1
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Weber SE, Roscher-Ehrig L, Kox T, Abbadi A, Stahl A, Snowdon RJ. Genomic prediction in Brassica napus: evaluating the benefit of imputed whole-genome sequencing data. Genome 2024; 67:210-222. [PMID: 38708850 DOI: 10.1139/gen-2023-0126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Advances in sequencing technology allow whole plant genomes to be sequenced with high quality. Combining genotypic and phenotypic data in genomic prediction helps breeders to select crossing partners in partially phenotyped populations. In plant breeding programs, the cost of sequencing entire breeding populations still exceeds available genotyping budgets. Hence, the method for genotyping is still mainly single nucleotide polymorphism (SNP) arrays; however, arrays are unable to assess the entire genome- and population-wide diversity. A compromise involves genotyping the entire population using an SNP array and a subset of the population with whole-genome sequencing. Both datasets can then be used to impute markers from whole-genome sequencing onto the entire population. Here, we evaluate whether imputation of whole-genome sequencing data enhances genomic predictions, using data from a nested association mapping population of rapeseed (Brassica napus). Employing two cross-validation schemes that mimic scenarios for the prediction of close and distant relatives, we show that imputed marker data do not significantly improve prediction accuracy, likely due to redundancy in relationship estimates and imputation errors. In simulation studies, only small improvements were observed, further corroborating the findings. We conclude that SNP arrays are already equipped with the information that is added by imputation through relationship and linkage disequilibrium.
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Affiliation(s)
- Sven E Weber
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Lennard Roscher-Ehrig
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | | | | | - Andreas Stahl
- Julius Kuehn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
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2
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Verwaaijen B, Alcock TD, Spitzer C, Liu Z, Fiebig A, Bienert MD, Bräutigam A, Bienert GP. The Brassica napus boron deficient inflorescence transcriptome resembles a wounding and infection response. PHYSIOLOGIA PLANTARUM 2023; 175:e14088. [PMID: 38148205 DOI: 10.1111/ppl.14088] [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: 05/17/2023] [Revised: 11/02/2023] [Accepted: 11/06/2023] [Indexed: 12/28/2023]
Abstract
Oilseed rape and other crops of Brassica napus have a high demand for boron (B). Boron deficiencies result in the inhibition of root growth, and eventually premature flower abortion. Understanding the genetic mechanisms underlying flower abortion in B-limiting conditions could provide the basis to enhance B-efficiency and prevent B-deficiency-related yield losses. In this study, we assessed transcriptomic responses to B-deficiency in diverse inflorescence tissues at multiple time points of soil-grown plants that were phenotypically unaffected by B-deficiency until early flowering. Whilst transcript levels of known B transporters were higher in B-deficient samples, these remained remarkably stable as the duration of B-deficiency increased. Meanwhile, GO-term enrichment analysis indicated a growing response resembling that of a pathogen or pest attack, escalating to a huge transcriptome response in shoot heads at mid-flowering. Grouping differentially expressed genes within this tissue into MapMan functional bins indicated enrichment of genes related to wounding, jasmonic acid and WRKY transcription factors. Individual candidate genes for controlling the "flowering-without-seed-setting" phenotype from within MapMan biotic stress bins include those of the metacaspase family, which have been implicated in orchestrating programmed cell death. Overall temporal expression patterns observed here imply a dynamic response to B-deficiency, first increasing expression of B transporters before recruiting various biotic stress-related pathways to coordinate targeted cell death, likely in response to as yet unidentified B-deficiency induced damage-associated molecular patterns (DAMPs). This response indicates new pathways to target and dissect to control B-deficiency-induced flower abortion and to develop more B-efficient crops.
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Affiliation(s)
- Bart Verwaaijen
- Computational Biology, Faculty for Biology, Bielefeld University, Bielefeld, Germany
- Center of Biotechnology, Bielefeld University, Bielefeld, Germany
- Department of Genetics, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Thomas David Alcock
- Crop Physiology, School of Life Sciences, Technical University of Munich, Freising, Germany
- HEF World Agricultural Systems Center, Technical University of Munich, Freising, Germany
| | - Christoph Spitzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Germany
| | - Zhaojun Liu
- Crop Physiology, School of Life Sciences, Technical University of Munich, Freising, Germany
- HEF World Agricultural Systems Center, Technical University of Munich, Freising, Germany
| | - Anne Fiebig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Germany
| | - Manuela Désirée Bienert
- HEF World Agricultural Systems Center, Technical University of Munich, Freising, Germany
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Germany
| | - Andrea Bräutigam
- Computational Biology, Faculty for Biology, Bielefeld University, Bielefeld, Germany
- Center of Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Gerd Patrick Bienert
- Crop Physiology, School of Life Sciences, Technical University of Munich, Freising, Germany
- HEF World Agricultural Systems Center, Technical University of Munich, Freising, Germany
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3
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Liu H, Zhao W, Hua W, Liu J. A large-scale population based organelle pan-genomes construction and phylogeny analysis reveal the genetic diversity and the evolutionary origins of chloroplast and mitochondrion in Brassica napus L. BMC Genomics 2022; 23:339. [PMID: 35501686 PMCID: PMC9063048 DOI: 10.1186/s12864-022-08573-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 04/19/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Allotetraploid oilseed rape (Brassica napus L.) is an important worldwide oil-producing crop. The origin of rapeseed is still undetermined due to the lack of wild resources. Despite certain genetic architecture and phylogenetic studies have been done focus on large group of Brassica nuclear genomes, the organelle genomes information under global pattern is largely unknown, which provide unique material for phylogenetic studies of B. napus. Here, based on de novo assemblies of 1,579 B. napus accessions collected globally, we constructed the chloroplast and mitochondrial pan-genomes of B. napus, and investigated the genetic diversity, phylogenetic relationships of B. napus, B. rapa and B. oleracea. RESULTS Based on mitotype-specific markers and mitotype-variant ORFs, four main cytoplasmic haplotypes were identified in our groups corresponding the nap, pol, ole, and cam mitotypes, among which the structure of chloroplast genomes was more conserved without any rearrangement than mitochondrial genomes. A total of 2,092 variants were detected in chloroplast genomes, whereas only 326 in mitochondrial genomes, indicating that chloroplast genomes exhibited a higher level of single-base polymorphism than mitochondrial genomes. Based on whole-genome variants diversity analysis, eleven genetic difference regions among different cytoplasmic haplotypes were identified on chloroplast genomes. The phylogenetic tree incorporating accessions of the B. rapa, B. oleracea, natural and synthetic populations of B. napus revealed multiple origins of B. napus cytoplasm. The cam-type and pol-type were both derived from B. rapa, while the ole-type was originated from B. oleracea. Notably, the nap-type cytoplasm was identified in both the B. rapa population and the synthetic B. napus, suggesting that B. rapa might be the maternal ancestor of nap-type B. napus. CONCLUSIONS The phylogenetic results provide novel insights into the organelle genomic evolution of Brassica species. The natural rapeseeds contained at least four cytoplastic haplotypes, of which the predominant nap-type might be originated from B. rapa. Besides, the organelle pan-genomes and the overall variation data offered useful resources for analysis of cytoplasmic inheritance related agronomical important traits of rapeseed, which can substantially facilitate the cultivation and improvement of rapeseed varieties.
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Affiliation(s)
- Hongfang Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Wei Zhao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Wei Hua
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, China.
| | - Jing Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, China.
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4
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Bayer PE, Scheben A, Golicz AA, Yuan Y, Faure S, Lee H, Chawla HS, Anderson R, Bancroft I, Raman H, Lim YP, Robbens S, Jiang L, Liu S, Barker MS, Schranz ME, Wang X, King GJ, Pires JC, Chalhoub B, Snowdon RJ, Batley J, Edwards D. Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2488-2500. [PMID: 34310022 PMCID: PMC8633514 DOI: 10.1111/pbi.13674] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/11/2021] [Accepted: 07/20/2021] [Indexed: 05/26/2023]
Abstract
Plant genomes demonstrate significant presence/absence variation (PAV) within a species; however, the factors that lead to this variation have not been studied systematically in Brassica across diploids and polyploids. Here, we developed pangenomes of polyploid Brassica napus and its two diploid progenitor genomes B. rapa and B. oleracea to infer how PAV may differ between diploids and polyploids. Modelling of gene loss suggests that loss propensity is primarily associated with transposable elements in the diploids while in B. napus, gene loss propensity is associated with homoeologous recombination. We use these results to gain insights into the different causes of gene loss, both in diploids and following polyploidization, and pave the way for the application of machine learning methods to understanding the underlying biological and physical causes of gene presence/absence.
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Affiliation(s)
- Philipp E. Bayer
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Armin Scheben
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Agnieszka A. Golicz
- Plant Molecular Biology and Biotechnology LaboratoryFaculty of Veterinary and Agricultural SciencesUniversity of MelbourneParkvilleVICAustralia
| | - Yuxuan Yuan
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | | | - HueyTyng Lee
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig University GiessenGiessenGermany
| | - Harmeet Singh Chawla
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig University GiessenGiessenGermany
| | - Robyn Anderson
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | | | - Harsh Raman
- NSW Department of Primary IndustriesWagga Wagga Agricultural Institute, PMBWagga WaggaNSWAustralia
| | - Yong Pyo Lim
- Department of HorticultureChungnam National UniversityDaejeonSouth Korea
| | | | - Lixi Jiang
- Institute of crop scienceDepartment of Agronomy and Plant BreedingZhejiang UniversityHangzhouChina
| | - Shengyi Liu
- Chinese Academy of Agricultural SciencesOil Crops Research InstituteWuhanChina
| | - Michael S. Barker
- Department of Ecology & Evolutionary BiologyUniversity of ArizonaTucsonAZUSA
| | - M. Eric Schranz
- Biosystematics GroupWageningen University and Research CenterWageningenThe Netherlands
| | - Xiaowu Wang
- Institute of Vegetables and FlowersChinese Academy of Agricultural Sciences (IVF, CAAS)BeijingChina
| | - Graham J. King
- Southern Cross Plant ScienceSouthern Cross UniversityLismoreNSWAustralia
| | - J. Chris Pires
- Division of Biological SciencesBond Life Sciences CenterUniversity of MissouriColumbiaMissouriUSA
| | - Boulos Chalhoub
- Institute of crop scienceDepartment of Agronomy and Plant BreedingZhejiang UniversityHangzhouChina
| | - Rod J. Snowdon
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig University GiessenGiessenGermany
| | - Jacqueline Batley
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - David Edwards
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
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5
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Hu D, Jing J, Snowdon RJ, Mason AS, Shen J, Meng J, Zou J. Exploring the gene pool of Brassica napus by genomics-based approaches. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1693-1712. [PMID: 34031989 PMCID: PMC8428838 DOI: 10.1111/pbi.13636] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 05/08/2023]
Abstract
De novo allopolyploidization in Brassica provides a very successful model for reconstructing polyploid genomes using progenitor species and relatives to broaden crop gene pools and understand genome evolution after polyploidy, interspecific hybridization and exotic introgression. B. napus (AACC), the major cultivated rapeseed species and the third largest oilseed crop in the world, is a young Brassica species with a limited genetic base resulting from its short history of domestication, cultivation, and intensive selection during breeding for target economic traits. However, the gene pool of B. napus has been significantly enriched in recent decades that has been benefit from worldwide effects by the successful introduction of abundant subgenomic variation and novel genomic variation via intraspecific, interspecific and intergeneric crosses. An important question in this respect is how to utilize such variation to breed crops adapted to the changing global climate. Here, we review the genetic diversity, genome structure, and population-level differentiation of the B. napus gene pool in relation to known exotic introgressions from various species of the Brassicaceae, especially those elucidated by recent genome-sequencing projects. We also summarize progress in gene cloning, trait-marker associations, gene editing, molecular marker-assisted selection and genome-wide prediction, and describe the challenges and opportunities of these techniques as molecular platforms to exploit novel genomic variation and their value in the rapeseed gene pool. Future progress will accelerate the creation and manipulation of genetic diversity with genomic-based improvement, as well as provide novel insights into the neo-domestication of polyploid crops with novel genetic diversity from reconstructed genomes.
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Affiliation(s)
- Dandan Hu
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jinjie Jing
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Rod J. Snowdon
- Department of Plant BreedingIFZ Research Centre for Biosystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Annaliese S. Mason
- Department of Plant BreedingIFZ Research Centre for Biosystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
- Plant Breeding DepartmentINRESThe University of BonnBonnGermany
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jinling Meng
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jun Zou
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
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6
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Raza A, Razzaq A, Mehmood SS, Hussain MA, Wei S, He H, Zaman QU, Xuekun Z, Hasanuzzaman M. Omics: The way forward to enhance abiotic stress tolerance in Brassica napus L. GM CROPS & FOOD 2021; 12:251-281. [PMID: 33464960 PMCID: PMC7833762 DOI: 10.1080/21645698.2020.1859898] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Plant abiotic stresses negative affects growth and development, causing a massive reduction in global agricultural production. Rapeseed (Brassica napus L.) is a major oilseed crop because of its economic value and oilseed production. However, its productivity has been reduced by many environmental adversities. Therefore, it is a prime need to grow rapeseed cultivars, which can withstand numerous abiotic stresses. To understand the various molecular and cellular mechanisms underlying the abiotic stress tolerance and improvement in rapeseed, omics approaches have been extensively employed in recent years. This review summarized the recent advancement in genomics, transcriptomics, proteomics, metabolomics, and their imploration in abiotic stress regulation in rapeseed. Some persisting bottlenecks have been highlighted, demanding proper attention to fully explore the omics tools. Further, the potential prospects of the CRISPR/Cas9 system for genome editing to assist molecular breeding in developing abiotic stress-tolerant rapeseed genotypes have also been explained. In short, the combination of integrated omics, genome editing, and speed breeding can alter rapeseed production worldwide.
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Affiliation(s)
- Ali Raza
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS) , Wuhan, China
| | - Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture , Faisalabad, Pakistan
| | - Sundas Saher Mehmood
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS) , Wuhan, China
| | - Muhammad Azhar Hussain
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS) , Wuhan, China
| | - Su Wei
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS) , Wuhan, China
| | - Huang He
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS) , Wuhan, China
| | - Qamar U Zaman
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS) , Wuhan, China
| | - Zhang Xuekun
- College of Agriculture, Engineering Research Center of Ecology and Agricultural Use of Wetland of Ministry of Education, Yangtze University Jingzhou , China
| | - Mirza Hasanuzzaman
- Department of Agronomy, Faculty of Agriculture, Sher-e-Bangla Agricultural University , Dhaka, Bangladesh
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7
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Bu S, Wu W, Zhang YM. A Multi-Locus Association Model Framework for Nested Association Mapping With Discriminating QTL Effects in Various Subpopulations. Front Genet 2021; 11:590012. [PMID: 33537057 PMCID: PMC7848182 DOI: 10.3389/fgene.2020.590012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 12/04/2020] [Indexed: 11/13/2022] Open
Abstract
Nested association mapping (NAM) has been an invaluable approach for plant genetics community and can dissect the genetic architecture of complex traits. As the most popular NAM analysis strategy, joint multifamily mapping can combine all information from diverse genetic backgrounds and increase population size. However, it is influenced by the genetic heterogeneity of quantitative trait locus (QTL) across various subpopulations. Multi-locus association mapping has been proven to be powerful in many cases of QTL mapping and genome-wide association studies. Therefore, we developed a multi-locus association model of multiple families in the NAM population, which could discriminate the effects of QTLs in all subpopulations. A series of simulations with a real maize NAM genomic data were implemented. The results demonstrated that the new method improves the statistical power in QTL detection and the accuracy in QTL effect estimation. The new approach, along with single-family linkage mapping, was used to identify QTLs for three flowering time traits in the maize NAM population. As a result, most QTLs detected in single family linkage mapping were identified by the new method. In addition, the new method also mapped some new QTLs with small effects, although their functions need to be identified in the future.
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Affiliation(s)
- Suhong Bu
- College of Agriculture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weiren Wu
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuan-Ming Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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8
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Scott MF, Ladejobi O, Amer S, Bentley AR, Biernaskie J, Boden SA, Clark M, Dell'Acqua M, Dixon LE, Filippi CV, Fradgley N, Gardner KA, Mackay IJ, O'Sullivan D, Percival-Alwyn L, Roorkiwal M, Singh RK, Thudi M, Varshney RK, Venturini L, Whan A, Cockram J, Mott R. Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding. Heredity (Edinb) 2020; 125:396-416. [PMID: 32616877 PMCID: PMC7784848 DOI: 10.1038/s41437-020-0336-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 06/16/2020] [Accepted: 06/16/2020] [Indexed: 11/21/2022] Open
Abstract
Crop populations derived from experimental crosses enable the genetic dissection of complex traits and support modern plant breeding. Among these, multi-parent populations now play a central role. By mixing and recombining the genomes of multiple founders, multi-parent populations combine many commonly sought beneficial properties of genetic mapping populations. For example, they have high power and resolution for mapping quantitative trait loci, high genetic diversity and minimal population structure. Many multi-parent populations have been constructed in crop species, and their inbred germplasm and associated phenotypic and genotypic data serve as enduring resources. Their utility has grown from being a tool for mapping quantitative trait loci to a means of providing germplasm for breeding programmes. Genomics approaches, including de novo genome assemblies and gene annotations for the population founders, have allowed the imputation of rich sequence information into the descendent population, expanding the breadth of research and breeding applications of multi-parent populations. Here, we report recent successes from crop multi-parent populations in crops. We also propose an ideal genotypic, phenotypic and germplasm 'package' that multi-parent populations should feature to optimise their use as powerful community resources for crop research, development and breeding.
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Affiliation(s)
| | | | - Samer Amer
- University of Reading, Reading, RG6 6AH, UK
- Faculty of Agriculture, Alexandria University, Alexandria, 23714, Egypt
| | - Alison R Bentley
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Jay Biernaskie
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Scott A Boden
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | | | | | - Laura E Dixon
- Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Carla V Filippi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET, Nicolas Repetto y Los Reseros s/n, 1686, Hurlingham, Buenos Aires, Argentina
| | - Nick Fradgley
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Keith A Gardner
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Ian J Mackay
- SRUC, West Mains Road, Kings Buildings, Edinburgh, EH9 3JG, UK
| | | | | | - Manish Roorkiwal
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rakesh Kumar Singh
- International Center for Biosaline Agriculture, Academic City, Dubai, United Arab Emirates
| | - Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev Kumar Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Alex Whan
- CSIRO, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - James Cockram
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Richard Mott
- UCL Genetics Institute, Gower Street, London, WC1E 6BT, UK
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9
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Yang S, Gill RA, Zaman QU, Ulhassan Z, Zhou W. Insights on SNP types, detection methods and their utilization in Brassica species: Recent progress and future perspectives. J Biotechnol 2020; 324:11-20. [PMID: 32979432 DOI: 10.1016/j.jbiotec.2020.09.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 09/15/2020] [Accepted: 09/20/2020] [Indexed: 01/09/2023]
Abstract
The genus Brassica, family Brassicaceae (Cruciferae), comprises many important species of oil crops, vegetables and medicinal plants including B. rapa, B. oleracea, B. nigra, B. napus, B. juncea, B. carinata. Genomic researches in Brassica species is constrained by polyploidization, mainly due to its complicated genomic structure. However, rapid development of methods for detecting single nucleotide polymorphisms (SNP), such as next generation sequencing and SNP microarray, has accelerated release of reference Brassica species genomes as well as discovery of large numbers and genome-wide SNPs, thus intensifying forward genetics in this genus. In this review, we summarize biological characteristics, classification and various methods for detecting SNPs, focusing on high-throughput techniques. Moreover, we describe the pivotal roles of SNPs in genetic diversity, linkage map construction and QTL mapping, comparative genomics, linkage disequilibrium and genome-wide association studies. These insights are expected to deepen our understanding and guide further advancements in Brassica species research.
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Affiliation(s)
- Su Yang
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Rafaqat Ali Gill
- Oil Crops Research Institute, Chinese Academy of Agricultural Science, Wuhan 430062, China.
| | - Qamar U Zaman
- Oil Crops Research Institute, Chinese Academy of Agricultural Science, Wuhan 430062, China
| | - Zaid Ulhassan
- Institute of Crop Science, Ministry of Agriculture and Rural Affairs Laboratory of Spectroscopy Sensing, Zhejiang University, Hangzhou 310058, China
| | - Weijun Zhou
- Institute of Crop Science, Ministry of Agriculture and Rural Affairs Laboratory of Spectroscopy Sensing, Zhejiang University, Hangzhou 310058, China
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10
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Gabur I, Chawla HS, Lopisso DT, von Tiedemann A, Snowdon RJ, Obermeier C. Gene presence-absence variation associates with quantitative Verticillium longisporum disease resistance in Brassica napus. Sci Rep 2020; 10:4131. [PMID: 32139810 PMCID: PMC7057980 DOI: 10.1038/s41598-020-61228-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 02/07/2020] [Indexed: 12/31/2022] Open
Abstract
Although copy number variation (CNV) and presence-absence variation (PAV) have been discovered in selected gene families in most crop species, the global prevalence of these polymorphisms in most complex genomes is still unclear and their influence on quantitatively inherited agronomic traits is still largely unknown. Here we analyze the association of gene PAV with resistance of oilseed rape (Brassica napus) against the important fungal pathogen Verticillium longisporum, as an example for a complex, quantitative disease resistance in the strongly rearranged genome of a recent allopolyploid crop species. Using Single Nucleotide absence Polymorphism (SNaP) markers to efficiently trace PAV in breeding populations, we significantly increased the resolution of loci influencing V. longisporum resistance in biparental and multi-parental mapping populations. Gene PAV, assayed by resequencing mapping parents, was observed in 23-51% of the genes within confidence intervals of quantitative trait loci (QTL) for V. longisporum resistance, and high-priority candidate genes identified within QTL were all affected by PAV. The results demonstrate the prominent role of gene PAV in determining agronomic traits, suggesting that this important class of polymorphism should be exploited more systematically in future plant breeding.
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Affiliation(s)
- Iulian Gabur
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Harmeet Singh Chawla
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Daniel Teshome Lopisso
- Section of General Plant Pathology and Crop Protection, Georg August University Göttingen, 37077, Göttingen, Germany
- College of Agriculture and Veterinary Medicine, Jimma University, Jimma, Ethiopia
| | - Andreas von Tiedemann
- Section of General Plant Pathology and Crop Protection, Georg August University Göttingen, 37077, Göttingen, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Christian Obermeier
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, 35392, Giessen, Germany.
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11
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Diehn TA, Bienert MD, Pommerrenig B, Liu Z, Spitzer C, Bernhardt N, Fuge J, Bieber A, Richet N, Chaumont F, Bienert GP. Boron demanding tissues of Brassica napus express specific sets of functional Nodulin26-like Intrinsic Proteins and BOR1 transporters. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:68-82. [PMID: 31148338 PMCID: PMC6852077 DOI: 10.1111/tpj.14428] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/01/2019] [Accepted: 05/28/2019] [Indexed: 05/22/2023]
Abstract
The sophisticated uptake and translocation regulation of the essential element boron (B) in plants is ensured by two transmembrane transporter families: the Nodulin26-like Intrinsic Protein (NIP) and BOR transporter family. Though the agriculturally important crop Brassica napus is highly sensitive to B deficiency, and NIPs and BORs have been suggested to be responsible for B efficiency in this species, functional information of these transporter subfamilies is extremely rare. Here, we molecularly characterized the NIP and BOR1 transporter family in the European winter-type cv. Darmor-PBY018. Our transport assays in the heterologous oocyte and yeast expression systems as well as in growth complementation assays in planta demonstrated B transport activity of NIP5, NIP6, NIP7 and BOR1 isoforms. Moreover, we provided functional and quantitative evidence that also members of the NIP2, NIP3 and NIP4 groups facilitate the transport of B. A detailed B- and tissue-dependent B-transporter expression map was generated by quantitative polymerase chain reaction. We showed that NIP5 isoforms are highly upregulated under B-deficient conditions in roots, but also in shoot tissues. Moreover, we detected transcripts of several B-permeable NIPs from various groups in floral tissues that contribute to the B distribution within the highly B deficiency-sensitive flowers.
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Affiliation(s)
- Till Arvid Diehn
- Metalloid Transport, Department of Physiology and Cell BiologyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466Germany
| | - Manuela Désirée Bienert
- Metalloid Transport, Department of Physiology and Cell BiologyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466Germany
| | - Benjamin Pommerrenig
- Metalloid Transport, Department of Physiology and Cell BiologyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466Germany
- Division of Plant PhysiologyUniversity KaiserslauternKaiserslautern67663Germany
| | - Zhaojun Liu
- Metalloid Transport, Department of Physiology and Cell BiologyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466Germany
| | - Christoph Spitzer
- Metalloid Transport, Department of Physiology and Cell BiologyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466Germany
| | - Nadine Bernhardt
- Experimental Taxonomy, Genebank DepartmentLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466Germany
| | - Jacqueline Fuge
- Metalloid Transport, Department of Physiology and Cell BiologyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466Germany
| | - Annett Bieber
- Metalloid Transport, Department of Physiology and Cell BiologyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466Germany
| | - Nicolas Richet
- Louvain Institute of Biomolecular Science and TechnologyUCLouvainLouvain‐la‐Neuve1348Belgium
| | - François Chaumont
- Louvain Institute of Biomolecular Science and TechnologyUCLouvainLouvain‐la‐Neuve1348Belgium
| | - Gerd Patrick Bienert
- Metalloid Transport, Department of Physiology and Cell BiologyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466Germany
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12
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Zou J, Mao L, Qiu J, Wang M, Jia L, Wu D, He Z, Chen M, Shen Y, Shen E, Huang Y, Li R, Hu D, Shi L, Wang K, Zhu Q, Ye C, Bancroft I, King GJ, Meng J, Fan L. Genome-wide selection footprints and deleterious variations in young Asian allotetraploid rapeseed. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1998-2010. [PMID: 30947395 PMCID: PMC6737024 DOI: 10.1111/pbi.13115] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 02/16/2019] [Accepted: 03/13/2019] [Indexed: 05/19/2023]
Abstract
Brassica napus (AACC, 2n = 38) is an important oilseed crop grown worldwide. However, little is known about the population evolution of this species, the genomic difference between its major genetic groups, such as European and Asian rapeseed, and the impacts of historical large-scale introgression events on this young tetraploid. In this study, we reported the de novo assembly of the genome sequences of an Asian rapeseed (B. napus), Ningyou 7, and its four progenitors and compared these genomes with other available genomic data from diverse European and Asian cultivars. Our results showed that Asian rapeseed originally derived from European rapeseed but subsequently significantly diverged, with rapid genome differentiation after hybridization and intensive local selective breeding. The first historical introgression of B. rapa dramatically broadened the allelic pool but decreased the deleterious variations of Asian rapeseed. The second historical introgression of the double-low traits of European rapeseed (canola) has reshaped Asian rapeseed into two groups (double-low and double-high), accompanied by an increase in genetic load in the double-low group. This study demonstrates distinctive genomic footprints and deleterious SNP (single nucleotide polymorphism) variants for local adaptation by recent intra- and interspecies introgression events and provides novel insights for understanding the rapid genome evolution of a young allopolyploid crop.
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Affiliation(s)
- Jun Zou
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Lingfeng Mao
- Institute of Crop Sciences & Institute of BioinformaticsZhejiang UniversityHangzhouChina
| | - Jie Qiu
- Institute of Crop Sciences & Institute of BioinformaticsZhejiang UniversityHangzhouChina
| | - Meng Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Lei Jia
- Institute of Crop Sciences & Institute of BioinformaticsZhejiang UniversityHangzhouChina
| | - Dongya Wu
- Institute of Crop Sciences & Institute of BioinformaticsZhejiang UniversityHangzhouChina
| | - Zhesi He
- Department of BiologyYork UniversityHeslingtonUK
| | - Meihong Chen
- Institute of Crop Sciences & Institute of BioinformaticsZhejiang UniversityHangzhouChina
| | - Yifei Shen
- Institute of Crop Sciences & Institute of BioinformaticsZhejiang UniversityHangzhouChina
| | - Enhui Shen
- Institute of Crop Sciences & Institute of BioinformaticsZhejiang UniversityHangzhouChina
| | - Yongji Huang
- Center for Genomics and BiotechnologyHaixia Institute of Science and Technology (HIST)Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Ruiyuan Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Dandan Hu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Lei Shi
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Kai Wang
- Center for Genomics and BiotechnologyHaixia Institute of Science and Technology (HIST)Fujian Agriculture and Forestry UniversityFuzhouChina
| | | | - Chuyu Ye
- Institute of Crop Sciences & Institute of BioinformaticsZhejiang UniversityHangzhouChina
| | - Ian Bancroft
- Department of BiologyYork UniversityHeslingtonUK
| | - Graham J. King
- Southern Cross Plant ScienceSouthern Cross UniversityLismoreNSWAustralia
| | - Jinling Meng
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Longjiang Fan
- Institute of Crop Sciences & Institute of BioinformaticsZhejiang UniversityHangzhouChina
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13
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Malmberg MM, Spangenberg GC, Daetwyler HD, Cogan NOI. Assessment of low-coverage nanopore long read sequencing for SNP genotyping in doubled haploid canola (Brassica napus L.). Sci Rep 2019; 9:8688. [PMID: 31213642 PMCID: PMC6582154 DOI: 10.1038/s41598-019-45131-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/28/2019] [Indexed: 11/16/2022] Open
Abstract
Despite the high accuracy of short read sequencing (SRS), there are still issues with attaining accurate single nucleotide polymorphism (SNP) genotypes at low sequencing coverage and in highly duplicated genomes due to misalignment. Long read sequencing (LRS) systems, including the Oxford Nanopore Technologies (ONT) minION, have become popular options for de novo genome assembly and structural variant characterisation. The current high error rate often requires substantial post-sequencing correction and would appear to prevent the adoption of this system for SNP genotyping, but nanopore sequencing errors are largely random. Using low coverage ONT minION sequencing for genotyping of pre-validated SNP loci was examined in 9 canola doubled haploids. The minION genotypes were compared to the Illumina sequences to determine the extent and nature of genotype discrepancies between the two systems. The significant increase in read length improved alignment to the genome and the absence of classical SRS biases results in a more even representation of the genome. Sequencing errors are present, primarily in the form of heterozygous genotypes, which can be removed in completely homozygous backgrounds but requires more advanced bioinformatics in heterozygous genomes. Developments in this technology are promising for routine genotyping in the future.
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Affiliation(s)
- M M Malmberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - G C Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - H D Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - N O I Cogan
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria, 3083, Australia. .,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3086, Australia.
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14
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Scheben A, Verpaalen B, Lawley CT, Chan CKK, Bayer PE, Batley J, Edwards D. CropSNPdb: a database of SNP array data for Brassica crops and hexaploid bread wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:142-152. [PMID: 30548723 DOI: 10.1111/tpj.14194] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 05/23/2023]
Abstract
Advances in sequencing technology have led to a rapid rise in the genomic data available for plants, driving new insights into the evolution, domestication and improvement of crops. Single nucleotide polymorphisms (SNPs) are a major component of crop genomic diversity, and are invaluable as genetic markers in research and breeding programs. High-throughput SNP arrays, or 'SNP chips', can generate reproducible sets of informative SNP markers and have been broadly adopted. Although there are many public repositories for sequencing data, which are routinely uploaded, there are no formal repositories for crop SNP array data. To make SNP array data more easily accessible, we have developed CropSNPdb (http://snpdb.appliedbioinformatics.com.au), a database for SNP array data produced by the Illumina Infinium™ hexaploid bread wheat (Triticum aestivum) 90K and Brassica 60K arrays. We currently host SNPs from datasets covering 526 Brassica lines and 309 bread wheat lines, and provide search, download and upload utilities for users. CropSNPdb provides a useful repository for these data, which can be applied for a range of genomics and molecular crop-breeding activities.
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Affiliation(s)
- Armin Scheben
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Brent Verpaalen
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | | | - Chon-Kit K Chan
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
- Australian Genome Research Facility, Melbourne, Vic., 3000, Australia
| | - Philipp E Bayer
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
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15
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Gabur I, Chawla HS, Liu X, Kumar V, Faure S, von Tiedemann A, Jestin C, Dryzska E, Volkmann S, Breuer F, Delourme R, Snowdon R, Obermeier C. Finding invisible quantitative trait loci with missing data. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:2102-2112. [PMID: 29729219 PMCID: PMC6230954 DOI: 10.1111/pbi.12942] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/26/2018] [Accepted: 04/28/2018] [Indexed: 05/21/2023]
Abstract
Evolutionary processes during plant polyploidization and speciation have led to extensive presence-absence variation (PAV) in crop genomes, and there is increasing evidence that PAV associates with important traits. Today, high-resolution genetic analysis in major crops frequently implements simple, cost-effective, high-throughput genotyping from single nucleotide polymorphism (SNP) hybridization arrays; however, these are normally not designed to distinguish PAV from failed SNP calls caused by hybridization artefacts. Here, we describe a strategy to recover valuable information from single nucleotide absence polymorphisms (SNaPs) by population-based quality filtering of SNP hybridization data to distinguish patterns associated with genuine deletions from those caused by technical failures. We reveal that including SNaPs in genetic analyses elucidate segregation of small to large-scale structural variants in nested association mapping populations of oilseed rape (Brassica napus), a recent polyploid crop with widespread structural variation. Including SNaP markers in genomewide association studies identified numerous quantitative trait loci, invisible using SNP markers alone, for resistance to two major fungal diseases of oilseed rape, Sclerotinia stem rot and blackleg disease. Our results indicate that PAV has a strong influence on quantitative disease resistance in B. napus and that SNaP analysis using cost-effective SNP array data can provide extensive added value from 'missing data'. This strategy might also be applicable for improving the precision of genetic mapping in many important crop species.
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Affiliation(s)
- Iulian Gabur
- Department of Plant BreedingJustus Liebig UniversityGiessenGermany
| | | | - Xiwei Liu
- Department of Plant BreedingJustus Liebig UniversityGiessenGermany
| | - Vinod Kumar
- IGEPP, INRA, AGROCAMPUS OUESTUniv RennesLe RheuFrance
| | | | - Andreas von Tiedemann
- Section of General Plant Pathology and Crop ProtectionGeorg August UniversityGöttingenGermany
| | | | | | | | | | | | - Rod Snowdon
- Department of Plant BreedingJustus Liebig UniversityGiessenGermany
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16
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Pommerrenig B, Junker A, Abreu I, Bieber A, Fuge J, Willner E, Bienert MD, Altmann T, Bienert GP. Identification of Rapeseed ( Brassica napus) Cultivars With a High Tolerance to Boron-Deficient Conditions. FRONTIERS IN PLANT SCIENCE 2018; 9:1142. [PMID: 30131820 PMCID: PMC6091279 DOI: 10.3389/fpls.2018.01142] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 07/17/2018] [Indexed: 05/22/2023]
Abstract
Boron (B) is an essential micronutrient for seed plants. Information on B-efficiency mechanisms and B-efficient crop and model plant genotypes is very scarce. Studies evaluating the basis and consequences of B-deficiency and B-efficiency are limited by the facts that B occurs as a trace contaminant essentially everywhere, its bioavailability is difficult to control and soil-based B-deficiency growth systems allowing a high-throughput screening of plant populations have hitherto been lacking. The crop plant Brassica napus shows a very high sensitivity toward B-deficient conditions. To reduce B-deficiency-caused yield losses in a sustainable manner, the identification of B-efficient B. napus genotypes is indispensable. We developed a soil substrate-based cultivation system which is suitable to study plant growth in automated high-throughput phenotyping facilities under defined and repeatable soil B conditions. In a comprehensive screening, using this system with soil B concentrations below 0.1 mg B (kg soil)-1, we identified three highly B-deficiency tolerant B. napus cultivars (CR2267, CR2280, and CR2285) among a genetically diverse collection comprising 590 accessions from all over the world. The B-efficiency classification of cultivars was based on a detailed assessment of various physical and high-throughput imaging-based shoot and root growth parameters in soil substrate or in in vitro conditions, respectively. We identified cultivar-specific patterns of B-deficiency-responsive growth dynamics. Elemental analysis revealed striking differences only in B contents between contrasting genotypes when grown under B-deficient but not under standard conditions. Results indicate that B-deficiency tolerant cultivars can grow with a very limited amount of B which is clearly below previously described critical B-tissue concentration values. These results suggest a higher B utilization efficiency of CR2267, CR2280, and CR2285 which would represent a unique trait among so far identified B-efficient B. napus cultivars which are characterized by a higher B-uptake capacity. Testing various other nutrient deficiency treatments, we demonstrated that the tolerance is specific for B-deficient conditions and is not conferred by a general growth vigor at the seedling stage. The identified B-deficiency tolerant cultivars will serve as genetic and physiological "tools" to further understand the mechanisms regulating the B nutritional status in rapeseed and to develop B-efficient elite genotypes.
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Affiliation(s)
- Benjamin Pommerrenig
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Astrid Junker
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Isidro Abreu
- Department of Biology, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Annett Bieber
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Jacqueline Fuge
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Evelin Willner
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Manuela D. Bienert
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Thomas Altmann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Gerd P. Bienert
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
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17
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Hurgobin B, Golicz AA, Bayer PE, Chan CK, Tirnaz S, Dolatabadian A, Schiessl SV, Samans B, Montenegro JD, Parkin IAP, Pires JC, Chalhoub B, King GJ, Snowdon R, Batley J, Edwards D. Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1265-1274. [PMID: 29205771 PMCID: PMC5999312 DOI: 10.1111/pbi.12867] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/17/2017] [Accepted: 10/19/2017] [Indexed: 05/08/2023]
Abstract
Homoeologous exchanges (HEs) have been shown to generate novel gene combinations and phenotypes in a range of polyploid species. Gene presence/absence variation (PAV) is also a major contributor to genetic diversity. In this study, we show that there is an association between these two events, particularly in recent Brassica napus synthetic accessions, and that these represent a novel source of genetic diversity, which can be captured for the improvement of this important crop species. By assembling the pangenome of B. napus, we show that 38% of the genes display PAV behaviour, with some of these variable genes predicted to be involved in important agronomic traits including flowering time, disease resistance, acyl lipid metabolism and glucosinolate metabolism. This study is a first and provides a detailed characterization of the association between HEs and PAVs in B. napus at the pangenome level.
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Affiliation(s)
- Bhavna Hurgobin
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
- School of Agriculture and Food SciencesUniversity of QueenslandSt. LuciaQLDAustralia
| | - Agnieszka A. Golicz
- Plant Molecular Biology and Biotechnology LaboratoryFaculty of Veterinary and Agricultural SciencesUniversity of MelbourneMelbourneVICAustralia
| | - Philipp E. Bayer
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Chon‐Kit Kenneth Chan
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Soodeh Tirnaz
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Aria Dolatabadian
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Sarah V. Schiessl
- Department of Plant BreedingIFZ Research Centre for Biosystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Birgit Samans
- Department of Plant BreedingIFZ Research Centre for Biosystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Juan D. Montenegro
- School of Agriculture and Food SciencesUniversity of QueenslandSt. LuciaQLDAustralia
| | | | - J. Chris Pires
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
| | - Boulos Chalhoub
- Institute of System and Synthetic Biology, Organization and Evolution of Complex GenomesInstitut National de la Recherche agronomique, GenopoleCentre National de la Recherche ScientifiqueUniversité d'Evry Val d'EssonneUniversité Paris‐SaclayEvryFrance
| | - Graham J. King
- Southern Cross Plant ScienceSouthern Cross UniversityLismoreNSWAustralia
| | - Rod Snowdon
- Department of Plant BreedingIFZ Research Centre for Biosystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Jacqueline Batley
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - David Edwards
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
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18
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Werner CR, Qian L, Voss-Fels KP, Abbadi A, Leckband G, Frisch M, Snowdon RJ. Genome-wide regression models considering general and specific combining ability predict hybrid performance in oilseed rape with similar accuracy regardless of trait architecture. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:299-317. [PMID: 29080901 DOI: 10.1007/s00122-017-3002-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 10/09/2017] [Indexed: 05/02/2023]
Abstract
Genomic prediction using the Brassica 60 k genotyping array is efficient in oilseed rape hybrids. Prediction accuracy is more dependent on trait complexity than on the prediction model. In oilseed rape breeding programs, performance prediction of parental combinations is of fundamental importance. Due to the phenomenon of heterosis, per se performance is not a reliable indicator for F1-hybrid performance, and selection of well-paired parents requires the testing of large quantities of hybrid combinations in extensive field trials. However, the number of potential hybrids, in general, dramatically exceeds breeding capacity and budget. Integration of genomic selection (GS) could substantially increase the number of potential combinations that can be evaluated. GS models can be used to predict the performance of untested individuals based only on their genotypic profiles, using marker effects previously predicted in a training population. This allows for a preselection of promising genotypes, enabling a more efficient allocation of resources. In this study, we evaluated the usefulness of the Illumina Brassica 60 k SNP array for genomic prediction and compared three alternative approaches based on a homoscedastic ridge regression BLUP and three Bayesian prediction models that considered general and specific combining ability (GCA and SCA, respectively). A total of 448 hybrids were produced in a commercial breeding program from unbalanced crosses between 220 paternal doubled haploid lines and five male-sterile testers. Predictive ability was evaluated for seven agronomic traits. We demonstrate that the Brassica 60 k genotyping array is an adequate and highly valuable platform to implement genomic prediction of hybrid performance in oilseed rape. Furthermore, we present first insights into the application of established statistical models for prediction of important agronomical traits with contrasting patterns of polygenic control.
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Affiliation(s)
- Christian R Werner
- Department of Plant Breeding, Justus Liebig University, 35392, Giessen, Germany
| | - Lunwen Qian
- Department of Plant Breeding, Justus Liebig University, 35392, Giessen, Germany
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China
| | - Kai P Voss-Fels
- Department of Plant Breeding, Justus Liebig University, 35392, Giessen, Germany
| | - Amine Abbadi
- NPZ Innovation GmbH, Hohenlieth, 24363, Holtsee, Germany
| | | | - Matthias Frisch
- Institute of Agronomy and Plant Breeding II, Justus Liebig University, 35392, Giessen, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, Justus Liebig University, 35392, Giessen, Germany.
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19
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Zou J, Hu D, Mason AS, Shen X, Wang X, Wang N, Grandke F, Wang M, Chang S, Snowdon RJ, Meng J. Genetic changes in a novel breeding population of Brassica napus synthesized from hundreds of crosses between B. rapa and B. carinata. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:507-519. [PMID: 28703467 PMCID: PMC5811809 DOI: 10.1111/pbi.12791] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 06/29/2017] [Accepted: 07/07/2017] [Indexed: 05/20/2023]
Abstract
Introgression of genomic variation between and within related crop species is a significant evolutionary approach for population differentiation, genome reorganization and trait improvement. Using the Illumina Infinium Brassica 60K SNP array, we investigated genomic changes in a panel of advanced generation new-type Brassica napus breeding lines developed from hundreds of interspecific crosses between 122 Brassica rapa and 74 Brassica carinata accessions, and compared them with representative accessions of their three parental species. The new-type B. napus population presented rich genetic diversity and abundant novel genomic alterations, consisting of introgressions from B. rapa and B. carinata, novel allelic combinations, reconstructed linkage disequilibrium patterns and haplotype blocks, and frequent deletions and duplications (nonrandomly distributed), particularly in the C subgenome. After a much shorter, but very intensive, selection history compared to traditional B. napus, a total of 15 genomic regions with strong selective sweeps and 112 genomic regions with putative signals of selective sweeps were identified. Some of these regions were associated with important agronomic traits that were selected for during the breeding process, while others were potentially associated with restoration of genome stability and fertility after interspecific hybridization. Our results demonstrate how a novel method for population-based crop genetic improvement can lead to rapid adaptation, restoration of genome stability and positive responses to artificial selection.
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Affiliation(s)
- Jun Zou
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Dandan Hu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Annaliese S. Mason
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Xueqi Shen
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Xiaohua Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Nian Wang
- College of Horticulture & Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Fabian Grandke
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Meng Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Shihao Chang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Rod J. Snowdon
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Jinling Meng
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
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20
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Malmberg MM, Shi F, Spangenberg GC, Daetwyler HD, Cogan NOI. Diversity and Genome Analysis of Australian and Global Oilseed Brassica napus L. Germplasm Using Transcriptomics and Whole Genome Re-sequencing. FRONTIERS IN PLANT SCIENCE 2018; 9:508. [PMID: 29725344 PMCID: PMC5917405 DOI: 10.3389/fpls.2018.00508] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/03/2018] [Indexed: 05/21/2023]
Abstract
Intensive breeding of Brassica napus has resulted in relatively low diversity, such that B. napus would benefit from germplasm improvement schemes that sustain diversity. As such, samples representative of global germplasm pools need to be assessed for existing population structure, diversity and linkage disequilibrium (LD). Complexity reduction genotyping-by-sequencing (GBS) methods, including GBS-transcriptomics (GBS-t), enable cost-effective screening of a large number of samples, while whole genome re-sequencing (WGR) delivers the ability to generate large numbers of unbiased genomic single nucleotide polymorphisms (SNPs), and identify structural variants (SVs). Furthermore, the development of genomic tools based on whole genomes representative of global oilseed diversity and orientated by the reference genome has substantial industry relevance and will be highly beneficial for canola breeding. As recent studies have focused on European and Chinese varieties, a global diversity panel as well as a substantial number of Australian spring types were included in this study. Focusing on industry relevance, 633 varieties were initially genotyped using GBS-t to examine population structure using 61,037 SNPs. Subsequently, 149 samples representative of global diversity were selected for WGR and both data sets used for a side-by-side evaluation of diversity and LD. The WGR data was further used to develop genomic resources consisting of a list of 4,029,750 high-confidence SNPs annotated using SnpEff, and SVs in the form of 10,976 deletions and 2,556 insertions. These resources form the basis of a reliable and repeatable system allowing greater integration between canola genomics studies, with a strong focus on breeding germplasm and industry applicability.
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Affiliation(s)
- M. Michelle Malmberg
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Fan Shi
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, Australia
| | - German C. Spangenberg
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Hans D. Daetwyler
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Noel O. I. Cogan
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
- *Correspondence: Noel O. I. Cogan,
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22
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Hu J, Guo C, Wang B, Ye J, Liu M, Wu Z, Xiao Y, Zhang Q, Li H, King GJ, Liu K. Genetic Properties of a Nested Association Mapping Population Constructed With Semi-Winter and Spring Oilseed Rapes. FRONTIERS IN PLANT SCIENCE 2018; 9:1740. [PMID: 30534135 PMCID: PMC6275288 DOI: 10.3389/fpls.2018.01740] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 11/08/2018] [Indexed: 05/17/2023]
Abstract
Nested association mapping (NAM) populations have been widely applied to dissect the genetic basis of complex quantitative traits in a variety of crops. In this study, we developed a Brassica napus NAM (BN-NAM) population consisting of 15 recombination inbred line (RIL) families with 2,425 immortal genotypes. Fifteen high-density genetic linkage maps were constructed by genotyping by sequencing (GBS) based on all RIL families, with further integration into a joint linkage map (JLM) having 30,209 unique markers in common with multiple linkage maps. Furthermore, an ultra-density whole-genome variation map was constructed by projecting 4,444,309 high-quality variants onto the JLM. The NAM population captured a total of 88,542 recombination events (REs). The uneven distribution of recombination rate along chromosomes is positively correlated with the densities of genes and markers, but negatively correlated with the density of transposable elements and linkage disequilibrium (LD). Analyses of population structure and principal components revealed that the BN-NAM population could be divided into three groups with weak stratification. The LD decay distance across genome varied between 170 and 2,400 Kb, with LD decay more rapid in the A than in the C sub-genome. The pericentromeric regions contained large LD blocks, especially in the C sub-genome. This NAM population provides a valuable resource for dissecting the genetic basis of important traits in rapeseed, especially in semi-winter oilseed rape.
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Affiliation(s)
- Jianlin Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Chaocheng Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Bo Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jiaqing Ye
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Meng Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zhikun Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Haitao Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Graham J. King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Kede Liu,
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23
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Perumal S, Waminal NE, Lee J, Lee J, Choi BS, Kim HH, Grandbastien MA, Yang TJ. Elucidating the major hidden genomic components of the A, C, and AC genomes and their influence on Brassica evolution. Sci Rep 2017; 7:17986. [PMID: 29269833 PMCID: PMC5740159 DOI: 10.1038/s41598-017-18048-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 12/04/2017] [Indexed: 11/09/2022] Open
Abstract
Decoding complete genome sequences is prerequisite for comprehensive genomics studies. However, the currently available reference genome sequences of Brassica rapa (A genome), B. oleracea (C) and B. napus (AC) cover 391, 540, and 850 Mbp and represent 80.6, 85.7, and 75.2% of the estimated genome size, respectively, while remained are hidden or unassembled due to highly repetitive nature of these genome components. Here, we performed the first comprehensive genome-wide analysis using low-coverage whole-genome sequences to explore the hidden genome components based on characterization of major repeat families in the B. rapa and B. oleracea genomes. Our analysis revealed 10 major repeats (MRs) including a new family comprising about 18.8, 10.8, and 11.5% of the A, C and AC genomes, respectively. Nevertheless, these 10 MRs represented less than 0.7% of each assembled reference genome. Genomic survey and molecular cytogenetic analyses validates our insilico analysis and also pointed to diversity, differential distribution, and evolutionary dynamics in the three Brassica species. Overall, our work elucidates hidden portions of three Brassica genomes, thus providing a resource for understanding the complete genome structures. Furthermore, we observed that asymmetrical accumulation of the major repeats might be a cause of diversification between the A and C genomes.
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Affiliation(s)
- Sampath Perumal
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada.,Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Nomar Espinosa Waminal
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.,Department of Life Science, Plant Biotechnology Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Jonghoon Lee
- Joeun Seed, Goesan-Gun, Chungcheongbuk-Do, 28051, Republic of Korea
| | - Junki Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Beom-Soon Choi
- Phyzen Genomics Institute, Seongnam, 13558, Republic of Korea
| | - Hyun Hee Kim
- Department of Life Science, Plant Biotechnology Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | | | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea. .,Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, 232-916, Republic of Korea.
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24
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Neik TX, Barbetti MJ, Batley J. Current Status and Challenges in Identifying Disease Resistance Genes in Brassica napus. FRONTIERS IN PLANT SCIENCE 2017; 8:1788. [PMID: 29163558 PMCID: PMC5681527 DOI: 10.3389/fpls.2017.01788] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 10/02/2017] [Indexed: 05/18/2023]
Abstract
Brassica napus is an economically important crop across different continents including temperate and subtropical regions in Europe, Canada, South Asia, China and Australia. Its widespread cultivation also brings setbacks as it plays host to fungal, oomycete and chytrid pathogens that can lead to serious yield loss. For sustainable crop production, identification of resistance (R) genes in B. napus has become of critical importance. In this review, we discuss four key pathogens affecting Brassica crops: Clubroot (Plasmodiophora brassicae), Blackleg (Leptosphaeria maculans and L. biglobosa), Sclerotinia Stem Rot (Sclerotinia sclerotiorum), and Downy Mildew (Hyaloperonospora parasitica). We first review current studies covering prevalence of these pathogens on Brassica crops and highlight the R genes and QTL that have been identified from Brassica species against these pathogens. Insights into the relationships between the pathogen and its Brassica host, the unique host resistance mechanisms and how these affect resistance outcomes is also presented. We discuss challenges in identification and deployment of R genes in B. napus in relation to highly specific genetic interactions between host subpopulations and pathogen pathotypes and emphasize the need for common or shared techniques and research materials or tighter collaboration between researchers to reconcile the inconsistencies in the research outcomes. Using current genomics tools, we provide examples of how characterization and cloning of R genes in B. napus can be carried out more effectively. Lastly, we put forward strategies to breed resistant cultivars through introgressions supported by genomic approaches and suggest prospects that can be implemented in the future for a better, pathogen-resistant B. napus.
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Affiliation(s)
- Ting Xiang Neik
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - Martin J. Barbetti
- School of Agriculture and Environment and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
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25
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Samans B, Chalhoub B, Snowdon RJ. Surviving a Genome Collision: Genomic Signatures of Allopolyploidization in the Recent Crop Species Brassica napus. THE PLANT GENOME 2017; 10. [PMID: 29293818 DOI: 10.3835/plantgenome2017.02.0013] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Polyploidization has played a major role in crop plant evolution, leading to advantageous traits that have been selected by humans. Here, we describe restructuring patterns in the genome of L., a recent allopolyploid species. Widespread segmental deletions, duplications, and homeologous chromosome exchanges were identified in diverse genome sequences from 32 natural and 20 synthetic accessions, indicating that homeologous exchanges are a major driver of postpolyploidization genome diversification. Breakpoints of genomic rearrangements are rich in microsatellite sequences that are known to interact with the meiotic recombination machinery. In both synthetic and natural , a subgenome bias was observed toward exchanges replacing larger chromosome segments from the C-subgenome by their smaller, homeologous A-subgenome segments, driving postpolyploidization genome size reduction. Selection in natural favored segmental deletions involving genes associated with immunity, reproduction, and adaptation. Deletions affecting mismatch repair system genes, which are assumed to control homeologous recombination, were also found to be under selection. Structural exchanges between homeologous subgenomes appear to be a major source of novel genetic diversity in de novo allopolyploids. Documenting the consequences of genomic collision by genomic resequencing gives insights into the adaptive processes accompanying allopolyploidization.
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26
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Werner CR, Qian L, Voss-Fels KP, Abbadi A, Leckband G, Frisch M, Snowdon RJ. Genome-wide regression models considering general and specific combining ability predict hybrid performance in oilseed rape with similar accuracy regardless of trait architecture. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017. [PMID: 29080901 DOI: 10.1007/s00122‐017‐3002‐5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
KEY MESSAGE Genomic prediction using the Brassica 60 k genotyping array is efficient in oilseed rape hybrids. Prediction accuracy is more dependent on trait complexity than on the prediction model. In oilseed rape breeding programs, performance prediction of parental combinations is of fundamental importance. Due to the phenomenon of heterosis, per se performance is not a reliable indicator for F1-hybrid performance, and selection of well-paired parents requires the testing of large quantities of hybrid combinations in extensive field trials. However, the number of potential hybrids, in general, dramatically exceeds breeding capacity and budget. Integration of genomic selection (GS) could substantially increase the number of potential combinations that can be evaluated. GS models can be used to predict the performance of untested individuals based only on their genotypic profiles, using marker effects previously predicted in a training population. This allows for a preselection of promising genotypes, enabling a more efficient allocation of resources. In this study, we evaluated the usefulness of the Illumina Brassica 60 k SNP array for genomic prediction and compared three alternative approaches based on a homoscedastic ridge regression BLUP and three Bayesian prediction models that considered general and specific combining ability (GCA and SCA, respectively). A total of 448 hybrids were produced in a commercial breeding program from unbalanced crosses between 220 paternal doubled haploid lines and five male-sterile testers. Predictive ability was evaluated for seven agronomic traits. We demonstrate that the Brassica 60 k genotyping array is an adequate and highly valuable platform to implement genomic prediction of hybrid performance in oilseed rape. Furthermore, we present first insights into the application of established statistical models for prediction of important agronomical traits with contrasting patterns of polygenic control.
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Affiliation(s)
- Christian R Werner
- Department of Plant Breeding, Justus Liebig University, 35392, Giessen, Germany
| | - Lunwen Qian
- Department of Plant Breeding, Justus Liebig University, 35392, Giessen, Germany.,Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China
| | - Kai P Voss-Fels
- Department of Plant Breeding, Justus Liebig University, 35392, Giessen, Germany
| | - Amine Abbadi
- NPZ Innovation GmbH, Hohenlieth, 24363, Holtsee, Germany
| | | | - Matthias Frisch
- Institute of Agronomy and Plant Breeding II, Justus Liebig University, 35392, Giessen, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, Justus Liebig University, 35392, Giessen, Germany.
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27
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Carbohydrate microarrays and their use for the identification of molecular markers for plant cell wall composition. Proc Natl Acad Sci U S A 2017; 114:6860-6865. [PMID: 28607074 DOI: 10.1073/pnas.1619033114] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genetic improvement of the plant cell wall has enormous potential to increase the quality of food, fibers, and fuels. However, the identification and characterization of genes involved in plant cell wall synthesis is far from complete. Association mapping is one of the few techniques that can help identify candidate genes without relying on our currently incomplete knowledge of cell wall synthesis. However, few cell wall phenotyping methodologies have proven sufficiently precise, robust, or scalable for association mapping to be conducted for specific cell wall polymers. Here, we created high-density carbohydrate microarrays containing chemically extracted cell wall polysaccharides collected from 331 genetically diverse Brassica napus cultivars and used them to obtain detailed, quantitative information describing the relative abundance of selected noncellulosic polysaccharide linkages and primary structures. We undertook genome-wide association analysis of data collected from 57 carbohydrate microarrays and identified molecular markers reflecting a diversity of specific xylan, xyloglucan, pectin, and arabinogalactan moieties. These datasets provide a detailed insight into the natural variations in cell wall carbohydrate moieties between B. napus genotypes and identify associated markers that could be exploited by marker-assisted breeding. The identified markers also have value beyond B. napus for functional genomics, facilitated by the close genetic relatedness to the model plant Arabidopsis Together, our findings provide a unique dissection of the genetic architecture that underpins plant cell wall biosynthesis and restructuring.
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28
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From plant genomes to phenotypes. J Biotechnol 2017; 261:46-52. [PMID: 28602791 DOI: 10.1016/j.jbiotec.2017.06.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/27/2017] [Accepted: 06/07/2017] [Indexed: 12/21/2022]
Abstract
Recent advances in sequencing technologies have greatly accelerated the rate of plant genome and applied breeding research. Despite this advancing trend, plant genomes continue to present numerous difficulties to the standard tools and pipelines not only for genome assembly but also gene annotation and downstream analysis. Here we give a perspective on tools, resources and services necessary to assemble and analyze plant genomes and link them to plant phenotypes.
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29
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Braatz J, Harloff HJ, Mascher M, Stein N, Himmelbach A, Jung C. CRISPR-Cas9 Targeted Mutagenesis Leads to Simultaneous Modification of Different Homoeologous Gene Copies in Polyploid Oilseed Rape ( Brassica napus). PLANT PHYSIOLOGY 2017; 174:935-942. [PMID: 28584067 PMCID: PMC5462057 DOI: 10.1104/pp.17.00426] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 04/13/2017] [Indexed: 05/18/2023]
Abstract
In polyploid species, altering a trait by random mutagenesis is highly inefficient due to gene redundancy. We have stably transformed tetraploid oilseed rape (Brassica napus) with a CRISPR-Cas9 construct targeting two ALCATRAZ (ALC) homoeologs. ALC is involved in valve margin development and, thus, contributes to seed shattering from mature fruits. Knocking out ALC would increase shatter resistance to avoid seed loss during mechanical harvest. We obtained a transgenic T1 plant with four alc mutant alleles by the use of a single target sequence. All mutations were stably inherited to the T2 progeny. The T2 generation was devoid of any wild-type alleles, proving that the underlying T1 was a nonchimeric double heterozygote. T-DNA and ALC loci were not linked, as indicated by random segregation in the T2 generation. Hence, we could select double mutants lacking the T-DNA already in the first offspring generation. However, whole-genome sequencing data revealed at least five independent insertions of vector backbone sequences. We did not detect any off-target effects in two genome regions homologous to the target sequence. The simultaneous alteration of multiple homoeologs by CRISPR-Cas9 mutagenesis without any background mutations will offer new opportunities for using mutant genotypes in rapeseed breeding.
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Affiliation(s)
- Janina Braatz
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, 24098 Kiel, Germany (J.B., H.-J.H., C.J.)
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, 06466 Stadt Seeland, Germany (M.M., N.S., A.H.); and
- German Centre for Integrative Biodiversity Research Halle-Jena-Leipzig, 04103 Leipzig, Germany (M.M.)
| | - Hans-Joachim Harloff
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, 24098 Kiel, Germany (J.B., H.-J.H., C.J.)
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, 06466 Stadt Seeland, Germany (M.M., N.S., A.H.); and
- German Centre for Integrative Biodiversity Research Halle-Jena-Leipzig, 04103 Leipzig, Germany (M.M.)
| | - Martin Mascher
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, 24098 Kiel, Germany (J.B., H.-J.H., C.J.)
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, 06466 Stadt Seeland, Germany (M.M., N.S., A.H.); and
- German Centre for Integrative Biodiversity Research Halle-Jena-Leipzig, 04103 Leipzig, Germany (M.M.)
| | - Nils Stein
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, 24098 Kiel, Germany (J.B., H.-J.H., C.J.)
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, 06466 Stadt Seeland, Germany (M.M., N.S., A.H.); and
- German Centre for Integrative Biodiversity Research Halle-Jena-Leipzig, 04103 Leipzig, Germany (M.M.)
| | - Axel Himmelbach
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, 24098 Kiel, Germany (J.B., H.-J.H., C.J.)
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, 06466 Stadt Seeland, Germany (M.M., N.S., A.H.); and
- German Centre for Integrative Biodiversity Research Halle-Jena-Leipzig, 04103 Leipzig, Germany (M.M.)
| | - Christian Jung
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, 24098 Kiel, Germany (J.B., H.-J.H., C.J.);
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, 06466 Stadt Seeland, Germany (M.M., N.S., A.H.); and
- German Centre for Integrative Biodiversity Research Halle-Jena-Leipzig, 04103 Leipzig, Germany (M.M.)
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30
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Hanhart P, Thieß M, Amari K, Bajdzienko K, Giavalisco P, Heinlein M, Kehr J. Bioinformatic and expression analysis of the Brassica napus L. cyclophilins. Sci Rep 2017; 7:1514. [PMID: 28473712 PMCID: PMC5431436 DOI: 10.1038/s41598-017-01596-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/29/2017] [Indexed: 12/15/2022] Open
Abstract
Cyclophilins (CYPs) are a group of ubiquitous proteins characterized by their ability to bind to the immunosuppressive drug cyclosporin A. The CYP family occurs in a wide range of organisms and contains a conserved peptidyl-prolyl cis/trans isomerase domain. In addition to fulfilling a basic role in protein folding, CYPs may also play diverse important roles, e.g. in protein degradation, mRNA processing, development, and stress responses. We performed a genome-wide database survey and identified a total of 94 CYP genes encoding 91 distinct proteins. Sequence alignment analysis of the putative BnCYP cyclophilin-like domains revealed highly conserved motifs. By using RNA-Seq, we could verify the presence of 77 BnCYP genes under control conditions. To identify phloem-specific BnCYP proteins in a complementary approach, we used LC-MS/MS to determine protein abundances in leaf and phloem extracts. We detected 26 BnCYPs in total with 12 being unique to phloem sap. Our analysis provides the basis for future studies concentrating on the functional characterization of individual members of this gene family in a plant of dual importance: as a crop and a model system for polyploidization and long-distance signalling.
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Affiliation(s)
- Patrizia Hanhart
- Molecular Plant Genetics, Universität Hamburg, Biozentrum Klein Flottbek, Ohnhorststraße 18, 22609, Hamburg, Germany
| | - Melanie Thieß
- Molecular Plant Genetics, Universität Hamburg, Biozentrum Klein Flottbek, Ohnhorststraße 18, 22609, Hamburg, Germany
| | - Khalid Amari
- Université de Strasbourg, CNRS, IBMP UPR 2357, 12 rue du Général Zimmer, F-67000, Strasbourg, France
| | - Krzysztof Bajdzienko
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Wissenschaftspark Potsdam-Golm, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Patrick Giavalisco
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Wissenschaftspark Potsdam-Golm, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Manfred Heinlein
- Université de Strasbourg, CNRS, IBMP UPR 2357, 12 rue du Général Zimmer, F-67000, Strasbourg, France
| | - Julia Kehr
- Molecular Plant Genetics, Universität Hamburg, Biozentrum Klein Flottbek, Ohnhorststraße 18, 22609, Hamburg, Germany.
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Mason AS, Higgins EE, Snowdon RJ, Batley J, Stein A, Werner C, Parkin IAP. A user guide to the Brassica 60K Illumina Infinium™ SNP genotyping array. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:621-633. [PMID: 28220206 DOI: 10.1007/s00122-016-2849-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 09/14/2016] [Indexed: 06/06/2023]
Abstract
The Brassica napus 60K Illumina Infinium™ SNP array has had huge international uptake in the rapeseed community due to the revolutionary speed of acquisition and ease of analysis of this high-throughput genotyping data, particularly when coupled with the newly available reference genome sequence. However, further utilization of this valuable resource can be optimized by better understanding the promises and pitfalls of SNP arrays. We outline how best to analyze Brassica SNP marker array data for diverse applications, including linkage and association mapping, genetic diversity and genomic introgression studies. We present data on which SNPs are locus-specific in winter, semi-winter and spring B. napus germplasm pools, rather than amplifying both an A-genome and a C-genome locus or multiple loci. Common issues that arise when analyzing array data will be discussed, particularly those unique to SNP markers and how to deal with these for practical applications in Brassica breeding applications.
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Affiliation(s)
- Annaliese S Mason
- Department of Plant Breeding, IFZ for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| | - Erin E Higgins
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N0X2, Canada
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Jacqueline Batley
- School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane, 4072, Australia
- School of Plant Biology and The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, Perth, Australia
| | - Anna Stein
- Department of Plant Breeding, IFZ for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Christian Werner
- Department of Plant Breeding, IFZ for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N0X2, Canada
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Cheng F, Liang J, Cai C, Cai X, Wu J, Wang X. Genome sequencing supports a multi-vertex model for Brassiceae species. CURRENT OPINION IN PLANT BIOLOGY 2017; 36:79-87. [PMID: 28242534 DOI: 10.1016/j.pbi.2017.01.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 01/24/2017] [Accepted: 01/26/2017] [Indexed: 06/06/2023]
Abstract
The economically important Brassica genus is a good system for studying the evolution of polyploids. Brassica genomes have undergone whole genome triplication (WGT). Subgenome dominance phenomena such as biased gene fractionation and dominant gene expression were observed in tripled genomes of Brassica. The genome of radish (Raphanus sativus), another important crop of tribe Brassiceae, was derived from the same WGT event and shows similar subgenome dominance. These findings and molecular dating indicate that radish occupies a similar evolutionary origin as that of Brassica species. Here, we extended the Brassica "triangle of U" to a multi-vertex model. This model describes the relationships or the potential of using more Brassiceae mesohexaploids in the creation of new allotetraploid oil or vegetable crop species.
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Affiliation(s)
- Feng Cheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Jianli Liang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Chengcheng Cai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Xu Cai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Jian Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
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33
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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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34
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Carlson MO, Gazave E, Gore MA, Smart CD. Temporal Genetic Dynamics of an Experimental, Biparental Field Population of Phytophthora capsici. Front Genet 2017; 8:26. [PMID: 28348576 PMCID: PMC5347166 DOI: 10.3389/fgene.2017.00026] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 02/20/2017] [Indexed: 01/01/2023] Open
Abstract
Defining the contributions of dispersal, reproductive mode, and mating system to the population structure of a pathogenic organism is essential to estimating its evolutionary potential. After introduction of the devastating plant pathogen, Phytophthora capsici, into a grower's field, a lack of aerial spore dispersal restricts migration. Once established, coexistence of both mating types results in formation of overwintering recombinant oospores, engendering persistent pathogen populations. To mimic these conditions, in 2008, we inoculated a field with two P. capsici isolates of opposite mating type. We analyzed pathogenic isolates collected in 2009-2013 from this experimental population, using genome-wide single-nucleotide polymorphism markers. By tracking heterozygosity across years, we show that the population underwent a generational shift; transitioning from exclusively F1 in 2009-2010, to multi-generational in 2011, and ultimately all inbred in 2012-2013. Survival of F1 oospores, characterized by heterozygosity excess, coupled with a low rate of selfing, delayed declines in heterozygosity due to inbreeding and attainment of equilibrium genotypic frequencies. Large allele and haplotype frequency changes in specific genomic regions accompanied the generational shift, representing putative signatures of selection. Finally, we identified an approximately 1.6 Mb region associated with mating type determination, constituting the first detailed genomic analysis of a mating type region (MTR) in Phytophthora. Segregation patterns in the MTR exhibited tropes of sex-linkage, where maintenance of allele frequency differences between isolates of opposite mating type was associated with elevated heterozygosity despite inbreeding. Characterizing the trajectory of this experimental system provides key insights into the processes driving persistent, sexual pathogen populations.
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Affiliation(s)
- Maryn O. Carlson
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell UniversityGeneva, NY, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell UniversityIthaca, NY, USA
| | - Elodie Gazave
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell UniversityIthaca, NY, USA
| | - Michael A. Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell UniversityIthaca, NY, USA
| | - Christine D. Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell UniversityGeneva, NY, USA
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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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36
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Schiessl SV, Huettel B, Kuehn D, Reinhardt R, Snowdon RJ. Flowering Time Gene Variation in Brassica Species Shows Evolutionary Principles. FRONTIERS IN PLANT SCIENCE 2017; 8:1742. [PMID: 29089948 PMCID: PMC5651034 DOI: 10.3389/fpls.2017.01742] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 09/25/2017] [Indexed: 05/02/2023]
Abstract
Flowering time genes have a strong influence on successful reproduction and life cycle adaptation. However, their regulation is highly complex and only well understood in diploid model systems. For crops with a polyploid background from the genus Brassica, data on flowering time gene variation are scarce, although indispensable for modern breeding techniques like marker-assisted breeding. We have deep-sequenced all paralogs of 35 Arabidopsis thaliana flowering regulators using Sequence Capture followed by Illumina sequencing in two selected accessions of the vegetable species Brassica rapa and Brassica oleracea, respectively. Using these data, we were able to call SNPs, InDels and copy number variations (CNVs) for genes from the total flowering time network including central flowering regulators, but also genes from the vernalisation pathway, the photoperiod pathway, temperature regulation, the circadian clock and the downstream effectors. Comparing the results to a complementary data set from the allotetraploid species Brassica napus, we detected rearrangements in B. napus which probably occurred early after the allopolyploidisation event. Those data are both a valuable resource for flowering time research in those vegetable species, as well as a contribution to speciation genetics.
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Affiliation(s)
- Sarah V. Schiessl
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
- *Correspondence: Sarah V. Schiessl
| | - Bruno Huettel
- Max Planck Institute for Breeding Research, Cologne, Germany
| | - Diana Kuehn
- Max Planck Institute for Breeding Research, Cologne, Germany
| | | | - Rod J. Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
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37
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Qian L, Voss-Fels K, Cui Y, Jan HU, Samans B, Obermeier C, Qian W, Snowdon RJ. Deletion of a Stay-Green Gene Associates with Adaptive Selection in Brassica napus. MOLECULAR PLANT 2016; 9:1559-1569. [PMID: 27825945 DOI: 10.1016/j.molp.2016.10.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/19/2016] [Accepted: 10/20/2016] [Indexed: 05/02/2023]
Abstract
Chlorophyll levels provide important information about plant growth and physiological plasticity in response to changing environments. The stay-green gene NON-YELLOWING 1 (NYE1) is believed to regulate chlorophyll degradation during senescence, concomitantly affecting the disassembly of the light-harvesting complex and hence indirectly influencing photosynthesis. We identified Brassica napus accessions carrying an NYE1 deletion associated with increased chlorophyll content, and with upregulated expression of light-harvesting complex and photosynthetic reaction center (PSI and PSII) genes. Comparative analysis of the seed oil content of accessions with related genetic backgrounds revealed that the B. napus NYE1 gene deletion (bnnye1) affected oil accumulation, and linkage disequilibrium signatures suggested that the locus has been subject to artificial selection by breeding in oilseed B. napus forms. Comparative analysis of haplotype diversity groups (haplogroups) between three different ecotypes of the allopolyploid B. napus and its A-subgenome diploid progenitor, Brassica rapa, indicated that introgression of the bnnye1 deletion from Asian B. rapa into winter-type B. napus may have simultaneously improved its adaptation to cooler environments experienced by autumn-sown rapeseed.
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Affiliation(s)
- Lunwen Qian
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Kai Voss-Fels
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Yixin Cui
- College of Agronomy and Biotechnology, Southwest University, 400716 Chongqing, China
| | - Habib U Jan
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Birgit Samans
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Christian Obermeier
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, 400716 Chongqing, China
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany.
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Mason AS, Snowdon RJ. Oilseed rape: learning about ancient and recent polyploid evolution from a recent crop species. PLANT BIOLOGY (STUTTGART, GERMANY) 2016; 18:883-892. [PMID: 27063780 DOI: 10.1111/plb.12462] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 04/06/2016] [Indexed: 05/18/2023]
Abstract
Oilseed rape (Brassica napus) is one of our youngest crop species, arising several times under cultivation in the last few thousand years and completely unknown in the wild. Oilseed rape originated from hybridisation events between progenitor diploid species B. rapa and B. oleracea, both important vegetable species. The diploid progenitors are also ancient polyploids, with remnants of two previous polyploidisation events evident in the triplicated genome structure. This history of polyploid evolution and human agricultural selection makes B. napus an excellent model with which to investigate processes of genomic evolution and selection in polyploid crops. The ease of de novo interspecific hybridisation, responsiveness to tissue culture, and the close relationship of oilseed rape to the model plant Arabidopsis thaliana, coupled with the recent availability of reference genome sequences and suites of molecular cytogenetic and high-throughput genotyping tools, allow detailed dissection of genetic, genomic and phenotypic interactions in this crop. In this review we discuss the past and present uses of B. napus as a model for polyploid speciation and evolution in crop species, along with current and developing analysis tools and resources. We further outline unanswered questions that may now be tractable to investigation.
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Affiliation(s)
- A S Mason
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany.
| | - R J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
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Arend D, Junker A, Scholz U, Schüler D, Wylie J, Lange M. PGP repository: a plant phenomics and genomics data publication infrastructure. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw033. [PMID: 27087305 PMCID: PMC4834206 DOI: 10.1093/database/baw033] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 02/26/2016] [Indexed: 11/22/2022]
Abstract
Plant genomics and phenomics represents the most promising tools for accelerating yield gains and overcoming emerging crop productivity bottlenecks. However, accessing this wealth of plant diversity requires the characterization of this material using state-of-the-art genomic, phenomic and molecular technologies and the release of subsequent research data via a long-term stable, open-access portal. Although several international consortia and public resource centres offer services for plant research data management, valuable digital assets remains unpublished and thus inaccessible to the scientific community. Recently, the Leibniz Institute of Plant Genetics and Crop Plant Research and the German Plant Phenotyping Network have jointly initiated the Plant Genomics and Phenomics Research Data Repository (PGP) as infrastructure to comprehensively publish plant research data. This covers in particular cross-domain datasets that are not being published in central repositories because of its volume or unsupported data scope, like image collections from plant phenotyping and microscopy, unfinished genomes, genotyping data, visualizations of morphological plant models, data from mass spectrometry as well as software and documents. The repository is hosted at Leibniz Institute of Plant Genetics and Crop Plant Research using e!DAL as software infrastructure and a Hierarchical Storage Management System as data archival backend. A novel developed data submission tool was made available for the consortium that features a high level of automation to lower the barriers of data publication. After an internal review process, data are published as citable digital object identifiers and a core set of technical metadata is registered at DataCite. The used e!DAL-embedded Web frontend generates for each dataset a landing page and supports an interactive exploration. PGP is registered as research data repository at BioSharing.org, re3data.org and OpenAIRE as valid EU Horizon 2020 open data archive. Above features, the programmatic interface and the support of standard metadata formats, enable PGP to fulfil the FAIR data principles—findable, accessible, interoperable, reusable. Database URL:http://edal.ipk-gatersleben.de/repos/pgp/
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Affiliation(s)
- Daniel Arend
- Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, Stadt Seeland, 06466, Gatersleben, Germany
| | - Astrid Junker
- Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, Stadt Seeland, 06466, Gatersleben, Germany
| | - Uwe Scholz
- Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, Stadt Seeland, 06466, Gatersleben, Germany
| | - Danuta Schüler
- Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, Stadt Seeland, 06466, Gatersleben, Germany
| | - Juliane Wylie
- Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, Stadt Seeland, 06466, Gatersleben, Germany
| | - Matthias Lange
- Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, Stadt Seeland, 06466, Gatersleben, Germany
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