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Wang T, van Dijk ADJ, Bucher J, Liang J, Wu J, Bonnema G, Wang X. Interploidy Introgression Shaped Adaptation during the Origin and Domestication History of Brassica napus. Mol Biol Evol 2023; 40:msad199. [PMID: 37707440 PMCID: PMC10504873 DOI: 10.1093/molbev/msad199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/15/2023] Open
Abstract
Polyploidy is recurrent across the tree of life and known as an evolutionary driving force in plant diversification and crop domestication. How polyploid plants adapt to various habitats has been a fundamental question that remained largely unanswered. Brassica napus is a major crop cultivated worldwide, resulting from allopolyploidy between unknown accessions of diploid B. rapa and B. oleracea. Here, we used whole-genome resequencing data of accessions representing the majority of morphotypes and ecotypes from the species B. rapa, B. oleracea, and B. napus to investigate the role of polyploidy during domestication. To do so, we first reconstructed the phylogenetic history of B. napus, which supported the hypothesis that the emergence of B. napus derived from the hybridization of European turnip of B. rapa and wild B. oleracea. These analyses also showed that morphotypes of swede and Siberian kale (used as vegetable and fodder) were domesticated before rapeseed (oil crop). We next observed that frequent interploidy introgressions from sympatric diploids were prominent throughout the domestication history of B. napus. Introgressed genomic regions were shown to increase the overall genetic diversity and tend to be localized in regions of high recombination. We detected numerous candidate adaptive introgressed regions and found evidence that some of the genes in these regions contributed to phenotypic diversification and adaptation of different morphotypes. Overall, our results shed light on the origin and domestication of B. napus and demonstrate interploidy introgression as an important mechanism that fuels rapid diversification in polyploid species.
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Affiliation(s)
- Tianpeng Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Aalt D J van Dijk
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Johan Bucher
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Jianli Liang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guusje Bonnema
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Xiaowu Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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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 Biotechnol J 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Boideau F, Pelé A, Tanguy C, Trotoux G, Eber F, Maillet L, Gilet M, Lodé-Taburel M, Huteau V, Morice J, Coriton O, Falentin C, Delourme R, Rousseau-Gueutin M, Chèvre AM. A Modified Meiotic Recombination in Brassica napus Largely Improves Its Breeding Efficiency. Biology (Basel) 2021; 10:biology10080771. [PMID: 34440003 PMCID: PMC8389541 DOI: 10.3390/biology10080771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/10/2021] [Accepted: 08/10/2021] [Indexed: 01/31/2023]
Abstract
Simple Summary The selection of varieties more resilient to disease and climate change requires generating new genetic diversity for breeding. The main mechanism for reshuffling genetic information is through the recombination of chromosomes during meiosis. We showed in oilseed rape (Brassica napus, AACC, 2n = 4x = 38), which is a natural hybrid formed from a cross between turnip (B. rapa, AA, 2n = 2x = 20) and cabbage (B. oleracea, CC, 2n = 2x = 18), that there is significantly more crossovers occurring along the entire A chromosomes in allotriploid AAC (crossbetween B. napus and B. rapa) than in diploid AA or allotetraploid AACC hybrids. We demonstrated that these allotriploid AAC hybrids are highly efficient to introduce new variability within oilseed rape varieties, notably by enabling the introduction of small genomic regions carrying genes controlling agronomically interesting traits. Abstract Meiotic recombination is the main tool used by breeders to generate biodiversity, allowing genetic reshuffling at each generation. It enables the accumulation of favorable alleles while purging deleterious mutations. However, this mechanism is highly regulated with the formation of one to rarely more than three crossovers, which are not randomly distributed. In this study, we showed that it is possible to modify these controls in oilseed rape (Brassica napus, AACC, 2n = 4x = 38) and that it is linked to AAC allotriploidy and not to polyploidy per se. To that purpose, we compared the frequency and the distribution of crossovers along A chromosomes from hybrids carrying exactly the same A nucleotide sequence, but presenting three different ploidy levels: AA, AAC and AACC. Genetic maps established with 202 SNPs anchored on reference genomes revealed that the crossover rate is 3.6-fold higher in the AAC allotriploid hybrids compared to AA and AACC hybrids. Using a higher SNP density, we demonstrated that smaller and numerous introgressions of B. rapa were present in AAC hybrids compared to AACC allotetraploid hybrids, with 7.6 Mb vs. 16.9 Mb on average and 21 B. rapa regions per plant vs. nine regions, respectively. Therefore, this boost of recombination is highly efficient to reduce the size of QTL carried in cold regions of the oilseed rape genome, as exemplified here for a QTL conferring blackleg resistance.
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Affiliation(s)
- Franz Boideau
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Alexandre Pelé
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, 61-614 Poznan, Poland
| | - Coleen Tanguy
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Gwenn Trotoux
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Frédérique Eber
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Loeiz Maillet
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Marie Gilet
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Maryse Lodé-Taburel
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Virginie Huteau
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Jérôme Morice
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Olivier Coriton
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Cyril Falentin
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Régine Delourme
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Mathieu Rousseau-Gueutin
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Anne-Marie Chèvre
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
- Correspondence: ; Tel.: +33-2-23-48-51-31
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Chu Y, Bertioli D, Levinson CM, Stalker HT, Holbrook CC, Ozias-Akins P. Homoeologous recombination is recurrent in the nascent synthetic allotetraploid Arachis ipaënsis × Arachis correntina4x and its derivatives. G3 (Bethesda) 2021; 11:6162164. [PMID: 33693764 PMCID: PMC8759810 DOI: 10.1093/g3journal/jkab066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/21/2021] [Indexed: 11/13/2022]
Abstract
Genome instability in newly synthesized allotetraploids of peanut has breeding implications that have not been fully appreciated. Synthesis of wild species-derived neo-tetraploids offers the opportunity to broaden the gene pool of peanut; however, the dynamics among the newly merged genomes creates predictable and unpredictable variation. Selfed progenies from the neo-tetraploid Arachis ipaënsis × Arachis correntina (A. ipaënsis × A. correntina)4x and F1 hybrids and F2 progenies from crosses between A. hypogaea × [A. ipaënsis × A. correntina]4x were genotyped by the Axiom Arachis 48 K SNP array. Homoeologous recombination between the A. ipaënsis and A. correntina derived subgenomes was observed in the S0 generation. Among the S1 progenies, these recombined segments segregated and new events of homoeologous recombination emerged. The genomic regions undergoing homoeologous recombination segregated mostly disomically in the F2 progenies from A. hypogaea × [A. ipaënsis × A. correntina]4x crosses. New homoeologous recombination events also occurred in the F2 population, mostly found on chromosomes 03, 04, 05, and 06. From the breeding perspective, these phenomena offer both possibilities and perils; recombination between genomes increases genetic diversity, but genome instability could lead to instability of traits or even loss of viability within lineages.
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Affiliation(s)
- Ye Chu
- Horticulture Department, University of Georgia, Tifton, GA 31793, USA
| | - David Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA.,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA.,Department of Crop and Soil Science, University of Georgia, Athens, GA 30602, USA
| | - Chandler M Levinson
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA
| | - H Thomas Stalker
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - C Corley Holbrook
- USDA- Agricultural Research Service, Crop Genetics and Breeding Research Unit, Tifton, GA 31793, USA
| | - Peggy Ozias-Akins
- Horticulture Department, University of Georgia, Tifton, GA 31793, USA.,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA
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Mei J, Shao C, Yang R, Feng Y, Gao Y, Ding Y, Li J, Qian W. Introgression and pyramiding of genetic loci from wild Brassica oleracea into B. napus for improving Sclerotinia resistance of rapeseed. Theor Appl Genet 2020; 133:1313-1319. [PMID: 32008057 DOI: 10.1007/s00122-020-03552-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 01/23/2020] [Indexed: 05/28/2023]
Abstract
Resistant rapeseed lines pyramided with multiple resistant QTLs derived from Brassica oleracea were developed via a hexaploidy strategy. Rapeseed (Brassica napus L.) suffers heavily from Sclerotinia stem rot, but the breeding of Sclerotinia-resistant rapeseed cultivar has been unsuccessful. During the study, interspecific hexaploids were generated between rapeseed variety 'Zhongshuang 9' and a wild B. oleracea which was highly resistant to S. sclerotiorum, followed by backcrossing with Zhongshuang 9 and successive selfing. By molecular marker-assisted selection, three major resistant QTLs were transferred and pyramided from B. oleracea into two BC1F8 lines which exhibited ~ 35% higher resistance level than Zhongshuang 9 and produced good seed yield and seed quality. It is the first report on successful development of Sclerotinia-resistant rapeseed lines by introducing multiple resistant loci from wild B. oleracea. This study revealed the effectiveness of pyramiding multiple QTLs in improving Sclerotinia resistance in rapeseed and provided a novel breeding strategy on utilization of B. oleracea in rapeseed improvement.
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Affiliation(s)
- Jiaqin Mei
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400716, China
| | - Chaoguo Shao
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400716, China
| | - Ruhan Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400716, China
| | - Yuxia Feng
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400716, China
| | - Yang Gao
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400716, China
| | - Yijuan Ding
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400716, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400716, China
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400716, China.
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Nikzad A, Kebede B, Pinzon J, Bhavikkumar J, Wang X, Yang RC, Rahman H. Potential of the C Genome of the Different Variants of Brassica oleracea for Heterosis in Spring B. napus Canola. Front Plant Sci 2020; 10:1691. [PMID: 32010170 PMCID: PMC6978715 DOI: 10.3389/fpls.2019.01691] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 11/29/2019] [Indexed: 05/14/2023]
Abstract
The genetic base of Brassica napus canola need to be broadened for exploitation of heterosis at a greater level in the breeding of F1 hybrid canola cultivars. In this study, we evaluated 228 inbred B. napus canola lines derived from six B. napus × B. oleracea interspecific crosses and following two breeding methods (F2- and BC1-derived lines) to understand the effect of the B. oleracea alleles on heterosis for different agronomic and seed quality traits. Test hybrids of the inbreds derived from crosses involving vars. botrytis (cauliflower), alboglabra (Chinese kale) and capitata (cabbage) cv. Badger Shipper, on an average, gave about 10% mid-parent heterosis (MPH), and about 67% of the test hybrids gave higher seed yield than the common B. napus parent indicating that B. oleracea alleles can contribute to heterosis for seed yield in spring B. napus canola hybrids. This was also evident from a positive correlation of the genetic distance of the inbred lines from the common B. napus parent with MPH for seed yield (r = 0.31) as well as with hybrid yield (r = 0.26). Almost no correlation was found between genetic distance and MPH for seed oil and protein content as well as with the performance of the test hybrids for these two traits. The occurrence of positive correlation between seed yield of the inbred lines and test hybrids suggested the importance of the genes exerting additive effect for high seed yield in the hybrids. Very little or almost no heterosis was found for the other agronomic traits as well as for seed oil and protein content. While comparing the two breeding methods, no significant difference was found for seed yield of the test hybrids or the level of MPH; however, the BC1-derived inbred and test hybrid populations flowered and matured earlier and had longer grain-filling period than the F2-derived population. Thus, the results suggested that the B. oleracea gene pool can be used in the breeding of spring B. napus canola to improve seed yield in hybrid cultivars.
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Affiliation(s)
- Azam Nikzad
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Berisso Kebede
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Jaime Pinzon
- Northern Forestry Centre, Natural Resources Canada, Edmonton, AB, Canada
| | - Jani Bhavikkumar
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Xin Wang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Rong-Cai Yang
- Crop Research and Extension Division, Alberta Agriculture and Rural Development, Edmonton, AB, Canada
| | - Habibur Rahman
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
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Zhang L, Zou J, Li S, Wang B, Raboanatahiry N, Li M. Characterization and expression profiles of miRNAs in the triploid hybrids of Brassica napus and Brassica rapa. BMC Genomics 2019; 20:649. [PMID: 31412776 PMCID: PMC6694508 DOI: 10.1186/s12864-019-6001-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 07/26/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Polyploidy provides a means of interspecific genome transfer to incorporate preferable traits from progenitor to progeny. However, few studies on miRNA expression profiles of interspecific hybrids of B. napus (AnAnCnCn) and B. rapa (ArAr) have been reported. RESULTS Here, we apply small RNA sequencing to explore miRNA expression patterns between B. napus, B. rapa and their F1 hybrid. Bioinformatics analysis identified 376, 378, 383 conserved miRNAs and 82, 76, 82 novel miRNAs in B. napus, B. rapa and the F1 hybrid, respectively. Moreover, 213 miRNAs were found to be differentially expressed between B. napus, B. rapa and the F1 hybrid. The present study also shows 211 miRNAs, including 77 upregulated and 134 downregulated miRNAs, to be nonadditively expressed in the F1 hybrid. Furthermore, miRNA synteny analysis revealed high genomic conservation between the genomes of B. napus, B. rapa and their F1 hybrid, with some miRNA loss and gain events in the F1 hybrid. CONCLUSIONS This study not only provides useful resources for exploring global miRNA expression patterns and genome structure but also facilitates genetic research on the roles of miRNAs in genomic interactions of Brassica allopolyploids.
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Affiliation(s)
- Libin Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jun Zou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shisheng Li
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 438000, China
| | - Baoshan Wang
- College of Life Science, Shandong Normal University, Jinan, 250000, China
| | - Nadia Raboanatahiry
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Maoteng Li
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China. .,Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 438000, China.
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Hu D, Zhang W, Zhang Y, Chang S, Chen L, Chen Y, Shi Y, Shen J, Meng J, Zou J. Reconstituting the genome of a young allopolyploid crop, Brassica napus, with its related species. Plant Biotechnol J 2019; 17:1106-1118. [PMID: 30467941 PMCID: PMC6523605 DOI: 10.1111/pbi.13041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 11/01/2018] [Accepted: 11/05/2018] [Indexed: 05/20/2023]
Abstract
Brassica napus (An An Cn Cn ) is an important worldwide oilseed crop, but it is a young allotetraploid with a short evolutionary history and limited genetic diversity. To significantly broaden its genetic diversity and create a novel heterotic population for sustainable rapeseed breeding, this study reconstituted the genome of B. napus by replacing it with the subgenomes from 122 accessions of Brassica rapa (Ar Ar ) and 74 accessions of Brassica carinata (Bc Bc Cc Cc ) and developing a novel gene pool of B. napus through five rounds of extensive recurrent selection. When compared with traditional B. napus using SSR markers and high-throughput SNP/Indel markers through genotyping by sequencing, the newly developed gene pool and its homozygous progenies exhibited a large genetic distance, rich allelic diversity, new alleles and exotic allelic introgression across all 19 AC chromosomes. In addition to the abundant genomic variation detected in the AC genome, we also detected considerable introgression from the eight chromosomes of the B genome. Extensive trait variation and some genetic improvements were present from the early recurrent selection to later generations. This novel gene pool produced equally rich phenotypic variation and should be valuable for rapeseed genetic improvement. By reconstituting the genome of B. napus by introducing subgenomic variation within and between the related species using intense selection and recombination, the whole genome could be substantially reorganized. These results serve as an example of the manipulation of the genome of a young allopolyploid and provide insights into its rapid genome evolution affected by interspecific and intraspecific crosses.
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Affiliation(s)
- Dandan Hu
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Wenshan Zhang
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yikai Zhang
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Shihao Chang
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Lunlin Chen
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yingying Chen
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yongdi Shi
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - 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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Shi L, Song J, Guo C, Wang B, Guan Z, Yang P, Chen X, Zhang Q, King GJ, Wang J, Liu K. A CACTA-like transposable element in the upstream region of BnaA9.CYP78A9 acts as an enhancer to increase silique length and seed weight in rapeseed. Plant J 2019; 98:524-539. [PMID: 30664290 DOI: 10.1111/tpj.14236] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/13/2019] [Accepted: 01/18/2019] [Indexed: 05/26/2023]
Abstract
Rapeseed (Brassica napus L.) is a model plant for polyploid crop research and the second-leading source of vegetable oil worldwide. Silique length (SL) and seed weight are two important yield-influencing traits in rapeseed. Using map-based cloning, we isolated qSLWA9, which encodes a P450 monooxygenase (BnaA9.CYP78A9) and functions as a positive regulator of SL. The expression level of BnaA9.CYP78A9 in silique valves of the long-silique variety is much higher than that in the regular-silique variety, which results in elongated cells and a prolonged phase of silique elongation. Plants of the long-silique variety and transgenic plants with high expression of BnaA9.CYP78A9 had a higher concentration of auxin in the developing silique; this induced a number of auxin-related genes but no genes in well-known auxin biosynthesis pathways, suggesting that BnaA9.CYP78A9 may influence auxin concentration by affecting auxin metabolism or an unknown auxin biosynthesis pathway. A 3.7-kb CACTA-like transposable element (TE) inserted in the 3.9-kb upstream regulatory sequence of BnaA9.CYP78A9 elevates the expression level, suggesting that the CACTA-like TE acts as an enhancer to stimulate high gene expression and silique elongation. Marker and sequence analysis revealed that the TE in B. napus had recently been introgressed from Brassica rapa by interspecific hybridization. The insertion of the TE is consistently associated with long siliques and large seeds in both B. napus and B. rapa collections. However, the frequency of the CACTA-like TE in rapeseed varieties is still very low, suggesting that this allele has not been widely used in rapeseed breeding programs and would be invaluable for yield improvement in rapeseed breeding.
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Affiliation(s)
- Liuliu Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jurong Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Chaocheng Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Bo Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zhilin Guan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Pu Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xun Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, 2480, Australia
| | - Jing Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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10
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Ma Y, Fang S, Peng Y, Gong Y, Wang D. Remote Estimation of Biomass in Winter Oilseed Rape (Brassica napus L.) Using Canopy Hyperspectral Data at Different Growth Stages. Applied Sciences 2019; 9:545. [DOI: 10.3390/app9030545] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The dry aboveground biomass (AGB) is an important parameter in assessing crop growth and predicting yield. This study aims to ascertain the optimal methods for the spectroscopic estimation of winter oilseed rape (WOR) biomass. The different fertilizer-N gradients WOR were planted to collect biomass data and canopy hyperspectral data in two years of field experiments. Correlation analyses and partial least squares regression (PLSR) were performed between canopy hyperspectral data and AGB, and the linear and non-linear regression models simulated the quantitative relation between the vegetation indices (VIs) and AGB at four different growth stages (seeding, bolting, flowering, and pod stage). The results indicated that VIs that were derived from canopy hyperspectral data could estimate AGB accurately: (1) At the seeding and bolting stage, the CIred edge showed excellent performance with the higher accuracy (R2 ranged from 0.60–0.95) as compared to the other six VIs (Green chlorophyll index (CIgreen), normalized difference vegetation index (NDVI), Green normalized difference vegetation index (GNDVI), ratio vegetation index (RVI), DVI, and soil adjusted vegetation index (SAVI)); (2) Correlation analyses and PLSR can effectively extract the feature wavelengths (800 nm and 1200 nm) for biomass estimation. The modified vegetation indices NDVI (800, 1200) significantly improved AGB estimation accuracy (R2 > 0.80, RMSE < 1530 kg/hm2, RPD > 2.3) without saturation phenomenon at the total for four stages, and retained good robustness and reduced the influence of flower and pod for estimating AGB; (3) it was vital to pay more attention to the near-infrared (NIR) bands that could represent WOR growth phenology, and selecting suitable VIs and modeling algorithms could also have a relatively large effect on the success of AGB estimation. The overall results indicated that WOR AGB could be reliably estimated by canopy hyperspectral data, although the plant architecture and coverage of WOR were significantly different during its entire growing period.
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Wang D, Fang S, Yang Z, Wang L, Tang W, Li Y, Tong C. A Regional Mapping Method for Oilseed Rape Based on HSV Transformation and Spectral Features. IJGI 2018; 7:224. [DOI: 10.3390/ijgi7060224] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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12
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Li Q, Chen Y, Yue F, Qian W, Song H. Microspore culture reveals high fitness of B. napus-like gametes in an interspecific hybrid between Brassica napus and B. oleracea. PLoS One 2018; 13:e0193548. [PMID: 29494698 PMCID: PMC5832323 DOI: 10.1371/journal.pone.0193548] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 02/13/2018] [Indexed: 11/18/2022] Open
Abstract
The strategies of crossing B. napus with parental species play important role in broadening and improving the genetic basis of B. napus by the introgression of genetic resources from parental species. With these strategies, it is easy to select new types of B. napus, but difficult to select new types of B. rapa or B. oleracea by self-pollination. This characteristic may be a consequence of high competition with B. napus gametes. To verify the role of gamete viability in producing new B. napus individuals, the meiotic chromosome behavior of the interspecific hybrid between B. napus (Zhongshuang 9) and B. oleracea (6m08) was studied, and microspore-derived (MD) individuals were analyzed. The highest fitness of the 9:19 (1.10%) pattern was observed with a 5.49-fold higher than theoretical expectation among the six chromosome segregation patterns in the hybrid. A total of 43 MD lines with more than 14 chromosomes were developed from the hybrid, and 8 (18.6%) of them were B. napus-like (n = 19) type gametes, having the potential to broaden the genetic basis of natural B. napus (GD = 0.43 ± 0.04). It is easy to produce B. napus-like gametes with 19 chromosomes, and these gametes showed high fitness and competition in the microspore-derived lines, suggesting it might be easy to select new types of B. napus from the interspecific hybrid between B. napus and B. oleracea.
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Affiliation(s)
- Qinfei Li
- College of Horticulture and Landscape, Southwest University, Chongqing, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yangui Chen
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Fang Yue
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- * E-mail: (WQ); (HS)
| | - Hongyuan Song
- College of Horticulture and Landscape, Southwest University, Chongqing, China
- * E-mail: (WQ); (HS)
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Yang Y, Shen Y, Li S, Ge X, Li Z. High Density Linkage Map Construction and QTL Detection for Three Silique-Related Traits in Orychophragmus violaceus Derived Brassica napus Population. Front Plant Sci 2017; 8:1512. [PMID: 28932230 PMCID: PMC5592274 DOI: 10.3389/fpls.2017.01512] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/16/2017] [Indexed: 05/08/2023]
Abstract
Seeds per silique (SS), seed weight (SW), and silique length (SL) are important determinant traits of seed yield potential in rapeseed (Brassica napus L.), and are controlled by naturally occurring quantitative trait loci (QTLs). Mapping QTLs to narrow chromosomal regions provides an effective means of characterizing the genetic basis of these complex traits. Orychophragmus violaceus is a crucifer with long siliques, many SS, and heavy seeds. A novel B. napus introgression line with many SS was previously selected from multiple crosses (B. rapa ssp. chinesis × O. violaceus) × B. napus. In present study, a doubled haploid (DH) population with 167 lines was established from a cross between the introgression line and a line with far fewer SS, in order to detect QTLs for silique-related traits. By screening with a Brassica 60K single nucleotide polymorphism (SNP) array, a high-density linkage map consisting of 1,153 bins and spanning a cumulative length of 2,209.1 cM was constructed, using 12,602 high-quality polymorphic SNPs in the DH population. The average recombination bin densities of the A and C subgenomes were 1.7 and 2.4 cM, respectively. 45 QTLs were identified for the three traits in all, which explained 4.0-34.4% of the total phenotypic variation; 20 of them were integrated into three unique QTLs by meta-analysis. These unique QTLs revealed a significant positive correlation between SS and SL and a significant negative correlation between SW and SS, and were mapped onto the linkage groups A05, C08, and C09. A trait-by-trait meta-analysis revealed eight, four, and seven consensus QTLs for SS, SW, and SL, respectively, and five major QTLs (cqSS.A09b, cqSS.C09, cqSW.A05, cqSW.C09, and cqSL.C09) were identified. Five, three, and four QTLs for SS, SW, and SL, respectively, might be novel QTLs because of the existence of alien genetic loci for these traits in the alien introgression. Thirty-eight candidate genes underlying nine QTLs for silique-related traits were identified.
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Zhang Y, Thomas CL, Xiang J, Long Y, Wang X, Zou J, Luo Z, Ding G, Cai H, Graham NS, Hammond JP, King GJ, White PJ, Xu F, Broadley MR, Shi L, Meng J. QTL meta-analysis of root traits in Brassica napus under contrasting phosphorus supply in two growth systems. Sci Rep 2016; 6:33113. [PMID: 27624881 PMCID: PMC5021999 DOI: 10.1038/srep33113] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 08/22/2016] [Indexed: 12/23/2022] Open
Abstract
A high-density SNP-based genetic linkage map was constructed and integrated with a previous map in the Tapidor x Ningyou7 (TNDH) Brassica napus population, giving a new map with a total of 2041 molecular markers and an average marker density which increased from 0.39 to 0.97 (0.82 SNP bin) per cM. Root and shoot traits were screened under low and 'normal' phosphate (Pi) supply using a 'pouch and wick' system, and had been screened previously in an agar based system. The P-efficient parent Ningyou7 had a shorter primary root length (PRL), greater lateral root density (LRD) and a greater shoot biomass than the P-inefficient parent Tapidor under both treatments and growth systems. Quantitative trait loci (QTL) analysis identified a total of 131 QTL, and QTL meta-analysis found four integrated QTL across the growth systems. Integration reduced the confidence interval by ~41%. QTL for root and shoot biomass were co-located on chromosome A3 and for lateral root emergence were co-located on chromosomes A4/C4 and C8/C9. There was a major QTL for LRD on chromosome C9 explaining ~18% of the phenotypic variation. QTL underlying an increased LRD may be a useful breeding target for P uptake efficiency in Brassica.
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Affiliation(s)
- Ying Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Catherine L. Thomas
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
| | - Jinxia Xiang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Yan Long
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaohua Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Ziliang Luo
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Guangda Ding
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongmei Cai
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Neil S. Graham
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
| | - John P. Hammond
- School of Agriculture, Policy and Development, University of Reading, Reading RG6 6AR, United Kingdom
- Southern Cross Plant Science, Southern Cross University, Lismore NSW 2480, Australia
| | - Graham J. King
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
- Southern Cross Plant Science, Southern Cross University, Lismore NSW 2480, Australia
| | - Philip J. White
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
- King Saud University, Riyadh 11451, Kingdom of Saudi Arabia
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Martin R. Broadley
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
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Tonosaki K, Osabe K, Kawanabe T, Fujimoto R. The importance of reproductive barriers and the effect of allopolyploidization on crop breeding. Breed Sci 2016; 66:333-49. [PMID: 27436943 PMCID: PMC4902455 DOI: 10.1270/jsbbs.15114] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/25/2016] [Indexed: 05/04/2023]
Abstract
Inter-specific hybrids are a useful source for increasing genetic diversity. Some reproductive barriers before and/or after fertilization prevent production of hybrid plants by inter-specific crossing. Therefore, techniques to overcome the reproductive barrier have been developed, and have contributed to hybridization breeding. In recent studies, identification of molecules involved in plant reproduction has been studied to understand the mechanisms of reproductive barriers. Revealing the molecular mechanisms of reproductive barriers may allow us to overcome reproductive barriers in inter-specific crossing, and to efficiently produce inter-specific hybrids in cross-combinations that cannot be produced through artificial techniques. Inter-specific hybrid plants can potentially serve as an elite material for plant breeding, produced through the merging of genomes of parental species by allopolyploidization. Allopolyploidization provides some benefits, such as heterosis, increased genetic diversity and phenotypic variability, which are caused by dynamic changes of the genome and epigenome. Understanding of allopolyploidization mechanisms is important for practical utilization of inter-specific hybrids as a breeding material. This review discusses the importance of reproductive barriers and the effect of allopolyploidization in crop breeding programs.
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Affiliation(s)
- Kaoru Tonosaki
- Kihara Institute for Biological Research, Yokohama City University,
641-12 Maioka, Totsuka, Yokohama, Kanagawa 244-0813,
Japan
- Corresponding author (e-mail: )
| | - Kenji Osabe
- Okinawa Institute of Science and Technology,
1919-1 Tancha, Onna-son, Kunigami, Okinawa 904-0495,
Japan
| | - Takahiro Kawanabe
- Graduate School of Agricultural Science, Kobe University,
Rokkodai, Nada-ku, Kobe 657-8501,
Japan
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University,
Rokkodai, Nada-ku, Kobe 657-8501,
Japan
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16
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Fang S, Tang W, Peng Y, Gong Y, Dai C, Chai R, Liu K. Remote Estimation of Vegetation Fraction and Flower Fraction in Oilseed Rape with Unmanned Aerial Vehicle Data. Remote Sensing 2016; 8:416. [DOI: 10.3390/rs8050416] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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17
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Jan HU, Abbadi A, Lücke S, Nichols RA, Snowdon RJ. Genomic Prediction of Testcross Performance in Canola (Brassica napus). PLoS One 2016; 11:e0147769. [PMID: 26824924 DOI: 10.1371/journal.pone.0147769] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 01/07/2016] [Indexed: 01/13/2023] Open
Abstract
Genomic selection (GS) is a modern breeding approach where genome-wide single-nucleotide polymorphism (SNP) marker profiles are simultaneously used to estimate performance of untested genotypes. In this study, the potential of genomic selection methods to predict testcross performance for hybrid canola breeding was applied for various agronomic traits based on genome-wide marker profiles. A total of 475 genetically diverse spring-type canola pollinator lines were genotyped at 24,403 single-copy, genome-wide SNP loci. In parallel, the 950 F1 testcross combinations between the pollinators and two representative testers were evaluated for a number of important agronomic traits including seedling emergence, days to flowering, lodging, oil yield and seed yield along with essential seed quality characters including seed oil content and seed glucosinolate content. A ridge-regression best linear unbiased prediction (RR-BLUP) model was applied in combination with 500 cross-validations for each trait to predict testcross performance, both across the whole population as well as within individual subpopulations or clusters, based solely on SNP profiles. Subpopulations were determined using multidimensional scaling and K-means clustering. Genomic prediction accuracy across the whole population was highest for seed oil content (0.81) followed by oil yield (0.75) and lowest for seedling emergence (0.29). For seed yieId, seed glucosinolate, lodging resistance and days to onset of flowering (DTF), prediction accuracies were 0.45, 0.61, 0.39 and 0.56, respectively. Prediction accuracies could be increased for some traits by treating subpopulations separately; a strategy which only led to moderate improvements for some traits with low heritability, like seedling emergence. No useful or consistent increase in accuracy was obtained by inclusion of a population substructure covariate in the model. Testcross performance prediction using genome-wide SNP markers shows considerable potential for pre-selection of promising hybrid combinations prior to resource-intensive field testing over multiple locations and years.
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Liu J, Wang J, Wang H, Wang W, Zhou R, Mei D, Cheng H, Yang J, Raman H, Hu Q. Multigenic Control of Pod Shattering Resistance in Chinese Rapeseed Germplasm Revealed by Genome-Wide Association and Linkage Analyses. Front Plant Sci 2016; 7:1058. [PMID: 27493651 PMCID: PMC4954820 DOI: 10.3389/fpls.2016.01058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 07/06/2016] [Indexed: 05/03/2023]
Abstract
The majority of rapeseed cultivars shatter seeds upon maturity especially under hot-dry and windy conditions, reducing yield and gross margin return to growers. Here, we identified quantitative trait loci (QTL) for resistance to pod shatter in an unstructured diverse panel of 143 rapeseed accessions, and two structured populations derived from bi-parental doubled haploid (DH) and inter-mated (IF2) crosses derived from R1 (resistant to pod shattering) and R2 (prone to pod shattering) accessions. Genome-wide association analysis identified six significant QTL for resistance to pod shatter located on chromosomes A01, A06, A07, A09, C02, and C05. Two of the QTL, qSRI.A09 delimited with the SNP marker Bn-A09-p30171993 (A09) and qSRI.A06 delimited with the SNP marker Bn-A06-p115948 (A06) could be repeatedly detected across environments in a diversity panel, DH and IF2 populations, suggesting that at least two loci on chromosomes A06 and A09 were the main contributors to pod shatter resistance in Chinese germplasm. Significant SNP markers identified in this study especially those that appeared repeatedly across environments provide a cost-effective and an efficient method for introgression and pyramiding of favorable alleles for pod shatter resistance via marker-assisted selection in rapeseed improvement programs.
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Affiliation(s)
- Jia Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Jun Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
- Graduate School of Chinese Academy of Agricultural SciencesBeijing, China
| | - Hui Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Wenxiang Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Rijin Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Desheng Mei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Hongtao Cheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Juan Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Harsh Raman
- Graham Centre for Agricultural Innovation (an Alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural InstituteWagga Wagga, NSW, Australia
- *Correspondence: Harsh Raman
| | - Qiong Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
- Qiong Hu
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Zhang J, Li G, Li H, Pu X, Jiang J, Chai L, Zheng B, Cui C, Yang Z, Zhu Y, Jiang L. Transcriptome Analysis of Interspecific Hybrid between Brassica napus and B. rapa Reveals Heterosis for Oil Rape Improvement. Int J Genomics 2015; 2015:230985. [PMID: 26448924 DOI: 10.1155/2015/230985] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Revised: 08/03/2015] [Accepted: 08/05/2015] [Indexed: 12/02/2022] Open
Abstract
The hybrid between Brassica napus and B. rapa displays obvious heterosis in both growth performance and stress tolerances. A comparative transcriptome analysis for B. napus (AnAnCC genome), B. rapa (ArAr genome), and its hybrid F1 (AnArC genome) was carried out to reveal the possible molecular mechanisms of heterosis at the gene expression level. A total of 40,320 nonredundant unigenes were identified using B. rapa (AA genome) and B. oleracea (CC genome) as reference genomes. A total of 6,816 differentially expressed genes (DEGs) were mapped in the A and C genomes with 4,946 DEGs displayed nonadditively by comparing the gene expression patterns among the three samples. The coexistence of nonadditive DEGs including high-parent dominance, low-parent dominance, overdominance, and underdominance was observed in the gene action modes of F1 hybrid, which were potentially related to the heterosis. The coexistence of multiple gene actions in the hybrid was observed and provided a list of candidate genes and pathways for heterosis. The expression bias of transposable element-associated genes was also observed in the hybrid compared to their parents. The present study could be helpful for the better understanding of the determination and regulation of mechanisms of heterosis to aid Brassica improvement.
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Dai S, Hou J, Long Y, Wang J, Li C, Xiao Q, Jiang X, Zou X, Zou J, Meng J. Widespread and evolutionary analysis of a MITE family Monkey King in Brassicaceae. BMC Plant Biol 2015; 15:149. [PMID: 26084405 PMCID: PMC4471910 DOI: 10.1186/s12870-015-0490-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/07/2015] [Indexed: 05/24/2023]
Abstract
BACKGROUND Miniature inverted repeat transposable elements (MITEs) are important components of eukaryotic genomes, with hundreds of families and many copies, which may play important roles in gene regulation and genome evolution. However, few studies have investigated the molecular mechanisms involved. In our previous study, a Tourist-like MITE, Monkey King, was identified from the promoter region of a flowering time gene, BnFLC.A10, in Brassica napus. Based on this MITE, the characteristics and potential roles on gene regulation of the MITE family were analyzed in Brassicaceae. RESULTS The characteristics of the Tourist-like MITE family Monkey King in Brassicaceae, including its distribution, copies and insertion sites in the genomes of major Brassicaceae species were analyzed in this study. Monkey King was actively amplified in Brassica after divergence from Arabidopsis, which was indicated by the prompt increase in copy number and by phylogenetic analysis. The genomic variations caused by Monkey King insertions, both intra- and inter-species in Brassica, were traced by PCR amplification. Genomic sequence analysis showed that most complete Monkey King elements are located in gene-rich regions, less than 3kb from genes, in both the B. rapa and A. thaliana genomes. Sixty-seven Brassica expressed sequence tags carrying Monkey King fragments were also identified from the NCBI database. Bisulfite sequencing identified specific DNA methylation of cytosine residues in the Monkey King sequence. A fragment containing putative TATA-box motifs in the MITE sequence could bind with nuclear protein(s) extracted from leaves of B. napus plants. A Monkey King-related microRNA, bna-miR6031, was identified in the microRNA database. In transgenic A. thaliana, when the Monkey King element was inserted upstream of 35S promoter, the promoter activity was weakened. CONCLUSION Monkey King, a Brassicaceae Tourist-like MITE family, has amplified relatively recently and has induced intra- and inter-species genomic variations in Brassica. Monkey King elements are most abundant in the vicinity of genes and may have a substantial effect on genome-wide gene regulation in Brassicaceae. Monkey King insertions potentially regulate gene expression and genome evolution through epigenetic modification and new regulatory motif production.
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Affiliation(s)
- Shutao Dai
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Jinna Hou
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
- Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhenzhou, Henan, 450002, China.
| | - Yan Long
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Jing Wang
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Cong Li
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Qinqin Xiao
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Xiaoxue Jiang
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Xiaoxiao Zou
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Jun Zou
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Jinling Meng
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
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Gupta M, Gupta S, Kumar H, Kumar N, Banga SS. Population structure and breeding value of a new type of Brassica juncea created by combining A and B genomes from related allotetraploids. Theor Appl Genet 2015; 128:221-34. [PMID: 25399317 DOI: 10.1007/s00122-014-2423-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 11/02/2014] [Indexed: 05/11/2023]
Abstract
Derived amphiploidy helped to resynthesize agronomically superior B. juncea germplasm which showed high heterosis in crosses with natural B. juncea . This new procedure facilitates a seamless flow of variation across Brassica digenomics. Brassica digenomics, artificially resynthesized by hybridizing extant genome donor diploids, show poor breeding value due to the linkage drag associated with diploid donors. We recently developed a method that involves resynthesis through hybridization between related allotetraploids. Derived B. juncea was created by combining A and B genomes extant in B. napus and B. carinata, respectively. Large genomic and agronomic modifications resulted. Population structure analysis based on the DNA polymorphism generated using 108 locus-specific SSR primers helped to identify three pools of allelic diversity. Thirteen progenies with determinate plant growth habit were discovered, and these aligned closely with B genome of the donor species like B. nigra and B. carinata. The indeterminate group showed greater genetic affinity with extant B. juncea. Derived genotypes possessed high agronomic potential. Importantly, high heterosis was observed in crosses between derived and natural B. juncea. Some derived juncea progenies figured in heterotic combinations during both the years of F 1 hybrid evaluation. In essence, the hybrids between derived B. juncea and natural B. juncea can be considered as interspecific hybrids between B. juncea and B. napus for A genome and between B. juncea and B. carinata for B genome. This possibly explains their high heterosis-inducing potential. Integrating genetic diversity with the inherent breeding value allowed more efficient prediction of heterosis. Besides generation of new novel variability of huge economic importance and operational simplicity, the method of derived amphiploidy allows a seamless flow of heritable variation across Brassica digenomics.
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Affiliation(s)
- Mehak Gupta
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141001, India
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Li F, Chen B, Xu K, Wu J, Song W, Bancroft I, Harper AL, Trick M, Liu S, Gao G, Wang N, Yan G, Qiao J, Li J, Li H, Xiao X, Zhang T, Wu X. Genome-wide association study dissects the genetic architecture of seed weight and seed quality in rapeseed (Brassica napus L.). DNA Res 2014; 21:355-67. [PMID: 24510440 PMCID: PMC4131830 DOI: 10.1093/dnares/dsu002] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 01/08/2014] [Indexed: 11/12/2022] Open
Abstract
Association mapping can quickly and efficiently dissect complex agronomic traits. Rapeseed is one of the most economically important polyploid oil crops, although its genome sequence is not yet published. In this study, a recently developed 60K Brassica Infinium(®) SNP array was used to analyse an association panel with 472 accessions. The single-nucleotide polymorphisms (SNPs) of the array were in silico mapped using 'pseudomolecules' representative of the genome of rapeseed to establish their hypothetical order and to perform association mapping of seed weight and seed quality. As a result, two significant associations on A8 and C3 of Brassica napus were detected for erucic acid content, and the peak SNPs were found to be only 233 and 128 kb away from the key genes BnaA.FAE1 and BnaC.FAE1. BnaA.FAE1 was also identified to be significantly associated with the oil content. Orthologues of Arabidopsis thaliana HAG1 were identified close to four clusters of SNPs associated with glucosinolate content on A9, C2, C7 and C9. For seed weight, we detected two association signals on A7 and A9, which were consistent with previous studies of quantitative trait loci mapping. The results indicate that our association mapping approach is suitable for fine mapping of the complex traits in rapeseed.
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Affiliation(s)
- Feng Li
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
| | - Biyun Chen
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
| | - Kun Xu
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
| | - Jinfeng Wu
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
| | - Weilin Song
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
| | - Ian Bancroft
- Department of Biology, University of York, York, UK
| | | | - Martin Trick
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Shengyi Liu
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
| | - Guizhen Gao
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
| | - Nian Wang
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
| | - Guixin Yan
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
| | - Jiangwei Qiao
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
| | - Jun Li
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
| | - Hao Li
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
| | - Xin Xiao
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
| | - Tianyao Zhang
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
| | - Xiaoming Wu
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
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Li Q, Mei J, Zhang Y, Li J, Ge X, Li Z, Qian W. A large-scale introgression of genomic components of Brassica rapa into B. napus by the bridge of hexaploid derived from hybridization between B. napus and B. oleracea. Theor Appl Genet 2013; 126:2073-2080. [PMID: 23699961 DOI: 10.1007/s00122-013-2119-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Accepted: 05/08/2013] [Indexed: 06/02/2023]
Abstract
Brassica rapa (AA) has been used to widen the genetic basis of B. napus (AACC), which is a new but important oilseed crop worldwide. In the present study, we have proposed a strategy to develop new type B. napus carrying genomic components of B. rapa by crossing B. rapa with hexaploid (AACCCC) derived from B. napus and B. oleracea (CC). The hexaploid exhibited large flowers and high frequency of normal chromosome segregation, resulting in good seed set (average of 4.48 and 12.53 seeds per pod by self and open pollination, respectively) and high pollen fertility (average of 87.05 %). It was easy to develop new type B. napus by crossing the hexaploid with 142 lines of B. rapa from three ecotype groups, with the average crossability of 9.24 seeds per pod. The genetic variation of new type B. napus was diverse from that of current B. napus, especially in the A subgenome, revealed by genome-specific simple sequence repeat markers. Our data suggest that the strategy proposed here is a large-scale and highly efficient method to introgress genomic components of B. rapa into B. napus.
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Affiliation(s)
- Qinfei Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
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24
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Xiong W, Li X, Fu D, Mei J, Li Q, Lu G, Qian L, Fu Y, Disi JO, Li J, Qian W. DNA Methylation Alterations at 5'-CCGG Sites in the Interspecific and Intraspecific Hybridizations Derived from Brassica rapa and B. napus. PLoS One 2013; 8:e65946. [PMID: 23824315 PMCID: PMC3688851 DOI: 10.1371/journal.pone.0065946] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 05/01/2013] [Indexed: 11/18/2022] Open
Abstract
DNA methylation is an important regulatory mechanism for gene expression that involved in the biological processes of development and differentiation in plants. To investigate the association of DNA methylation with heterosis in Brassica, a set of intraspecific hybrids in Brassica rapa and B. napus and interspecific hybrids between B. rapa and B. napus, together with parental lines, were used to monitor alterations in cytosine methylation at 5'-CCGG sites in seedlings and buds by methylation-sensitive amplification polymorphism analysis. The methylation status of approximately a quarter of the methylation sites changed between seedlings and buds. These alterations were related closely to the genomic structure and heterozygous status among accessions. The methylation status in the majority of DNA methylation sites detected in hybrids was the same as that in at least one of the parental lines in both seedlings and buds. However, the association between patterns of cytosine methylation and heterosis varied among different traits and between tissues in hybrids of Brassica, although a few methylation loci were associated with heterosis. Our data suggest that changes in DNA methylation at 5'-CCGG sites are not associated simply with heterosis in the interspecific and intraspecific hybridizations derived from B. rapa and B. napus.
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Affiliation(s)
- Wanshan Xiong
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Xiaorong Li
- College of Pharmaceutical Science, Southwest University, Chongqing, China
| | - Donghui Fu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Jiaqin Mei
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Qinfei Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Guanyuan Lu
- Oil Crop Institute, China Academy of Agricultural Science, Wuhan, China
| | - Lunwen Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yin Fu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | | | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- * E-mail:
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25
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Malek MA, Ismail MR, Rafii MY, Rahman M. Synthetic Brassica napus L.: development and studies on morphological characters, yield attributes, and yield. ScientificWorldJournal 2012; 2012:416901. [PMID: 22701356 PMCID: PMC3373182 DOI: 10.1100/2012/416901] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 03/27/2012] [Indexed: 11/17/2022] Open
Abstract
Brassica napus was synthesized by hybridization between its diploid progenitor species B. rapa and B. oleracea followed by chromosome doubling. Cross with B. rapa as a female parent was only successful. Among three colchicine treatments (0.10, 0.15, and 0.20%), 0.15% gave the highest success (86%) of chromosome doubling in the hybrids (AC; 2n = 19). Synthetic B. napus (AACC, 2n = 38) was identified with bigger petals, fertile pollens and seed setting. Synthetic B. napus had increased growth over parents and exhibited wider ranges with higher coefficients of variations than parents for morphological and yield contributing characters, and yield per plant. Siliqua length as well as beak length in synthetic B. napus was longer than those of the parents. Number of seeds per siliqua, 1000-seed weight and seed yield per plant in synthetic B. napus were higher than those of the parents. Although flowering time in synthetic B. napus was earlier than both parents, however the days to maturity was little higher over early maturing B. rapa parent. The synthesized B. napus has great potential to produce higher seed yield. Further screening and evaluation is needed for selection of desirable genotypes having improved yield contributing characters and higher seed yield.
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Affiliation(s)
- M A Malek
- Plant Breeding Division, Bangladesh Institute of Nuclear Agriculture, Mymensingh 2202, Bangladesh.
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Zou J, Fu D, Gong H, Qian W, Xia W, Pires JC, Li R, Long Y, Mason AS, Yang TJ, Lim YP, Park BS, Meng J. De novo genetic variation associated with retrotransposon activation, genomic rearrangements and trait variation in a recombinant inbred line population of Brassica napus derived from interspecific hybridization with Brassica rapa. Plant J 2011; 68:212-24. [PMID: 21689170 DOI: 10.1111/j.1365-313x.2011.04679.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Interspecific hybridization is a significant evolutionary force as well as a powerful method for crop breeding. Partial substitution of the AA subgenome in Brassica napus (A(n) A(n) C(n) C(n) ) with the Brassica rapa (A(r) A(r) ) genome by two rounds of interspecific hybridization resulted in a new introgressed type of B. napus (A(r) A(r) C(n) C(n) ). In this study, we construct a population of recombinant inbred lines of the new introgressed type of B. napus. Microsatellite, intron-based and retrotransposon markers were used to characterize this experimental population with genetic mapping, genetic map comparison and specific marker cloning analysis. Yield-related traits were also recorded for identification of quantitative trait loci (QTLs). A remarkable range of novel genomic alterations was observed in the population, including simple sequence repeat (SSR) mutations, chromosomal rearrangements and retrotransposon activations. Most of these changes occurred immediately after interspecific hybridization, in the early stages of genome stabilization and derivation of experimental lines. These novel genomic alterations affected yield-related traits in the introgressed B. napus to an even greater extent than the alleles alone that were introgressed from the A(r) subgenome of B. rapa, suggesting that genomic changes induced by interspecific hybridization are highly significant in both genome evolution and crop improvement.
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Affiliation(s)
- Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Jiang C, Ramchiary N, Ma Y, Jin M, Feng J, Li R, Wang H, Long Y, Choi SR, Zhang C, Cowling WA, Park BS, Lim YP, Meng J. Structural and functional comparative mapping between the Brassica A genomes in allotetraploid Brassica napus and diploid Brassica rapa. Theor Appl Genet 2011; 123:927-941. [PMID: 21761162 DOI: 10.1007/s00122-011-1637-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Accepted: 06/13/2011] [Indexed: 05/29/2023]
Abstract
Brassica napus (AACC genome) is an important oilseed crop that was formed by the fusion of the diploids B. rapa (AA) and B. oleracea (CC). The complete genomic sequence of the Brassica A genome will be available soon from the B. rapa genome sequencing project, but it is not clear how informative the A genome sequence in B. rapa (A(r)) will be for predicting the structure and function of the A subgenome in the allotetraploid Brassica species B. napus (A(n)). In this paper, we report the results of structural and functional comparative mapping between the A subgenomes of B. napus and B. rapa based on genetic maps that were anchored with bacterial artificial chromosomes (BACs)-sequence of B. rapa. We identified segmental conservation that represented by syntenic blocks in over one third of the A genome; meanwhile, comparative mapping of quantitative trait loci for seed quality traits identified a dozen homologous regions with conserved function in the A genome of the two species. However, several genomic rearrangement events, such as inversions, intra- and inter-chromosomal translocations, were also observed, covering totally at least 5% of the A genome, between allotetraploid B. napus and diploid B. rapa. Based on these results, the A genomes of B. rapa and B. napus are mostly functionally conserved, but caution will be necessary in applying the full sequence data from B. rapa to the B. napus as a result of genomic rearrangements in the A genome between the two species.
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Affiliation(s)
- Congcong Jiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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28
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Tian E, Jiang Y, Chen L, Zou J, Liu F, Meng J. Synthesis of a Brassica trigenomic allohexaploid (B. carinata × B. rapa) de novo and its stability in subsequent generations. Theor Appl Genet 2010; 121:1431-40. [PMID: 20607208 DOI: 10.1007/s00122-010-1399-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Accepted: 06/19/2010] [Indexed: 05/11/2023]
Abstract
Allopolyploidy plays an important role in plant evolution and confers obvious advantages on crop growth and breeding compared to low ploidy levels. The present investigation was aimed at synthesising the first known chromosomally stable hexaploid Brassica with the genome constitution AABBCC. More than 2,000 putative hexaploid plants were obtained through large-scale hybridisation from various combinations of crosses between different cultivars of Brassica carinata (BBCC) and B. rapa (AA). The majority of plants after two generations of selfing within selected hexaploid plants (H(2)) were aneuploid, and only 80 plants (4.6%) had the expected hexaploid chromosome number (2n = 54). The hexaploid ratio increased to an average of 23.0 and 26.3% in the H(3) and H(4) generations, respectively, and was accompanied by an increase in pollen fertility. The appearance of aneuploid plants in each generation could be detected having various chromosomal abnormalities at meiosis. The frequency of hexaploid plants varied significantly among different cultivar combinations, from 0 to 56% in the H(4) generation, and it showed a positive correlation with pollen fertility. The frequency of SSR allelic fragments lost or novel alleles gained was significantly lower in H(4) than in H(2) and H(3), which reflects increasing genome stability in H(4). The A and C genomes were significantly less stable than the B genome, which may mainly result from frequent homoeologous pairing and rearrangements between the A and C genomes. Methods to establish a stable hexaploid Brassica crop by intercrossing these lines followed by intensive selection are also discussed.
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Affiliation(s)
- Entang Tian
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 1 Shizishan, 430070, Wuhan, China
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Zou J, Jiang C, Cao Z, Li R, Long Y, Chen S, Meng J. Association mapping of seed oil content in Brassica napus and comparison with quantitative trait loci identified from linkage mappingThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”. Genome 2010; 53:908-16. [DOI: 10.1139/g10-075] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Association mapping has been used increasingly in natural populations with rich genetic diversity to detect DNA-based markers that are associated with important agronomic traits. Brassica napus is an important oil crop with limited genetic diversity. “New-type” B. napus that is introgressed with subgenomic components from related species has been developed to broaden the genetic basis of “traditional” B. napus . In this study, new-type B. napus lines and a collection of traditional B. napus varieties from different countries were used as two different populations to evaluate seed oil content and to determine the efficacy of association mapping by comparison with previous study of linkage mapping. Relatively rich genetic diversity, but a higher level of linkage disequilibrium was observed in the new-type B. napus as compared with the traditional B. napus . Similarly, a larger variation in oil content and a greater number of associated markers were detected in the population of new-type B. napus . Meanwhile, more than half of the genetic loci, to which the associated markers corresponded, were located within the quantitative trait loci intervals identified previously in linkage mapping experiments, which demonstrated the power of association mapping in B. napus .
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Affiliation(s)
- Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- School of Plant Biology, and International Centre for Plant Breeding Education and Research, The University of Western Australia, Crawley, WA 6009, Australia
| | - Congcong Jiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- School of Plant Biology, and International Centre for Plant Breeding Education and Research, The University of Western Australia, Crawley, WA 6009, Australia
| | - Zhengying Cao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- School of Plant Biology, and International Centre for Plant Breeding Education and Research, The University of Western Australia, Crawley, WA 6009, Australia
| | - Ruiyuan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- School of Plant Biology, and International Centre for Plant Breeding Education and Research, The University of Western Australia, Crawley, WA 6009, Australia
| | - Yan Long
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- School of Plant Biology, and International Centre for Plant Breeding Education and Research, The University of Western Australia, Crawley, WA 6009, Australia
| | - Sheng Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- School of Plant Biology, and International Centre for Plant Breeding Education and Research, The University of Western Australia, Crawley, WA 6009, Australia
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- School of Plant Biology, and International Centre for Plant Breeding Education and Research, The University of Western Australia, Crawley, WA 6009, Australia
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Xiao Y, Chen L, Zou J, Tian E, Xia W, Meng J. Development of a population for substantial new type Brassica napus diversified at both A/C genomes. Theor Appl Genet 2010; 121:1141-1150. [PMID: 20556596 DOI: 10.1007/s00122-010-1378-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2009] [Accepted: 06/03/2010] [Indexed: 05/29/2023]
Abstract
Intersubgenomic heterosis in rapeseed has been revealed in previous studies by using traditional Brassica napus (A(n)A(n)C(n)C(n)) to cross partial new type B. napus with A(r)/C(c) introgression from the genomes of B. rapa and B. carinata, respectively. To further enlarge the genetic basis of B. napus and to facilitate a sustained heterosis breeding in rapeseed, it is crucial to create a population for substantial new type B. napus diversified at both A/C genomes. In this experiment, hundreds of artificial hexaploid plants (A(r)A(r)B(c)B(c)C(c)C(c)) involving hundreds of B. carinata/B. rapa combinations were first crossed with elite lines of partial new type B. napus. The pentaploid plants (AABCC) were open-pollinated in isolated conditions, and their offspring were successively self-pollinated and intensively selected for two generations. Thereafter, a population of substantial new type B. napus mainly with a genomic composition of A(r)A(r)C(c)C(c) harbouring genetic diversity from 25 original cultivars of B. rapa and 72 accessions of B. carinata was constructed. The population was cytologically verified to have the correct chromosome constitution of AACC and differed genetically from traditional B. napus, in terms of the genome components of A(r)/C(c) and B(c) as well as the novel genetic variations induced by the interspecific hybridisation process. Synchronously, rich phenotypic variation with plenty of novel valuable traits was observed in the population. The origin of the novel variations and the value of the population are discussed.
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Affiliation(s)
- Yong Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070, Hubei, China
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Wang N, Shi L, Tian F, Ning H, Wu X, Long Y, Meng J. Assessment of FAE1 polymorphisms in three Brassica species using EcoTILLING and their association with differences in seed erucic acid contents. BMC Plant Biol 2010; 10:137. [PMID: 20594317 PMCID: PMC3017795 DOI: 10.1186/1471-2229-10-137] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2009] [Accepted: 07/01/2010] [Indexed: 05/04/2023]
Abstract
BACKGROUND FAE1 (fatty acid elongase1) is the key gene in the control of erucic acid synthesis in seeds of Brassica species. Due to oil with low erucic acid (LEA) content is essential for human health and not enough LEA resource could be available, thus new LEA genetic resources are being sought for Brassica breeding. EcoTILLING, a powerful genotyping method, can readily be used to identify polymorphisms in Brassica. RESULTS Seven B. rapa, nine B. oleracea and 101 B. napus accessions were collected for identification of FAE1 polymorphisms. Three polymorphisms were detected in the two FAE1 paralogues of B. napus using EcoTILLING and were found to be strongly associated with differences in the erucic acid contents of seeds. In genomic FAE1 sequences obtained from seven B. rapa accessions, one SNP in the coding region was deduced to cause loss of gene function. Molecular evolution analysis of FAE1 homologues showed that the relationship between the Brassica A and C genomes is closer than that between the A/C genomes and Arabidopsis genome. Alignment of the coding sequences of these FAE1 homologues indicated that 18 SNPs differed between the A and C genomes and could be used as genome-specific markers in Brassica. CONCLUSION This study showed the applicability of EcoTILLING for detecting gene polymorphisms in Brassica. The association between B. napus FAE1 polymorphisms and the erucic acid contents of seeds may provide useful guidance for LEA breeding. The discovery of the LEA resource in B. rapa can be exploited in Brasscia cultivation.
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Affiliation(s)
- Nian Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Fang Tian
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Huicai Ning
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaoming Wu
- Oil Crops Research Institute, Chinese Academic of Agriculture Science, Wuhan, 430062, China
| | - Yan Long
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
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Zou J, Zhu J, Huang S, Tian E, Xiao Y, Fu D, Tu J, Fu T, Meng J. Broadening the avenue of intersubgenomic heterosis in oilseed Brassica. Theor Appl Genet 2010; 120:283-90. [PMID: 19911158 DOI: 10.1007/s00122-009-1201-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Accepted: 10/17/2009] [Indexed: 05/05/2023]
Abstract
Accumulated evidence has shown that each of the three basic Brassica genomes (A, B and C) has undergone profound changes in different species, and has led to the concept of the "subgenome". Significant intersubgenomic heterosis was observed in hybrids between traditional Brassica napus and first generation lines of new type B. napus. The latter were produced by the partial introgression of subgenomic components from different species into B. napus. To increase the proportion of exotic subgenomic components and thus achieve stronger heterosis, lines of first generation new type B. napus were intercrossed with each other, and subjected to intensive marker-assisted selection to develop the second generation of new type B. napus. The second generation showed better agronomic traits and a higher proportion of introgression of subgenomic components than did the first generation. Compared with the commercial hybrid and the hybrids produced with the first generation new type B. napus, the novel hybrids showed stronger heterosis for seed yield during the 2 years of field trials. The extent of heterosis showed a significant positive correlation with the introgressed subgenomic components in the parental new type B. napus. To increase the content of the exotic subgenomic components further and to allow sustainable breeding of novel lines of new type B. napus, we initiated the development of a gene pool for new type B. napus that contained a substantial amount of genetic variation in the A(r) and C(c) genome. We discuss new approaches to broaden the avenue of intersubgenomic heterosis in oilseed Brassica.
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Affiliation(s)
- Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
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Liu RH, Meng JL. RFLP and AFLP analysis of inter- and intraspecific variation of Brassica rapa and B. napus shows that B. rapa is an important genetic resource for B. napus improvement. ACTA ACUST UNITED AC 2009; 33:814-23. [PMID: 16980128 DOI: 10.1016/s0379-4172(06)60115-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2005] [Accepted: 04/27/2006] [Indexed: 11/19/2022]
Abstract
Fingerprinting of 29 accessions of oilseed rape, including seven accessions of Brassica napus, and 22 accessions of B. rapa (B. campestris) from Europe, North America, and China was analyzed using RFLP and AFLP markers. In total, 1,477 polymorphic RFLP bands and 183 polymorphic AFLP bands from 166 enzyme-probe combinations and two pairs of AFLP primers, respectively, were scored for the 29 accessions. On average, RFLP analysis showed that the Arabidopsis EST probe detected more polymorphic bands in Brassica than the random genomic probe performed. More polymorphic RFLP markers were detected with the digestion of EcoR I or BamH I than HindIII. According to the number of bands amplified from each accession, the copy numbers of each gene in the genomes of B. rapa and B. napus were estimated. The average copy numbers in B. rapa of China, B. rapa of Europe, and B. napus, were 3.2, 3.1, and 2.9, respectively. Genetic distance based on the AFLP data was well correlated with that based on the RFLP data (r = 0.72, P<0.001), but 0.39 smaller on average. Genetic diversity analysis showed that Chinese B. rapa was more polymorphic than Chinese B. napus and European materials. Some European B. napus accessions were clustered into European B. rapa, which were distinctly different from Chinese B. napus. The larger variations of Chinese accessions of B. rapa suggest that they are valuable in oilseed rape breeding. Novel strategies to use intersubgenomic heterosis between genome of B. rapa (A(r)A(r)) and genome of B. napus (A(n)A(n)C(n)C(n)) were elucidated.
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Affiliation(s)
- Ren-Hu Liu
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Chen X, Li M, Shi J, Fu D, Qian W, Zou J, Zhang C, Meng J. Gene expression profiles associated with intersubgenomic heterosis in Brassica napus. Theor Appl Genet 2008; 117:1031-40. [PMID: 18754099 DOI: 10.1007/s00122-008-0842-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Accepted: 06/28/2008] [Indexed: 05/21/2023]
Abstract
In order to understand the genetic mechanism of heterosis that has been observed in hybrids between Brassica napus and partial new-type B. napus which had exotic genome components from relative species, this study focused on the difference in gene expression patterns among partial new-typed B. napus lines, B. napus cultivars and their hybrids using the cDNA amplified fragment length polymorphism technique (cDNA-AFLP) technique. First, three partial new-type B. napus lines were compared with their original parents. One new line contained the exotic genomic components from B. rapa, and the other two new lines were obtained by the introgression of genomic components from B. rapa and B. carinata. The experimental results showed that the introgression of A(r) and C(c) genome components from B. rapa and B. carinata led to considerable differences in the gene expression profiles of the partial new-type lines when compared with their parents. Secondly, the gene expression profiles of nine cross-combinations between three partial new-type lines and three B. napus cultivars were compared. Twenty transcript-derived fragments (TDFs) associated with intersubgenomic heterosis were randomly selected and converted into PCR-based molecular markers. Some of them were mapped in the confidence intervals of quantitative trait loci (QTLs) for yield and yield-related traits in three segregative populations of B. napus. These results suggested that a proportion of the heterosis-associated TDFs were really responsible for fluctuating seed yield in rapeseed.
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Affiliation(s)
- Xin Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
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35
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Qian W, Sass O, Meng J, Li M, Frauen M, Jung C. Heterotic patterns in rapeseed (Brassica napus L.): I. Crosses between spring and Chinese semi-winter lines. Theor Appl Genet 2007; 115:27-34. [PMID: 17453172 DOI: 10.1007/s00122-007-0537-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2006] [Accepted: 03/10/2007] [Indexed: 05/05/2023]
Abstract
Chinese semi-winter rapeseed is genetically diverse from Canadian and European spring rapeseed. This study was conducted to evaluate the potential of semi-winter rapeseed for spring rapeseed hybrid breeding, to assess the genetic effects involved, and to estimate the correlation of parental genetic distance (GD) with hybrid performance, heterosis, general combining ability (GCA) and specific combining ability (SCA) in crosses between spring and semi-winter rapeseed lines. Four spring male sterile lines from Germany and Canada as testers were crossed with 13 Chinese semi-winter rapeseed lines to develop 52 hybrids, which were evaluated together with their parents and commercial hybrids for seed yield and oil content in three sets of field trials with 8 environments in Canada and Europe. The Chinese parental lines were not adapted to local environmental conditions as demonstrated by poor seed yields per se. However, the hybrids between the Chinese parents and the adapted spring rapeseed lines exhibited high heterosis for seed yield. The average mid-parent heterosis was 15% and ca. 50% of the hybrids were superior to the respective hybrid control across three sets of field trials. Additive gene effects mainly contributed to hybrid performance since the mean squares of GCA were higher as compared to SCA. The correlation between parental GD and hybrid performance and heterosis was found to be low whereas the correlation between GCA((f + m)) and hybrid performance was high and significant in each set of field trials, with an average of r = 0.87 for seed yield and r = 0.89 for oil content, indicating that hybrid performance can be predicted by GCA((f + m)). These results demonstrate that Chinese semi-winter rapeseed germplasm has a great potential to increase seed yield in spring rapeseed hybrid breeding programs in Canada and Europe.
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Affiliation(s)
- W Qian
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Kiel 24118, Germany
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36
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Li M, Liu J, Wang Y, Yu L, Meng J. Production of Partial New-typed Brassica Napus by Introgression of Genomic Components from B. rapa and B. carinata. J Genet Genomics 2007; 34:460-8. [PMID: 17560532 DOI: 10.1016/s1673-8527(07)60050-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Accepted: 11/27/2006] [Indexed: 11/25/2022]
Abstract
A breeding strategy for widening the germplasm of Brassica napus was proposed by introgression of the A(r) subgenome of B. rapa (A(r)A(r)) and C(c) of B. carinata (B(c)B(c)C(c)C(c)) into natural B. napus (A(n)A(n)C(n)C(n)). The progenies with 38 chromosomes that were derived from the self-pollinated seeds of pentaploid hybrids (A(r)A(n)B(c)C(c)C(n)) were used for further research. Some of the partial new-typed B. napus showed normal meiotic behavior, high portion of germinated pollen and normal embryological development. This indicates that the selected new-typed B. napus had a balanced genetic base. Molecular analysis showed that about 50% of the genome in the new-typed B. napus was replaced by A(r) and C(c) subgenome from B. rapa and B. carinata. Considering the genetic diversity among different lines of new-typed B. napus it was deduced that the introgression of the genomic components from B. rapa and B. carinata could widen the genetic diversity of rapeseed.
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Affiliation(s)
- Maoteng Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
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37
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Qian W, Meng J, Li M, Frauen M, Sass O, Noack J, Jung C. Introgression of genomic components from Chinese Brassica rapa contributes to widening the genetic diversity in rapeseed (B. napus L.), with emphasis on the evolution of Chinese rapeseed. Theor Appl Genet 2006; 113:49-54. [PMID: 16604336 DOI: 10.1007/s00122-006-0269-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2005] [Accepted: 03/17/2006] [Indexed: 05/02/2023]
Abstract
In spite of its short history of being an oil crop in China, the Chinese semi-winter rapeseed (Brassica napus L., 2n = 38, AACC) has been improved rapidly by intentional introgression of genomic components from Chinese B. rapa (2n = 20, AA). As a result, the Chinese semi-winter rapeseed has diversified genetically from the spring and winter rapeseed grown in the other regions such as Europe and North America. The objectives of this study were to investigate the roles of the introgression of the genomic components from the Chinese B. rapa in widening the genetic diversity of rapeseed and to verify the role of this introgression in the evolution of the Chinese rapeseed. Ten lines of the new type of rapeseed, which were produced by introgression of Chinese B. rapa to Chinese normal rapeseed, were compared for genetic diversity using amplified fragment length polymorphism (AFLP) with three groups of 35 lines of the normal rapeseed, including 9 semi-winter rapeseed lines from China, 9 winter rapeseed lines from Europe and 17 spring rapeseed lines from Northern Europe, Canada and Australia. Analysis of 799 polymorphic fragments revealed that within the groups, the new type rapeseed had the highest genetic diversity, followed by the semi-winter normal rapeseed from China. Spring and winter rapeseed had the lowest genetic diversity. Among the groups, the new type rapeseed group had the largest average genetic distance to the other three groups. Principal component analysis and cluster analysis, however, could not separate the new type rapeseed group from Chinese normal rapeseed group. Our data suggested that the introgression of Chinese B. rapa could significantly diversify the genetic basis of the rapeseed and play an important role in the evolution of Chinese rapeseed. The use of new genetic variation for the exploitation of heterosis in Brassica hybrid breeding is discussed.
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Affiliation(s)
- W Qian
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
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