu Z, Sun F, Lim YP, Lyons E, Town CD, Bancroft I, Wang X, Meng J, Ma J, Pires JC, King GJ, Brunel D, Delourme R, Renard M, Aury JM, Adams KL, Batley J, Snowdon RJ, Tost J, Edwards D, Zhou Y, Hua W, Sharpe AG, Paterson AH, Guan C, Wincker P. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 2014. [PMID: 25146293 DOI: 10.1126/science.125343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.
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Affiliation(s)
- Boulos Chalhoub
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France.
| | - France Denoeud
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France. Université d'Evry Val d'Essone, UMR 8030, CP5706, Evry, France. Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706, Evry, France
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada.
| | - Haibao Tang
- J. Craig Venter Institute, Rockville, MD 20850, USA. Center for Genomics and Biotechnology, Fujian Agriculture and Forestry, University, Fuzhou 350002, Fujian Province, China
| | - Xiyin Wang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA. Center of Genomics and Computational Biology, School of Life Sciences, Hebei United University, Tangshan, Hebei 063000, China
| | - Julien Chiquet
- Laboratoire de Mathématiques et Modélisation d'Evry-UMR 8071 CNRS/Université d'Evry val d'Essonne-USC INRA, Evry, France
| | - Harry Belcram
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Chaobo Tong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Birgit Samans
- Department of Plant Breeding, Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Margot Corréa
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Corinne Da Silva
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Jérémy Just
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Cyril Falentin
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Chu Shin Koh
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Isabelle Le Clainche
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Maria Bernard
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Pascal Bento
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Benjamin Noel
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Karine Labadie
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Adriana Alberti
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Mathieu Charles
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Dominique Arnaud
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Hui Guo
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Christian Daviaud
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91000 Evry, France
| | - Salman Alamery
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Kamel Jabbari
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France. Cologne Center for Genomics, University of Cologne, Weyertal 115b, 50931 Köln, Germany
| | - Meixia Zhao
- Department of Agronomy, Purdue University, WSLR Building B018, West Lafayette, IN 47907, USA
| | - Patrick P Edger
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Houda Chelaifa
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - David Tack
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Gilles Lassalle
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Imen Mestiri
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Nicolas Schnel
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Marie-Christine Le Paslier
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Guangyi Fan
- Beijing Genome Institute-Shenzhen, Shenzhen 518083, China
| | - Victor Renault
- Fondation Jean Dausset-Centre d'Étude du Polymorphisme Humain, 27 rue Juliette Dodu, 75010 Paris, France
| | - Philippe E Bayer
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Agnieszka A Golicz
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Sahana Manoli
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Tae-Ho Lee
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Vinh Ha Dinh Thi
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Smahane Chalabi
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Qiong Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Reece Tollenaere
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Yunhai Lu
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Christophe Battail
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | | | - Xinfa Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Aurélie Canaguier
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Aurélie Chauveau
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Aurélie Bérard
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Gwenaëlle Deniot
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Mei Guan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Zhongsong Liu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Fengming Sun
- Beijing Genome Institute-Shenzhen, Shenzhen 518083, China
| | - Yong Pyo Lim
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon-305764, South Korea
| | - Eric Lyons
- School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, AZ, USA
| | | | - Ian Bancroft
- Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianxin Ma
- Department of Agronomy, Purdue University, WSLR Building B018, West Lafayette, IN 47907, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | - Dominique Brunel
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Régine Delourme
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Michel Renard
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Keith L Adams
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Jacqueline Batley
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia. School of Plant Biology, University of Western Australia, WA 6009, Australia
| | - Rod J Snowdon
- Department of Plant Breeding, Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Jorg Tost
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91000 Evry, France
| | - David Edwards
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia. School of Plant Biology, University of Western Australia, WA 6009, Australia.
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
| | - Wei Hua
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Andrew G Sharpe
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada.
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA.
| | - Chunyun Guan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China.
| | - Patrick Wincker
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France. Université d'Evry Val d'Essone, UMR 8030, CP5706, Evry, France. Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706, Evry, France.
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13
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Chalhoub B, Denoeud F, Liu S, Parkin IAP, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B, Corréa M, Da Silva C, Just J, Falentin C, Koh CS, Le Clainche I, Bernard M, Bento P, Noel B, Labadie K, Alberti A, Charles M, Arnaud D, Guo H, Daviaud C, Alamery S, Jabbari K, Zhao M, Edger PP, Chelaifa H, Tack D, Lassalle G, Mestiri I, Schnel N, Le Paslier MC, Fan G, Renault V, Bayer PE, Golicz AA, Manoli S, Lee TH, Thi VHD, Chalabi S, Hu Q, Fan C, Tollenaere R, Lu Y, Battail C, Shen J, Sidebottom CHD, Wang X, Canaguier A, Chauveau A, Bérard A, Deniot G, Guan M, Liu Z, Sun F, Lim YP, Lyons E, Town CD, Bancroft I, Wang X, Meng J, Ma J, Pires JC, King GJ, Brunel D, Delourme R, Renard M, Aury JM, Adams KL, Batley J, Snowdon RJ, Tost J, Edwards D, Zhou Y, Hua W, Sharpe AG, Paterson AH, Guan C, Wincker P. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 2014; 345:950-3. [PMID: 25146293 DOI: 10.1126/science.1253435] [Citation(s) in RCA: 1362] [Impact Index Per Article: 136.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.
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Affiliation(s)
- Boulos Chalhoub
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France.
| | - France Denoeud
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France. Université d'Evry Val d'Essone, UMR 8030, CP5706, Evry, France. Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706, Evry, France
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada.
| | - Haibao Tang
- J. Craig Venter Institute, Rockville, MD 20850, USA. Center for Genomics and Biotechnology, Fujian Agriculture and Forestry, University, Fuzhou 350002, Fujian Province, China
| | - Xiyin Wang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA. Center of Genomics and Computational Biology, School of Life Sciences, Hebei United University, Tangshan, Hebei 063000, China
| | - Julien Chiquet
- Laboratoire de Mathématiques et Modélisation d'Evry-UMR 8071 CNRS/Université d'Evry val d'Essonne-USC INRA, Evry, France
| | - Harry Belcram
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Chaobo Tong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Birgit Samans
- Department of Plant Breeding, Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Margot Corréa
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Corinne Da Silva
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Jérémy Just
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Cyril Falentin
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Chu Shin Koh
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Isabelle Le Clainche
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Maria Bernard
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Pascal Bento
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Benjamin Noel
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Karine Labadie
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Adriana Alberti
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Mathieu Charles
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Dominique Arnaud
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Hui Guo
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Christian Daviaud
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91000 Evry, France
| | - Salman Alamery
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Kamel Jabbari
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France. Cologne Center for Genomics, University of Cologne, Weyertal 115b, 50931 Köln, Germany
| | - Meixia Zhao
- Department of Agronomy, Purdue University, WSLR Building B018, West Lafayette, IN 47907, USA
| | - Patrick P Edger
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Houda Chelaifa
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - David Tack
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Gilles Lassalle
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Imen Mestiri
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Nicolas Schnel
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Marie-Christine Le Paslier
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Guangyi Fan
- Beijing Genome Institute-Shenzhen, Shenzhen 518083, China
| | - Victor Renault
- Fondation Jean Dausset-Centre d'Étude du Polymorphisme Humain, 27 rue Juliette Dodu, 75010 Paris, France
| | - Philippe E Bayer
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Agnieszka A Golicz
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Sahana Manoli
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Tae-Ho Lee
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Vinh Ha Dinh Thi
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Smahane Chalabi
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Qiong Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Reece Tollenaere
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Yunhai Lu
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Christophe Battail
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | | | - Xinfa Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Aurélie Canaguier
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Aurélie Chauveau
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Aurélie Bérard
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Gwenaëlle Deniot
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Mei Guan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Zhongsong Liu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Fengming Sun
- Beijing Genome Institute-Shenzhen, Shenzhen 518083, China
| | - Yong Pyo Lim
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon-305764, South Korea
| | - Eric Lyons
- School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, AZ, USA
| | | | - Ian Bancroft
- Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianxin Ma
- Department of Agronomy, Purdue University, WSLR Building B018, West Lafayette, IN 47907, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | - Dominique Brunel
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Régine Delourme
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Michel Renard
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Keith L Adams
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Jacqueline Batley
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia. School of Plant Biology, University of Western Australia, WA 6009, Australia
| | - Rod J Snowdon
- Department of Plant Breeding, Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Jorg Tost
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91000 Evry, France
| | - David Edwards
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia. School of Plant Biology, University of Western Australia, WA 6009, Australia.
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
| | - Wei Hua
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Andrew G Sharpe
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada.
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA.
| | - Chunyun Guan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China.
| | - Patrick Wincker
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France. Université d'Evry Val d'Essone, UMR 8030, CP5706, Evry, France. Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706, Evry, France.
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Fopa Fomeju B, Falentin C, Lassalle G, Manzanares-Dauleux MJ, Delourme R. Homoeologous duplicated regions are involved in quantitative resistance of Brassica napus to stem canker. BMC Genomics 2014; 15:498. [PMID: 24948032 PMCID: PMC4082613 DOI: 10.1186/1471-2164-15-498] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 06/11/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several major crop species are current or ancient polyploids. To better describe the genetic factors controlling traits of agronomic interest (QTL), it is necessary to understand the structural and functional organisation of these QTL regions in relation to genome duplication. We investigated quantitative resistance to the fungal disease stem canker in Brassica napus, a highly duplicated amphidiploid species, to assess the proportion of resistance QTL located at duplicated positions. RESULTS Genome-wide association analysis on a panel of 116 oilseed rape varieties genotyped with 3228 SNP indicated that 321 markers, corresponding to 64 genomic regions, are associated with resistance to stem canker. These genomic regions are relatively equally distributed on the A (53%) and C (47%) genomes of B. napus. Overall, 44% of these regions (28/64) are duplicated homoeologous regions. They are located in duplications of six (E, J, R, T, U and W) of the 24 ancestral blocks that constitute the B. napus genome. Overall, these six ancestral blocks have 34 duplicated copies in the B.napus genome. Almost all of the duplicated copies (82% of the 34 regions) harboured resistance associated markers for stem canker resistance, which suggests structural and functional conservation of genetic factors involved in this trait in B. napus. CONCLUSIONS Our study provides information on the involvement of duplicated loci in the control of stem canker resistance in B. napus. Further investigation of the similarity/divergence in sequence and gene content of these duplicated regions will provide insight into the conservation and allelic diversity of the underlying genes.
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Delourme R, Falentin C, Fomeju BF, Boillot M, Lassalle G, André I, Duarte J, Gauthier V, Lucante N, Marty A, Pauchon M, Pichon JP, Ribière N, Trotoux G, Blanchard P, Rivière N, Martinant JP, Pauquet J. High-density SNP-based genetic map development and linkage disequilibrium assessment in Brassica napus L. BMC Genomics 2013; 14:120. [PMID: 23432809 PMCID: PMC3600037 DOI: 10.1186/1471-2164-14-120] [Citation(s) in RCA: 150] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 02/11/2013] [Indexed: 11/30/2022] Open
Abstract
Background High density genetic maps built with SNP markers that are polymorphic in various genetic backgrounds are very useful for studying the genetics of agronomical traits as well as genome organization and evolution. Simultaneous dense SNP genotyping of segregating populations and variety collections was applied to oilseed rape (Brassica napus L.) to obtain a high density genetic map for this species and to study the linkage disequilibrium pattern. Results We developed an integrated genetic map for oilseed rape by high throughput SNP genotyping of four segregating doubled haploid populations. A very high level of collinearity was observed between the four individual maps and a large number of markers (>59%) was common to more than two maps. The precise integrated map comprises 5764 SNP and 1603 PCR markers. With a total genetic length of 2250 cM, the integrated map contains a density of 3.27 markers (2.56 SNP) per cM. Genotyping of these mapped SNP markers in oilseed rape collections allowed polymorphism level and linkage disequilibrium (LD) to be studied across the different collections (winter vs spring, different seed quality types) and along the linkage groups. Overall, polymorphism level was higher and LD decayed faster in spring than in “00” winter oilseed rape types but this was shown to vary greatly along the linkage groups. Conclusions Our study provides a valuable resource for further genetic studies using linkage or association mapping, for marker assisted breeding and for Brassica napus sequence assembly and genome organization analyses.
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Lu YH, Arnaud D, Belcram H, Falentin C, Rouault P, Piel N, Lucas MO, Just J, Renard M, Delourme R, Chalhoub B. A dominant point mutation in a RINGv E3 ubiquitin ligase homoeologous gene leads to cleistogamy in Brassica napus. Plant Cell 2012; 24:4875-91. [PMID: 23277363 PMCID: PMC3556963 DOI: 10.1105/tpc.112.104315] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
In the allopolyploid Brassica napus, we obtained a petal-closed flower mutation by ethyl methanesulfonate mutagenesis. Here, we report cloning and characterization of the Bn-CLG1A (CLG for cleistogamy) gene and the Bn-clg1A-1D mutant allele responsible for the cleistogamy phenotype. Bn-CLG1A encodes a RINGv E3 ubiquitin ligase that is highly conserved across eukaryotes. In the Bn-clg1A-1D mutant allele, a C-to-T transition converts a Pro at position 325 to a Leu (P325L), causing a dominant mutation leading to cleistogamy. B. napus and Arabidopsis thaliana plants transformed with a Bn-clg1A-1D allele show cleistogamous flowers, and characterization of these flowers suggests that the Bn-clg1A-1D mutation causes a pronounced negative regulation of cutin biosynthesis or loading and affects elongation or differentiation of petal and sepal cells. This results in an inhibition or a delay of petal development, leading to folded petals. A homoeologous gene (Bn-CLG1C), which shows 99.5% amino acid identity and is also constitutively and equally expressed to the wild-type Bn-CLG1A gene, was also identified. We showed that P325L is not a loss-of-function mutation and did not affect expression of Bn-clg1A-1D or Bn-CLG1C. Our findings suggest that P325L is a gain-of-function semidominant mutation, which led to either hyper- or neofunctionalization of a redundant homoeologous gene.
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Affiliation(s)
- Yun-Hai Lu
- Unité de Recherche en Génomique Végétale (Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université d'Evry Val d'Essonnes), Organization and Evolution of Plant Genomes, 91057 Evry cedex, France
| | - Dominique Arnaud
- Unité de Recherche en Génomique Végétale (Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université d'Evry Val d'Essonnes), Organization and Evolution of Plant Genomes, 91057 Evry cedex, France
| | - Harry Belcram
- Unité de Recherche en Génomique Végétale (Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université d'Evry Val d'Essonnes), Organization and Evolution of Plant Genomes, 91057 Evry cedex, France
| | - Cyril Falentin
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1349 Institut de Génétique, Environnement et Protection des Plantes, F-35653 Le Rheu, France
| | - Patricia Rouault
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1349 Institut de Génétique, Environnement et Protection des Plantes, F-35653 Le Rheu, France
| | - Nathalie Piel
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1349 Institut de Génétique, Environnement et Protection des Plantes, F-35653 Le Rheu, France
| | - Marie-Odile Lucas
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1349 Institut de Génétique, Environnement et Protection des Plantes, F-35653 Le Rheu, France
| | - Jérémy Just
- Unité de Recherche en Génomique Végétale (Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université d'Evry Val d'Essonnes), Organization and Evolution of Plant Genomes, 91057 Evry cedex, France
| | - Michel Renard
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1349 Institut de Génétique, Environnement et Protection des Plantes, F-35653 Le Rheu, France
| | - Régine Delourme
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1349 Institut de Génétique, Environnement et Protection des Plantes, F-35653 Le Rheu, France
| | - Boulos Chalhoub
- Unité de Recherche en Génomique Végétale (Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université d'Evry Val d'Essonnes), Organization and Evolution of Plant Genomes, 91057 Evry cedex, France
- Address correspondence to
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Wang J, Lydiate DJ, Parkin IAP, Falentin C, Delourme R, Carion PWC, King GJ. Integration of linkage maps for the Amphidiploid Brassica napus and comparative mapping with Arabidopsis and Brassica rapa. BMC Genomics 2011; 12:101. [PMID: 21306613 PMCID: PMC3042011 DOI: 10.1186/1471-2164-12-101] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 02/09/2011] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The large number of genetic linkage maps representing Brassica chromosomes constitute a potential platform for studying crop traits and genome evolution within Brassicaceae. However, the alignment of existing maps remains a major challenge. The integration of these genetic maps will enhance genetic resolution, and provide a means to navigate between sequence-tagged loci, and with contiguous genome sequences as these become available. RESULTS We report the first genome-wide integration of Brassica maps based on an automated pipeline which involved collation of genome-wide genotype data for sequence-tagged markers scored on three extensively used amphidiploid Brassica napus (2n = 38) populations. Representative markers were selected from consolidated maps for each population, and skeleton bin maps were generated. The skeleton maps for the three populations were then combined to generate an integrated map for each LG, comparing two different approaches, one encapsulated in JoinMap and the other in MergeMap. The BnaWAIT_01_2010a integrated genetic map was generated using JoinMap, and includes 5,162 genetic markers mapped onto 2,196 loci, with a total genetic length of 1,792 cM. The map density of one locus every 0.82 cM, corresponding to 515 Kbp, increases by at least three-fold the locus and marker density within the original maps. Within the B. napus integrated map we identified 103 conserved collinearity blocks relative to Arabidopsis, including five previously unreported blocks. The BnaWAIT_01_2010a map was used to investigate the integrity and conservation of order proposed for genome sequence scaffolds generated from the constituent A genome of Brassica rapa. CONCLUSIONS Our results provide a comprehensive genetic integration of the B. napus genome from a range of sources, which we anticipate will provide valuable information for rapeseed and Canola research.
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Affiliation(s)
- Jun Wang
- Department of Plant Sciences, Rothamsted Research, Harpenden, AL5 2JQ, UK
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18
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Heesch S, Cho GY, Peters AF, Le Corguillé G, Falentin C, Boutet G, Coëdel S, Jubin C, Samson G, Corre E, Coelho SM, Cock JM. A sequence-tagged genetic map for the brown alga Ectocarpus siliculosus provides large-scale assembly of the genome sequence. New Phytol 2010; 188:42-51. [PMID: 20456050 DOI: 10.1111/j.1469-8137.2010.03273.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
• Ectocarpus siliculosus has been proposed as a genetic and genomic model for the brown algae and the 214 Mbp genome of this organism has been sequenced. The aim of this project was to obtain a chromosome-scale view of the genome by constructing a genetic map using microsatellite markers that were designed based on the sequence supercontigs. • To map genetic markers, a segregating F(2) population was generated from a cross between the sequenced strain (Ec 32) and a compatible strain from northern Chile. Amplified fragment length polymorphism (AFLP) analysis indicated a significant degree of polymorphism (41%) between the genomes of these two parental strains. Of 1,152 microsatellite markers that were selected for analysis based on their location on long supercontigs, their potential as markers and their predicted ability to amplify a single genomic locus, 407 were found to be polymorphic. • A genetic map was constructed using 406 markers, resulting in 34 linkage groups. The 406 markers anchor 325 of the longest supercontigs on to the map, representing 70.1% of the genome sequence. • The Ectocarpus genetic map described here not only provides a large-scale assembly of the genome sequence, but also represents an important tool for future genetic analysis using this organism.
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Affiliation(s)
- Svenja Heesch
- UPMC Univ. Paris 06, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France
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Delourme R, Piel N, Horvais R, Pouilly N, Domin C, Vallée P, Falentin C, Manzanares-Dauleux MJ, Renard M. Molecular and phenotypic characterization of near isogenic lines at QTL for quantitative resistance to Leptosphaeria maculans in oilseed rape (Brassica napus L.). Theor Appl Genet 2008; 117:1055-67. [PMID: 18696043 DOI: 10.1007/s00122-008-0844-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2008] [Revised: 06/20/2008] [Accepted: 06/28/2008] [Indexed: 05/09/2023]
Abstract
The most common and effective way to control phoma stem canker (blackleg) caused by Leptosphaeria maculans in oilseed rape (Brassica napus) is by breeding resistant cultivars. Specific resistance genes have been identified in B. napus and related species but in some B. napus cultivars resistance is polygenic [mediated by quantitative trait loci (QTL)], postulated to be race non-specific and durable. The genetic basis of quantitative resistance in the French winter oilseed rape 'Darmor', which was derived from 'Jet Neuf', was previously examined in two genetic backgrounds. Stable QTL involved in blackleg resistance across year and genetic backgrounds were identified. In this study, near isogenic lines (NILs) were produced in the susceptible background 'Yudal' for four of these QTL using marker-assisted selection. Various strategies were used to develop new molecular markers, which were mapped in these QTL regions. These were used to characterize the length and homozygosity of the 'Darmor-bzh' introgressed segment in the NILs. Individuals from each NIL were evaluated in blackleg disease field trials and assessed for their level of stem canker in comparison to the recurrent line 'Yudal'. The effect of QTL LmA2 was clearly validated and to a lesser extent, QTL LmA9 also showed an effect on the disease level. This work provides valuable material that can be used to study the mode of action of genetic factors involved in L. maculans quantitative resistance.
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Affiliation(s)
- R Delourme
- UMR 118 Amélioration des Plantes et Biotechnologies Végétales, INRA, BP 35327, 35653 Le Rheu Cedex, France.
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Abstract
Oilseed rape (Brassica napus L.) is a major oil crop that also supplies proteins for the feed industry. In order to reduce total cost production, the objective is to increase oil yield while reducing crop inputs (especially nitrogen and pesticides). Concomitantly, it is necessary to anticipate specific uses (e.g., fatty acid composition) and to ensure the valorisation of the by-products (rapeseed meal). By the past, improvement of seed quality focused on fatty acid balance and low seed glucosinolate content. Current goals include the breeding of yellow-seeded rapeseed lines with high content of seed oil. The use of molecular tools and the exploitation of Arabidopsis knowledge will be presented and discussed.
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Affiliation(s)
- Nathalie Nesi
- INRA-Agrocampus Rennes-University of Rennes1 Joint Laboratory, UMR118, Plant Genetics and Biotechnologies, BP 35327, 35653 Le Rheu cedex, France.
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21
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Delourme R, Falentin C, Huteau V, Clouet V, Horvais R, Gandon B, Specel S, Hanneton L, Dheu JE, Deschamps M, Margale E, Vincourt P, Renard M. Genetic control of oil content in oilseed rape (Brassica napus L.). Theor Appl Genet 2006; 113:1331-45. [PMID: 16960716 DOI: 10.1007/s00122-006-0386-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Accepted: 07/31/2006] [Indexed: 05/11/2023]
Abstract
In oilseed rape (Brassica napus L.) like in most oleaginous crops, seed oil content is the main qualitative determinant that confers its economic value to the harvest. Increasing seed oil content is then still an important objective in oilseed rape breeding. In the objective to get better knowledge on the genetic determinism of seed oil content, a genetic study was undertaken in two genetic backgrounds. Two populations of 445 and a 242 doubled haploids (DH) derived from the crosses "Darmor-bzh" x "Yudal" (DY) and "Rapid" x "NSL96/25" (RNSL), respectively, were genotyped and evaluated for oil content in different trials. QTL mapping in the two populations indicate that additive effects are the main factors contributing to variation in oil content. A total of 14 and 10 genomic regions were involved in seed oil content in DY and RNSL populations, respectively, of which five and two were consistently revealed across the three trials performed for each population. Most of the QTL detected were not colocalised to QTL involved in flowering time. Few epistatic QTL involved regions that carry additive QTL in one or the other population. Only one QTL located on linkage group N3 was potentially common to the two populations. The comparisons of the QTL location in this study and in the literature showed that: (i) some of the QTL were more consistently revealed across different genetic backgrounds. The QTL on N3 was revealed in all the studies and the QTL on N1, N8 and N13 were revealed in three studies out of five, (ii) some of the QTL were specific to one genetic background with potentially some original alleles, (iii) some QTL were located in homeologous regions, and (iv) some of the regions carrying QTL for oil content in oilseed rape and in Arabidopsis could be collinear. These results show the possibility to combine favourable alleles at different QTL to increase seed oil content and to use Arabidopsis genomic data to derive markers for oilseed rape QTL and identify candidate genes, as well as the interest to combine information from different segregating populations in order to build a consolidated map of QTL involved in a specific trait.
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Affiliation(s)
- R Delourme
- UMR INRA Agrocampus Rennes, Amélioration des Plantes et Biotechnologies Végétales, BP 35327, 35653, Le Rheu Cedex, France.
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Giancola S, Marhadour S, Desloire S, Clouet V, Falentin-Guyomarc'h H, Laloui W, Falentin C, Pelletier G, Renard M, Bendahmane A, Delourme R, Budar F. Characterization of a radish introgression carrying the Ogura fertility restorer gene Rfo in rapeseed, using the Arabidopsis genome sequence and radish genetic mapping. Theor Appl Genet 2003; 107:1442-1451. [PMID: 12942173 DOI: 10.1007/s00122-003-1381-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2003] [Accepted: 06/13/2003] [Indexed: 05/24/2023]
Abstract
The radish Rfo gene restores male fertility in radish or rapeseed plants carrying Ogura cytoplasmic male-sterility. This system was first discovered in radish and was transferred to rapeseed for the production of F1 hybrid seeds. We aimed to identify the region of the Arabidopsis genome syntenic to the Rfo locus and to characterize the radish introgression in restored rapeseed. We used two methods: amplified consensus genetic markers (ACGMs) in restored rapeseed plants and construction of a precise genetic map around the Rfo gene in a segregating radish population. The use of ACGMs made it possible to detect radish orthologs of Arabidopsis genes in the restored rapeseed genome. We identified radish genes, linked to Rfo in rapeseed and whose orthologs in Arabidopsis are carried by chromosomes 1, 4 and 5. This indicates several breaks in colinearity between radish and Arabidopsis genomes in this region. We determined the positions of markers relative to each other and to the Rfo gene, using the progeny of a rapeseed plant with unstable meiotic transmission of the radish introgression. This enabled us to produce a schematic diagram of the radish introgression in rapeseed. Markers which could be mapped both on radish and restored rapeseed indicate that at least 50 cM of the radish genome is integrated in restored rapeseed. Using markers closely linked to the Rfo gene in rapeseed and radish, we identified a contig spanning six bacterial artificial chromosome (BAC) clones on Arabidopsis chromosome 1, which is likely to carry the orthologous Rfo gene.
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Affiliation(s)
- Sandra Giancola
- Station de Génétique et d'Amélioration des Plantes, INRA, Route de Saint-Cyr, 78026, Versailles cedex, France
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Desloire S, Gherbi H, Laloui W, Marhadour S, Clouet V, Cattolico L, Falentin C, Giancola S, Renard M, Budar F, Small I, Caboche M, Delourme R, Bendahmane A. Identification of the fertility restoration locus, Rfo, in radish, as a member of the pentatricopeptide-repeat protein family. EMBO Rep 2003; 4:588-94. [PMID: 12740605 PMCID: PMC1319198 DOI: 10.1038/sj.embor.embor848] [Citation(s) in RCA: 249] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2003] [Revised: 03/19/2003] [Accepted: 04/08/2003] [Indexed: 11/09/2022] Open
Abstract
Ogura cytoplasmic male sterility (CMS) in radish (Raphanus sativus) is caused by an aberrant mitochondrial gene, Orf138, that prevents the production of functional pollen without affecting female fertility. Rfo, a nuclear gene that restores male fertility, alters the expression of Orf138 at the post-transcriptional level. The Ogura CMS/Rfo two-component system is a useful model for investigating nuclear-cytoplasmic interactions, as well as the physiological basis of fertility restoration. Using a combination of positional cloning and microsynteny analysis of Arabidopsis thaliana and radish, we genetically and physically delimited the Rfo locus to a 15-kb DNA segment. Analysis of this segment shows that Rfo is a member of the pentatricopeptide repeat (PPR) family. In Arabidopsis, this family contains more than 450 members of unknown function, although most of them are predicted to be targeted to mitochondria and chloroplasts and are thought to have roles in organellar gene expression.
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Affiliation(s)
- Sophie Desloire
- Unité de Recherches en Génomique Végétale INRA CNRS, 2 Rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France
- These authors contributed equally to this work
| | - Hassen Gherbi
- Unité de Recherches en Génomique Végétale INRA CNRS, 2 Rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France
- These authors contributed equally to this work
| | - Wassila Laloui
- Unité de Recherches en Génomique Végétale INRA CNRS, 2 Rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France
| | - Sylvie Marhadour
- UMR INRA-ENSAR, Amélioration des Plantes et Biotechnologies Végétales, BP 35327, F35653 Le Rheu Cedex, France
| | - Vanessa Clouet
- UMR INRA-ENSAR, Amélioration des Plantes et Biotechnologies Végétales, BP 35327, F35653 Le Rheu Cedex, France
| | - Laurence Cattolico
- Centre National de Séquençage, 2 Rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France
| | - Cyril Falentin
- UMR INRA-ENSAR, Amélioration des Plantes et Biotechnologies Végétales, BP 35327, F35653 Le Rheu Cedex, France
| | - Sandra Giancola
- Station de Génétique et d'Amélioration des Plantes, INRA, Route de Saint-Cyr, 78026 Versailles Cedex, France
| | - Michel Renard
- UMR INRA-ENSAR, Amélioration des Plantes et Biotechnologies Végétales, BP 35327, F35653 Le Rheu Cedex, France
| | - Françoise Budar
- Station de Génétique et d'Amélioration des Plantes, INRA, Route de Saint-Cyr, 78026 Versailles Cedex, France
| | - Ian Small
- Unité de Recherches en Génomique Végétale INRA CNRS, 2 Rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France
| | - Michel Caboche
- Unité de Recherches en Génomique Végétale INRA CNRS, 2 Rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France
| | - Régine Delourme
- UMR INRA-ENSAR, Amélioration des Plantes et Biotechnologies Végétales, BP 35327, F35653 Le Rheu Cedex, France
| | - Abdelhafid Bendahmane
- Unité de Recherches en Génomique Végétale INRA CNRS, 2 Rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France
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