1
|
Pei D, Yu X, Fu W, Ma X, Fang J. The evolution and formation of centromeric repeats analysis in Vitis vinifera. PLANTA 2024; 259:99. [PMID: 38522063 DOI: 10.1007/s00425-024-04374-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/03/2024] [Indexed: 03/25/2024]
Abstract
MAIN CONCLUSION Six grape centromere-specific markers for cytogenetics were mined by combining genetic and immunological assays, and the possible evolution mechanism of centromeric repeats was analyzed. Centromeric histone proteins are functionally conserved; however, centromeric repetitive DNA sequences may represent considerable diversity in related species. Therefore, studying the characteristics and structure of grape centromere repeat sequences contributes to a deeper understanding of the evolutionary process of grape plants, including their origin and mechanisms of polyploidization. Plant centromeric regions are mainly composed of repetitive sequences, including SatDNA and transposable elements (TE). In this research, the characterization of centromere sequences in the whole genome of grapevine (Vitis vinifera L.) has been conducted. Five centromeric tandem repeat sequences (Vv1, Vv2, Vv5, Vv6, and Vv8) and one long terminal repeat (LTR) sequence Vv24 were isolated. These sequences had different centromeric distributions, which indicates that grape centromeric sequences may undergo rapid evolution. The existence of extrachromosomal circular DNA (eccDNA) and gene expression in CenH3 subdomain region may provide various potential mechanisms for the generation of new centromeric regions.
Collapse
Affiliation(s)
- Dan Pei
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xue Yu
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Weihong Fu
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xuhui Ma
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277000, China
| | - Jinggui Fang
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing, China.
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, Nanjing, 210095, China.
| |
Collapse
|
2
|
Zhang YY, Li HK, Huang X, Yuan YJ, Zhang XF, Gao XS, Wang XJ, Wei MM, Huang HS, Li W. Heterozygosity analysis of spontaneous 2n female gametes and centromere mapping of the diploid Hevea brasiliensis based on full-sib triploid populations. PLANT REPRODUCTION 2024; 37:47-56. [PMID: 37758937 DOI: 10.1007/s00497-023-00481-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023]
Abstract
KEY MESSAGE Unreduced megagametophytes via second-division restitution were confirmed through heterozygosity analysis, and four candidate physical centromeres of rubber were located for the first time. The evaluation of maternal heterozygosity restitution (MHR) is vital in identifying the mechanism of 2n gametogenesis and assessing the utilization value of 2n gametes. In this study, three full-sib triploid populations were employed to evaluate the MHR of 2n female gametes of rubber tree clone GT1 and to confirm their genetic derivation. The 2n female gametes of GT1 were derived from second-division restitution (SDR) and transmitted more than half of the parental heterozygosity. In addition, low recombination frequency markers were developed, and four candidate physical centromeres of rubber tree were located for the first time. The confirmation that 2n female gametes of rubber tree clone GT1 are derived from SDR provides insights into the molecular mechanisms of 2n gametogenesis. In addition, the identified centromere location will aid in the development of centromeric markers for the rapid identification of the 2n gametogenesis mechanism.
Collapse
Affiliation(s)
- Yuan-Yuan Zhang
- State Key Laboratory of Tropical Crop Breeding, State Centre for Rubber Breeding, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.
| | - Hong-Kun Li
- Dehong Institute of Tropical Agricultural Sciences of Yunnan Province, Ruili, 678600, Yunnan, China
| | - Xiao Huang
- State Key Laboratory of Tropical Crop Breeding, State Centre for Rubber Breeding, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Yu-Jiao Yuan
- College of Tropical Crops, Yunnan Agricultural University, Puer, 665099, Yunnan, China
| | - Xiao-Fei Zhang
- State Key Laboratory of Tropical Crop Breeding, State Centre for Rubber Breeding, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Xin-Sheng Gao
- State Key Laboratory of Tropical Crop Breeding, State Centre for Rubber Breeding, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Xiang-Jun Wang
- State Key Laboratory of Tropical Crop Breeding, State Centre for Rubber Breeding, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Ming-Ming Wei
- State Key Laboratory of Tropical Crop Breeding, State Centre for Rubber Breeding, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Hua-Sun Huang
- State Key Laboratory of Tropical Crop Breeding, State Centre for Rubber Breeding, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Weiguo Li
- State Key Laboratory of Tropical Crop Breeding, State Centre for Rubber Breeding, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.
| |
Collapse
|
3
|
Katche E, Katche EI, Vasquez-Teuber P, Idris Z, Lo YT, Nugent D, Zou J, Batley J, Mason AS. Genome composition in Brassica interspecific hybrids affects chromosome inheritance and viability of progeny. Chromosome Res 2023; 31:22. [PMID: 37596507 PMCID: PMC10439240 DOI: 10.1007/s10577-023-09733-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/04/2023] [Accepted: 08/01/2023] [Indexed: 08/20/2023]
Abstract
Interspecific hybridization is widespread in nature and can result in the formation of new hybrid species as well as the transfer of traits between species. However, the fate of newly formed hybrid lineages is relatively understudied. We undertook pairwise crossing between multiple genotypes of three Brassica allotetraploid species Brassica juncea (2n = AABB), Brassica carinata (2n = BBCC), and Brassica napus (2n = AACC) to generate AABC, BBAC, and CCAB interspecific hybrids and investigated chromosome inheritance and fertility in these hybrids and their self-pollinated progeny. Surprisingly, despite the presence of a complete diploid genome in all hybrids, hybrid fertility was very low. AABC and BBAC first generation (F1) hybrids both averaged ~16% pollen viability compared to 3.5% in CCAB hybrids: most CCAB hybrid flowers were male-sterile. AABC and CCAB F1 hybrid plants averaged 5.5 and 0.5 seeds per plant, respectively, and BBAC F1 hybrids ~56 seeds/plant. In the second generation (S1), all confirmed self-pollinated progeny resulting from CCAB hybrids were sterile, producing no self-pollinated seeds. Three AABC S1 hybrids putatively resulting from unreduced gametes produced 3, 14, and 182 seeds each, while other AABC S1 hybrids averaged 1.5 seeds/plant (0-8). BBAC S1 hybrids averaged 44 seeds/plant (range 0-403). We also observed strong bias towards retention rather than loss of the haploid genomes, suggesting that the subgenomes in the Brassica allotetraploids are already highly interdependent, such that loss of one subgenome is detrimental to fertility and viability. Our results suggest that relationships between subgenomes determine hybridization outcomes in these species.
Collapse
Affiliation(s)
- Elvis Katche
- Plant Breeding Department, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Elizabeth Ihien Katche
- Plant Breeding Department, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
- Plant Breeding Department, University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Paula Vasquez-Teuber
- Plant Breeding Department, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
- Plant Breeding Department, University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, 4072, Australia
- Department of Plant Production, Faculty of Agronomy, University of Concepción, Av. Vicente Méndez, 595, Chillán, Chile
| | - Zurianti Idris
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Yu-Tzu Lo
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - David Nugent
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jacqueline Batley
- School of Biological Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, Perth, 6009, Australia
| | - Annaliese S Mason
- Plant Breeding Department, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
- Plant Breeding Department, University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany.
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, 4072, Australia.
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
Dong J, Tu W, Wang H, Zuo Y, Liu T, Zhao Q, Ying J, Wu J, Liu Y, Cai X, Song B. Genome sequence analysis provides insights into the mode of 2n egg formation in Solanum malmeanum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:157. [PMID: 37340281 DOI: 10.1007/s00122-023-04406-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/13/2023] [Indexed: 06/22/2023]
Abstract
KEY MESSAGE Our genomic investigation confirms the mechanism of 2n eggs formation in S. malmeanum and aid in optimizing the use of wild germplasm. Wild potatoes are a valuable source of agronomic traits. However, substantial reproductive barriers limit gene flow into cultivated species. 2n gametes are instrumental in preventing endosperm abortion caused by genetic imbalances in the endosperm. However, little is known about the molecular mechanisms underlying the formation of 2n gametes. Here, the wild species Solanum malmeanum Bitter (2x, 1EBN, endosperm balance number) was used in inter- and intrapoloid crosses with other Solanum species, with viable seeds being produced only when S. malmeanum was used as the female parent to cross the 2EBN Solanum genus and with the likely involvement of 2n gametes. Subsequently, we substantiated the formation of 2n eggs in S. malmeanum using fluorescence in situ hybridization (FISH) and genomic sequencing technology. Additionally, the transmission rate of maternal heterozygous polymorphism sites was assessed from a genomic perspective to analyze the mode of 2n egg formation in S. malmeanum × S. tuberosum and S. malmeanum × S. chacoense crosses; each cross acquired an average of 31.12% and 22.79% maternal sites, respectively. This confirmed that 2n egg formation in S. malmeanum attributed to second-division restitution (SDR) coupled with the occurrence of exchange events. The high-throughput sequencing technology used in this study has strong advantages over traditional cytological analyses. Furthermore, S. malmeanum, which has a variety of excellent traits not available from present cultivated potato genepool, has received little research attention and has successfully achieved gene flow in cultivated species in the current study. These findings will facilitate the understanding and optimization of wild germplasm utilization in potatoes.
Collapse
Affiliation(s)
- Jianke Dong
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wei Tu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, China
| | - Haibo Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, 445000, China
| | - Yingtao Zuo
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tengfei Liu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qinghao Zhao
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jingwen Ying
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianghai Wu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuanyuan Liu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xingkui Cai
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Botao Song
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
6
|
Fell H, Muthayil Ali A, Wells R, Mitrousia GK, Woolfenden H, Schoonbeek HJ, Fitt BDL, Ridout CJ, Stotz HU. Novel gene loci associated with susceptibility or cryptic quantitative resistance to Pyrenopeziza brassicae in Brassica napus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:71. [PMID: 36952022 PMCID: PMC10036280 DOI: 10.1007/s00122-023-04243-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
Quantitative disease resistance (QDR) controls the association of the light leaf spot pathogen with Brassica napus; four QDR loci that were in linkage disequilibrium and eight gene expression markers were identified. Quantitative disease resistance (QDR) can provide durable control of pathogens in crops in contrast to resistance (R) gene-mediated resistance which can break down due to pathogen evolution. QDR is therefore a desirable trait in crop improvement, but little is known about the causative genes, and so it is difficult to incorporate into breeding programmes. Light leaf spot, caused by Pyrenopeziza brassicae, is an important disease of oilseed rape (canola, Brassica napus). To identify new QDR gene loci, we used a high-throughput screening pathosystem with P. brassicae on 195 lines of B. napus combined with an association transcriptomics platform. We show that all resistance against P. brassicae was associated with QDR and not R gene-mediated. We used genome-wide association analysis with an improved B. napus population structure to reveal four gene loci significantly (P = 0.0001) associated with QDR in regions showing linkage disequilibrium. On chromosome A09, enhanced resistance was associated with heterozygosity for a cytochrome P450 gene co-localising with a previously described locus for seed glucosinolate content. In addition, eight significant gene expression markers with a false discovery rate of 0.001 were associated with QDR against P. brassicae. For seven of these, expression was positively correlated with resistance, whereas for one, a HXXXD-type acyl-transferase, negative correlation indicated a potential susceptibility gene. The study identifies novel QDR loci for susceptibility and resistance, including novel cryptic QDR genes associated with heterozygosity, that will inform future crop improvement.
Collapse
Affiliation(s)
- Heather Fell
- Centre for Agriculture, Food and Environmental Management, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK
| | - Ajisa Muthayil Ali
- Centre for Agriculture, Food and Environmental Management, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK
| | - Rachel Wells
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Georgia K Mitrousia
- Centre for Agriculture, Food and Environmental Management, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK
- Communication and Engagement Office, Science Innovation Engagement Partnerships, Rothamsted Research Ltd, West Common, Harpenden, AL5 2JQ, UK
| | - Hugh Woolfenden
- Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Henk-Jan Schoonbeek
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Bruce D L Fitt
- Centre for Agriculture, Food and Environmental Management, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK
| | - Christopher J Ridout
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Henrik U Stotz
- Centre for Agriculture, Food and Environmental Management, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK.
| |
Collapse
|
7
|
Orantes-Bonilla M, Makhoul M, Lee H, Chawla HS, Vollrath P, Langstroff A, Sedlazeck FJ, Zou J, Snowdon RJ. Frequent spontaneous structural rearrangements promote rapid genome diversification in a Brassica napus F1 generation. FRONTIERS IN PLANT SCIENCE 2022; 13:1057953. [PMID: 36466276 PMCID: PMC9716091 DOI: 10.3389/fpls.2022.1057953] [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: 09/30/2022] [Accepted: 10/31/2022] [Indexed: 05/26/2023]
Abstract
In a cross between two homozygous Brassica napus plants of synthetic and natural origin, we demonstrate that novel structural genome variants from the synthetic parent cause immediate genome diversification among F1 offspring. Long read sequencing in twelve F1 sister plants revealed five large-scale structural rearrangements where both parents carried different homozygous alleles but the heterozygous F1 genomes were not identical heterozygotes as expected. Such spontaneous rearrangements were part of homoeologous exchanges or segmental deletions and were identified in different, individual F1 plants. The variants caused deletions, gene copy-number variations, diverging methylation patterns and other structural changes in large numbers of genes and may have been causal for unexpected phenotypic variation between individual F1 sister plants, for example strong divergence of plant height and leaf area. This example supports the hypothesis that spontaneous de novo structural rearrangements after de novo polyploidization can rapidly overcome intense allopolyploidization bottlenecks to re-expand crops genetic diversity for ecogeographical expansion and human selection. The findings imply that natural genome restructuring in allopolyploid plants from interspecific hybridization, a common approach in plant breeding, can have a considerably more drastic impact on genetic diversity in agricultural ecosystems than extremely precise, biotechnological genome modifications.
Collapse
Affiliation(s)
- Mauricio Orantes-Bonilla
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Manar Makhoul
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - HueyTyng Lee
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Harmeet Singh Chawla
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Paul Vollrath
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Anna Langstroff
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China
| | - Rod J. Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| |
Collapse
|
8
|
Yang Z, Jiang Y, Gong J, Li Q, Dun B, Liu D, Yin F, Yuan L, Zhou X, Wang H, Wang J, Zhan Z, Shah N, Nwafor CC, Zhou Y, Chen P, Zhu L, Li S, Wang B, Xiang J, Zhou Y, Li Z, Piao Z, Yang Q, Zhang C. R gene triplication confers European fodder turnip with improved clubroot resistance. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1502-1517. [PMID: 35445530 PMCID: PMC9342621 DOI: 10.1111/pbi.13827] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 03/30/2022] [Accepted: 04/10/2022] [Indexed: 05/08/2023]
Abstract
Clubroot is one of the most important diseases for many important cruciferous vegetables and oilseed crops worldwide. Different clubroot resistance (CR) loci have been identified from only limited species in Brassica, making it difficult to compare and utilize these loci. European fodder turnip ECD04 is considered one of the most valuable resources for CR breeding. To explore the genetic and evolutionary basis of CR in ECD04, we sequenced the genome of ECD04 using de novo assembly and identified 978 candidate R genes. Subsequently, the 28 published CR loci were physically mapped to 15 loci in the ECD04 genome, including 62 candidate CR genes. Among them, two CR genes, CRA3.7.1 and CRA8.2.4, were functionally validated. Phylogenetic analysis revealed that CRA3.7.1 and CRA8.2.4 originated from a common ancestor before the whole-genome triplication (WGT) event. In clubroot susceptible Brassica species, CR-gene homologues were affected by transposable element (TE) insertion, resulting in the loss of CR function. It can be concluded that the current functional CR genes in Brassica rapa and non-functional CR genes in other Brassica species were derived from a common ancestral gene before WGT. Finally, a hypothesis for CR gene evolution is proposed for further discussion.
Collapse
Affiliation(s)
- Zhiquan Yang
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Yingfen Jiang
- Institute of Crop ScienceAnhui Academy of Agricultural ScienceHefeiChina
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jianfang Gong
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Qian Li
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Bicheng Dun
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Yangtze River Rare Plant Research InstituteChina Three Gorges CorporationYichangChina
| | - Dongxu Liu
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Feifan Yin
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Lei Yuan
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Xueqing Zhou
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Huiying Wang
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jing Wang
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Zongxiang Zhan
- College of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Nadil Shah
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Chinedu Charles Nwafor
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yuanwei Zhou
- Yichang Academy of Agricultural ScienceYichangChina
| | - Peng Chen
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Li Zhu
- Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains and College of Biology and Agriculture ResourceHuanggang Normal UniversityHuanggangChina
| | - Shisheng Li
- Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains and College of Biology and Agriculture ResourceHuanggang Normal UniversityHuanggangChina
| | - Bingrui Wang
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jun Xiang
- Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains and College of Biology and Agriculture ResourceHuanggang Normal UniversityHuanggangChina
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Zaiyun Li
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Zhongyun Piao
- College of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Qingyong Yang
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Chunyu Zhang
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| |
Collapse
|
9
|
Bayer PE, Scheben A, Golicz AA, Yuan Y, Faure S, Lee H, Chawla HS, Anderson R, Bancroft I, Raman H, Lim YP, Robbens S, Jiang L, Liu S, Barker MS, Schranz ME, Wang X, King GJ, Pires JC, Chalhoub B, Snowdon RJ, Batley J, Edwards D. Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2488-2500. [PMID: 34310022 PMCID: PMC8633514 DOI: 10.1111/pbi.13674] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/11/2021] [Accepted: 07/20/2021] [Indexed: 05/26/2023]
Abstract
Plant genomes demonstrate significant presence/absence variation (PAV) within a species; however, the factors that lead to this variation have not been studied systematically in Brassica across diploids and polyploids. Here, we developed pangenomes of polyploid Brassica napus and its two diploid progenitor genomes B. rapa and B. oleracea to infer how PAV may differ between diploids and polyploids. Modelling of gene loss suggests that loss propensity is primarily associated with transposable elements in the diploids while in B. napus, gene loss propensity is associated with homoeologous recombination. We use these results to gain insights into the different causes of gene loss, both in diploids and following polyploidization, and pave the way for the application of machine learning methods to understanding the underlying biological and physical causes of gene presence/absence.
Collapse
Affiliation(s)
- Philipp E. Bayer
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Armin Scheben
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Agnieszka A. Golicz
- Plant Molecular Biology and Biotechnology LaboratoryFaculty of Veterinary and Agricultural SciencesUniversity of MelbourneParkvilleVICAustralia
| | - Yuxuan Yuan
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | | | - HueyTyng Lee
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig University GiessenGiessenGermany
| | - Harmeet Singh Chawla
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig University GiessenGiessenGermany
| | - Robyn Anderson
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | | | - Harsh Raman
- NSW Department of Primary IndustriesWagga Wagga Agricultural Institute, PMBWagga WaggaNSWAustralia
| | - Yong Pyo Lim
- Department of HorticultureChungnam National UniversityDaejeonSouth Korea
| | | | - Lixi Jiang
- Institute of crop scienceDepartment of Agronomy and Plant BreedingZhejiang UniversityHangzhouChina
| | - Shengyi Liu
- Chinese Academy of Agricultural SciencesOil Crops Research InstituteWuhanChina
| | - Michael S. Barker
- Department of Ecology & Evolutionary BiologyUniversity of ArizonaTucsonAZUSA
| | - M. Eric Schranz
- Biosystematics GroupWageningen University and Research CenterWageningenThe Netherlands
| | - Xiaowu Wang
- Institute of Vegetables and FlowersChinese Academy of Agricultural Sciences (IVF, CAAS)BeijingChina
| | - Graham J. King
- Southern Cross Plant ScienceSouthern Cross UniversityLismoreNSWAustralia
| | - J. Chris Pires
- Division of Biological SciencesBond Life Sciences CenterUniversity of MissouriColumbiaMissouriUSA
| | - Boulos Chalhoub
- Institute of crop scienceDepartment of Agronomy and Plant BreedingZhejiang UniversityHangzhouChina
| | - Rod J. Snowdon
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig University GiessenGiessenGermany
| | - Jacqueline Batley
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - David Edwards
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| |
Collapse
|
10
|
Boideau F, Pelé A, Tanguy C, Trotoux G, Eber F, Maillet L, Gilet M, Lodé-Taburel M, Huteau V, Morice J, Coriton O, Falentin C, Delourme R, Rousseau-Gueutin M, Chèvre AM. A Modified Meiotic Recombination in Brassica napus Largely Improves Its Breeding Efficiency. BIOLOGY 2021; 10:biology10080771. [PMID: 34440003 PMCID: PMC8389541 DOI: 10.3390/biology10080771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/10/2021] [Accepted: 08/10/2021] [Indexed: 01/31/2023]
Abstract
Simple Summary The selection of varieties more resilient to disease and climate change requires generating new genetic diversity for breeding. The main mechanism for reshuffling genetic information is through the recombination of chromosomes during meiosis. We showed in oilseed rape (Brassica napus, AACC, 2n = 4x = 38), which is a natural hybrid formed from a cross between turnip (B. rapa, AA, 2n = 2x = 20) and cabbage (B. oleracea, CC, 2n = 2x = 18), that there is significantly more crossovers occurring along the entire A chromosomes in allotriploid AAC (crossbetween B. napus and B. rapa) than in diploid AA or allotetraploid AACC hybrids. We demonstrated that these allotriploid AAC hybrids are highly efficient to introduce new variability within oilseed rape varieties, notably by enabling the introduction of small genomic regions carrying genes controlling agronomically interesting traits. Abstract Meiotic recombination is the main tool used by breeders to generate biodiversity, allowing genetic reshuffling at each generation. It enables the accumulation of favorable alleles while purging deleterious mutations. However, this mechanism is highly regulated with the formation of one to rarely more than three crossovers, which are not randomly distributed. In this study, we showed that it is possible to modify these controls in oilseed rape (Brassica napus, AACC, 2n = 4x = 38) and that it is linked to AAC allotriploidy and not to polyploidy per se. To that purpose, we compared the frequency and the distribution of crossovers along A chromosomes from hybrids carrying exactly the same A nucleotide sequence, but presenting three different ploidy levels: AA, AAC and AACC. Genetic maps established with 202 SNPs anchored on reference genomes revealed that the crossover rate is 3.6-fold higher in the AAC allotriploid hybrids compared to AA and AACC hybrids. Using a higher SNP density, we demonstrated that smaller and numerous introgressions of B. rapa were present in AAC hybrids compared to AACC allotetraploid hybrids, with 7.6 Mb vs. 16.9 Mb on average and 21 B. rapa regions per plant vs. nine regions, respectively. Therefore, this boost of recombination is highly efficient to reduce the size of QTL carried in cold regions of the oilseed rape genome, as exemplified here for a QTL conferring blackleg resistance.
Collapse
Affiliation(s)
- Franz Boideau
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Alexandre Pelé
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, 61-614 Poznan, Poland
| | - Coleen Tanguy
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Gwenn Trotoux
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Frédérique Eber
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Loeiz Maillet
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Marie Gilet
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Maryse Lodé-Taburel
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Virginie Huteau
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Jérôme Morice
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Olivier Coriton
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Cyril Falentin
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Régine Delourme
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Mathieu Rousseau-Gueutin
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Anne-Marie Chèvre
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
- Correspondence: ; Tel.: +33-2-23-48-51-31
| |
Collapse
|
11
|
Ferreira de Carvalho J, Stoeckel S, Eber F, Lodé-Taburel M, Gilet MM, Trotoux G, Morice J, Falentin C, Chèvre AM, Rousseau-Gueutin M. Untangling structural factors driving genome stabilization in nascent Brassica napus allopolyploids. THE NEW PHYTOLOGIST 2021; 230:2072-2084. [PMID: 33638877 DOI: 10.1111/nph.17308] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 02/22/2021] [Indexed: 05/28/2023]
Abstract
Allopolyploids have globally higher fitness than their diploid progenitors; however, by comparison, most resynthesized allopolyploids have poor fertility and highly unstable genome. Elucidating the evolutionary processes promoting genome stabilization and fertility is thus essential to comprehend allopolyploid success. Using the Brassica model, we mimicked the speciation process of a nascent allopolyploid species by resynthesizing allotetraploid Brassica napus and systematically selecting for euploid individuals over eight generations in four independent allopolyploidization events with contrasted genetic backgrounds, cytoplasmic donors, and polyploid formation type. We evaluated the evolution of meiotic behavior and fertility and identified rearrangements in S1 to S9 lineages to explore the positive consequences of euploid selection on B. napus genome stability. Recurrent selection of euploid plants for eight generations drastically reduced the percentage of aneuploid progenies as early as the fourth generation, concomitantly with a decrease in number of newly fixed homoeologous rearrangements. The consequences of homoeologous rearrangements on meiotic behavior and seed number depended strongly on the genetic background and cytoplasm donor. The combined use of both self-fertilization and recurrent euploid selection allowed identification of genomic regions associated with fertility and meiotic behavior, providing complementary evidence to explain B. napus speciation success.
Collapse
Affiliation(s)
| | - Solenn Stoeckel
- IGEPP, INRAE, Institut Agro, Université de Rennes, Le Rheu, 35650, France
| | - Frédérique Eber
- IGEPP, INRAE, Institut Agro, Université de Rennes, Le Rheu, 35650, France
| | | | | | - Gwenn Trotoux
- IGEPP, INRAE, Institut Agro, Université de Rennes, Le Rheu, 35650, France
| | - Jérôme Morice
- IGEPP, INRAE, Institut Agro, Université de Rennes, Le Rheu, 35650, France
| | - Cyril Falentin
- IGEPP, INRAE, Institut Agro, Université de Rennes, Le Rheu, 35650, France
| | - Anne-Marie Chèvre
- IGEPP, INRAE, Institut Agro, Université de Rennes, Le Rheu, 35650, France
| | | |
Collapse
|
12
|
Katche E, Gaebelein R, Idris Z, Vasquez-Teuber P, Lo YT, Nugent D, Batley J, Mason AS. Stable, fertile lines produced by hybridization between allotetraploids Brassica juncea (AABB) and Brassica carinata (BBCC) have merged the A and C genomes. THE NEW PHYTOLOGIST 2021; 230:1242-1257. [PMID: 33476056 DOI: 10.1111/nph.17225] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 01/12/2021] [Indexed: 06/12/2023]
Abstract
Many flowering plant taxa contain allopolyploids that share one or more genomes in common. In the Brassica genus, crop species Brassica juncea and Brassica carinata share the B genome, with 2n = AABB and 2n = BBCC genome complements, respectively. Hybridization results in 2n = BBAC hybrids, but the fate of these hybrids over generations of self-pollination has never been reported. We produced and characterized B. juncea × B. carinata (2n = BBAC) interspecific hybrids over six generations of self-pollination under selection for high fertility using a combination of genotyping, fertility phenotyping, and cytogenetics techniques. Meiotic pairing behaviour improved from 68% bivalents in the F1 to 98% in the S5 /S6 generations, and initially low hybrid fertility also increased to parent species levels. The S5 /S6 hybrids contained an intact B genome (16 chromosomes) plus a new, stable A/C genome (18-20 chromosomes) resulting from recombination and restructuring of A and C-genome chromosomes. Our results provide the first experimental evidence that two genomes can come together to form a new, restructured genome in hybridization events between two allotetraploid species that share a common genome. This mechanism should be considered in interpreting phylogenies in taxa with multiple allopolyploid species.
Collapse
Affiliation(s)
- Elvis Katche
- Plant Breeding Department, Justus Liebig University, Heinrich-Buff-Ring 26-32, Giessen, 35392, Germany
| | - Roman Gaebelein
- Plant Breeding Department, Justus Liebig University, Heinrich-Buff-Ring 26-32, Giessen, 35392, Germany
| | - Zurianti Idris
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Paula Vasquez-Teuber
- Plant Breeding Department, Justus Liebig University, Heinrich-Buff-Ring 26-32, Giessen, 35392, Germany
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
- Department of Plant Production, Faculty of Agronomy, University of Concepción, Av. Vicente Méndez 595, Chillán, Chile
| | - Yu-Tzu Lo
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - David Nugent
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jacqueline Batley
- School of Biological Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, Perth, WA, 6009, Australia
| | - Annaliese S Mason
- Plant Breeding Department, Justus Liebig University, Heinrich-Buff-Ring 26-32, Giessen, 35392, Germany
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
- Plant Breeding Department, University of Bonn, Katzenburgweg 5, Bonn, 53115, Germany
| |
Collapse
|
13
|
Tourrette E, Falque M, Martin OC. Enhancing backcross programs through increased recombination. Genet Sel Evol 2021; 53:25. [PMID: 33750291 PMCID: PMC7941899 DOI: 10.1186/s12711-021-00619-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/24/2021] [Indexed: 11/28/2022] Open
Abstract
Background Introgression of a quantitative trait locus (QTL) by successive backcrosses is used to improve elite lines (recurrent parent) by introducing alleles from exotic material (donor parent). In the absence of selection, the proportion of the donor genome decreases by half at each generation. However, since selection is for the donor allele at the QTL, elimination of the donor genome around that QTL will be much slower than in the rest of the genome (i.e. linkage drag). Using markers to monitor the genome around the QTL and in the genetic background can accelerate the return to the recurrent parent genome. Successful introgression of a locus depends partly on the occurrence of crossovers at favorable positions. However, the number of crossovers per generation is limited and their distribution along the genome is heterogeneous. Recently, techniques have been developed to modify these two recombination parameters. Results In this paper, we assess, by simulations in the context of Brassicaceae, the effect of increased recombination on the efficiency of introgression programs by studying the decrease in linkage drag and the recovery of the recurrent genome. The simulated selection schemes begin by two generations of foreground selection and continue with one or more generations of background selection. Our results show that, when the QTL is in a region that initially lacked crossovers, an increase in recombination rate can decrease linkage drag by nearly ten-fold after the foreground selection and improves the return to the recurrent parent. However, if the QTL is in a region that is already rich in crossovers, an increase in recombination rate is detrimental. Conclusions Depending on the recombination rate in the region targeted for introgression, increasing it can be beneficial or detrimental. Thus, the simulations analysed in this paper help us understand how an increase in recombination rate can be beneficial. They also highlight the best methods that can be used to increase recombination rate, depending on the situation. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00619-0.
Collapse
Affiliation(s)
- Elise Tourrette
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Matthieu Falque
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France.
| | - Olivier C Martin
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France.,Université Paris-Saclay, INRAE, CNRS, Univ. Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France.,Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| |
Collapse
|
14
|
Rousseau-Gueutin M, Belser C, Da Silva C, Richard G, Istace B, Cruaud C, Falentin C, Boideau F, Boutte J, Delourme R, Deniot G, Engelen S, de Carvalho JF, Lemainque A, Maillet L, Morice J, Wincker P, Denoeud F, Chèvre AM, Aury JM. Long-read assembly of the Brassica napus reference genome Darmor-bzh. Gigascience 2020; 9:giaa137. [PMID: 33319912 PMCID: PMC7736779 DOI: 10.1093/gigascience/giaa137] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/18/2020] [Accepted: 11/09/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The combination of long reads and long-range information to produce genome assemblies is now accepted as a common standard. This strategy not only allows access to the gene catalogue of a given species but also reveals the architecture and organization of chromosomes, including complex regions such as telomeres and centromeres. The Brassica genus is not exempt, and many assemblies based on long reads are now available. The reference genome for Brassica napus, Darmor-bzh, which was published in 2014, was produced using short reads and its contiguity was extremely low compared with current assemblies of the Brassica genus. FINDINGS Herein, we report the new long-read assembly of Darmor-bzh genome (Brassica napus) generated by combining long-read sequencing data and optical and genetic maps. Using the PromethION device and 6 flowcells, we generated ∼16 million long reads representing 93× coverage and, more importantly, 6× with reads longer than 100 kb. This ultralong-read dataset allows us to generate one of the most contiguous and complete assemblies of a Brassica genome to date (contig N50 > 10 Mb). In addition, we exploited all the advantages of the nanopore technology to detect modified bases and sequence transcriptomic data using direct RNA to annotate the genome and focus on resistance genes. CONCLUSION Using these cutting-edge technologies, and in particular by relying on all the advantages of the nanopore technology, we provide the most contiguous Brassica napus assembly, a resource that will be valuable to the Brassica community for crop improvement and will facilitate the rapid selection of agronomically important traits.
Collapse
Affiliation(s)
| | - Caroline Belser
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Gautier Richard
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France
| | - Benjamin Istace
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Cyril Falentin
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France
| | - Franz Boideau
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France
| | - Julien Boutte
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France
| | - Regine Delourme
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France
| | - Gwenaëlle Deniot
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France
| | - Stefan Engelen
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | | | - Arnaud Lemainque
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Loeiz Maillet
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France
| | - Jérôme Morice
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | - France Denoeud
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Anne-Marie Chèvre
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| |
Collapse
|
15
|
Xia QM, Miao LK, Xie KD, Yin ZP, Wu XM, Chen CL, Grosser JW, Guo WW. Localization and characterization of Citrus centromeres by combining half-tetrad analysis and CenH3-associated sequence profiling. PLANT CELL REPORTS 2020; 39:1609-1622. [PMID: 32897396 DOI: 10.1007/s00299-020-02587-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 08/26/2020] [Indexed: 06/11/2023]
Abstract
The physical locations of citrus centromere are revealed by combining genetic and immunological assays for the first time and nine citrus centromere-specific markers for cytogenetics are mined. Centromere localization is challenging, because highly redundant repetitive sequences in centromeric regions make sequence assembly difficult. Although several citrus genomes have been released, the centromeric regions and their characteristics remain to be elucidated. Here, we mapped citrus centromeres through half-tetrad analysis (HTA) that included the genotyping of 54 tetraploid hybrids derived from 2n megagametophytes of Nadorcott tangor with 212 single nucleotide polymorphism (SNP) markers. The sizes of centromeric regions, which estimated based on the heterozygosity restitution rate pattern along the chromosomes, ranged from 1.12 to 18.19 Mb. We also profiled the binding sequences with the centromere-specific histone variant CenH3 by chromatin immunoprecipitation sequencing (ChIP-seq). Based on the positions of the top ten CenH3-enriched contigs, the sizes of centromeric regions were estimated to range from 0.01 to 7.60 Mb and were either adjacent to or included in the centromeric regions identified by HTA. We used DNA probes from two repeats selected from the centromeric regions and seven CenH3-binding centromeric repeats to verify centromeric locations by fluorescence in situ hybridization (FISH). Centromere localization in citrus will contribute to the mining of centromeric/pericentromeric markers, thus to facilitate the rapid identification of mechanisms underlying 2n gamete formation and serve the polyploidy breeding.
Collapse
Affiliation(s)
- Qiang-Ming Xia
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lu-Ke Miao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kai-Dong Xie
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Zhao-Ping Yin
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiao-Meng Wu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chun-Li Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jude W Grosser
- Citrus Research and Education Center, University of Florida, 700 Experiment Station Road, Lake Alfred, FL, 33850, USA
| | - Wen-Wu Guo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| |
Collapse
|
16
|
Tourrette E, Bernardo R, Falque M, Martin OC. Assessing by Modeling the Consequences of Increased Recombination in Recurrent Selection of Oryza sativa and Brassica rapa. G3 (BETHESDA, MD.) 2019; 9:4169-4181. [PMID: 31628152 PMCID: PMC6893184 DOI: 10.1534/g3.119.400545] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/15/2019] [Indexed: 02/08/2023]
Abstract
Meiotic recombination generates genetic diversity but in most species the number of crossovers per meiosis is limited. Previous modeling studies showed that increasing recombination can enhance response to selection. However, such studies did not assume a specific method of modifying recombination. Our objective was to test whether two methods used to increase recombination in plants could increase genetic gain in a population undergoing recurrent selection such as in genomic selection programs. The first method, in Oryza sativa, used a mutant of anti-crossover genes, increasing global recombination without affecting the recombination landscape shape. The second one used the ploidy level of a cross between Brassica rapa and Brassica napus, increasing recombination especially in pericentromeric regions. Our modeling framework used these recombination landscapes and sampled quantitative trait loci positions from the actual gene distributions. We simulated selection programs with initially a cross between two inbred lines, for two species. Increased recombination enhanced the response to selection. The amount of enhancement in the cumulative gain largely depended on the species and the number of quantitative trait loci (2, 10, 20, 50, 200 or 1000 per chromosome). Genetic gains were increased up to 30% after 20 generations. Furthermore, increasing recombination in cold regions was the most effective: the gain was larger by 25% with the first method and 34% with the second one in B. rapa, and 12% compared to 16% in O. sativa In summary, increased recombination enhances the genetic gain in long-term selection programs, with visible effects after four to five generations.
Collapse
Affiliation(s)
- Elise Tourrette
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France and
| | - Rex Bernardo
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul
| | - Matthieu Falque
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France and
| | - Olivier C Martin
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France and
| |
Collapse
|
17
|
Gohar M, Gäbelein R, Mason AS. A quartet pollen phenotype identified in a population of Brassica interspecific hybrids shows incomplete penetrance and variable response to temperature. PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20:894-901. [PMID: 29883021 DOI: 10.1111/plb.12854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 06/03/2018] [Indexed: 06/08/2023]
Abstract
Quartet pollen, where pollen grains remain attached to each other post-meiosis, is useful for tetrad analysis, crossover assessment and centromere mapping. We observed the quartet pollen phenotype for the first time in the agriculturally significant Brassica genus, in an experimental population of allohexaploid Brassica hybrids derived from the cross (Brassica napus × B. carinata) × B. juncea followed by two self-pollination generations. Quartet pollen production was assessed in 144 genotypes under glasshouse conditions, following which a set of 16 genotypes were selected to further investigate the effect of environment (warm: 25 °C and cold: 10 °C temperatures) on quartet pollen production in growth cabinets. Under glasshouse phenotyping conditions, only 92 out of 144 genotypes produced enough pollen to score: of these, 30 did not produce any observable quartet pollen, while 62 genotypes produced quartet pollen at varying frequencies. Quartet pollen production appeared quantitative and did not clearly fall into phenotypic or qualitative categories indicative of major gene expression. No consistent effect of temperature on quartet pollen production was identified, with some genotypes producing more and some producing less quartet pollen under different temperature treatments. The genetic heterogeneity and frequent pollen infertility of this population prevents strong conclusions being made. However, it is clear that the quartet phenotype in this Brassica population does not show complete penetrance and shows variable (likely genotype-specific) response to temperature stress. In future, identification of quartet phenotypes in Brassica would perhaps best be carried out via screening of diploid (e.g. B. rapa) TILLING populations.
Collapse
Affiliation(s)
- M Gohar
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | - R Gäbelein
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | - A S Mason
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| |
Collapse
|
18
|
Zou J, Hu D, Mason AS, Shen X, Wang X, Wang N, Grandke F, Wang M, Chang S, Snowdon RJ, Meng J. Genetic changes in a novel breeding population of Brassica napus synthesized from hundreds of crosses between B. rapa and B. carinata. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:507-519. [PMID: 28703467 PMCID: PMC5811809 DOI: 10.1111/pbi.12791] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 06/29/2017] [Accepted: 07/07/2017] [Indexed: 05/20/2023]
Abstract
Introgression of genomic variation between and within related crop species is a significant evolutionary approach for population differentiation, genome reorganization and trait improvement. Using the Illumina Infinium Brassica 60K SNP array, we investigated genomic changes in a panel of advanced generation new-type Brassica napus breeding lines developed from hundreds of interspecific crosses between 122 Brassica rapa and 74 Brassica carinata accessions, and compared them with representative accessions of their three parental species. The new-type B. napus population presented rich genetic diversity and abundant novel genomic alterations, consisting of introgressions from B. rapa and B. carinata, novel allelic combinations, reconstructed linkage disequilibrium patterns and haplotype blocks, and frequent deletions and duplications (nonrandomly distributed), particularly in the C subgenome. After a much shorter, but very intensive, selection history compared to traditional B. napus, a total of 15 genomic regions with strong selective sweeps and 112 genomic regions with putative signals of selective sweeps were identified. Some of these regions were associated with important agronomic traits that were selected for during the breeding process, while others were potentially associated with restoration of genome stability and fertility after interspecific hybridization. Our results demonstrate how a novel method for population-based crop genetic improvement can lead to rapid adaptation, restoration of genome stability and positive responses to artificial selection.
Collapse
Affiliation(s)
- Jun Zou
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Dandan Hu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Annaliese S. Mason
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Xueqi Shen
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Xiaohua Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Nian Wang
- College of Horticulture & Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Fabian Grandke
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Meng Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Shihao Chang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Rod J. Snowdon
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Jinling Meng
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| |
Collapse
|
19
|
Hu J, Guo C, Wang B, Ye J, Liu M, Wu Z, Xiao Y, Zhang Q, Li H, King GJ, Liu K. Genetic Properties of a Nested Association Mapping Population Constructed With Semi-Winter and Spring Oilseed Rapes. FRONTIERS IN PLANT SCIENCE 2018; 9:1740. [PMID: 30534135 PMCID: PMC6275288 DOI: 10.3389/fpls.2018.01740] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 11/08/2018] [Indexed: 05/17/2023]
Abstract
Nested association mapping (NAM) populations have been widely applied to dissect the genetic basis of complex quantitative traits in a variety of crops. In this study, we developed a Brassica napus NAM (BN-NAM) population consisting of 15 recombination inbred line (RIL) families with 2,425 immortal genotypes. Fifteen high-density genetic linkage maps were constructed by genotyping by sequencing (GBS) based on all RIL families, with further integration into a joint linkage map (JLM) having 30,209 unique markers in common with multiple linkage maps. Furthermore, an ultra-density whole-genome variation map was constructed by projecting 4,444,309 high-quality variants onto the JLM. The NAM population captured a total of 88,542 recombination events (REs). The uneven distribution of recombination rate along chromosomes is positively correlated with the densities of genes and markers, but negatively correlated with the density of transposable elements and linkage disequilibrium (LD). Analyses of population structure and principal components revealed that the BN-NAM population could be divided into three groups with weak stratification. The LD decay distance across genome varied between 170 and 2,400 Kb, with LD decay more rapid in the A than in the C sub-genome. The pericentromeric regions contained large LD blocks, especially in the C sub-genome. This NAM population provides a valuable resource for dissecting the genetic basis of important traits in rapeseed, especially in semi-winter oilseed rape.
Collapse
Affiliation(s)
- Jianlin Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Chaocheng Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Bo Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jiaqing Ye
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Meng Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zhikun Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Haitao Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Graham J. King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Kede Liu,
| |
Collapse
|
20
|
Stein A, Coriton O, Rousseau‐Gueutin M, Samans B, Schiessl SV, Obermeier C, Parkin IA, Chèvre A, Snowdon RJ. Mapping of homoeologous chromosome exchanges influencing quantitative trait variation in Brassica napus. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1478-1489. [PMID: 28370938 PMCID: PMC5633767 DOI: 10.1111/pbi.12732] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 03/10/2017] [Accepted: 03/17/2017] [Indexed: 05/20/2023]
Abstract
Genomic rearrangements arising during polyploidization are an important source of genetic and phenotypic variation in the recent allopolyploid crop Brassica napus. Exchanges among homoeologous chromosomes, due to interhomoeologue pairing, and deletions without compensating homoeologous duplications are observed in both natural B. napus and synthetic B. napus. Rearrangements of large or small chromosome segments induce gene copy number variation (CNV) and can potentially cause phenotypic changes. Unfortunately, complex genome restructuring is difficult to deal with in linkage mapping studies. Here, we demonstrate how high-density genetic mapping with codominant, physically anchored SNP markers can detect segmental homoeologous exchanges (HE) as well as deletions and accurately link these to QTL. We validated rearrangements detected in genetic mapping data by whole-genome resequencing of parental lines along with cytogenetic analysis using fluorescence in situ hybridization with bacterial artificial chromosome probes (BAC-FISH) coupled with PCR using primers specific to the rearranged region. Using a well-known QTL region influencing seed quality traits as an example, we confirmed that HE underlies the trait variation in a DH population involving a synthetic B. napus trait donor, and succeeded in narrowing the QTL to a small defined interval that enables delineation of key candidate genes.
Collapse
Affiliation(s)
- Anna Stein
- Department of Plant BreedingIFZ Research Centre for Biosystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Olivier Coriton
- IGEPPINRAAgrocampus OuestUniversité de Rennes 1Le RheuFrance
| | | | - Birgit Samans
- Department of Plant BreedingIFZ Research Centre for Biosystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Sarah V. Schiessl
- Department of Plant BreedingIFZ Research Centre for Biosystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Christian Obermeier
- Department of Plant BreedingIFZ Research Centre for Biosystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| | | | | | - Rod J. Snowdon
- Department of Plant BreedingIFZ Research Centre for Biosystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| |
Collapse
|
21
|
Gene Introgression in Weeds Depends on Initial Gene Location in the Crop: Brassica napus- Raphanus raphanistrum Model. Genetics 2017; 206:1361-1372. [PMID: 28533439 DOI: 10.1534/genetics.117.201715] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/07/2017] [Indexed: 11/18/2022] Open
Abstract
The effect of gene location within a crop genome on its transfer to a weed genome remains an open question for gene flow assessment. To elucidate this question, we analyzed advanced generations of intergeneric hybrids, derived from an initial pollination of known oilseed rape varieties (Brassica napus, AACC, 2n = 38) by a local population of wild radish (Raphanus raphanistrum, RrRr, 2n = 18). After five generations of recurrent pollination, 307 G5 plants with a chromosome number similar to wild radish were genotyped using 105 B. napus specific markers well distributed along the chromosomes. They revealed that 49.8% of G5 plants carried at least one B. napus genomic region. According to the frequency of B. napus markers (0-28%), four classes were defined: Class 1 (near zero frequency), with 75 markers covering ∼70% of oilseed rape genome; Class 2 (low frequency), with 20 markers located on 11 genomic regions; Class 3 (high frequency), with eight markers on three genomic regions; and Class 4 (higher frequency), with two adjacent markers detected on A10. Therefore, some regions of the oilseed rape genome are more prone than others to be introgressed into wild radish. Inheritance and growth of plant progeny revealed that genomic regions of oilseed rape could be stably introduced into wild radish and variably impact the plant fitness (plant height and seed number). Our results pinpoint that novel technologies enabling the targeted insertion of transgenes should select genomic regions that are less likely to be introgressed into the weed genome, thereby reducing gene flow.
Collapse
|
22
|
Pelé A, Falque M, Trotoux G, Eber F, Nègre S, Gilet M, Huteau V, Lodé M, Jousseaume T, Dechaumet S, Morice J, Poncet C, Coriton O, Martin OC, Rousseau-Gueutin M, Chèvre AM. Amplifying recombination genome-wide and reshaping crossover landscapes in Brassicas. PLoS Genet 2017; 13:e1006794. [PMID: 28493942 PMCID: PMC5444851 DOI: 10.1371/journal.pgen.1006794] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 05/25/2017] [Accepted: 05/02/2017] [Indexed: 11/19/2022] Open
Abstract
Meiotic recombination by crossovers (COs) is tightly regulated, limiting its key role in producing genetic diversity. However, while COs are usually restricted in number and not homogenously distributed along chromosomes, we show here how to disrupt these rules in Brassica species by using allotriploid hybrids (AAC, 2n = 3x = 29), resulting from the cross between the allotetraploid rapeseed (B. napus, AACC, 2n = 4x = 38) and one of its diploid progenitors (B. rapa, AA, 2n = 2x = 20). We produced mapping populations from different genotypes of both diploid AA and triploid AAC hybrids, used as female and/or as male. Each population revealed nearly 3,000 COs that we studied with SNP markers well distributed along the A genome (on average 1 SNP per 1.25 Mbp). Compared to the case of diploids, allotriploid hybrids showed 1.7 to 3.4 times more overall COs depending on the sex of meiosis and the genetic background. Most surprisingly, we found that such a rise was always associated with (i) dramatic changes in the shape of recombination landscapes and (ii) a strong decrease of CO interference. Hybrids carrying an additional C genome exhibited COs all along the A chromosomes, even in the vicinity of centromeres that are deprived of COs in diploids as well as in most studied species. Moreover, in male allotriploid hybrids we found that Class I COs are mostly responsible for the changes of CO rates, landscapes and interference. These results offer the opportunity for geneticists and plant breeders to dramatically enhance the generation of diversity in Brassica species by disrupting the linkage drag coming from limits on number and distribution of COs.
Collapse
Affiliation(s)
- Alexandre Pelé
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Matthieu Falque
- GQE-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif sur Yvette, France
| | - Gwenn Trotoux
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Frédérique Eber
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Sylvie Nègre
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Marie Gilet
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Virginie Huteau
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Maryse Lodé
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | | | - Sylvain Dechaumet
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Jérôme Morice
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | | | - Olivier Coriton
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Olivier C. Martin
- GQE-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif sur Yvette, France
| | | | - Anne-Marie Chèvre
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
- * E-mail:
| |
Collapse
|
23
|
Mwathi MW, Gupta M, Atri C, Banga SS, Batley J, Mason AS. Segregation for fertility and meiotic stability in novel Brassica allohexaploids. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:767-776. [PMID: 28097399 DOI: 10.1007/s00122-016-2850-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 12/27/2016] [Indexed: 05/15/2023]
Abstract
Allohexaploid Brassica populations reveal ongoing segregation for fertility, while genotype influences fertility and meiotic stability. Creation of a new Brassica allohexaploid species is of interest for the development of a crop type with increased heterosis and adaptability. At present, no naturally occurring, meiotically stable Brassica allohexaploid exists, with little data available on chromosome behaviour and meiotic control in allohexaploid germplasm. In this study, 100 plants from the cross B. carinata × B. rapa (A2 allohexaploid population) and 69 plants from the cross (B. napus × B. carinata) × B. juncea (H2 allohexaploid population) were assessed for fertility and meiotic behaviour. Estimated pollen viability, self-pollinated seed set, number of seeds on the main shoot, number of pods on the main shoot, seeds per ten pods and plant height were measured for both the A2 and H2 populations and for a set of reference control cultivars. The H2 population had high segregation for pollen viability and meiotic stability, while the A2 population was characterised by low pollen fertility and a high level of chromosome loss. Both populations were taller, but had lower average fertility trait values than the control cultivar samples. The study also characterises fertility and meiotic chromosome behaviour in genotypes and progeny sets in heterozygous allotetraploid Brassica derived lines, and indicates that genotypes of the parents and H1 hybrids are affecting chromosome pairing and fertility phenotypes in the H2 population. The identification and characterisation of factors influencing stability in novel allohexaploid Brassica populations will assist in the development of this as a new crop species for food and agricultural benefit.
Collapse
Affiliation(s)
- Margaret W Mwathi
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, 4072, Australia
- School of Plant Biology, The University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia
| | - Mehak Gupta
- Department of Plant Breeding and Genetics, DBT Centre of Excellence on Brassicas, Punjab Agricultural University, Ludhiana, 141001, India
| | - Chaya Atri
- Department of Plant Breeding and Genetics, DBT Centre of Excellence on Brassicas, Punjab Agricultural University, Ludhiana, 141001, India
| | - Surinder S Banga
- Department of Plant Breeding and Genetics, DBT Centre of Excellence on Brassicas, Punjab Agricultural University, Ludhiana, 141001, India
| | - Jacqueline Batley
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, 4072, Australia
- School of Plant Biology, The University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia
| | - Annaliese S Mason
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, 4072, Australia.
- Department of Plant Breeding, Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| |
Collapse
|
24
|
Pelé A, Trotoux G, Eber F, Lodé M, Gilet M, Deniot G, Falentin C, Nègre S, Morice J, Rousseau-Gueutin M, Chèvre AM. The poor lonesome A subgenome of Brassica napus var. Darmor (AACC) may not survive without its mate. THE NEW PHYTOLOGIST 2017; 213:1886-1897. [PMID: 27575298 DOI: 10.1111/nph.14147] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/12/2016] [Indexed: 06/06/2023]
Abstract
Constitutive genomes of allopolyploid species evolve throughout their life span. However, the consequences of long-term alterations on the interdependency between each original genome have not been established. Here, we attempted an approach corresponding to subgenome extraction from a previously sequenced natural allotetraploid, offering a unique opportunity to evaluate plant viability and structural evolution of one of its diploid components. We employed two different strategies to extract the diploid AA component of the Brassica napus variety 'Darmor' (AACC, 2n = 4x = 38) and we assessed the genomic structure of the latest AA plants obtained (after four to five rounds of selection), using a 60K single nucleotide polymorphism Illumina array. Only one strategy was successful and the diploid AA plants that were structurally characterized presented a lower proportion of the B. napus A subgenome extracted than expected. In addition, our analyses revealed that some genes lost in a polyploid context appeared to be compensated for plant survival, either by conservation of genomic regions from B. rapa, used in the initial cross, or by some introgressions from the B. napus C subgenome. We conclude that as little as c. 7500 yr of coevolution could lead to subgenome interdependency in the allotetraploid B. napus as a result of structural modifications.
Collapse
Affiliation(s)
- Alexandre Pelé
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | - Gwenn Trotoux
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | - Frédérique Eber
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | - Maryse Lodé
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | - Marie Gilet
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | - Gwenaelle Deniot
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | - Cyril Falentin
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | - Sylvie Nègre
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | - Jérôme Morice
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | | | - Anne-Marie Chèvre
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
| |
Collapse
|
25
|
The Impact of Open Pollination on the Structural Evolutionary Dynamics, Meiotic Behavior, and Fertility of Resynthesized Allotetraploid Brassica napus L. G3-GENES GENOMES GENETICS 2017; 7:705-717. [PMID: 28007837 PMCID: PMC5295613 DOI: 10.1534/g3.116.036517] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Allopolyploidy, which results from the merger and duplication of two divergent genomes, has played a major role in the evolution and diversification of flowering plants. The genomic changes that occur in resynthesized or natural neopolyploids have been extensively studied, but little is known about the effects of the reproductive mode in the initial generations that may precede its successful establishment. To truly reflect the early generations of a nascent polyploid, two resynthesized allotetraploid Brassica napus populations were obtained for the first time by open pollination. In these populations, we detected a much lower level of aneuploidy (third generation) compared with those previously published populations obtained by controlled successive selfing. We specifically studied 33 resynthesized B. napus individuals from our two open pollinated populations, and showed that meiosis was affected in both populations. Their genomes were deeply shuffled after allopolyploidization: up to 8.5 and 3.5% of the C and A subgenomes were deleted in only two generations. The identified deletions occurred mainly at the distal part of the chromosome, and to a significantly greater extent on the C rather than the A subgenome. Using Fluorescent In Situ Hybridization (BAC-FISH), we demonstrated that four of these deletions corresponded to fixed translocations (via homeologous exchanges). We were able to evaluate the size of the structural variations and their impact on the whole genome size, gene content, and allelic diversity. In addition, the evolution of fertility was assessed, to better understand the difficulty encountered by novel polyploid individuals before the putative formation of a novel stable species.
Collapse
|
26
|
Li H, Zhang L, Hu J, Zhang F, Chen B, Xu K, Gao G, Li H, Zhang T, Li Z, Wu X. Genome-Wide Association Mapping Reveals the Genetic Control Underlying Branch Angle in Rapeseed ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2017; 8:1054. [PMID: 28674549 PMCID: PMC5474488 DOI: 10.3389/fpls.2017.01054] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/31/2017] [Indexed: 05/20/2023]
Abstract
Plant architecture is vital not only for crop yield, but also for field management, such as mechanical harvesting. The branch angle is one of the key factors determining plant architecture. With the aim of revealing the genetic control underlying branch angle in rapeseed (Brassica napus L.), the positional variation of branch angles on individual plants was evaluated, and the branch angle increased with the elevation of branch position. Furthermore, three middle branches of individual plants were selected to measure the branch angle because they exhibited the most representative phenotypic values. An association panel with 472 diverse accessions was estimated for branch angle trait in six environments and genotyped with a 60K Brassica Infinium® SNP array. As a result of association mapping, 46 and 38 significantly-associated loci were detected using a mixed linear model (MLM) and a multi-locus random-SNP-effect mixed linear model (MRMLM), which explained up to 62.2 and 66.2% of the cumulative phenotypic variation, respectively. Numerous highly-promising candidate genes were identified by annotating against Arabidopsis thaliana homologous, including some first found in rapeseed, such as TAC1, SGR1, SGR3, and SGR5. These findings reveal the genetic control underlying branch angle and provide insight into genetic improvements that are possible in the plant architecture of rapeseed.
Collapse
Affiliation(s)
- Hongge Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of AgricultureWuhan, China
- National Key Lab of Crop Genetic Improvement, National Center of Crop molecular Breeding, National Center of Oil Crop Improvement, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Liping Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of AgricultureWuhan, China
| | - Jihong Hu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of AgricultureWuhan, China
| | - Fugui Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of AgricultureWuhan, China
| | - Biyun Chen
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of AgricultureWuhan, China
| | - Kun Xu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of AgricultureWuhan, China
| | - Guizhen Gao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of AgricultureWuhan, China
| | - Hao Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of AgricultureWuhan, China
| | - Tianyao Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of AgricultureWuhan, China
| | - Zaiyun Li
- National Key Lab of Crop Genetic Improvement, National Center of Crop molecular Breeding, National Center of Oil Crop Improvement, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
- *Correspondence: Zaiyun Li
| | - Xiaoming Wu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of AgricultureWuhan, China
- Xiaoming Wu
| |
Collapse
|
27
|
Gazave E, Tassone EE, Ilut DC, Wingerson M, Datema E, Witsenboer HMA, Davis JB, Grant D, Dyer JM, Jenks MA, Brown J, Gore MA. Population Genomic Analysis Reveals Differential Evolutionary Histories and Patterns of Diversity across Subgenomes and Subpopulations of Brassica napus L. FRONTIERS IN PLANT SCIENCE 2016; 7:525. [PMID: 27148342 PMCID: PMC4838616 DOI: 10.3389/fpls.2016.00525] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 04/04/2016] [Indexed: 05/08/2023]
Abstract
The allotetraploid species Brassica napus L. is a global crop of major economic importance, providing canola oil (seed) and vegetables for human consumption and fodder and meal for livestock feed. Characterizing the genetic diversity present in the extant germplasm pool of B. napus is fundamental to better conserve, manage and utilize the genetic resources of this species. We used sequence-based genotyping to identify and genotype 30,881 SNPs in a diversity panel of 782 B. napus accessions, representing samples of winter and spring growth habits originating from 33 countries across Europe, Asia, and America. We detected strong population structure broadly concordant with growth habit and geography, and identified three major genetic groups: spring (SP), winter Europe (WE), and winter Asia (WA). Subpopulation-specific polymorphism patterns suggest enriched genetic diversity within the WA group and a smaller effective breeding population for the SP group compared to WE. Interestingly, the two subgenomes of B. napus appear to have different geographic origins, with phylogenetic analysis placing WE and WA as basal clades for the other subpopulations in the C and A subgenomes, respectively. Finally, we identified 16 genomic regions where the patterns of diversity differed markedly from the genome-wide average, several of which are suggestive of genomic inversions. The results obtained in this study constitute a valuable resource for worldwide breeding efforts and the genetic dissection and prediction of complex B. napus traits.
Collapse
Affiliation(s)
- Elodie Gazave
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, IthacaNY, USA
| | - Erica E. Tassone
- Plant Physiology and Genetics Research Unit, U.S. Arid Land Agricultural Research Center, United States Department of Agriculture – Agricultural Research Service, MaricopaAZ, USA
| | - Daniel C. Ilut
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, IthacaNY, USA
| | - Megan Wingerson
- Department of Plant, Soil and Entomological Sciences, University of Idaho, MoscowID, USA
| | | | | | - James B. Davis
- Department of Plant, Soil and Entomological Sciences, University of Idaho, MoscowID, USA
| | - David Grant
- Corn Insects and Crop Genetics Research Unit, United States Department of Agriculture – Agricultural Research Service, AmesIA, USA
| | - John M. Dyer
- Plant Physiology and Genetics Research Unit, U.S. Arid Land Agricultural Research Center, United States Department of Agriculture – Agricultural Research Service, MaricopaAZ, USA
| | - Matthew A. Jenks
- Division of Plant and Soil Sciences, West Virginia University, MorgantownWV, USA
| | - Jack Brown
- Department of Plant, Soil and Entomological Sciences, University of Idaho, MoscowID, USA
| | - Michael A. Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, IthacaNY, USA
| |
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|