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Gepts P. Biocultural diversity and crop improvement. Emerg Top Life Sci 2023; 7:151-196. [PMID: 38084755 PMCID: PMC10754339 DOI: 10.1042/etls20230067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/30/2023]
Abstract
Biocultural diversity is the ever-evolving and irreplaceable sum total of all living organisms inhabiting the Earth. It plays a significant role in sustainable productivity and ecosystem services that benefit humanity and is closely allied with human cultural diversity. Despite its essentiality, biodiversity is seriously threatened by the insatiable and inequitable human exploitation of the Earth's resources. One of the benefits of biodiversity is its utilization in crop improvement, including cropping improvement (agronomic cultivation practices) and genetic improvement (plant breeding). Crop improvement has tended to decrease agricultural biodiversity since the origins of agriculture, but awareness of this situation can reverse this negative trend. Cropping improvement can strive to use more diverse cultivars and a broader complement of crops on farms and in landscapes. It can also focus on underutilized crops, including legumes. Genetic improvement can access a broader range of biodiversity sources and, with the assistance of modern breeding tools like genomics, can facilitate the introduction of additional characteristics that improve yield, mitigate environmental stresses, and restore, at least partially, lost crop biodiversity. The current legal framework covering biodiversity includes national intellectual property and international treaty instruments, which have tended to limit access and innovation to biodiversity. A global system of access and benefit sharing, encompassing digital sequence information, would benefit humanity but remains an elusive goal. The Kunming-Montréal Global Biodiversity Framework sets forth an ambitious set of targets and goals to be accomplished by 2030 and 2050, respectively, to protect and restore biocultural diversity, including agrobiodiversity.
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Affiliation(s)
- Paul Gepts
- Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Davis, CA 95616-8780, U.S.A
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2
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Bilgrami S, Darzi Ramandi H, Farokhzadeh S, Rousseau-Gueutin M, Sobhani Najafabadi A, Ghaderian M, Huang P, Liu L. Meta-analysis of seed weight QTLome using a consensus and highly dense genetic map in Brassica napus L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:161. [PMID: 37354229 DOI: 10.1007/s00122-023-04401-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/02/2023] [Indexed: 06/26/2023]
Abstract
KEY MESSAGE We report here the discovery of high-confidence MQTL regions and of putative candidate genes associated with seed weight in B. napus using a highly dense consensus genetic map and by comparing various large-scale multiomics datasets. Seed weight (SW) is a direct determinant of seed yield in Brassica napus and is controlled by many loci. To unravel the main genomic regions associated with this complex trait, we used 13 available genetic maps to construct a consensus and highly dense map, comprising 40,401 polymorphic markers and 9191 genetic bins, harboring a cumulative length of 3047.8 cM. Then, we performed a meta-analysis using 639 projected SW quantitative trait loci (QTLs) obtained from studies conducted since 1999, enabling the identification of 57 meta-QTLS (MQTLs). The confidence intervals of our MQTLs were 9.8 and 4.3 times lower than the average CIs of the original QTLs for the A and C subgenomes, respectively, resulting in the detection of some key genes and several putative novel candidate genes associated with SW. By comparing the genes identified in MQTL intervals with multiomics datasets and coexpression analyses of common genes, we defined a more reliable and shorter list of putative candidate genes potentially involved in the regulation of seed maturation and SW. As an example, we provide a list of promising genes with high expression levels in seeds and embryos (e.g., BnaA03g04230D, BnaC03g08840D, BnaA10g29580D and BnaA03g27410D) that can be more finely studied through functional genetics experiments or that may be useful for MQTL-assisted breeding for SW. The high-density genetic consensus map and the single nucleotide polymorphism (SNP) physical map generated from the latest B. napus cv. Darmor-bzh v10 assembly will be a valuable resource for further mapping and map-based cloning of other important traits.
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Affiliation(s)
- Sayedehsaba Bilgrami
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Hadi Darzi Ramandi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
| | - Sara Farokhzadeh
- Department of Plant Production, College of Agriculture and Natural Resources of Darab, Shiraz University, Darab, Iran
| | | | - Ahmad Sobhani Najafabadi
- Department of Biotechnology, Agricultural Biotechnology Research Institute of Iran - Isfahan Branch, Agricultural Research, Education and Extension Organization (AREEO), Isfahan, Iran
| | - Mostafa Ghaderian
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA
| | - Pu Huang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China.
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3
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Zhai L, Xie L, Xu J, Xu B, Dong J, Zhang X. Study on exogenous application of thidiazuron on seed size of Brassica napus L. FRONTIERS IN PLANT SCIENCE 2022; 13:998698. [PMID: 36147221 PMCID: PMC9486165 DOI: 10.3389/fpls.2022.998698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 08/16/2022] [Indexed: 06/16/2023]
Abstract
Thidiazuron (TDZ) is a novel and efficient cytokinin commonly used in tissue culture, and numerous studies have demonstrated that TDZ can increase berry size. However, no study to date has explored the effect of TDZ on seed size of Brassica napus and the mechanism. To shed light on the effect of TDZ on the seed size of B. napus, four different concentrations of TDZ were applied to B. napus. Results indicated that TDZ treatment could increase the seed diameter and silique length of B. napus to varying degrees and 100 and 200 μmol/L TDZ treatments were the most effective with a 3.6 and 4.6% increase in seed diameter, respectively. In addition, the yield of B. napus was also substantially increased under TDZ treatment. On the other hand, confocal micrographs of embryos and cotyledon cells suggested that embryos and their cotyledon epidermal cells treated with 200 μmol/L TDZ were obviously larger in size than the control. Furthermore, TDZ promoted the upregulation of some key maternal tissue growth-related genes, including two G-protein signaling genes (AGG3 and RGA1) and two transcriptional regulators (ANT and GS2). The expression analysis of genes related to the auxin metabolic pathways, G-protein signaling, endosperm growth and transcriptional regulators confirmed that treatment with TDZ negatively regulated the key genes ABI5, AGB1, AP2, ARF2, and ARF18 during bud development stage and florescence. The results strongly suggested that TDZ might regulate the transcriptional levels of key genes involved in auxin metabolic pathways, G-protein signaling, endosperm growth and transcriptional regulators, which resulted in bigger cotyledon epidermal cells and seed size in B. napus. This study explored the mechanism of TDZ treatment on the seed size of B. napus and provided an important reference for improving rapeseed yield.
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Affiliation(s)
- Lu Zhai
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, Yangtze University, Hubei, China
- College of Life Science, Yangtze University, Hubei, China
| | - Lingli Xie
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, Yangtze University, Hubei, China
- College of Life Science, Yangtze University, Hubei, China
| | - JinSong Xu
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, Yangtze University, Hubei, China
- College of Agriculture, Yangtze University, Hubei, China
| | - Benbo Xu
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, Yangtze University, Hubei, China
- College of Life Science, Yangtze University, Hubei, China
| | - Jing Dong
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Hubei, China
| | - XueKun Zhang
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, Yangtze University, Hubei, China
- College of Agriculture, Yangtze University, Hubei, China
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4
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Raboanatahiry N, Chao H, He J, Li H, Yin Y, Li M. Construction of a Quantitative Genomic Map, Identification and Expression Analysis of Candidate Genes for Agronomic and Disease-Related Traits in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:862363. [PMID: 35360294 PMCID: PMC8963808 DOI: 10.3389/fpls.2022.862363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 02/15/2022] [Indexed: 06/12/2023]
Abstract
Rapeseed is the second most important oil crop in the world. Improving seed yield and seed oil content are the two main highlights of the research. Unfortunately, rapeseed development is frequently affected by different diseases. Extensive research has been made through many years to develop elite cultivars with high oil, high yield, and/or disease resistance. Quantitative trait locus (QTL) analysis has been one of the most important strategies in the genetic deciphering of agronomic characteristics. To comprehend the distribution of these QTLs and to uncover the key regions that could simultaneously control multiple traits, 4,555 QTLs that have been identified during the last 25 years were aligned in one unique map, and a quantitative genomic map which involved 128 traits from 79 populations developed in 12 countries was constructed. The present study revealed 517 regions of overlapping QTLs which harbored 2,744 candidate genes and might affect multiple traits, simultaneously. They could be selected to customize super-rapeseed cultivars. The gene ontology and the interaction network of those candidates revealed genes that highly interacted with the other genes and might have a strong influence on them. The expression and structure of these candidate genes were compared in eight rapeseed accessions and revealed genes of similar structures which were expressed differently. The present study enriches our knowledge of rapeseed genome characteristics and diversity, and it also provided indications for rapeseed molecular breeding improvement in the future.
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Affiliation(s)
- Nadia Raboanatahiry
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hongbo Chao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Jianjie He
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Huaixin Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yongtai Yin
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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5
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Khan SU, Saeed S, Khan MHU, Fan C, Ahmar S, Arriagada O, Shahzad R, Branca F, Mora-Poblete F. Advances and Challenges for QTL Analysis and GWAS in the Plant-Breeding of High-Yielding: A Focus on Rapeseed. Biomolecules 2021; 11:1516. [PMID: 34680149 PMCID: PMC8533950 DOI: 10.3390/biom11101516] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 12/15/2022] Open
Abstract
Yield is one of the most important agronomic traits for the breeding of rapeseed (Brassica napus L), but its genetic dissection for the formation of high yield remains enigmatic, given the rapid population growth. In the present review, we review the discovery of major loci underlying important agronomic traits and the recent advancement in the selection of complex traits. Further, we discuss the benchmark summary of high-throughput techniques for the high-resolution genetic breeding of rapeseed. Biparental linkage analysis and association mapping have become powerful strategies to comprehend the genetic architecture of complex agronomic traits in crops. The generation of improved crop varieties, especially rapeseed, is greatly urged to enhance yield productivity. In this sense, the whole-genome sequencing of rapeseed has become achievable to clone and identify quantitative trait loci (QTLs). Moreover, the generation of high-throughput sequencing and genotyping techniques has significantly enhanced the precision of QTL mapping and genome-wide association study (GWAS) methodologies. Furthermore, this study demonstrates the first attempt to identify novel QTLs of yield-related traits, specifically focusing on ovule number per pod (ON). We also highlight the recent breakthrough concerning single-locus-GWAS (SL-GWAS) and multi-locus GWAS (ML-GWAS), which aim to enhance the potential and robust control of GWAS for improved complex traits.
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Affiliation(s)
- Shahid Ullah Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.U.K.); (S.S.); (M.H.U.K.)
| | - Sumbul Saeed
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.U.K.); (S.S.); (M.H.U.K.)
| | - Muhammad Hafeez Ullah Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.U.K.); (S.S.); (M.H.U.K.)
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.U.K.); (S.S.); (M.H.U.K.)
| | - Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3465548, Chile;
| | - Osvin Arriagada
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile;
| | - Raheel Shahzad
- Department of Biotechnology, Faculty of Science & Technology, Universitas Muhammadiyah Bandung, Bandung 40614, Indonesia;
| | - Ferdinando Branca
- Department of Agriculture, Food and Environment (Di3A), University of Catania, 95123 Catania, Italy;
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3465548, Chile;
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6
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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. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 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] [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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7
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Stahl A, Vollrath P, Samans B, Frisch M, Wittkop B, Snowdon RJ. Effect of breeding on nitrogen use efficiency-associated traits in oilseed rape. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1969-1986. [PMID: 30753580 PMCID: PMC6436158 DOI: 10.1093/jxb/erz044] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 01/06/2019] [Indexed: 05/21/2023]
Abstract
Oilseed rape is one of the most important dicotyledonous field crops in the world, where it plays a key role in productive cereal crop rotations. However, its production requires high nitrogen fertilization and its nitrogen footprint exceeds that of most other globally important crops. Hence, increased nitrogen use efficiency (NUE) in this crop is of high priority for sustainable agriculture. We report a comprehensive study of macrophysiological characteristics associated with breeding progress, conducted under contrasting nitrogen fertilization levels in a large panel of elite oilseed rape varieties representing breeding progress over the past 20 years. The results indicate that increased plant biomass at flowering, along with increases in primary yield components, have increased NUE in modern varieties. Nitrogen uptake efficiency has improved through breeding, particularly at high nitrogen. Despite low heritability, the number of seeds per silique is associated positively with increased yield in modern varieties. Seed weight remains unaffected by breeding progress; however, recent selection for high seed oil content and for high seed yields appears to have promoted a negative correlation (r= -0.39 at high and r= -0.49 at low nitrogen) between seed weight and seed oil concentration. Overall, our results reveal valuable breeding targets to improve NUE in oilseed rape.
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Affiliation(s)
- Andreas Stahl
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
- Correspondence:
| | - Paul Vollrath
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Birgit Samans
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Matthias Frisch
- Department of Biometry and Population Genetics, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Benjamin Wittkop
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
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8
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Lloyd A, Blary A, Charif D, Charpentier C, Tran J, Balzergue S, Delannoy E, Rigaill G, Jenczewski E. Homoeologous exchanges cause extensive dosage-dependent gene expression changes in an allopolyploid crop. THE NEW PHYTOLOGIST 2018; 217:367-377. [PMID: 29034956 DOI: 10.1111/nph.14836] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Accepted: 08/02/2017] [Indexed: 05/22/2023]
Abstract
Structural variation is a major source of genetic diversity and an important substrate for selection. In allopolyploids, homoeologous exchanges (i.e. between the constituent subgenomes) are a very frequent type of structural variant. However, their direct impact on gene content and gene expression had not been determined. Here, we used a tissue-specific mRNA-Seq dataset to measure the consequences of homoeologous exchanges (HE) on gene expression in Brassica napus, a representative allotetraploid crop. We demonstrate that expression changes are proportional to the change in gene copy number triggered by the HEs. Thus, when homoeologous gene pairs have unbalanced transcriptional contributions before the HE, duplication of one copy does not accurately compensate for loss of the other and combined homoeologue expression also changes. These effects are, however, mitigated over time. This study sheds light on the origins, timing and functional consequences of homeologous exchanges in allopolyploids. It demonstrates that the interplay between new structural variation and the resulting impacts on gene expression, influences allopolyploid genome evolution.
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Affiliation(s)
- Andrew Lloyd
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles Cedex, 78000, France
| | - Aurélien Blary
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles Cedex, 78000, France
| | - Delphine Charif
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles Cedex, 78000, France
| | - Catherine Charpentier
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles Cedex, 78000, France
| | - Joseph Tran
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles Cedex, 78000, France
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, Orsay, 91405, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, Orsay, 91405, France
| | - Sandrine Balzergue
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, Orsay, 91405, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, Orsay, 91405, France
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, Beaucouzé cedex, 49071, France
| | - Etienne Delannoy
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, Orsay, 91405, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, Orsay, 91405, France
| | - Guillem Rigaill
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, Orsay, 91405, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, Orsay, 91405, France
- Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), Université d'Evry Val d'Essonne, UMR CNRS 8071, ENSIIE, USC INRA, Évry Cedex, France
| | - Eric Jenczewski
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles Cedex, 78000, France
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9
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Raboanatahiry N, Chao H, Dalin H, Pu S, Yan W, Yu L, Wang B, Li M. QTL Alignment for Seed Yield and Yield Related Traits in Brassica napus. FRONTIERS IN PLANT SCIENCE 2018; 9:1127. [PMID: 30116254 PMCID: PMC6083399 DOI: 10.3389/fpls.2018.01127] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/12/2018] [Indexed: 05/17/2023]
Abstract
Worldwide consumption of oil is increasing with the growing population in need for edible oil and the expansion of industry using biofuels. Then, demand for high yielding varieties of oil crops is always increasing. Brassica napus (rapeseed) is one of the most important oil crop in the world, therefore, increasing rapeseed yield through breeding is inevitable in order to cater for the high demand of vegetable oil and high-quality protein for live stocks. Quantitative trait loci (QTL) analysis is a powerful tool to identify important loci and which is also valuable for molecular marker assisted breeding. Seed-yield (SY) is a complex trait that is controlled by multiple loci and is affected directly by seed weight, seeds per silique and silique number. Some yield-related traits, such as plant height, biomass yield, flowering time, and so on, also affect the SY indirectly. This study reports the assembly of QTLs identified for seed-yield and yield-related traits in rapeseed, in one unique map. A total of 972 QTLs for seed-yield and yield-related were aligned into the physical map of B. napus Darmor-bzh and 92 regions where 198 QTLs overlapped, could be discovered on 16 chromosomes. Also, 147 potential candidate genes were discovered in 65 regions where 131 QTLs overlapped, and might affect nine different traits. At the end, interaction network of candidate genes was studied, and showed nine genes that could highly interact with the other genes, and might have more influence on them. The present results would be helpful to develop molecular markers for yield associated traits and could be used for breeding improvement in B. napus.
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Affiliation(s)
- Nadia Raboanatahiry
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, China
| | - Hongbo Chao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, China
| | - Hou Dalin
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, China
| | - Shi Pu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Yan
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Longjiang Yu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Baoshan Wang
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, China
- *Correspondence: Maoteng Li,
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10
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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. FRONTIERS IN PLANT SCIENCE 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] [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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11
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Zheng M, Peng C, Liu H, Tang M, Yang H, Li X, Liu J, Sun X, Wang X, Xu J, Hua W, Wang H. Genome-Wide Association Study Reveals Candidate Genes for Control of Plant Height, Branch Initiation Height and Branch Number in Rapeseed ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2017; 8:1246. [PMID: 28769955 PMCID: PMC5513965 DOI: 10.3389/fpls.2017.01246] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 06/30/2017] [Indexed: 05/13/2023]
Abstract
Plant architecture is crucial for rapeseed yield and is determined by plant height (PH), branch initiation height (BIH), branch number (BN) and leaf and inflorescence morphology. In this study, we measured three major factors (PH, BIH, and BN) in a panel of 333 rapeseed accessions across 4 years. A genome-wide association study (GWAS) was performed via Q + K model and the panel was genotyped using the 60 k Brassica Infinium SNP array. We identified seven loci for PH, four for BIH, and five for BN. Subsequently, by determining linkage disequilibrium (LD) decay associated with 38 significant SNPs, we gained 31, 15, and 17 candidate genes for these traits, respectively. We also showed that PH is significantly correlated with BIH, while no other correlation was revealed. Notably, a GA signaling gene (BnRGA) and a flowering gene (BnFT) located on chromosome A02 were identified as the most likely candidate genes associated with PH regulation. Furthermore, a meristem initiation gene (BnLOF2) and a NAC domain transcriptional factor (BnCUC3) that may be associated with BN were identified on the chromosome A07. This study reveals novel insight into the genetic control of plant architecture and may facilitate marker-based breeding for rapeseed.
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Affiliation(s)
- Ming Zheng
- 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
| | - Cheng Peng
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Hongfang 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
| | - Min Tang
- 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
| | - Hongli 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
| | - Xiaokang Li
- 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
| | - Jinglin 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
| | - Xingchao Sun
- 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
| | - Xinfa 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
| | - Junfeng Xu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Wei Hua
- 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
| | - Hanzhong 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
- *Correspondence: Hanzhong Wang
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12
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Li F, Chen B, Xu K, Gao G, Yan G, Qiao J, Li J, Li H, Li L, Xiao X, Zhang T, Nishio T, Wu X. A genome-wide association study of plant height and primary branch number in rapeseed (Brassica napus). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:169-177. [PMID: 26566834 DOI: 10.1016/j.plantsci.2015.05.012] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 05/14/2015] [Accepted: 05/17/2015] [Indexed: 05/18/2023]
Abstract
Crop plant architecture plays a highly important role in its agronomic performance. Plant height (PH) and primary branch number (PB) are two major factors that affect the plant architecture of rapeseed (Brassica napus). Previous studies have shown that these two traits are controlled by multiple quantitative trait loci (QTL); however, QTLs have not been delimited to regions less than 10cM. Genome-wide association study (GWAS) is a highly efficient approach for identifying genetic loci controlling traits at relatively high resolution. In this study, variations in PH and PB of a panel of 472 rapeseed accessions that had previously been analyzed by a 60k SNP array were investigated for three consecutive years and studied by GWAS. Eight QTLs on chromosome A03, A05, A07 and C07 were identified for PH, and five QTLs on A01, A03, A07 and C07 were identified for PB. Although most QTLs have been detected in previous studies based on linkage analyses, the two QTLs of PH on A05 and the QTL of PB on C07 were novel. In the genomic regions close to the GWAS peaks, orthologs of the genes involved in flower development, phytohormone biosynthesis, metabolism and signaling in Arabidopsis were identified.
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Affiliation(s)
- Feng Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Biyun Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Kun Xu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Guizhen Gao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Guixin Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Jiangwei Qiao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Jun Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Hao Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Lixia Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Xin Xiao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Tianyao Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Takeshi Nishio
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
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13
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Zhao W, Wang X, Wang H, Tian J, Li B, Chen L, Chao H, Long Y, Xiang J, Gan J, Liang W, Li M. Genome-Wide Identification of QTL for Seed Yield and Yield-Related Traits and Construction of a High-Density Consensus Map for QTL Comparison in Brassica napus. FRONTIERS IN PLANT SCIENCE 2016; 7:17. [PMID: 26858737 PMCID: PMC4729939 DOI: 10.3389/fpls.2016.00017] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 01/08/2016] [Indexed: 05/18/2023]
Abstract
Seed yield (SY) is the most important trait in rapeseed, is determined by multiple seed yield-related traits (SYRTs) and is also easily subject to environmental influence. Many quantitative trait loci (QTLs) for SY and SYRTs have been reported in Brassica napus; however, no studies have focused on seven agronomic traits simultaneously affecting SY. Genome-wide QTL analysis for SY and seven SYRTs in eight environments was conducted in a doubled haploid population containing 348 lines. Totally, 18 and 208 QTLs for SY and SYRTs were observed, respectively, and then these QTLs were integrated into 144 consensus QTLs using a meta-analysis. Three major QTLs for SY were observed, including cqSY-C6-2 and cqSY-C6-3 that were expressed stably in winter cultivation area for 3 years and cqSY-A2-2 only expressed in spring rapeseed area. Trait-by-trait meta-analysis revealed that the 144 consensus QTLs were integrated into 72 pleiotropic unique QTLs. Among them, all the unique QTLs affected SY, except for uq.A6-1, including uq.A2-3, uq.C1-2, uq.C1-3, uq.C6-1, uq.C6-5, and uq.C6-6 could also affect more than two SYRTs. According to the constructed high-density consensus map and QTL comparison from literatures, 36 QTLs from five populations were co-localized with QTLs identified in this study. In addition, 13 orthologous genes were observed, including five each gene for SY and thousand seed weight, and one gene each for biomass yield, branch height, and plant height. The genomic information of these QTLs will be valuable in hybrid cultivar breeding and in analyzing QTL expression in different environments.
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Affiliation(s)
- Weiguo Zhao
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic ImprovementYangling, China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Xiaodong Wang
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Hao Wang
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic ImprovementYangling, China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- *Correspondence: Hao Wang
| | - Jianhua Tian
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic ImprovementYangling, China
| | - Baojun Li
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic ImprovementYangling, China
| | - Li Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Hongbo Chao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Yan Long
- Institute of Biotechnology, Chinese Academy of Agricultural SciencesBeijing, China
| | - Jun Xiang
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
| | - Jianping Gan
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
| | - Wusheng Liang
- Department of Applied Biological Science, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
- Maoteng Li
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14
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Sun C, Wang B, Yan L, Hu K, Liu S, Zhou Y, Guan C, Zhang Z, Li J, Zhang J, Chen S, Wen J, Ma C, Tu J, Shen J, Fu T, Yi B. Genome-Wide Association Study Provides Insight into the Genetic Control of Plant Height in Rapeseed (Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2016; 7:1102. [PMID: 27512396 PMCID: PMC4961929 DOI: 10.3389/fpls.2016.01102] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 07/12/2016] [Indexed: 05/18/2023]
Abstract
Plant height is a key morphological trait of rapeseed. In this study, we measured plant height of a rapeseed population across six environments. This population contains 476 inbred lines representing the major Chinese rapeseed genepool and 44 lines from other countries. The 60K Brassica Infinium® SNP array was utilized to genotype the association panel. A genome-wide association study (GWAS) was performed via three methods, including a robust, novel, nonparametric Anderson-Darling (A-D) test. Consequently, 68 loci were identified as significantly associated with plant height (P < 5.22 × 10(-5)), and more than 70% of the loci (48) overlapped the confidence intervals of reported QTLs from nine mapping populations. Moreover, 24 GWAS loci were detected with selective sweep signals, which reflected the signatures of historical semi-dwarf breeding. In the linkage disequilibrium (LD) decay range up-and downstream of 65 loci (r (2) > 0.1), we found plausible candidates orthologous to the documented Arabidopsis genes involved in height regulation. One significant association found by GWAS colocalized with the established height locus BnRGA in rapeseed. Our results provide insights into the genetic basis of plant height in rapeseed and may facilitate marker-based breeding.
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Affiliation(s)
- Chengming Sun
- National Key Laboratory of Crop Genetic Improvement, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural UniversityWuhan, China
| | - Benqi Wang
- National Key Laboratory of Crop Genetic Improvement, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural UniversityWuhan, China
| | - Lei Yan
- National Key Laboratory of Crop Genetic Improvement, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural UniversityWuhan, China
| | - Kaining Hu
- National Key Laboratory of Crop Genetic Improvement, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural UniversityWuhan, China
| | - Sheng Liu
- National Key Laboratory of Crop Genetic Improvement, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural UniversityWuhan, China
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural UniversityWuhan, China
| | - Chunyun Guan
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops, College of Agronomy, Hunan Agricultural UniversityChangsha, China
| | - Zhenqian Zhang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops, College of Agronomy, Hunan Agricultural UniversityChangsha, China
| | - Jiana Li
- Chongqing Rapeseed Engineering Technology Research Center, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Jiefu Zhang
- Key Laboratory of Cotton and Rapeseed, Jiangsu Academy of Agricultural ScienceNanjing, China
| | - Song Chen
- Key Laboratory of Cotton and Rapeseed, Jiangsu Academy of Agricultural ScienceNanjing, China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural UniversityWuhan, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural UniversityWuhan, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural UniversityWuhan, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural UniversityWuhan, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural UniversityWuhan, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural UniversityWuhan, China
- *Correspondence: Bin Yi
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15
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Sim SC, Robbins MD, Wijeratne S, Wang H, Yang W, Francis DM. Association Analysis for Bacterial Spot Resistance in a Directionally Selected Complex Breeding Population of Tomato. PHYTOPATHOLOGY 2015; 105:1437-45. [PMID: 26509802 DOI: 10.1094/phyto-02-15-0051-r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Bacterial spot of tomato is caused by at least four species of Xanthomonas with multiple physiological races. We developed a complex breeding population for simultaneous discovery of marker-trait linkage, validation of existing quantitative trait loci (QTL), and pyramiding of resistance. Six advanced accessions with resistance from distinct sources were crossed in all combinations and their F1 hybrids were intercrossed. Over 1,100 segregating progeny were evaluated in the field following inoculation with X. euvesicatoria race T1 strains. We selected 5% of the most resistant and 5% of the most susceptible progeny for evaluation as plots in two subsequent replicated field trials inoculated with T1 and T3 (X. perforans) strains. The estimated heritability of T1 resistance was 0.32. In order to detect previously reported resistance genes, as well as novel QTL, we explored methods to correct for population structure and analysis based on single markers or haplotypes. Both single-point and haplotype analyses identified strong associations in the genomic regions known to carry Rx-3 (chromosome 5) and Rx-4/Xv3 (chromosome 11). Accounting for kinship and structure generally improved the fit of statistical models. Detection of known loci was improved by adding kinship or a combination of kinship and structure using a Q matrix from model-based clustering. Additional QTL were detected on chromosomes 1, 4, 6, and 7 for T1 resistance and chromosomes 2, 4, and 6 for T3 resistance (P < 0.01). Haplotype analysis improved our ability to trace the origin of positive alleles. These results demonstrate that both known and novel associations can be identified using complex breeding populations that have experienced directional selection.
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Affiliation(s)
- Sung-Chur Sim
- First, second, and sixth authors: Department of Horticulture and Crop Science, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691; first author: Department of Bioresources Engineering, Sejong University, 98 Gunja-dong Gwangjin-gu Seoul, 143-747 Korea; second author: USDA Forage & Range Research Laboratory, Logan, UT 84322; third author: Molecular and Cellular Imaging Center, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691; fourth and fifth authors: Department of Vegetable Science, China Agricultural University, Beijing 100193, China; and fourth author: Dupont Pioneer, Woodstock, ON, N4S 7V6, Canada
| | - Matthew D Robbins
- First, second, and sixth authors: Department of Horticulture and Crop Science, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691; first author: Department of Bioresources Engineering, Sejong University, 98 Gunja-dong Gwangjin-gu Seoul, 143-747 Korea; second author: USDA Forage & Range Research Laboratory, Logan, UT 84322; third author: Molecular and Cellular Imaging Center, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691; fourth and fifth authors: Department of Vegetable Science, China Agricultural University, Beijing 100193, China; and fourth author: Dupont Pioneer, Woodstock, ON, N4S 7V6, Canada
| | - Saranga Wijeratne
- First, second, and sixth authors: Department of Horticulture and Crop Science, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691; first author: Department of Bioresources Engineering, Sejong University, 98 Gunja-dong Gwangjin-gu Seoul, 143-747 Korea; second author: USDA Forage & Range Research Laboratory, Logan, UT 84322; third author: Molecular and Cellular Imaging Center, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691; fourth and fifth authors: Department of Vegetable Science, China Agricultural University, Beijing 100193, China; and fourth author: Dupont Pioneer, Woodstock, ON, N4S 7V6, Canada
| | - Hui Wang
- First, second, and sixth authors: Department of Horticulture and Crop Science, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691; first author: Department of Bioresources Engineering, Sejong University, 98 Gunja-dong Gwangjin-gu Seoul, 143-747 Korea; second author: USDA Forage & Range Research Laboratory, Logan, UT 84322; third author: Molecular and Cellular Imaging Center, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691; fourth and fifth authors: Department of Vegetable Science, China Agricultural University, Beijing 100193, China; and fourth author: Dupont Pioneer, Woodstock, ON, N4S 7V6, Canada
| | - Wencai Yang
- First, second, and sixth authors: Department of Horticulture and Crop Science, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691; first author: Department of Bioresources Engineering, Sejong University, 98 Gunja-dong Gwangjin-gu Seoul, 143-747 Korea; second author: USDA Forage & Range Research Laboratory, Logan, UT 84322; third author: Molecular and Cellular Imaging Center, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691; fourth and fifth authors: Department of Vegetable Science, China Agricultural University, Beijing 100193, China; and fourth author: Dupont Pioneer, Woodstock, ON, N4S 7V6, Canada
| | - David M Francis
- First, second, and sixth authors: Department of Horticulture and Crop Science, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691; first author: Department of Bioresources Engineering, Sejong University, 98 Gunja-dong Gwangjin-gu Seoul, 143-747 Korea; second author: USDA Forage & Range Research Laboratory, Logan, UT 84322; third author: Molecular and Cellular Imaging Center, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691; fourth and fifth authors: Department of Vegetable Science, China Agricultural University, Beijing 100193, China; and fourth author: Dupont Pioneer, Woodstock, ON, N4S 7V6, Canada
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16
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Wang X, Wang H, Long Y, Liu L, Zhao Y, Tian J, Zhao W, Li B, Chen L, Chao H, Li M. Dynamic and comparative QTL analysis for plant height in different developmental stages of Brassica napus L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1175-92. [PMID: 25796183 DOI: 10.1007/s00122-015-2498-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 03/10/2015] [Indexed: 05/04/2023]
Abstract
This report describes a dynamic QTL analysis for plant height at various stages using a large doubled haploid population and performs a QTL comparison between different populations in Brassica napus. Plant height (PH) not only plays an important role in determining plant architecture, but is also an important character related to yield. The process of determining PH occurs through a series of steps; however, no studies have focused on developmental behavior factors affecting PH in Brassica napus. In the present study, KN DH, a large doubled haploid population containing 348 lines was used for a dynamic quantitative trait locus (QTL) analysis for PH in six experiments. In all, 20 QTLs were identified at maturity, whereas 50 QTLs were detected by conditional m apping method and the same number was identified by unconditional mapping strategies. Interestingly, five unconditional QTLs ucPH.A2-2, ucPH.A3-2, ucPH.C5-1, ucPH.C6-2 and ucPH.C6-3 were identified that were consistent over the all growth stages of one or two particular experiments, and one conditional QTL cPH.A2-3 was expressed throughout the entire growth process in one experiment. A total of 70 QTLs were obtained after combining QTLs identified at maturity, by conditional and unconditional mapping strategies, in which 25 showed opposite genetic effects in different periods/stages and experiments. A consensus map containing 1357 markers was constructed to compare QTLs identified in the KN population with five previously mapped populations. Alignment of the QTLs detected in different populations onto the consensus map showed that 27 were repeatedly detected in different genetic backgrounds. These findings will enhance our understanding of the genetic control of PH regulation in B. napus, and will be useful for rapeseed genetic manipulation through molecular marker-assisted selection.
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Affiliation(s)
- Xiaodong Wang
- College of Life Science and Technology, Key Laboratory of Molecular Biology, Physics of Ministry of Education, Huazhong University of Science and Technology, Wuhan, 430074, China
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17
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Andargie M, Pasquet RS, Muluvi GM, Timko MP. Quantitative trait loci analysis of flowering time related traits identified in recombinant inbred lines of cowpea (Vigna unguiculata). Genome 2013; 56:289-94. [DOI: 10.1139/gen-2013-0028] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Flowering time is a major adaptive trait in plants and an important selection criterion in the breeding for genetic improvement of crop species. QTLs for the time of flower opening and days to flower were identified in a cross between a short duration domesticated cowpea (Vigna unguiculata (L.) Walp.) variety, 524B, and a relatively long duration wild accession, 219-01. A set of 159 F7 lines was grown under greenhouse conditions and scored for the flowering time associated phenotypes of time of flower opening and days to flower. Using a LOD threshold of 2.0, putative QTLs were identified and placed on a linkage map consisting of 202 SSR markers and four morphological loci. A total of five QTLs related to the time of flower opening were identified, accounting for 8.8%–29.8% of the phenotypic variation. Three QTLs for days to flower were detected, accounting for 5.7%–18.5% of the phenotypic variation. The major QTL of days to flower and time of flower opening were both mapped on linkage group 1. The QTLs identified in this study provide a strong foundation for further validation and fine mapping for developing an efficient way to restrain the gene flow between the cultivated and wild plants.
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Affiliation(s)
- Mebeasealassie Andargie
- International Center of Insect Physiology and Ecology, Molecular Biology & Biotechnology Department, Nairobi, Kenya
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Remy S. Pasquet
- International Center of Insect Physiology and Ecology, Molecular Biology & Biotechnology Department, Nairobi, Kenya
- Institut de recherche pour le développement, UR072, LEGS, BP1, 91198 Gif-sur-Yvette cedex, France
| | - Geoffrey M. Muluvi
- Department of Biochemistry and Biotechnology, Kenyatta University, Nairobi, Kenya
| | - Michael P. Timko
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
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18
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Raman H, Raman R, Eckermann P, Coombes N, Manoli S, Zou X, Edwards D, Meng J, Prangnell R, Stiller J, Batley J, Luckett D, Wratten N, Dennis E. Genetic and physical mapping of flowering time loci in canola (Brassica napus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:119-32. [PMID: 22955939 DOI: 10.1007/s00122-012-1966-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Accepted: 08/10/2012] [Indexed: 05/18/2023]
Abstract
We identified quantitative trait loci (QTL) underlying variation for flowering time in a doubled haploid (DH) population of vernalisation-responsive canola (Brassica napus L.) cultivars Skipton and Ag-Spectrum and aligned them with physical map positions of predicted flowering genes from the Brassica rapa genome. Significant genetic variation in flowering time and response to vernalisation were observed among the DH lines from Skipton/Ag-Spectrum. A molecular linkage map was generated comprising 674 simple sequence repeat, sequence-related amplified polymorphism, sequence characterised amplified region, Diversity Array Technology, and candidate gene based markers loci. QTL analysis indicated that flowering time is a complex trait and is controlled by at least 20 loci, localised on ten different chromosomes. These loci each accounted for between 2.4 and 28.6% of the total genotypic variation for first flowering and response to vernalisation. However, identification of consistent QTL was found to be dependant upon growing environments. We compared the locations of QTL with the physical positions of predicted flowering time genes located on the sequenced genome of B. rapa. Some QTL associated with flowering time on A02, A03, A07, and C06 may represent homologues of known flowering time genes in Arabidopsis; VERNALISATION INSENSITIVE 3, APETALA1, CAULIFLOWER, FLOWERING LOCUS C, FLOWERING LOCUS T, CURLY LEAF, SHORT VEGETATIVE PHASE, GA3 OXIDASE, and LEAFY. Identification of the chromosomal location and effect of the genes influencing flowering time may hasten the development of canola varieties having an optimal time for flowering in target environments such as for low rainfall areas, via marker-assisted selection.
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Affiliation(s)
- Harsh Raman
- EH Graham Centre for Agricultural Innovation (an alliance between NSWDPI and Charles Sturt University), Wagga Wagga, Australia.
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19
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Raman H, Raman R, Eckermann P, Coombes N, Manoli S, Zou X, Edwards D, Meng J, Prangnell R, Stiller J, Batley J, Luckett D, Wratten N, Dennis E. Genetic and physical mapping of flowering time loci in canola (Brassica napus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:119-132. [PMID: 22955939 DOI: 10.1007/s00122-012-1966-1968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Accepted: 08/10/2012] [Indexed: 05/24/2023]
Abstract
We identified quantitative trait loci (QTL) underlying variation for flowering time in a doubled haploid (DH) population of vernalisation-responsive canola (Brassica napus L.) cultivars Skipton and Ag-Spectrum and aligned them with physical map positions of predicted flowering genes from the Brassica rapa genome. Significant genetic variation in flowering time and response to vernalisation were observed among the DH lines from Skipton/Ag-Spectrum. A molecular linkage map was generated comprising 674 simple sequence repeat, sequence-related amplified polymorphism, sequence characterised amplified region, Diversity Array Technology, and candidate gene based markers loci. QTL analysis indicated that flowering time is a complex trait and is controlled by at least 20 loci, localised on ten different chromosomes. These loci each accounted for between 2.4 and 28.6% of the total genotypic variation for first flowering and response to vernalisation. However, identification of consistent QTL was found to be dependant upon growing environments. We compared the locations of QTL with the physical positions of predicted flowering time genes located on the sequenced genome of B. rapa. Some QTL associated with flowering time on A02, A03, A07, and C06 may represent homologues of known flowering time genes in Arabidopsis; VERNALISATION INSENSITIVE 3, APETALA1, CAULIFLOWER, FLOWERING LOCUS C, FLOWERING LOCUS T, CURLY LEAF, SHORT VEGETATIVE PHASE, GA3 OXIDASE, and LEAFY. Identification of the chromosomal location and effect of the genes influencing flowering time may hasten the development of canola varieties having an optimal time for flowering in target environments such as for low rainfall areas, via marker-assisted selection.
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Affiliation(s)
- Harsh Raman
- EH Graham Centre for Agricultural Innovation (an alliance between NSWDPI and Charles Sturt University), Wagga Wagga, Australia.
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20
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Yang P, Shu C, Chen L, Xu J, Wu J, Liu K. Identification of a major QTL for silique length and seed weight in oilseed rape (Brassica napus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:285-96. [PMID: 22406980 DOI: 10.1007/s00122-012-1833-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2011] [Accepted: 02/17/2012] [Indexed: 05/18/2023]
Abstract
Silique length (SL) and seed weight (SW) are two important yield-related traits controlled by quantitative trait loci (QTL) in oilseed rape (Brassica napus L.). The genetic bases underlying these two traits are largely unknown at present. In this study, we conducted QTL analyses for SL and SW using 186 recombinant inbred lines (RILs) derived from a cross between S1, an EMS mutant with extremely long siliques and large seeds, and S2, an inbred line with regular silique length and seed size. RILs were grown in Wuhan in the 2008/09 (SS09) and 2009/10 (SS10) growing seasons, and mean SL and SW for each line were investigated. Ten non-redundant QTL were identified for SL. Of these, a major QTL, cqSLA9, consistently explained as much as 53.4% of SL variation across environments. The others are minor QTL and individually explained less than 10% of the SL variation. Nine non-redundant QTL were identified for SW. Of which, one major QTL, cqSWA9, explained as much as 28.2% of the total SW variation in the SS09 and SS10 environments. In addition, three additive by additive interactions with small effects were detected for SL, and no interactions were detected for SW. Interestingly, the two major QTL, cqSLA9 for SL and cqSWA9 for SW colocalized in the same chromosomal region and were integrated into a unique QTL, uqA9. The S1 allele at this locus increases both SL and SW, suggesting that uqA9 has pleiotropic effects on both SL and SW. The existence and effect of uqA9 was confirmed in genetically different RILs derived from the cross between S1 and No2127, a resynthesized DH line having regular silique length and seed size. Individuals in one residual heterozygous line for cqSLA9 showed significant difference in silique length. The results in this study revealed that silique length in the S1 mutant is mainly controlled by the cqSLA9 locus, which will be suitable for fine mapping and marker-assisted selection in rapeseed breeding for high yield.
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Affiliation(s)
- Pu Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research Wuhan, Huazhong Agricultural University, Wuhan 430070, China
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21
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Wang N, Qian W, Suppanz I, Wei L, Mao B, Long Y, Meng J, Müller AE, Jung C. Flowering time variation in oilseed rape (Brassica napus L.) is associated with allelic variation in the FRIGIDA homologue BnaA.FRI.a. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:5641-58. [PMID: 21862478 PMCID: PMC3223056 DOI: 10.1093/jxb/err249] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 07/20/2011] [Accepted: 07/22/2011] [Indexed: 05/18/2023]
Abstract
Oilseed rape (Brassica napus L.) is a major oil crop which is grown worldwide. Adaptation to different environments and regional climatic conditions involves variation in the regulation of flowering time. Winter types have a strong vernalization requirement whereas semi-winter and spring types have a low vernalization requirement or flower without exposure to cold, respectively. In Arabidopsis thaliana, FRIGIDA (FRI) is a key regulator which inhibits floral transition through activation of FLOWERING LOCUS C (FLC), a central repressor of flowering which controls vernalization requirement and response. Here, four FRI homologues in B. napus were identified by BAC library screening and PCR-based cloning. While all homologues are expressed, two genes were found to be differentially expressed in aerial plant organs. One of these, BnaA.FRI.a, was mapped to a region on chromosome A03 which co-localizes with a major flowering time quantitative trait locus in multiple environments in a doubled-haploid mapping population. Association analysis of BnaA.FRI.a revealed that six SNPs, including at least one at a putative functional site, and one haplotype block, respectively, are associated with flowering time variation in 248 accessions, with flowering times differing by 13-19 d between extreme haplotypes. The results from both linkage analysis and association mapping indicate that BnaA.FRI.a is a major determinant of flowering time in oilseed rape, and suggest further that this gene also contributes to the differentiation between growth types. The putative functional polymorphisms identified here may facilitate adaptation of this crop to specific environments through marker-assisted breeding.
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Affiliation(s)
- Nian Wang
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Wei Qian
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400716, China
| | - Ida Suppanz
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | - Lijuan Wei
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400716, China
| | - Bizeng Mao
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310029, China
| | - Yan Long
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Andreas E. Müller
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
- To whom correspondence should be addressed. E-mail:
| | - Christian Jung
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
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22
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Cai CC, Tu JX, Fu TD, Chen BY. The genetic basis of flowering time and photoperiod sensitivity in rapeseed Brassica napus L. RUSS J GENET+ 2011. [DOI: 10.1134/s1022795408030137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Fan C, Cai G, Qin J, Li Q, Yang M, Wu J, Fu T, Liu K, Zhou Y. Mapping of quantitative trait loci and development of allele-specific markers for seed weight in Brassica napus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:1289-301. [PMID: 20574694 DOI: 10.1007/s00122-010-1388-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Accepted: 06/04/2010] [Indexed: 05/18/2023]
Abstract
Seed weight is an important component of grain yield in oilseed rape (Brassica napus L.), but the genetic basis for the important quantitative trait is still not clear. In order to identify the genes for seed weight in oilseed rape, QTL mapping for thousand seed weight (TSW) was conducted with a doubled haploid (DH) population and an F(2) population. A complete linkage map of the DH population was constructed using 297 simple sequence repeat (SSR) markers. Among nine TSW QTLs detected, two major QTLs, TSWA7a and TSWA7b, were stably identified across years and collectively explained 27.6-37.9% of the trait variation in the DH population. No significant epistatic interactions for TSW detected in the DH population indicate that the seed weight variation may be primarily attributed to additive effects. The stability and significance of TSWA7a and TSWA7b were further validated in the F(2) population with different genetic backgrounds. By cloning BnMINI3a and BnTTG2a, two B. napus homologous genes to Arabidopsis thaliana, allele-specific markers were developed for TSWA5b and TSWA5c, two TSW QTLs on A5, respectively. The importance of the major and minor QTLs identified was further demonstrated by analysis of the allelic effects on TSW in the DH population.
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Affiliation(s)
- Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
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24
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Zhang L, Wang S, Li H, Deng Q, Zheng A, Li S, Li P, Li Z, Wang J. Effects of missing marker and segregation distortion on QTL mapping in F2 populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:1071-1082. [PMID: 20535442 DOI: 10.1007/s00122-010-1372-z] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Accepted: 05/21/2010] [Indexed: 05/27/2023]
Abstract
Missing marker and segregation distortion are commonly encountered in actual quantitative trait locus (QTL) mapping populations. Our objective in this study was to investigate the impact of the two factors on QTL mapping through computer simulations. Results indicate that detection power decreases with increasing levels of missing markers, and the false discovery rate increases. Missing markers have greater effects on smaller effect QTL and smaller size populations. The effect of missing markers can be quantified by a population with a reduced size similar to the marker missing rate. As for segregation distortion, if the distorted marker is not closely linked with any QTL, it will not have significant impact on QTL mapping; otherwise, the impact of the distortion will depend on the degree of dominance of QTL, frequencies of the three marker types, the linkage distance between the distorted marker and QTL, and the mapping population size. Sometimes, the distortion can result in a higher genetic variance than that of non-distortion, and therefore benefits the detection of linked QTL. A formula of the ratio of genetic variance explained by QTL under distortion and non-distortion was given in this study, so as to easily determine whether the segregation distortion marker (SDM) increases or decreases the QTL detection power. The effect of SDM decreases rapidly as its linkage relationship with QTL becomes looser. In general, distorted markers will not have a great effect on the position and effect estimations of QTL, and their effects can be ignored in large-size mapping populations.
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Affiliation(s)
- Luyan Zhang
- School of Mathematical Sciences, Beijing Normal University, Beijing, 100875, China
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25
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LI YL, DONG YB, NIU SZ, CUI DQ. Identification of QTL for Popping Characteristics Using a BC2F2 Population and Comparison with Its F2:3 Population in Popcorn. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/s1671-2927(09)60020-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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26
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Flowering time quantitative trait Loci analysis of oilseed brassica in multiple environments and genomewide alignment with Arabidopsis. Genetics 2008; 177:2433-44. [PMID: 18073439 DOI: 10.1534/genetics.107.080705] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Most agronomical traits exhibit quantitative variation, which is controlled by multiple genes and are environmentally dependent. To study the genetic variation of flowering time in Brassica napus, a DH population and its derived reconstructed F(2) population were planted in 11 field environments. The flowering time varied greatly with environments; 60% of the phenotypic variation was attributed to genetic effects. Five to 18 QTL at a statistically significant level (SL-QTL) were detected in each environment and, on average, two new SL-QTL were discovered with each added environment. Another type of QTL, micro-real QTL (MR-QTL), was detected repeatedly from at least 2 of the 11 environments; resulting in a total of 36 SL-QTL and 6 MR-QTL. Sixty-three interacting pairs of loci were found; 50% of them were involved in QTL. Hundreds of floral transition genes in Arabidopsis were aligned with the linkage map of B. napus by in silico mapping; 28% of them aligned with QTL regions and 9% were consistent with interacting loci. One locus, BnFLC10, in N10 and a QTL cluster in N16 were specific to spring- and winter-cropped environments respectively. The number of QTL, interacting loci, and aligned functional genes revealed a complex genetic network controlling flowering time in B. napus.
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27
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Gaeta RT, Pires JC, Iniguez-Luy F, Leon E, Osborn TC. Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. THE PLANT CELL 2007; 19:3403-17. [PMID: 18024568 PMCID: PMC2174891 DOI: 10.1105/tpc.107.054346] [Citation(s) in RCA: 399] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2007] [Revised: 10/05/2007] [Accepted: 10/21/2007] [Indexed: 05/18/2023]
Abstract
Many previous studies have provided evidence for genome changes in polyploids, but there are little data on the overall population dynamics of genome change and whether it causes phenotypic variability. We analyzed genetic, epigenetic, gene expression, and phenotypic changes in approximately 50 resynthesized Brassica napus lines independently derived by hybridizing double haploids of Brassica oleracea and Brassica rapa. A previous analysis of the first generation (S0) found that genetic changes were rare, and cytosine methylation changes were frequent. Our analysis of a later generation found that most S0 methylation changes remained fixed in their S5 progeny, although there were some reversions and new methylation changes. Genetic changes were much more frequent in the S5 generation, occurring in every line with lines normally distributed for number of changes. Genetic changes were detected on 36 of the 38 chromosomes of the S5 allopolyploids and were not random across the genome. DNA fragment losses within lines often occurred at linked marker loci, and most fragment losses co-occurred with intensification of signal from homoeologous markers, indicating that the changes were due to homoeologous nonreciprocal transpositions (HNRTs). HNRTs between chromosomes A1 and C1 initiated in early generations, occurred in successive generations, and segregated, consistent with a recombination mechanism. HNRTs and deletions were correlated with qualitative changes in the expression of specific homoeologous genes and anonymous cDNA amplified fragment length polymorphisms and with phenotypic variation among S5 polyploids. Our data indicate that exchanges among homoeologous chromosomes are a major mechanism creating novel allele combinations and phenotypic variation in newly formed B. napus polyploids.
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Affiliation(s)
- Robert T Gaeta
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin, USA
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28
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Abstract
An ultimate objective of QTL mapping is cloning genes responsible for quantitative traits. However, projects seldom go beyond segments <5 cM without subsequent breeding and genotyping lines to identify additional crossovers in a genomic region of interest. We report on a QTL analysis performed as a preliminary step in the development of a resource for map-based cloning of domestication and improvement genes in corn. A large backcross (BC)1 population derived from a cross between maize (Zea mays ssp. mays) and teosinte (ssp. parviglumis) was grown for the analysis. A total of 1749 progenies were genotyped for 304 markers and measured for 22 morphological traits. The results are in agreement with earlier studies showing a small number of genomic regions having greater impact on the morphological traits distinguishing maize and teosinte. Despite considerable power to detect epistasis, few QTL interactions were identified. To create a permanent resource, seed of BC1 plants was archived and 1000 BC2S6 BC1-derived lines are in development for fine mapping and cloning. The identification of four BC1 progeny with crossovers in a single gene, tb1, indicated that enough derived lines already exist to clone many QTL without the need to generate and identify additional crossovers.
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29
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Ramchiary N, Padmaja KL, Sharma S, Gupta V, Sodhi YS, Mukhopadhyay A, Arumugam N, Pental D, Pradhan AK. Mapping of yield influencing QTL in Brassica juncea: implications for breeding of a major oilseed crop of dryland areas. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 115:807-17. [PMID: 17646960 DOI: 10.1007/s00122-007-0610-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2006] [Accepted: 07/07/2007] [Indexed: 05/16/2023]
Abstract
Quantitative trait loci (QTL) analysis of yield influencing traits was carried out in Brassica juncea (AABB) using a doubled haploid (DH) mapping population of 123 lines derived from a cross between Varuna (a line representing the Indian gene pool) and Heera (representing the east European gene pool) to identify potentially useful alleles from both the parents. The existing AFLP based map of B. juncea was further saturated with RFLP and SSR markers which led to the identification of the linkage groups belonging to the A (B. rapa) and B (B. nigra) genome components of B. juncea. For QTL dissection, the DH lines were evaluated at three different environments and phenotyped for 12 quantitative traits. A total of 65 QTL spread over 13 linkage groups (LG) were identified from the three environments. QTL analysis showed that the A genome has contributed more than the B genome to productivity (68% of the total QTL detected) suggesting a more prominent role of the A genome towards domestication of this crop. The east European line, Heera, carried favorable alleles for 42% of the detected QTL and the remaining 58% were in the Indian gene pool line, Varuna. We observed clustering of major QTL in a few linkage groups, particularly in J7 and J10 of the A genome, with QTL of different traits having agronomically antagonistic allelic effects co-mapping to the same genetic interval. QTL analysis also identified some well-separated QTL which could be readily transferred between the two pools. Based on the QTL analysis, we propose that improvement in yield could be achieved more readily by heterosis breeding rather than by pure line breeding.
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Affiliation(s)
- N Ramchiary
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
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30
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Chen W, Zhang Y, Liu X, Chen B, Tu J, Tingdong F. Detection of QTL for six yield-related traits in oilseed rape (Brassica napus) using DH and immortalized F(2) populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 115:849-58. [PMID: 17665168 DOI: 10.1007/s00122-007-0613-2] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2007] [Accepted: 07/08/2007] [Indexed: 05/16/2023]
Abstract
The inheritance of yield-related traits in rapeseed (Brassica napus) is poorly understood, and the investigations on mapping of quantitative trait loci (QTL) for such traits are only few. QTL related to six traits were mapped which include plant height (PH), height of lowest primary effective branch (HPB), length of main inflorescence (LMI), silique length (SL), number of primary branches (FB) and silique density (SD). A set of 258 doubled haploid (DH) lines derivatives of a cross between a canola variety Quantum and a resynthesized B. napus line No.2127-17, and a fixed immortalized F(2) (designated as IF(2)) population generated by randomly permutated intermating of these DHs were investigated. A genetic linkage map was constructed using 208 SSR and 189 SRAP markers for the DH population. Phenotypic data were collected from three environments for the two populations. Using composite interval mapping analyses, 30 and 22 significant QTL were repeatedly detected across environments for the six traits in the DH and IF(2) populations, respectively. Twenty-nine QTL were common between the two populations. The directions of parental contribution for all common QTL were the same, showing a great potential for marker-assisted selection in improving these traits. Some chromosomal regions harbor QTL for multiple traits, which were consistent with significant phenotypic correlations observed among traits. The results provided a better understanding of the genetic factors controlling yield-related traits in rapeseed.
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Affiliation(s)
- Wei Chen
- National Key Laboratory of Crop Genetic Improvement, National Sub-center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
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31
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Kim JS, Chung TY, King GJ, Jin M, Yang TJ, Jin YM, Kim HI, Park BS. A sequence-tagged linkage map of Brassica rapa. Genetics 2006; 174:29-39. [PMID: 16988107 PMCID: PMC1569789 DOI: 10.1534/genetics.106.060152] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A detailed genetic linkage map of Brassica rapa has been constructed containing 545 sequence-tagged loci covering 1287 cM, with an average mapping interval of 2.4 cM. The loci were identified using a combination of 520 RFLP and 25 PCR-based markers. RFLP probes were derived from 359 B. rapa EST clones and amplification products of 11 B. rapa and 26 Arabidopsis. Including 21 SSR markers provided anchors to previously published linkage maps for B. rapa and B. napus and is followed as the referenced mapping of R1-R10. The sequence-tagged markers allowed interpretation of the pattern of chromosome duplications within the B. rapa genome and comparison with Arabidopsis. A total of 62 EST markers showing a single RFLP band were mapped through 10 linkage groups, indicating that these can be valuable anchoring markers for chromosome-based genome sequencing of B. rapa. Other RFLP probes gave rise to 2-5 loci, inferring that B. rapa genome duplication is a general phenomenon through 10 chromosomes. The map includes five loci of FLC paralogues, which represent the previously reported BrFLC-1, -2, -3, and -5 and additionally identified BrFLC3 paralogues derived from local segmental duplication on R3.
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Affiliation(s)
- Jung Sun Kim
- National Institute of Agricultural Biotechnology (NIAB), Rural Development Administration, Suwon, 441-707, Korea
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32
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Saito M, Kubo N, Matsumoto S, Suwabe K, Tsukada M, Hirai M. Fine mapping of the clubroot resistance gene, Crr3, in Brassica rapa. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 114:81-91. [PMID: 17039346 DOI: 10.4141/cjps10073] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Accepted: 09/08/2006] [Indexed: 05/26/2023]
Abstract
A linkage map of Chinese cabbage (Brassica rapa) was constructed to localize the clubroot resistance (CR) gene, Crr3. Quantitative trait loci analysis using an F(3) population revealed a sharp peak in the logarithm of odds score around the sequence-tagged site (STS) marker, OPC11-2S. Therefore, this region contained Crr3. Nucleotide sequences of OPC11-2S and its proximal markers showed homology to sequences in the top arm of Arabidopsis chromosome 3, suggesting a synteny between the two species. For fine mapping of Crr3, a number of STS markers were developed based on genomic information from Arabidopsis. We obtained polymorphisms in 23 Arabidopsis-derived STS markers, 11 of which were closely linked to Crr3. The precise position of Crr3 was determined using a population of 888 F(2) plants. Eighty plants showing recombination around Crr3 locus were selected and used for the mapping. A fine map of 4.74 cM was obtained, in which two markers (BrSTS-41 and BrSTS-44) and three markers (OPC11-2S, BrSTS-54 and BrSTS-61) were cosegregated. Marker genotypes of the 21 selected F(2) families and CR tests of their progenies strongly suggested that the Crr3 gene is located in a 0.35 cM segment between the two markers, BrSTS-33 and BrSTS-78.
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Affiliation(s)
- M Saito
- Graduate School of Agriculture, Kyoto Prefectural University, Kyoto Prefectural Institute of Agricultural Biotechnology, 74 Oji, Kitainayazuma, Seika, Soraku, Kyoto, 619-0244, Japan
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Mahmood T, Rahman MH, Stringam GR, Yeh F, Good AG. Identification of quantitative trait loci (QTL) for oil and protein contents and their relationships with other seed quality traits in Brassica juncea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:1211-20. [PMID: 16960718 DOI: 10.1007/s00122-006-0376-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2005] [Accepted: 07/15/2006] [Indexed: 05/11/2023]
Abstract
A detailed RFLP-genomic map was used to study the genetics of oil, seed and meal protein and sum of oil and seed/meal protein contents in a recombinant doubled-haploid population developed by crossing black- and yellow-seeded Brassica juncea lines. Two yellow seed color genes (SC-B4, SC-A6) and one QTL for erucic acid content (E(1b)) showed pleiotropic effect for oil, protein and sum of oil and seed/meal protein contents. Six (O-A1, O-A6, O-A9, O-B3, O-B4, O-B5) and five (SP-A1, SP-A9, SP-B4, SP-B6, SP-C) QTLs were significant for oil and seed protein contents, respectively. Tight linkage of three of these QTLs (SP-A1, SP-A9, SP-B4, O-A1, O-A9, O-B4), with opposite effects, poses challenge to the plant breeders for simultaneous improvement of negatively correlated (r = -0.7**) oil and seed protein contents. However, one QTL for oil content (O-B3) and two for seed protein content (SP-B6, SP-C) were found to be unlinked, which offer the possibility for simultaneous improvement of these two traits. QTLs significant for meal protein (MP-A1, MP-A6, MP-A9, MP-B5, MP-B6) were significant at least for oil, seed protein or sum of oil and seed/meal protein contents (T-A6, T-A7, T-B4, T-B5). Sum of oil and seed protein contents and sum of oil and meal protein contents had a perfect correlation, as well as same epistatic interactions and QTLs with similar additive effect. This indicates that protein in seed or meal has practically the same meaning for breeding purposes. Epistatic interactions were significant for the quality traits, and their linkage reflected association among the traits.
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Affiliation(s)
- T Mahmood
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
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Quijada PA, Udall JA, Lambert B, Osborn TC. Quantitative trait analysis of seed yield and other complex traits in hybrid spring rapeseed (Brassica napus L.): 1. Identification of genomic regions from winter germplasm. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:549-61. [PMID: 16767447 DOI: 10.1007/s00122-006-0323-1] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2005] [Accepted: 05/13/2006] [Indexed: 05/10/2023]
Abstract
The introgression of winter germplasm into spring canola (Brassica napus L.) represents a novel approach to improve seed yield of hybrid spring canola. In this study, quantitative trait loci (QTL) for seed yield and other traits were genetically mapped to determine the effects of genomic regions introgressed from winter germplasm into spring canola. Plant materials used comprised of two populations of doubled haploid (DH) lines having winter germplasm introgression from two related French winter cultivars and their testcrosses with a spring line used in commercial hybrids. These populations were evaluated for 2 years at two locations (Wisconsin, USA and Saskatchewan, Canada). Genetic linkage maps based on RFLP loci were constructed for each DH population. Six QTL were detected in the testcross populations for which the winter alleles increased seed yield. One of these QTL explained 11 and 19% of the phenotypic variation in the two Canadian environments. The winter allele for another QTL that increased seed yield was linked in coupling to a QTL allele for high glucosinolate content, suggesting that the transition of rapeseed into canola could have resulted in the loss of favorable seed yield alleles. Most QTL for which the introgressed allele decreased seed yield of hybrids mapped to genomic regions having homoeologous non-reciprocal transpositions. This suggests that allelic configurations created by these rearrangements might make an important contribution to genetic variation for complex traits in oilseed B. napus and could account for a portion of the heterotic effects in hybrids.
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Affiliation(s)
- Pablo A Quijada
- Plant Breeding and Plant Genetics Program, and Department of Agronomy, University of Wisconsin, Madison, WI 53706, USA
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35
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Udall JA, Quijada PA, Lambert B, Osborn TC. Quantitative trait analysis of seed yield and other complex traits in hybrid spring rapeseed (Brassica napus L.): 2. Identification of alleles from unadapted germplasm. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:597-609. [PMID: 16767446 DOI: 10.1007/s00122-006-0324-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2005] [Accepted: 05/13/2006] [Indexed: 05/10/2023]
Abstract
Unadapted germplasm may contain alleles that could improve hybrid cultivars of spring oilseed Brassica napus. Quantitative trait loci (QTL) mapping was used to identify potentially useful alleles from two unadapted germplasm sources, a Chinese winter cultivar and a re-synthesized B. napus, that increase seed yield when introgressed into a B. napus spring hybrid combination. Two populations of 160 doubled haploid (DH) lines were created from crosses between the unadapted germplasm source and a genetically engineered male-fertility restorer line (P1804). A genetically engineered male-sterile tester line was used to create hybrids with each DH line (testcrosses). The two DH line populations were evaluated in two environments and the two testcross populations were evaluated in three or four environments for seed yield and other agronomic traits. Several genomic regions were found in the two testcross populations which contained QTL for seed yield. The map positions of QTL for days to flowering and resistance to a bacterial leaf blight disease coincided with QTL for seed yield and other agronomic traits, suggesting the occurrence of pleiotropic or linked effects. For two hybrid seed yield QTL, the favorable alleles increasing seed yield originated from the unadapted parents, and one of these QTL was detected in multiple environments and in both populations. In this QTL region, a chromosome rearrangement was identified in P1804, which may have affected seed yield.
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Affiliation(s)
- Joshua A Udall
- Plant Breeding and Plant Genetics Program, and Department of Agronomy, University of Wisconsin, Madison, WI 53706, USA
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36
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Zhao J, Becker HC, Zhang D, Zhang Y, Ecke W. Conditional QTL mapping of oil content in rapeseed with respect to protein content and traits related to plant development and grain yield. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:33-8. [PMID: 16614833 DOI: 10.1007/s00122-006-0267-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2005] [Accepted: 03/17/2006] [Indexed: 05/08/2023]
Abstract
Oil content in rapeseed (Brassica napus L.) is generally regarded as a character with high heritability that is negatively correlated with protein content and influenced by plant developmental and yield related traits. To evaluate possible genetic interrelationships between these traits and oil content, QTL for oil content were mapped using data on oil content and on oil content conditioned on the putatively interrelated traits. Phenotypic data were evaluated in a segregating doubled haploid population of 282 lines derived from the F(1) of a cross between the old German cultivar Sollux and the Chinese cultivar Gaoyou. The material was tested at four locations, two each in Germany and in China. QTLMapper version 1.0 was used for mapping unconditional and conditional QTL with additive (a) and locus pairs with additive x additive epistatic (aa) effects. Clear evidence was found for a strong genetic relationship between oil and protein content. Six QTL and nine epistatic locus pairs were found, which had pleiotropic effects on both traits. Nevertheless, two QTL were also identified, which control oil content independent from protein content and which could be used in practical breeding programs to increase oil content without affecting seed protein content. In addition, six additional QTL with small effects were only identified in the conditional mapping. Some evidence was apparent for a genetic interrelationship between oil content and the number of seeds per silique but no evidence was found for a genetic relationship between oil content and flowering time, grain filling period or single seed weight. The results indicate that for closely correlated traits conditional QTL mapping can be used to dissect the genetic interrelationship between two traits at the level of individual QTL. Furthermore, conditional QTL mapping can reveal additional QTL with small effects that are undetectable in unconditional mapping.
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Affiliation(s)
- Jianyi Zhao
- Crop Research Institute, Zhejiang Academy of Agricultural Sciences, 310021 Hangzhou, People's Republic of China
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37
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Lukens LN, Pires JC, Leon E, Vogelzang R, Oslach L, Osborn T. Patterns of sequence loss and cytosine methylation within a population of newly resynthesized Brassica napus allopolyploids. PLANT PHYSIOLOGY 2006; 140:336-48. [PMID: 16377753 PMCID: PMC1326055 DOI: 10.1104/pp.105.066308] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2005] [Revised: 09/21/2005] [Accepted: 11/01/2005] [Indexed: 05/05/2023]
Abstract
Allopolyploid formation requires the adaptation of two nuclear genomes within a single cytoplasm, which may involve programmed genetic and epigenetic changes during the initial generations following genome fusion. To study the dynamics of genome change, we synthesized 49 isogenic Brassica napus allopolyploids and surveyed them with 76 restriction fragment length polymorphism (RFLP) probes and 30 simple sequence repeat (SSR) primer pairs. Here, we report on the types and distribution of genetic and epigenetic changes within the S(1) genotypes. We found that insertion/deletion (indel) events were rare, but not random. Of the 57,710 (54,383 RFLP and 3,327 SSR) parental fragments expected among the amphidiploids, we observed 56,676 or 99.9%. Three loci derived from Brassica rapa had indels, and one indel occurred repeatedly across 29% (14/49) of the lines. Loss of one parental fragment was due to the 400-bp reduction of a guanine-adenine dinucleotide repeat-rich sequence. In contrast to the 4% (3/76) RFLP probes that detected indels, 48% (35/73) detected changes in the CpG methylation status between parental genomes and the S1 lines. Some loci were far more likely than others to undergo epigenetic change, but the number of methylation changes within each synthetic polyploid was remarkably similar to others. Clear de novo methylation occurred at a much higher frequency than de novo demethylation within allopolyploid sequences derived from B. rapa. Our results suggest that there is little genetic change in the S(0) generation of resynthesized B. napus polyploids. In contrast, DNA methylation was altered extensively in a pattern that indicates tight regulation of epigenetic changes.
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Affiliation(s)
- Lewis N Lukens
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada N1G 2W1.
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38
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Zeyl C. The number of mutations selected during adaptation in a laboratory population of Saccharomyces cerevisiae. Genetics 2005; 169:1825-31. [PMID: 15744058 PMCID: PMC1449599 DOI: 10.1534/genetics.104.027102] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
There is currently limited empirical and theoretical support for the prevailing view that adaptation typically results from the fixation of many mutations, each with small phenotypic effects. Recent theoretical work suggests that, on the contrary, most of the phenotypic change during an episode of adaptation can result from the selection of a few mutations with relatively large effects. I studied the genetics of adaptation by populations of budding yeast to a culture regime of daily hundredfold dilution and transfer in a glucose-limited minimal liquid medium. A single haploid genotype isolated after 2000 generations showed a 76% fitness increase over its ancestor. This evolved haploid was crossed with its ancestor, and tetrad dissections were used to isolate a complete series of six meiotic tetrads. The Castle-Wright estimator of the number of loci at which adaptive mutations had been selected, modified to account for linkage and variation among mutations in the size of their effect, is 4.4. The estimate for a second haploid genotype, isolated from a separate population and with a fitness gain of 60%, was 2.7 loci. Backcrosses to the ancestor with the first evolved genotype support the inference that adaptation resulted primarily from two to five mutations. These backcrosses also indicated that deleterious mutations had hitchhiked with adaptive mutations in this evolved genotype.
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Affiliation(s)
- Clifford Zeyl
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina 27109, USA.
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Matsumoto E, Hayashida N, Sakamoto K, Ohi M. Behavior of DNA Markers Linked to a Clubroot Resistance Gene in Segregating Populations of Chinese Cabbage (Brassica rapa ssp. pekinensis). ACTA ACUST UNITED AC 2005. [DOI: 10.2503/jjshs.74.367] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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40
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Udall JA, Quijada PA, Osborn TC. Detection of chromosomal rearrangements derived from homologous recombination in four mapping populations of Brassica napus L. Genetics 2004; 169:967-79. [PMID: 15520255 PMCID: PMC1449096 DOI: 10.1534/genetics.104.033209] [Citation(s) in RCA: 208] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Genetic maps of Brassica napus were constructed from four segregating populations of doubled haploid lines. Each mapping population had the same male parent and used the same set of RFLP probes, facilitating the construction of a consensus map. Chromosomal rearrangements were identified in each population by molecular marker analysis and were classified as de novo homologous nonreciprocal transpositions (HNRTs), preexisting HNRTs, and homologous reciprocal transpositions (HRTs). Ninety-nine de novo HNRTs were identified by the presence of a few lines having duplication of a chromosomal region and loss of the corresponding homologous region. These de novo HNRTs were more prevalent in one population that had a resynthesized B. napus as a parent. Preexisting HNRTs were identified by fragment duplication or fragment loss in many DH lines due to the segregation of HNRTs preexisting in one of the parents. Nine preexisting HNRTs were identified in the three populations involving natural B. napus parents, which likely originated from previous homologous exchanges. The male parent had a previously described HRT between N7 and N16, which segregated in each population. These data suggest that chromosomal rearrangements caused by homologous recombination are widespread in B. napus. The effects of these rearrangements on allelic and phenotypic diversity are discussed.
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Affiliation(s)
- Joshua A Udall
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin 53706, USA
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41
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PIRES JCHRIS, ZHAO JIANWEI, SCHRANZ MERIC, LEON ENRIQUEJ, QUIJADA PABLOA, LUKENS LEWISN, OSBORN THOMASC. Flowering time divergence and genomic rearrangements in resynthesized Brassica polyploids (Brassicaceae). Biol J Linn Soc Lond 2004. [DOI: 10.1111/j.1095-8312.2004.00350.x] [Citation(s) in RCA: 263] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Osborn TC, Butrulle DV, Sharpe AG, Pickering KJ, Parkin IAP, Parker JS, Lydiate DJ. Detection and Effects of a Homeologous Reciprocal Transposition in Brassica napus. Genetics 2003; 165:1569-77. [PMID: 14668403 PMCID: PMC1462855 DOI: 10.1093/genetics/165.3.1569] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
A reciprocal chromosomal transposition was identified in several annual oilseed Brassica napus genotypes used as parents in crosses to biennial genotypes for genetic mapping studies. The transposition involved an exchange of interstitial homeologous regions on linkage groups N7 and N16, and its detection was made possible by the use of segregating populations of doubled haploid lines and codominant RFLP markers. RFLP probes detected pairs of homeologous loci on N7 and N16 for which the annual and biennial parents had identical alleles in regions expected to be homeologous. The existence of an interstitial reciprocal transposition was confirmed by cytological analysis of synaptonemal complexes of annual × biennial F1 hybrids. Although it included approximately one-third of the physical length of the N7 and N16 chromosomes, few recombination events within the region were recovered in the progenies of the hybrids. Significantly higher seed yields were associated with the parental configurations of the rearrangement in segregating progenies. These progenies contained complete complements of homeologous chromosomes from the diploid progenitors of B. napus, and thus their higher seed yields provide evidence for the selective advantage of allopolyploidy through the fixation of intergenomic heterozygosity.
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Affiliation(s)
- Thomas C Osborn
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin 53706, USA.
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Mahmood T, Ekuere U, Yeh F, Good AG, Stringam GR. RFLP linkage analysis and mapping genes controlling the fatty acid profile of Brassica juncea using reciprocal DH populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2003; 107:283-290. [PMID: 12669199 DOI: 10.1007/s00122-003-1244-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2002] [Accepted: 11/05/2002] [Indexed: 05/24/2023]
Abstract
An RFLP linkage map, comprising 300 linked and 16 unlinked loci, was constructed using reciprocal DH populations of Brassica juncea. The linked loci were organized into 18 linkage groups and seven unlinked segments, covering a total map distance of 1,564 cM. The A and B genomes were identified. The chi(2) test showed that 96.1% of the common intervals in the two populations differed non-significantly for recombination fractions, thus strongly suggesting the absence of sex-based differences for recombination fractions in B. juncea. Two QTLs, E(1a) and E(1b), significantly affected erucic acid content, and individually explained 53.7% and 32.1%, respectively, and collectively 85.8% of the phenotypic variation in the population. The QTLs E(1a) and E(1b) showed epistasis, and the full model including epistasis explained nearly all of the phenotypic variation in the population. The QTLs E(1a) and E(1b) were also associated with contents of oleic, linoleic and linolenic acids. Three additional QTLs (LN(2), LN(3) and LN(4)) significantly influenced linolenic acid content. The QTL LN(2) accounted for 35.4% of the phenotypic variation in the population. Epistatic interactions were observed between the QTLs E1a and LN(2). The stability of the detected QTLs across years and locations, and breeding strategies for improving the fatty acid profile of B. juncea, are discussed.
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Affiliation(s)
- T Mahmood
- Lembke Research Ltd, P.O Box 2499, Morden, MB, R6M 1C2
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44
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Sharpe AG, Lydiate DJ. Mapping the mosaic of ancestral genotypes in a cultivar of oilseed rape (Brassica napus) selected via pedigree breeding. Genome 2003; 46:461-8. [PMID: 12834063 DOI: 10.1139/g03-031] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Recent oilseed rape breeding has produced low glucosinolate cultivars that yield proteinaceous meal suitable for animal feed. The low glucosinolate character was introduced into modern cultivars from Brassica napus 'Bronowski', a cultivar that is agronomically inferior in most other respects. Residual segments of 'Bronowski' genotype in modern cultivars probably cause reduced yield, poorer winter hardiness, and lower oil content. The quantity and distribution of the 'Bronowski' genotype in the modern oilseed rape cultivar Brassica napus 'Tapidor' was investigated using a segregating population derived from a cross between 'Tapidor' and its high glucosinolate progenitor. This population was analyzed with 65 informative Brassica RFLP probes and a genetic linkage map, based on the segregation at 77 polymorphic loci, was constructed. The mapping identified 15 residual segments of donor genotype in 'Tapidor', which together occupy approximately 29% of the B. napus genome. Mapping the loci that control variation for the accumulation of total seed glucosinolates in the segregating population has identified three loci that together explain >90% of the variation for this character. All of these loci are in donor segments of the 'Tapidor' genome. This result shows the extent to which conventional breeding programmes have difficulty in eliminating residual segments of donor genotype from elite material.
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Affiliation(s)
- A G Sharpe
- Brassica Genetics Group, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK.
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45
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Burns MJ, Barnes SR, Bowman JG, Clarke MHE, Werner CP, Kearsey MJ. QTL analysis of an intervarietal set of substitution lines in Brassica napus: (i) Seed oil content and fatty acid composition. Heredity (Edinb) 2003; 90:39-48. [PMID: 12522424 DOI: 10.1038/sj.hdy.6800176] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Backcross breeding with marker-assisted selection was used to construct an intervarietal set of part chromosome substitution lines in Brassica napus, formed from a cross between two winter varieties of oilseed rape: Tapidor and Victor. A total of 22 lines from this substitution library were examined over a 3-year period, in a total of nine field trials, for seed oil fatty acid composition and seed oil content. Trialing of the substitution lines gave evidence for the existence of 13 quantitative trait loci (QTL). All 13 QTL affected fatty acid composition of the seed, and were distributed among linkage groups 1, 3, 6, 7, 8, 11, 13, 14, 18, and 19. Seven of these QTL, on linkage groups 3, 6, 8, 13, 14, 18, and 19, also affected total seed oil content. The positions of these QTL are compared to those in the published literature and with respect to erucic acid QTL previously identified in a backcross population of the same cross. The substitution line approach gives increased precision and sensitivity for QTL mapping compared to other methods.
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Affiliation(s)
- M J Burns
- Plant Genetics and Cell Biology Group, School of Biosciences, The University of Birmingham, UK.
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46
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47
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Doganlar S, Frary A, Ku HM, Tanksley SD. Mapping quantitative trait loci in inbred backcross lines of Lycopersicon pimpinellifolium (LA1589). Genome 2002; 45:1189-202. [PMID: 12502266 DOI: 10.1139/g02-091] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Although tomato has been the subject of extensive quantitative trait loci (QTLs) mapping experiments, most of this work has been conducted on transient populations (e.g., F2 or backcross) and few homozygous, permanent mapping populations are available. To help remedy this situation, we have developed a set of inbred backcross lines (IBLs) from the interspecific cross between Lycopersicon esculentum cv. E6203 and L. pimpinellifolium (LA1589). A total of 170 BC2F1 plants were selfed for five generations to create a set of homozygous BC2F6 lines by single-seed descent. These lines were then genotyped for 127 marker loci covering the entire tomato genome. These IBLs were evaluated for 22 quantitative traits. In all, 71 significant QTLs were identified, 15% (11/71) of which mapped to the same chromosomal positions as QTLs identified in earlier studies using the same cross. For 48% (34/71) of the detected QTLs, the wild allele was associated with improved agronomic performance. A number of new QTLs were identified including several of significant agronomic importance for tomato production: fruit shape, firmness, fruit color, scar size, seed and flower number, leaf curliness, plant growth, fertility, and flowering time. To improve the utility of the IBL population, a subset of 100 lines giving the most uniform genome coverage and map resolution was selected using a randomized greedy algorithm as implemented in the software package MapPop (http://www.bio.unc.edu/faculty/vision/lab/ mappop/). The map, phenotypic data, and seeds for the IBL population are publicly available (http://soldb.cit.cornell.edu) and will provide tomato geneticists and breeders with a genetic resource for mapping, gene discovery, and breeding.
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Affiliation(s)
- Sami Doganlar
- Department of Plant Breeding and Plant Biology, 252 Emerson Hall, Cornell University, Ithaca, NY 14853-1902, USA
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48
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Schranz ME, Quijada P, Sung SB, Lukens L, Amasino R, Osborn TC. Characterization and effects of the replicated flowering time gene FLC in Brassica rapa. Genetics 2002; 162:1457-68. [PMID: 12454088 PMCID: PMC1462321 DOI: 10.1093/genetics/162.3.1457] [Citation(s) in RCA: 147] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Functional genetic redundancy is widespread in plants and could have an important impact on phenotypic diversity if the multiple gene copies act in an additive or dosage-dependent manner. We have cloned four Brassica rapa homologs (BrFLC) of the MADS-box flowering-time regulator FLC, located at the top of chromosome 5 of Arabidopsis thaliana. Relative rate tests revealed no evidence for differential rates of evolution and the ratios of nonsynonymous-to-synonymous substitutions suggest BrFLC loci are not under strong purifying selection. BrFLC1, BrFLC2, and BrFLC3 map to genomic regions that are collinear with the top of At5, consistent with a polyploid origin. BrFLC5 maps near a junction of two collinear regions to Arabidopsis, one of which includes an FLC-like gene (AGL31). However, all BrFLC sequences are more closely related to FLC than to AGL31. BrFLC1, BrFLC2, and BrFLC5 cosegregate with flowering-time loci evaluated in populations derived by backcrossing late-flowering alleles from a biennial parent into an annual parent. Two loci segregating in a single backcross population affected flowering in a completely additive manner. Thus, replicated BrFLC genes appear to have a similar function and interact in an additive manner to modulate flowering time.
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Affiliation(s)
- M Eric Schranz
- Department of Agronomy, University of Wisconsin, Madison, 53706, USA
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Kabelka E, Franchino B, Francis DM. Two Loci from Lycopersicon hirsutum LA407 Confer Resistance to Strains of Clavibacter michiganensis subsp. michiganensis. PHYTOPATHOLOGY 2002; 92:504-10. [PMID: 18943024 DOI: 10.1094/phyto.2002.92.5.504] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
ABSTRACT We used molecular markers to identify quantitative trait loci (QTL) that contribute to resistance to bacterial canker of tomato caused by Clavibacter michiganensis subsp. michiganensis. Resistance was first identified as a marker-trait association in an inbred backcross (IBC) population derived from crossing Lycopersicon hirsutum accession (LA407) with L. esculentum. Single-marker QTL analysis suggested that at least two loci originating from L. hirsutum LA407, Rcm 2.0 on chromosome 2 and Rcm 5.1 on chromosome 5, contribute to resistance in replicated trials. Two segregating F(2) populations were developed by crossing resistant inbred backcross lines (IBLs) to elite L. esculentum lines and used to confirm QTL associations detected in the IBC population. In these populations, realized heritability estimates were higher for selection based on maximal disease than for selection based on disease progression. Realized heritability in the population carrying Rcm 2.0 was 0.63 and 0.14, respectively, for each selection criteria. Realized heritability estimates were 0.85 for selection based on maximal disease and 0.37 for selection based on disease progression in a population carrying Rcm 5.1. The disease response of F(3) families selected for resistance suggested that both Rcm 2.0 and Rcm 5.1 confer resistance to bacterial strains in the repetitive sequence-based polymerase chain reaction DNA fingerprint classes A and C. Markers linked to Rcm 2.0 explained up to 56% of the total phenotypic variation for resistance in one population, and markers linked to Rcm 5.1 explained up to 73% of the total phenotypic variation for resistance in a separate population.
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Kole C, Williams PH, Rimmer SR, Osborn TC. Linkage mapping of genes controlling resistance to white rust (Albugo candida) in Brassica rapa (syn. campestris) and comparative mapping to Brassica napus and Arabidopsis thaliana. Genome 2002; 45:22-7. [PMID: 11908664 DOI: 10.1139/g01-123] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Genes for resistance to white rust (Albugo candida) in oilseed Brassica rapa were mapped using a recombinant inbred (RI) population and a genetic linkage map consisting of 144 restriction fragment length polymorphism (RFLP) markers and 3 phenotypic markers. Young seedlings were evaluated by inoculating cotyledons with A. candida race 2 (AC2) and race 7 (AC7) and scoring the interaction phenotype (IP) on a 0-9 scale. The IP of each line was nearly identical for the two races and the population showed bimodal distributions, suggesting that a single major gene (or tightly linked genes) controlled resistance to the two races. The IP scores were converted to categorical resistant and susceptible scores, and these data were used to map a single Mendelian gene controlling resistance to both races on linkage group 4 where resistance to race 2 had been mapped previously. A quantitative trait loci (QTL) mapping approach using the IP scores detected the same major resistance locus for both races, plus a second minor QTL effect for AC2 on linkage group 2. These results indicate that either a dominant allele at a single locus (Acal) or two tightly linked loci control seedling resistance to both races of white rust in the biennial turnip rape cultivar Per. The map positions of white rust resistance genes in B. rapa and Brassica napus were compared and the results indicate where additional loci that have not been mapped may be located. Alignment of these maps to the physical map of the Arabidopsis genome identified regions to target for comparative fine mapping using this model organism.
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Affiliation(s)
- C Kole
- Department of Agronomy, University of Wisconsin, Madison 53706, USA
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