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Haelterman L, Louvieaux J, Chiodi C, Bouchet AS, Kupcsik L, Stahl A, Rousseau-Gueutin M, Snowdon R, Laperche A, Nesi N, Hermans C. Genetic control of root morphology in response to nitrogen across rapeseed diversity. PHYSIOLOGIA PLANTARUM 2024; 176:e14315. [PMID: 38693794 DOI: 10.1111/ppl.14315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/03/2024] [Accepted: 04/11/2024] [Indexed: 05/03/2024]
Abstract
Rapeseed (Brassica napus L.) is an oil-containing crop of great economic value but with considerable nitrogen requirement. Breeding root systems that efficiently absorb nitrogen from the soil could be a driver to ensure genetic gains for more sustainable rapeseed production. The aim of this study is to identify genomic regions that regulate root morphology in response to nitrate availability. The natural variability offered by 300 inbred lines was screened at two experimental locations. Seedlings grew hydroponically with low or elevated nitrate levels. Fifteen traits related to biomass production and root morphology were measured. On average across the panel, a low nitrate level increased the root-to-shoot biomass ratio and the lateral root length. A large phenotypic variation was observed, along with important heritability values and genotypic effects, but low genotype-by-nitrogen interactions. Genome-wide association study and bulk segregant analysis were used to identify loci regulating phenotypic traits. The first approach nominated 319 SNPs that were combined into 80 QTLs. Three QTLs identified on the A07 and C07 chromosomes were stable across nitrate levels and/or experimental locations. The second approach involved genotyping two groups of individuals from an experimental F2 population created by crossing two accessions with contrasting lateral root lengths. These individuals were found in the tails of the phenotypic distribution. Co-localized QTLs found in both mapping approaches covered a chromosomal region on the A06 chromosome. The QTL regions contained some genes putatively involved in root organogenesis and represent selection targets for redesigning the root morphology of rapeseed.
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Affiliation(s)
- Loïc Haelterman
- Crop Production and Biostimulation Laboratory (CPBL), Brussels Bioengineering School, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Julien Louvieaux
- Crop Production and Biostimulation Laboratory (CPBL), Brussels Bioengineering School, Université libre de Bruxelles (ULB), Brussels, Belgium
- Laboratory of Applied Plant Ecophysiology, Haute Ecole Provinciale de Hainaut Condorcet, Centre pour l'Agronomie et l'Agro-industrie de la Province de Hainaut (CARAH), Belgium
| | - Claudia Chiodi
- Crop Production and Biostimulation Laboratory (CPBL), Brussels Bioengineering School, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Anne-Sophie Bouchet
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Institut Agro, Université de Rennes, Le Rheu, France
| | - Laszlo Kupcsik
- Crop Production and Biostimulation Laboratory (CPBL), Brussels Bioengineering School, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Andreas Stahl
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Mathieu Rousseau-Gueutin
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Institut Agro, Université de Rennes, Le Rheu, France
| | - Rod Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Germany
| | - Anne Laperche
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Institut Agro, Université de Rennes, Le Rheu, France
| | - Nathalie Nesi
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Institut Agro, Université de Rennes, Le Rheu, France
| | - Christian Hermans
- Crop Production and Biostimulation Laboratory (CPBL), Brussels Bioengineering School, Université libre de Bruxelles (ULB), Brussels, Belgium
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2
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Katche EI, Schierholt A, Schiessl SV, He F, Lv Z, Batley J, Becker HC, Mason AS. Genetic factors inherited from both diploid parents interact to affect genome stability and fertility in resynthesized allotetraploid Brassica napus. G3 (BETHESDA, MD.) 2023; 13:jkad136. [PMID: 37313757 PMCID: PMC10411605 DOI: 10.1093/g3journal/jkad136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 04/24/2023] [Accepted: 05/31/2023] [Indexed: 06/15/2023]
Abstract
Established allopolyploids are known to be genomically stable and fertile. However, in contrast, most newly resynthesized allopolyploids are infertile and meiotically unstable. Identifying the genetic factors responsible for genome stability in newly formed allopolyploid is key to understanding how 2 genomes come together to form a species. One hypothesis is that established allopolyploids may have inherited specific alleles from their diploid progenitors which conferred meiotic stability. Resynthesized Brassica napus lines are often unstable and infertile, unlike B. napus cultivars. We tested this hypothesis by characterizing 41 resynthesized B. napus lines produced by crosses between 8 Brassica rapa and 8 Brassica oleracea lines for copy number variation resulting from nonhomologous recombination events and fertility. We resequenced 8 B. rapa and 5 B. oleracea parent accessions and analyzed 19 resynthesized lines for allelic variation in a list of meiosis gene homologs. SNP genotyping was performed using the Illumina Infinium Brassica 60K array for 3 individuals per line. Self-pollinated seed set and genome stability (number of copy number variants) were significantly affected by the interaction between both B. rapa and B. oleracea parental genotypes. We identified 13 putative meiosis gene candidates which were significantly associated with frequency of copy number variants and which contained putatively harmful mutations in meiosis gene haplotypes for further investigation. Our results support the hypothesis that allelic variants inherited from parental genotypes affect genome stability and fertility in resynthesized rapeseed.
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Affiliation(s)
- Elizabeth Ihien Katche
- Plant Breeding Department, University of Bonn, Bonn 53115, Germany
- Department of Plant Breeding, Justus Liebig University, Giessen 35392, Germany
| | - Antje Schierholt
- Department of Crop Sciences, Division of Plant Breeding Methodology, Georg-August University Göttingen, Göttingen 37073, Germany
| | - Sarah-Veronica Schiessl
- Department of Plant Breeding, Justus Liebig University, Giessen 35392, Germany
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main D-60325, Germany
| | - Fei He
- Plant Breeding Department, University of Bonn, Bonn 53115, Germany
| | - Zhenling Lv
- Plant Breeding Department, University of Bonn, Bonn 53115, Germany
- Department of Plant Breeding, Justus Liebig University, Giessen 35392, Germany
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Heiko C Becker
- Department of Crop Sciences, Division of Plant Breeding Methodology, Georg-August University Göttingen, Göttingen 37073, Germany
| | - Annaliese S Mason
- Plant Breeding Department, University of Bonn, Bonn 53115, Germany
- Department of Plant Breeding, Justus Liebig University, Giessen 35392, Germany
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3
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Menendez YC, Sanchez DH, Snowdon RJ, Rondanini DP, Botto JF. Unraveling the impact on agronomic traits of the genetic architecture underlying plant-density responses in canola. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5426-5441. [PMID: 33940608 DOI: 10.1093/jxb/erab191] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
Plant density defines vegetative architecture and the competition for light between individuals. Brassica napus (canola, rapeseed) presents a radically different plant architecture compared to traditional crops commonly cultivated at high density, and can act as a model system of indeterminate growth. Using a panel of 152 spring-type accessions and a double-haploid population of 99 lines from a cross between the cultivars Lynx and Monty, we performed genome-wide association studies (GWAS) and quantitative trait locus (QTL) mapping for 12 growth and yield traits at two contrasting plant densities of 15 and 60 plants m-2. The most significant associations were found for time to flowering, biomass at harvest, plant height, silique and seed numbers, and seed yield. These were generally independent of plant density, but some density-dependent associations were found in low-density populations. RNA-seq transcriptomic analysis revealed distinctive latent gene-regulatory responses to simulated shade between Lynx and Monty. Having identified candidate genes within the canola QTLs, we further examined their influence on density responses in Arabidopsis lines mutated in certain homologous genes. The results suggested that TCP1 might promote growth independently of plant density, while HY5 could increase biomass and seed yield specifically at high plant density. For flowering time, the results suggested that PIN genes might accelerate flowering in plant a density-dependent manner whilst FT, HY5, and TCP1 might accelerate it in a density-independent. This work highlights the advantages of using agronomic field experiments together with genetic and transcriptomic approaches to decipher quantitative complex traits that potentially mediate improved crop productivity.
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Affiliation(s)
- Yesica C Menendez
- IFEVA (CONICET-UBA), Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina
- Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina
| | - Diego H Sanchez
- IFEVA (CONICET-UBA), Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina
- Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina
- CONICET, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Av. Godoy Cruz 2290, C1425FQB, Ciudad Autónoma de Buenos Aires, Argentina
| | - Rod J Snowdon
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Deborah P Rondanini
- Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina
- CONICET, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Av. Godoy Cruz 2290, C1425FQB, Ciudad Autónoma de Buenos Aires, Argentina
| | - Javier F Botto
- IFEVA (CONICET-UBA), Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina
- Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina
- CONICET, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Av. Godoy Cruz 2290, C1425FQB, Ciudad Autónoma de Buenos Aires, Argentina
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Vollrath P, Chawla HS, Schiessl SV, Gabur I, Lee H, Snowdon RJ, Obermeier C. A novel deletion in FLOWERING LOCUS T modulates flowering time in winter oilseed rape. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1217-1231. [PMID: 33471161 PMCID: PMC7973412 DOI: 10.1007/s00122-021-03768-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/06/2021] [Indexed: 05/05/2023]
Abstract
A novel structural variant was discovered in the FLOWERING LOCUS T orthologue BnaFT.A02 by long-read sequencing. Nested association mapping in an elite winter oilseed rape population revealed that this 288 bp deletion associates with early flowering, putatively by modification of binding-sites for important flowering regulation genes. Perfect timing of flowering is crucial for optimal pollination and high seed yield. Extensive previous studies of flowering behavior in Brassica napus (canola, rapeseed) identified mutations in key flowering regulators which differentiate winter, semi-winter and spring ecotypes. However, because these are generally fixed in locally adapted genotypes, they have only limited relevance for fine adjustment of flowering time in elite cultivar gene pools. In crosses between ecotypes, the ecotype-specific major-effect mutations mask minor-effect loci of interest for breeding. Here, we investigated flowering time in a multiparental mapping population derived from seven elite winter oilseed rape cultivars which are fixed for major-effect mutations separating winter-type rapeseed from other ecotypes. Association mapping revealed eight genomic regions on chromosomes A02, C02 and C03 associating with fine modulation of flowering time. Long-read genomic resequencing of the seven parental lines identified seven structural variants coinciding with candidate genes for flowering time within chromosome regions associated with flowering time. Segregation patterns for these variants in the elite multiparental population and a diversity set of winter types using locus-specific assays revealed significant associations with flowering time for three deletions on chromosome A02. One of these was a previously undescribed 288 bp deletion within the second intron of FLOWERING LOCUS T on chromosome A02, emphasizing the advantage of long-read sequencing for detection of structural variants in this size range. Detailed analysis revealed the impact of this specific deletion on flowering-time modulation under extreme environments and varying day lengths in elite, winter-type oilseed rape.
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Affiliation(s)
- Paul Vollrath
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | - Harmeet S Chawla
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | - Sarah V Schiessl
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | - Iulian Gabur
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | - HueyTyng Lee
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
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Schiessl SV, Quezada-Martinez D, Orantes-Bonilla M, Snowdon RJ. Transcriptomics reveal high regulatory diversity of drought tolerance strategies in a biennial oil crop. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 297:110515. [PMID: 32563455 DOI: 10.1016/j.plantsci.2020.110515] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/23/2020] [Accepted: 04/25/2020] [Indexed: 05/19/2023]
Abstract
Spring droughts are expected to become more frequent in Central Europe as a result of climate change. Their coincidence with flowering of biennial crops like winter oilseed rape (Brassica napus) can cause major impact for yield development. However, no data is available on the diversity of genetic regulation of drought tolerance during this stage under realistic conditions. Here, we assessed the phenotypic plasticity of drought response for eight diverse B. napus accessions under field-like conditions and linked their stress response to gene and miRNA expression during early and late stress. We observed highly diverse responses, both on the phenotypic and on the gene expression level. Our data suggest that drought tolerant accessions have more effective molecular protection mechanisms like ROS scavenging, source/sink ratio and regulation of developmental timing, compared to otherwise phenotypically similar accessions. Bna.MAP3K13.C05 expression was found to be protective independently of the tolerance mechanism, indicating cross-talk to nitrogen signaling. Moreover, we identified putative miRNA genes in the B. napus genome which respond to stress and may also be involved in protective mechanisms, representing possible breeding targets.
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Affiliation(s)
- Sarah V Schiessl
- Department of Plant Breeding, Justus Liebig University, IFZ Research Centre for Biosystems, Land Use and Nutrition, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany; Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.
| | - Daniela Quezada-Martinez
- Department of Plant Breeding, Justus Liebig University, IFZ Research Centre for Biosystems, Land Use and Nutrition, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany.
| | - Mauricio Orantes-Bonilla
- Department of Plant Breeding, Justus Liebig University, IFZ Research Centre for Biosystems, Land Use and Nutrition, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany.
| | - Rod J Snowdon
- Department of Plant Breeding, Justus Liebig University, IFZ Research Centre for Biosystems, Land Use and Nutrition, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany.
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6
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The vernalisation regulator FLOWERING LOCUS C is differentially expressed in biennial and annual Brassica napus. Sci Rep 2019; 9:14911. [PMID: 31624282 PMCID: PMC6797750 DOI: 10.1038/s41598-019-51212-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 09/26/2019] [Indexed: 11/11/2022] Open
Abstract
Plants in temperate areas evolved vernalisation requirement to avoid pre-winter flowering. In Brassicaceae, a period of extended cold reduces the expression of the flowering inhibitor FLOWERING LOCUS C (FLC) and paves the way for the expression of downstream flowering regulators. As with all polyploid species of the Brassicaceae, the model allotetraploid Brassica napus (rapeseed, canola) is highly duplicated and carries 9 annotated copies of Bna.FLC. To investigate whether these multiple homeologs and paralogs have retained their original function in vernalisation or undergone subfunctionalisation, we compared the expression patterns of all 9 copies between vernalisation-dependent (biennial, winter type) and vernalisation-independent (annual, spring type) accessions, using RT-qPCR with copy-specific primers and RNAseq data from a diversity set. Our results show that only 3 copies – Bna.FLC.A03b, Bna.FLC.A10 and to some extent Bna.FLC.C02 – are differentially expressed between the two growth types, showing that expression of the other 6 copies does not correlate with growth type. One of those 6 copies, Bna.FLC.C03b, was not expressed at all, indicating a pseudogene, while three further copies, Bna.FLC.C03a and Bna.FLC.C09ab, did not respond to cold treatment. Sequence variation at the COOLAIR binding site of Bna.FLC.A10 was found to explain most of the variation in gene expression. However, we also found that Bna.FLC.A10 expression is not fully predictive of growth type.
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Schiessl S, Williams N, Specht P, Staiger D, Johansson M. Different copies of SENSITIVITY TO RED LIGHT REDUCED 1 show strong subfunctionalization in Brassica napus. BMC PLANT BIOLOGY 2019; 19:372. [PMID: 31438864 PMCID: PMC6704554 DOI: 10.1186/s12870-019-1973-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 08/13/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Correct timing of flowering is critical for plants to produce enough viable offspring. In Arabidopsis thaliana (Arabidopsis), flowering time is regulated by an intricate network of molecular signaling pathways. Arabidopsis srr1-1 mutants lacking SENSITIVITY TO RED LIGHT REDUCED 1 (SRR1) expression flower early, particularly under short day (SD) conditions (1). SRR1 ensures that plants do not flower prematurely in such non-inductive conditions by controlling repression of the key florigen FT. Here, we have examined the role of SRR1 in the closely related crop species Brassica napus. RESULTS Arabidopsis SRR1 has five homologs in Brassica napus. They can be divided into two groups, where the A02 and C02 copies show high similarity to AtSRR1 on the protein level. The other group, including the A03, A10 and C09 copies all carry a larger deletion in the amino acid sequence. Three of the homologs are expressed at detectable levels: A02, C02 and C09. Notably, the gene copies show a differential expression pattern between spring and winter type accessions of B. napus. When the three expressed gene copies were introduced into the srr1-1 background, only A02 and C02 were able to complement the srr1-1 early flowering phenotype, while C09 could not. Transcriptional analysis of known SRR1 targets in Bna.SRR1-transformed lines showed that CYCLING DOF FACTOR 1 (CDF1) expression is key for flowering time control via SRR1. CONCLUSIONS We observed subfunctionalization of the B. napus SRR1 gene copies, with differential expression between early and late flowering accessions of some Bna.SRR1 copies. This suggests involvement of Bna.SRR1 in regulation of seasonal flowering in B. napus. The C09 gene copy was unable to complement srr1-1 plants, but is highly expressed in B. napus, suggesting specialization of a particular function. Furthermore, the C09 protein carries a deletion which may pinpoint a key region of the SRR1 protein potentially important for its molecular function. This is important evidence of functional domain annotation in the highly conserved but unique SRR1 amino acid sequence.
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Affiliation(s)
- Sarah Schiessl
- Department of Plant Breeding, Justus Liebig University, IFZ Research Centre for Biosystems, Land Use and Nutrition, Heinrich-Buff-Ring 26-32, 35392 Giessen, Giessen, Germany
| | - Natalie Williams
- RNA Biology and Molecular Physiology, Faculty for Biology, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Pascal Specht
- Department of Plant Breeding, Justus Liebig University, IFZ Research Centre for Biosystems, Land Use and Nutrition, Heinrich-Buff-Ring 26-32, 35392 Giessen, Giessen, Germany
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty for Biology, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Mikael Johansson
- RNA Biology and Molecular Physiology, Faculty for Biology, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
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Šamec D, Urlić B, Salopek-Sondi B. Kale ( Brassica oleracea var. acephala) as a superfood: Review of the scientific evidence behind the statement. Crit Rev Food Sci Nutr 2018; 59:2411-2422. [PMID: 29557674 DOI: 10.1080/10408398.2018.1454400] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Kale (Brassica oleracea var. acephala) is a cruciferous vegetable, characterized by leaves along the stem, which, in recent years, have gained a great popularity as a ´superfood´. Consequently, in a popular culture it is listed in many ´lists of the healthiest vegetables´. Without the doubt, a scientific evidences support the fact that cruciferous vegetables included in human diet can positively affect health and well-being, but remains unclear why kale is declared superior in comparison with other cruciferous. It is questionable if this statement about kale is triggered by scientific evidence or by some other factors. Our review aims to bring an overview of kale's botanical characteristics, agronomic requirements, contemporary and traditional use, macronutrient and phytochemical content and biological activity, in order to point out the reasons for tremendous kale popularity.
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Affiliation(s)
- Dunja Šamec
- a Ruđer Bošković Institute, Department for Molecular Biology , Zagreb , Croatia
| | - Branimir Urlić
- b Institute for Adriatic Crops and Karst Reclamation , Split , Croatia
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9
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Friedt W, Tu J, Fu T. Academic and Economic Importance of Brassica napus Rapeseed. COMPENDIUM OF PLANT GENOMES 2018. [DOI: 10.1007/978-3-319-43694-4_1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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10
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Grandke F, Snowdon R, Samans B. gsrc: an R package for genome structure rearrangement calling. Bioinformatics 2017; 33:545-546. [PMID: 27797758 DOI: 10.1093/bioinformatics/btw648] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 10/11/2016] [Indexed: 11/13/2022] Open
Abstract
Summary Genome structure rearrangements are a common phenomenon in allopolyploid species. Deletions, duplications and homeologous non-reciprocal translocations (HNRT) between the highly similar subgenomes can be observed, which are known to have a large impact on phenotypic traits. Current research is limited because these rearrangements can be located genome wide only by cost intensive sequencing approaches and not reliably in high-density array genotyping data. We developed gsrc, an R-package to detect genome structure rearrangements from genotyping data in allopolyploid species including exchanges between subgenomes. We exemplarily apply gsrc to a publicly available Brassica napus dataset. Availability and Implementation The compiled R-package and source code are available at http://cran.r-project.org/web/packages/gsrc/ . Contact birgit.samans@uni-giessen.de. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Fabian Grandke
- Department of Plant Breeding, IFZ Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392 Giessen, Germany
| | - Rod Snowdon
- Department of Plant Breeding, IFZ Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392 Giessen, Germany
| | - Birgit Samans
- Department of Plant Breeding, IFZ Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392 Giessen, Germany
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11
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Schiessl S, Huettel B, Kuehn D, Reinhardt R, Snowdon RJ. Targeted deep sequencing of flowering regulators in Brassica napus reveals extensive copy number variation. Sci Data 2017; 4:170013. [PMID: 28291231 PMCID: PMC5349243 DOI: 10.1038/sdata.2017.13] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/05/2017] [Indexed: 01/23/2023] Open
Abstract
Gene copy number variation (CNV) is increasingly implicated in control of complex trait networks, particularly in polyploid plants like rapeseed (Brassica napus L.) with an evolutionary history of genome restructuring. Here we performed sequence capture to assay nucleotide variation and CNV in a panel of central flowering time regulatory genes across a species-wide diversity set of 280 B. napus accessions. The genes were chosen based on prior knowledge from Arabidopsis thaliana and related Brassica species. Target enrichment was performed using the Agilent SureSelect technology, followed by Illumina sequencing. A bait (probe) pool was developed based on results of a preliminary experiment with representatives from different B. napus morphotypes. A very high mean target coverage of ~670x allowed reliable calling of CNV, single nucleotide polymorphisms (SNPs) and insertion-deletion (InDel) polymorphisms. No accession exhibited no CNV, and at least one homolog of every gene we investigated showed CNV in some accessions. Some CNV appear more often in specific morphotypes, indicating a role in diversification.
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Affiliation(s)
- Sarah Schiessl
- Department of Plant Breeding, Justus Liebig University, IFZ Research Centre for Biosystems, Land Use and Nutrition, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Bruno Huettel
- Max Planck Institute for Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Diana Kuehn
- Max Planck Institute for Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Richard Reinhardt
- Max Planck Institute for Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, Justus Liebig University, IFZ Research Centre for Biosystems, Land Use and Nutrition, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
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12
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Schiessl S, Huettel B, Kuehn D, Reinhardt R, Snowdon R. Post-polyploidisation morphotype diversification associates with gene copy number variation. Sci Rep 2017; 7:41845. [PMID: 28165502 PMCID: PMC5292959 DOI: 10.1038/srep41845] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/03/2017] [Indexed: 11/24/2022] Open
Abstract
Genetic models for polyploid crop adaptation provide important information relevant for future breeding prospects. A well-suited model is Brassica napus, a recent allopolyploid closely related to Arabidopsis thaliana. Flowering time is a major adaptation trait determining life cycle synchronization with the environment. Here we unravel natural genetic variation in B. napus flowering time regulators and investigate associations with evolutionary diversification into different life cycle morphotypes. Deep sequencing of 35 flowering regulators was performed in 280 diverse B. napus genotypes. High sequencing depth enabled high-quality calling of single-nucleotide polymorphisms (SNPs), insertion-deletions (InDels) and copy number variants (CNVs). By combining these data with genotyping data from the Brassica 60 K Illumina® Infinium SNP array, we performed a genome-wide marker distribution analysis across the 4 ecogeographical morphotypes. Twelve haplotypes, including Bna.FLC.A10, Bna.VIN3.A02 and the Bna.FT promoter on C02_random, were diagnostic for the diversification of winter and spring types. The subspecies split between oilseed/kale (B. napus ssp. napus) and swedes/rutabagas (B. napus ssp. napobrassica) was defined by 13 haplotypes, including genomic rearrangements encompassing copies of Bna.FLC, Bna.PHYA and Bna.GA3ox1. De novo variation in copies of important flowering-time genes in B. napus arose during allopolyploidisation, enabling sub-functionalisation that allowed different morphotypes to appropriately fine-tune their lifecycle.
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Affiliation(s)
- Sarah Schiessl
- Department of Plant Breeding, Justus Liebig University, IFZ Research Centre for Biosystems, Land Use and Nutrition, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Bruno Huettel
- Max Planck Institute for Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Diana Kuehn
- Max Planck Institute for Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Richard Reinhardt
- Max Planck Institute for Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Rod Snowdon
- Department of Plant Breeding, Justus Liebig University, IFZ Research Centre for Biosystems, Land Use and Nutrition, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
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Joint genome-wide association and transcriptome sequencing reveals a complex polygenic network underlying hypocotyl elongation in rapeseed (Brassica napus L.). Sci Rep 2017; 7:41561. [PMID: 28139730 PMCID: PMC5282501 DOI: 10.1038/srep41561] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 12/20/2016] [Indexed: 11/08/2022] Open
Abstract
Hypocotyl elongation is considered an important typical seedling trait contributing directly to an increase in and stabilization of the yield in Brassica napus, but its molecular genetic mechanism is poorly understood. In the present study, hypocotyl lengths of 210 lines were measured in an illuminated culture room. A genome-wide association study (GWAS) was performed with 23,435 single nucleotide polymorphisms (SNPs) for hypocotyl length. Three lines with long hypocotyl length and three lines with short hypocotyl length from one doubled haploid line (DH) population were used for transcriptome sequencing. A GWAS followed by transcriptome analysis identified 29 differentially expressed genes associated with significant SNPs in B. napus. These genes regulate hypocotyl elongation by mediating flowering morphogenesis, circadian clock, hormone biosynthesis, or important metabolic signaling pathways. Among these genes, BnaC07g46770D negatively regulates hypocotyl elongation directly, as well as flowering time. Our results indicate that a joint GWAS and transcriptome analysis has significant potential for identifying the genes responsible for hypocotyl elongation; The extension of hypocotyl is a complex biological process regulated by a polygenic network.
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Alcock TD, Havlickova L, He Z, Bancroft I, White PJ, Broadley MR, Graham NS. Identification of Candidate Genes for Calcium and Magnesium Accumulation in Brassica napus L. by Association Genetics. FRONTIERS IN PLANT SCIENCE 2017; 8:1968. [PMID: 29187860 PMCID: PMC5694822 DOI: 10.3389/fpls.2017.01968] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 10/31/2017] [Indexed: 05/07/2023]
Abstract
Calcium (Ca) and magnesium (Mg) are essential plant nutrients and vital for human and animal nutrition. Biofortification of crops has previously been suggested to alleviate widespread human Ca and Mg deficiencies. In this study, new candidate genes influencing the leaf accumulation of Ca and Mg were identified in young Brassica napus plants using associative transcriptomics of ionomics datasets. A total of 247 and 166 SNP markers were associated with leaf Ca and Mg concentration, respectively, after false discovery rate correction and removal of SNPs with low second allele frequency. Gene expression markers at similar positions were also associated with leaf Ca and Mg concentration, including loci on chromosomes A10 and C2, within which lie previously identified transporter genes ACA8 and MGT7. Further candidate genes were selected from seven loci and the mineral composition of whole Arabidopsis thaliana shoots were characterized from lines mutated in orthologous genes. Four and two mutant lines had reduced shoot Ca and Mg concentration, respectively, compared to wild type plants. Three of these mutations were found to have tissue specific effects; notably reduced silique Ca in all three such mutant lines. This knowledge could be applied in targeted breeding, with the possibility of increasing Ca and Mg in plant tissue for improving human and livestock nutrition.
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Affiliation(s)
- Thomas D. Alcock
- Plant and Crop Sciences Division, University of Nottingham, Loughborough, United Kingdom
| | | | - Zhesi He
- Department of Biology, University of York, York, United Kingdom
| | - Ian Bancroft
- Department of Biology, University of York, York, United Kingdom
| | - Philip J. White
- The James Hutton Institute, Dundee, United Kingdom
- Distinguished Scientist Fellowship Program, King Saud University, Riyadh, Saudi Arabia
| | - Martin R. Broadley
- Plant and Crop Sciences Division, University of Nottingham, Loughborough, United Kingdom
| | - Neil S. Graham
- Plant and Crop Sciences Division, University of Nottingham, Loughborough, United Kingdom
- *Correspondence: Neil S. Graham,
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Thomas CL, Alcock TD, Graham NS, Hayden R, Matterson S, Wilson L, Young SD, Dupuy LX, White PJ, Hammond JP, Danku JMC, Salt DE, Sweeney A, Bancroft I, Broadley MR. Root morphology and seed and leaf ionomic traits in a Brassica napus L. diversity panel show wide phenotypic variation and are characteristic of crop habit. BMC PLANT BIOLOGY 2016; 16:214. [PMID: 27716103 PMCID: PMC5050600 DOI: 10.1186/s12870-016-0902-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 09/25/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Mineral nutrient uptake and utilisation by plants are controlled by many traits relating to root morphology, ion transport, sequestration and translocation. The aims of this study were to determine the phenotypic diversity in root morphology and leaf and seed mineral composition of a polyploid crop species, Brassica napus L., and how these traits relate to crop habit. Traits were quantified in a diversity panel of up to 387 genotypes: 163 winter, 127 spring, and seven semiwinter oilseed rape (OSR) habits, 35 swede, 15 winter fodder, and 40 exotic/unspecified habits. Root traits of 14 d old seedlings were measured in a 'pouch and wick' system (n = ~24 replicates per genotype). The mineral composition of 3-6 rosette-stage leaves, and mature seeds, was determined on compost-grown plants from a designed experiment (n = 5) by inductively coupled plasma-mass spectrometry (ICP-MS). RESULTS Seed size explained a large proportion of the variation in root length. Winter OSR and fodder habits had longer primary and lateral roots than spring OSR habits, with generally lower mineral concentrations. A comparison of the ratios of elements in leaf and seed parts revealed differences in translocation processes between crop habits, including those likely to be associated with crop-selection for OSR seeds with lower sulphur-containing glucosinolates. Combining root, leaf and seed traits in a discriminant analysis provided the most accurate characterisation of crop habit, illustrating the interdependence of plant tissues. CONCLUSIONS High-throughput morphological and composition phenotyping reveals complex interrelationships between mineral acquisition and accumulation linked to genetic control within and between crop types (habits) in B. napus. Despite its recent genetic ancestry (<10 ky), root morphology, and leaf and seed composition traits could potentially be used in crop improvement, if suitable markers can be identified and if these correspond with suitable agronomy and quality traits.
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Affiliation(s)
- C. L. Thomas
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
| | - T. D. Alcock
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - N. S. Graham
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - R. Hayden
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - S. Matterson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - L. Wilson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - S. D. Young
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - L. X. Dupuy
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
| | - P. J. White
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
- Distinguished Scientist Fellowship Program, King Saud University, Riyadh, 11451 Kingdom of Saudi Arabia
| | - J. P. Hammond
- School of Agriculture, Policy and Development and the Centre for Food Security, University of Reading, Whiteknights, PO Box 237, Reading, RG6 6AR UK
| | - J. M. C. Danku
- University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UU UK
| | - D. E. Salt
- University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UU UK
| | - A. Sweeney
- Department of Biology, University of York, Heslington, York, YO10 5DD UK
| | - I. Bancroft
- Department of Biology, University of York, Heslington, York, YO10 5DD UK
| | - M. R. Broadley
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
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Thomas CL, Graham NS, Hayden R, Meacham MC, Neugebauer K, Nightingale M, Dupuy LX, Hammond JP, White PJ, Broadley MR. High-throughput phenotyping (HTP) identifies seedling root traits linked to variation in seed yield and nutrient capture in field-grown oilseed rape (Brassica napus L.). ANNALS OF BOTANY 2016; 118:655-665. [PMID: 27052342 PMCID: PMC5055618 DOI: 10.1093/aob/mcw046] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 11/16/2015] [Accepted: 12/21/2015] [Indexed: 05/02/2023]
Abstract
Background and Aims Root traits can be selected for crop improvement. Techniques such as soil excavations can be used to screen root traits in the field, but are limited to genotypes that are well-adapted to field conditions. The aim of this study was to compare a low-cost, high-throughput root phenotyping (HTP) technique in a controlled environment with field performance, using oilseed rape (OSR; Brassica napus) varieties. Methods Primary root length (PRL), lateral root length and lateral root density (LRD) were measured on 14-d-old seedlings of elite OSR varieties (n = 32) using a 'pouch and wick' HTP system (∼40 replicates). Six field experiments were conducted using the same varieties at two UK sites each year for 3 years. Plants were excavated at the 6- to 8-leaf stage for general vigour assessments of roots and shoots in all six experiments, and final seed yield was determined. Leaves were sampled for mineral composition from one of the field experiments. Key Results Seedling PRL in the HTP system correlated with seed yield in four out of six (r = 0·50, 0·50, 0·33, 0·49; P < 0·05) and with emergence in three out of five (r = 0·59, 0·22, 0·49; P < 0·05) field experiments. Seedling LRD correlated positively with leaf concentrations of some minerals, e.g. calcium (r = 0·46; P < 0·01) and zinc (r = 0·58; P < 0·001), but did not correlate with emergence, general early vigour or yield in the field. Conclusions Associations between PRL and field performance are generally related to early vigour. These root traits might therefore be of limited additional selection value, given that vigour can be measured easily on shoots/canopies. In contrast, LRD cannot be assessed easily in the field and, if LRD can improve nutrient uptake, then it may be possible to use HTP systems to screen this trait in both elite and more genetically diverse, non-field-adapted OSR.
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Affiliation(s)
- C. L. Thomas
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - N. S. Graham
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - R. Hayden
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - M. C. Meacham
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - K. Neugebauer
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | | | - L. X. Dupuy
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - J. P. Hammond
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, PO Box 237, Reading RG6 6AR, UK and
| | - P. J. White
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
- Distinguished Scientist Fellowship Program, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia
| | - M. R. Broadley
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
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Körber N, Bus A, Li J, Parkin IAP, Wittkop B, Snowdon RJ, Stich B. Agronomic and Seed Quality Traits Dissected by Genome-Wide Association Mapping in Brassica napus. FRONTIERS IN PLANT SCIENCE 2016; 7:386. [PMID: 27066036 PMCID: PMC4814720 DOI: 10.3389/fpls.2016.00386] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/14/2016] [Indexed: 05/18/2023]
Abstract
In Brassica napus breeding, traits related to commercial success are of highest importance for plant breeders. However, such traits can only be assessed in an advanced developmental stage. Molecular markers genetically linked to such traits have the potential to accelerate the breeding process of B. napus by marker-assisted selection. Therefore, the objectives of this study were to identify (i) genome regions associated with the examined agronomic and seed quality traits, (ii) the interrelationship of population structure and the detected associations, and (iii) candidate genes for the revealed associations. The diversity set used in this study consisted of 405 B. napus inbred lines which were genotyped using a 6K single nucleotide polymorphism (SNP) array and phenotyped for agronomic and seed quality traits in field trials. In a genome-wide association study, we detected a total of 112 associations between SNPs and the seed quality traits as well as 46 SNP-trait associations for the agronomic traits with a P < 1.28e-05 (Bonferroni correction of α = 0.05) for the inbreds of the spring and winter trial. For the seed quality traits, a single SNP-sulfur concentration in seeds (SUL) association explained up to 67.3% of the phenotypic variance, whereas for the agronomic traits, a single SNP-blossom color (BLC) association explained up to 30.2% of the phenotypic variance. In a basic local alignment search tool (BLAST) search within a distance of 2.5 Mbp around these SNP-trait associations, 62 hits of potential candidate genes with a BLAST-score of ≥100 and a sequence identity of ≥70% to A. thaliana or B. rapa could be found for the agronomic SNP-trait associations and 187 hits of potential candidate genes for the seed quality SNP-trait associations.
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Affiliation(s)
- Niklas Körber
- Quantitative Crop Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
- Plant Breeding and Biotechnology, Institute of Crop Science and Resource Conservation, University of BonnBonn, Germany
- *Correspondence: Niklas Körber
| | - Anja Bus
- Quantitative Crop Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
- Plant Breeding and Biotechnology, Institute of Crop Science and Resource Conservation, University of BonnBonn, Germany
| | - Jinquan Li
- Quantitative Crop Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | | | - Benjamin Wittkop
- Department of Plant Breeding, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig UniversityGiessen, Germany
| | - Rod J. Snowdon
- Department of Plant Breeding, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig UniversityGiessen, Germany
| | - Benjamin Stich
- Quantitative Crop Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
- Benjamin Stich
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Schiessl S, Iniguez-Luy F, Qian W, Snowdon RJ. Diverse regulatory factors associate with flowering time and yield responses in winter-type Brassica napus. BMC Genomics 2015; 16:737. [PMID: 26419915 PMCID: PMC4589123 DOI: 10.1186/s12864-015-1950-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 09/23/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Flowering time, plant height and seed yield are strongly influenced by climatic and day-length adaptation in crop plants. To investigate these traits under highly diverse field conditions in the important oilseed crop Brassica napus, we performed a genome-wide association study using data from diverse agroecological environments spanning three continents. METHODS A total of 158 European winter-type B.napus inbred lines were genotyped with 21,623 unique, single-locus single-nucleotide polymorphism (SNP) markers using the Brassica 60 K-SNP Illumina® Infinium consortium array. Phenotypic associations were calculated in the panel over the years 2010-2012 for flowering time, plant height and seed yield in 5 highly diverse locations in Germany, China and Chile, adding up to 11 diverse environments in total. RESULTS We identified 101 genome regions associating with the onset of flowering, 69 with plant height, 36 with seed yield and 68 cross-trait regions with potential adaptive value. Within these regions, B.napus orthologs for a number of candidate adaptation genes were detected, including central circadian clock components like CIRCADIAN CLOCK- ASSOCIATED 1 (Bna.CCA1) and the important flowering-time regulators FLOWERING LOCUS T (Bna.FT) and FRUITFUL (Bna.FUL). DISCUSSION Gene ontology (GO) enrichment analysis of candidate regions suggested that selection of genes involved in post-transcriptional and epigenetic regulation of flowering time may play a potential role in adaptation of B. napus to highly divergent environments. The classical flowering time regulators Bna.FLC and Bna.CO were not found among the candidate regions, although both show functional variation. Allelic effects were additive for plant height and yield, but not for flowering time. The scarcity of positive minor alleles for yield in this breeding pool points to a lack of diversity for adaptation that could restrict yield gain in the face of environmental change. CONCLUSIONS Our study provides a valuable framework to further improve the adaptability and yield stability of this recent allopolyploid crop under changing environments. The results suggest that flowering time regulation within an adapted B. napus breeding pool is driven by a high number of small modulating processes rather than major transcription factors like Bna.CO. In contrast, yield regulation appears highly parallel, therefore yield could be increased by pyramiding positively associated haplotypes.
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Affiliation(s)
- Sarah Schiessl
- Department of Plant Breeding, Justus Liebig University, IFZ Research Centre for Biosystems, Land Use and Nutrition, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| | - Federico Iniguez-Luy
- Agriaquaculture Nutritional Genomic Center (CGNA), Genomics and Bioinformatics Unit, Km 10 Camino Cajón-Vilcún, INIA, Temuco, Chile.
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, 400716, Chongqing, China.
| | - Rod J Snowdon
- Department of Plant Breeding, Justus Liebig University, IFZ Research Centre for Biosystems, Land Use and Nutrition, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
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Körber N, Bus A, Li J, Higgins J, Bancroft I, Higgins EE, Parkin IAP, Salazar-Colqui B, Snowdon RJ, Stich B. Seedling development traits in Brassica napus examined by gene expression analysis and association mapping. BMC PLANT BIOLOGY 2015; 15:136. [PMID: 26055390 PMCID: PMC4459455 DOI: 10.1186/s12870-015-0496-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 04/20/2015] [Indexed: 05/23/2023]
Abstract
BACKGROUND An optimal seedling development of Brassica napus plants leads to a higher yield stability even under suboptimal growing conditions and has therefore a high importance for plant breeders. The objectives of our study were to (i) examine the expression levels of candidate genes in seedling leaves of B. napus and correlate these with seedling development as well as (ii) detect genome regions associated with gene expression levels and seedling development traits in B. napus by genome-wide association mapping. RESULTS The expression levels of the 15 candidate genes examined in the 509 B. napus inbreds showed an averaged standard deviation of 5.6 across all inbreds and ranged from 3.2 to 8.8. The gene expression differences between the 509 B. napus inbreds were more than adequate for the correlation with phenotypic variation of seedling development. The average of the absolute value correlations of the correlation coefficients of 0.11 were observed with a range from 0.00 to 0.39. The candidate genes GER1, AILP1, PECT, and FBP were strongly correlated with the seedling development traits. In a genome-wide association study, we detected a total of 63 associations between single nucleotide polymorphisms (SNPs) and the seedling development traits and 31 SNP-gene associations for the candidate genes with a P-value < 0.0001. For the projected leaf area traits we identified five different association hot spots on the chromosomes A2, A7, C3, C6, and C7. CONCLUSION A total of 99.4% of the adjacent SNPs on the A genome and 93.0% of the adjacent SNPs on the C genome had a distance smaller than the average range of linkage disequilibrium. Therefore, this genome-wide association study is expected to result on average in 14.7% of the possible power. Compared to previous studies in B. napus, the SNP marker density of our study is expected to provide a higher power to detect SNP-trait/-gene associations in the B. napus diversity set. The large number of associations detected for the examined 14 seedling development traits indicated that these are genetically complex inherited. The results of our analyses suggested that the studied genes ribulose 1,5-bisphosphate carboxylase/oxygenase small subunit (RBC) on the chromosomes A4 and C4 and fructose-1,6-bisphosphatase precursor (FBP) on the chromosomes A9 and C8 are cis-regulated.
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Affiliation(s)
- Niklas Körber
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Köln, 50829, Germany.
- Institute of Crop Science and Resource Conservation, Plant Breeding and Biotechnology, University of Bonn, Katzenburgweg 5, Bonn, 53115, Germany.
| | - Anja Bus
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Köln, 50829, Germany.
- Institute of Crop Science and Resource Conservation, Plant Breeding and Biotechnology, University of Bonn, Katzenburgweg 5, Bonn, 53115, Germany.
| | - Jinquan Li
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Köln, 50829, Germany.
| | - Janet Higgins
- The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Ian Bancroft
- John Innes Centre, Norwich Research Park, NR4 7UH, Norwich, UK.
- Department of Biology, Wentworth Way, University of York, Heslington, York, YO41 5DD, UK.
| | - Erin Eileen Higgins
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N OX2, Canada.
| | | | - Bertha Salazar-Colqui
- Department of Plant Breeding, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, Giessen, 35392, Germany.
| | - Rod John Snowdon
- Department of Plant Breeding, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, Giessen, 35392, Germany.
| | - Benjamin Stich
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Köln, 50829, Germany.
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Montoya C, Cochard B, Flori A, Cros D, Lopes R, Cuellar T, Espeout S, Syaputra I, Villeneuve P, Pina M, Ritter E, Leroy T, Billotte N. Genetic architecture of palm oil fatty acid composition in cultivated oil palm (Elaeis guineensis Jacq.) compared to its wild relative E. oleifera (H.B.K) Cortés. PLoS One 2014; 9:e95412. [PMID: 24816555 PMCID: PMC4015976 DOI: 10.1371/journal.pone.0095412] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 03/26/2014] [Indexed: 12/02/2022] Open
Abstract
We searched for quantitative trait loci (QTL) associated with the palm oil fatty acid composition of mature fruits of the oil palm E. guineensis Jacq. in comparison with its wild relative E. oleifera (H.B.K) Cortés. The oil palm cross LM2T x DA10D between two heterozygous parents was considered in our experiment as an intraspecific representative of E. guineensis. Its QTLs were compared to QTLs published for the same traits in an interspecific Elaeis pseudo-backcross used as an indirect representative of E. oleifera. Few correlations were found in E. guineensis between pulp fatty acid proportions and yield traits, allowing for the rather independent selection of both types of traits. Sixteen QTLs affecting palm oil fatty acid proportions and iodine value were identified in oil palm. The phenotypic variation explained by the detected QTLs was low to medium in E. guineensis, ranging between 10% and 36%. The explained cumulative variation was 29% for palmitic acid C16:0 (one QTL), 68% for stearic acid C18:0 (two QTLs), 50% for oleic acid C18:1 (three QTLs), 25% for linoleic acid C18:2 (one QTL), and 40% (two QTLs) for the iodine value. Good marker co-linearity was observed between the intraspecific and interspecific Simple Sequence Repeat (SSR) linkage maps. Specific QTL regions for several traits were found in each mapping population. Our comparative QTL results in both E. guineensis and interspecific materials strongly suggest that, apart from two common QTL zones, there are two specific QTL regions with major effects, which might be one in E. guineensis, the other in E. oleifera, which are independent of each other and harbor QTLs for several traits, indicating either pleiotropic effects or linkage. Using QTL maps connected by highly transferable SSR markers, our study established a good basis to decipher in the future such hypothesis at the Elaeis genus level.
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Affiliation(s)
- Carmenza Montoya
- Oil Palm Biology and Breeding Program, Corporación Centro de Investigación en Palma de Aceite (Cenipalma), Bogotá D.C., Colombia
| | - Benoit Cochard
- Umr Agap, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Montpellier, France
| | - Albert Flori
- Umr Agap, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Montpellier, France
| | - David Cros
- Umr Agap, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Montpellier, France
| | - Ricardo Lopes
- Laboratory of Molecular Biology, Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA), Manaus, Brazil
| | - Teresa Cuellar
- Umr Agap, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Montpellier, France
| | - Sandra Espeout
- Umr Agap, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Montpellier, France
| | - Indra Syaputra
- Agricultural Department, SOCFINDO (PT Socfin-Indonesia), Medan, Indonesia
| | - Pierre Villeneuve
- Umr Iate 1208, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Montpellier, France
| | - Michel Pina
- Umr Iate 1208, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Montpellier, France
| | - Enrique Ritter
- Biotechnology Department, Instituto Vasco de Investigación y Desarrollo Agrario (NEIKER), Vitoria, Spain
| | - Thierry Leroy
- Umr Agap, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Montpellier, France
| | - Norbert Billotte
- Umr Agap, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Montpellier, France
- * E-mail:
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Schiessl S, Samans B, Hüttel B, Reinhard R, Snowdon RJ. Capturing sequence variation among flowering-time regulatory gene homologs in the allopolyploid crop species Brassica napus. FRONTIERS IN PLANT SCIENCE 2014; 5:404. [PMID: 25202314 PMCID: PMC4142343 DOI: 10.3389/fpls.2014.00404] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 07/29/2014] [Indexed: 05/18/2023]
Abstract
Flowering, the transition from the vegetative to the generative phase, is a decisive time point in the lifecycle of a plant. Flowering is controlled by a complex network of transcription factors, photoreceptors, enzymes and miRNAs. In recent years, several studies gave rise to the hypothesis that this network is also strongly involved in the regulation of other important lifecycle processes ranging from germination and seed development through to fundamental developmental and yield-related traits. In the allopolyploid crop species Brassica napus, (genome AACC), homoeologous copies of flowering time regulatory genes are implicated in major phenological variation within the species, however the extent and control of intraspecific and intergenomic variation among flowering-time regulators is still unclear. To investigate differences among B. napus morphotypes in relation to flowering-time gene variation, we performed targeted deep sequencing of 29 regulatory flowering-time genes in four genetically and phenologically diverse B. napus accessions. The genotype panel included a winter-type oilseed rape, a winter fodder rape, a spring-type oilseed rape (all B. napus ssp. napus) and a swede (B. napus ssp. napobrassica), which show extreme differences in winter-hardiness, vernalization requirement and flowering behavior. A broad range of genetic variation was detected in the targeted genes for the different morphotypes, including non-synonymous SNPs, copy number variation and presence-absence variation. The results suggest that this broad variation in vernalization, clock and signaling genes could be a key driver of morphological differentiation for flowering-related traits in this recent allopolyploid crop species.
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Affiliation(s)
- Sarah Schiessl
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, GiessenGiessen, Germany
- *Correspondence: Sarah Schiessl, Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, Giessen 35392, Germany e-mail:
| | - Birgit Samans
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, GiessenGiessen, Germany
| | - Bruno Hüttel
- Max Planck Genome Centre Cologne, Max Planck Institute for Breeding ResearchCologne, Germany
| | - Richard Reinhard
- Max Planck Genome Centre Cologne, Max Planck Institute for Breeding ResearchCologne, Germany
| | - Rod J. Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, GiessenGiessen, Germany
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Bus A, Körber N, Parkin IAP, Samans B, Snowdon RJ, Li J, Stich B. Species- and genome-wide dissection of the shoot ionome in Brassica napus and its relationship to seedling development. FRONTIERS IN PLANT SCIENCE 2014; 5:485. [PMID: 25324847 PMCID: PMC4179769 DOI: 10.3389/fpls.2014.00485] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 09/02/2014] [Indexed: 05/22/2023]
Abstract
Knowing the genetic basis of the plant ionome is essential for understanding the control of nutrient transport and accumulation. The aim of this research was to (i) study mineral nutrient concentrations in a large and diverse set of Brassica napus, (ii) describe the relationships between the shoot ionome and seedling development, and (iii) identify genetic regions associated with variation of the shoot ionome. The plant material under study was a germplasm set consisting of 509 inbred lines that was genotyped by a 6K single nucleotide polymorphism (SNP) array and phenotyped by analyzing the concentrations of eleven mineral nutrients in the shoots of 30 days old seedlings. Among mineral concentrations, positive correlations were found, whereas mineral concentrations were mainly negatively correlated with seedling development traits from earlier studies. In a genome-wide association mapping approach, altogether 29 significantly associated loci were identified across seven traits after correcting for multiple testing. The associations included a locus with effects on the concentrations of Cu, Mn, and Zn on chromosome C3, and a genetic region with multiple associations for Na concentration on chromosome A9. This region was situated within an association hotspot close to SOS1, a key gene for Na tolerance in plants.
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Affiliation(s)
- Anja Bus
- Quantitative Crop Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
- Crop Genetics and Biotechnology Unit, Institute of Crop Science and Resource Conservation, University of BonnBonn, Germany
| | - Niklas Körber
- Quantitative Crop Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
- Crop Genetics and Biotechnology Unit, Institute of Crop Science and Resource Conservation, University of BonnBonn, Germany
| | - Isobel A. P. Parkin
- Saskatoon Research Centre, Agriculture and Agri-Food CanadaSaskatoon, SK, Canada
| | - Birgit Samans
- Department of Plant Breeding, Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig UniversityGiessen, Germany
| | - Rod J. Snowdon
- Department of Plant Breeding, Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig UniversityGiessen, Germany
| | - Jinquan Li
- Quantitative Crop Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Benjamin Stich
- Quantitative Crop Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
- *Correspondence: Benjamin Stich, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany e-mail:
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Clarke WE, Parkin IA, Gajardo HA, Gerhardt DJ, Higgins E, Sidebottom C, Sharpe AG, Snowdon RJ, Federico ML, Iniguez-Luy FL. Genomic DNA enrichment using sequence capture microarrays: a novel approach to discover sequence nucleotide polymorphisms (SNP) in Brassica napus L. PLoS One 2013; 8:e81992. [PMID: 24312619 PMCID: PMC3849492 DOI: 10.1371/journal.pone.0081992] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 10/20/2013] [Indexed: 12/24/2022] Open
Abstract
Targeted genomic selection methodologies, or sequence capture, allow for DNA enrichment and large-scale resequencing and characterization of natural genetic variation in species with complex genomes, such as rapeseed canola (Brassica napus L., AACC, 2n=38). The main goal of this project was to combine sequence capture with next generation sequencing (NGS) to discover single nucleotide polymorphisms (SNPs) in specific areas of the B. napus genome historically associated (via quantitative trait loci –QTL– analysis) to traits of agronomical and nutritional importance. A 2.1 million feature sequence capture platform was designed to interrogate DNA sequence variation across 47 specific genomic regions, representing 51.2 Mb of the Brassica A and C genomes, in ten diverse rapeseed genotypes. All ten genotypes were sequenced using the 454 Life Sciences chemistry and to assess the effect of increased sequence depth, two genotypes were also sequenced using Illumina HiSeq chemistry. As a result, 589,367 potentially useful SNPs were identified. Analysis of sequence coverage indicated a four-fold increased representation of target regions, with 57% of the filtered SNPs falling within these regions. Sixty percent of discovered SNPs corresponded to transitions while 40% were transversions. Interestingly, fifty eight percent of the SNPs were found in genic regions while 42% were found in intergenic regions. Further, a high percentage of genic SNPs was found in exons (65% and 64% for the A and C genomes, respectively). Two different genotyping assays were used to validate the discovered SNPs. Validation rates ranged from 61.5% to 84% of tested SNPs, underpinning the effectiveness of this SNP discovery approach. Most importantly, the discovered SNPs were associated with agronomically important regions of the B. napus genome generating a novel data resource for research and breeding this crop species.
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Affiliation(s)
- Wayne E. Clarke
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Isobel A. Parkin
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Humberto A. Gajardo
- Genomics and Bioinformatics Unit, Agriaquaculture Nutritional Genomic Center (CGNA), Temuco, Louisiana, United States of America Araucanía, Chile
| | | | - Erin Higgins
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Christine Sidebottom
- Plant Biotechnology Institute, National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Andrew G. Sharpe
- Plant Biotechnology Institute, National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Rod J. Snowdon
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | - Maria L. Federico
- Genomics and Bioinformatics Unit, Agriaquaculture Nutritional Genomic Center (CGNA), Temuco, Louisiana, United States of America Araucanía, Chile
| | - Federico L. Iniguez-Luy
- Genomics and Bioinformatics Unit, Agriaquaculture Nutritional Genomic Center (CGNA), Temuco, Louisiana, United States of America Araucanía, Chile
- * E-mail:
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