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Li C, Fu L, Wang Q, Liu H, Chen G, Qi F, Zhang M, Jia Y, Li X, Huang B, Dong W, Du P, Zhang X. Development and application of whole-chromosome painting of chromosomes 7A and 8A of Arachis duranensis based on chromosome-specific single-copy oligonucleotides. Genome 2024; 67:178-188. [PMID: 38394647 DOI: 10.1139/gen-2023-0116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
For peanut, the lack of stable cytological markers is a barrier to tracking specific chromosomes, elucidating the genetic relationships between genomes and identifying chromosomal variations. Chromosome mapping using single-copy oligonucleotide (oligo) probe libraries has unique advantages for identifying homologous chromosomes and chromosomal rearrangements. In this study, we developed two whole-chromosome single-copy oligo probe libraries, LS-7A and LS-8A, based on the reference genome sequences of chromosomes 7A and 8A of Arachis duranensis. Fluorescence in situ hybridization (FISH) analysis confirmed that the libraries could specifically paint chromosomes 7 and 8. In addition, sequential FISH and electronic localization of LS-7A and LS-8A in A. duranensis (AA) and A. ipaensis (BB) showed that chromosomes 7A and 8A contained translocations and inversions relative to chromosomes 7B and 8B. Analysis of the chromosomes of wild Arachis species using LS-8A confirmed that this library could accurately and effectively identify A genome species. Finally, LS-7A and LS-8A were used to paint the chromosomes of interspecific hybrids and their progenies, which verified the authenticity of the interspecific hybrids and identified a disomic addition line. This study provides a model for developing specific oligo probes to identify the structural variations of other chromosomes in Arachis and demonstrates the practical utility of LS-7A and LS-8A.
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Affiliation(s)
- Chenyu Li
- College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Liuyang Fu
- College of Life Science, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Qian Wang
- College of Life Science, Zhengzhou University, Zhengzhou, Henan 450001, China
- The Shennong Laboratory/Nation Industrial Innovation Centre for Bio-Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement/Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Hua Liu
- The Shennong Laboratory/Nation Industrial Innovation Centre for Bio-Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement/Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Guoquan Chen
- College of Life Science, Zhengzhou University, Zhengzhou, Henan 450001, China
- The Shennong Laboratory/Nation Industrial Innovation Centre for Bio-Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement/Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Feiyan Qi
- The Shennong Laboratory/Nation Industrial Innovation Centre for Bio-Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement/Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Maoning Zhang
- College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yaoguang Jia
- College of Life Science, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Xiaona Li
- College of Life Science, Zhengzhou University, Zhengzhou, Henan 450001, China
- The Shennong Laboratory/Nation Industrial Innovation Centre for Bio-Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement/Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Bingyan Huang
- The Shennong Laboratory/Nation Industrial Innovation Centre for Bio-Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement/Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Wenzhao Dong
- The Shennong Laboratory/Nation Industrial Innovation Centre for Bio-Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement/Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Pei Du
- The Shennong Laboratory/Nation Industrial Innovation Centre for Bio-Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement/Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Xinyou Zhang
- College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- The Shennong Laboratory/Nation Industrial Innovation Centre for Bio-Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement/Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
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Leal-Bertioli SCM, de Blas FJ, Carolina Chavarro M, Simpson CE, Valls JFM, Tallury SP, Moretzsohn MC, Custodio AR, Thomas Stalker H, Seijo G, Bertioli DJ. Relationships of the wild peanut species, section Arachis: A resource for botanical classification, crop improvement, and germplasm management. AMERICAN JOURNAL OF BOTANY 2024; 111:e16357. [PMID: 38898619 DOI: 10.1002/ajb2.16357] [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: 03/08/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 06/21/2024]
Abstract
PREMISE Wild species are strategic sources of valuable traits to be introduced into crops through hybridization. For peanut, the 33 currently described wild species in the section Arachis are particularly important because of their sexual compatibility with the domesticated species, Arachis hypogaea. Although numerous wild accessions are carefully preserved in seed banks, their morphological similarities pose challenges to routine classification. METHODS Using a high-density array, we genotyped 272 accessions encompassing all diploid species in section Arachis. Detailed relationships between accessions and species were revealed through phylogenetic analyses and interpreted using the expertise of germplasm collectors and curators. RESULTS Two main groups were identified: one with A genome species and the other with B, D, F, G, and K genomes. Species groupings generally showed clear boundaries. Structure within groups was informative, for instance, revealing the history of the proto-domesticate A. stenosperma. However, some groupings suggested multiple sibling species. Others were polyphyletic, indicating the need for taxonomic revision. Annual species were better defined than perennial ones, revealing limitations in applying classical and phylogenetic species concepts to the genus. We suggest new species assignments for several accessions. CONCLUSIONS Curated by germplasm collectors and curators, this analysis of species relationships lays the foundation for future species descriptions, classification of unknown accessions, and germplasm use for peanut improvement. It supports the conservation and curation of current germplasm, both critical tasks considering the threats to the genus posed by habitat loss and the current restrictions on new collections and germplasm transfer.
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Affiliation(s)
- Soraya C M Leal-Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, 30602, GA, USA
- Department of Plant Pathology, University of Georgia, Athens, 30602, GA, USA
| | - Francisco J de Blas
- Center for Applied Genetic Technologies, University of Georgia, Athens, 30602, GA, USA
- Botanical Institute of the Northeast (IBONE), CC 209, Corrientes, W3402, Argentina
| | - M Carolina Chavarro
- Center for Applied Genetic Technologies, University of Georgia, Athens, 30602, GA, USA
| | - Charles E Simpson
- Texas AgriLife Research, Texas A&M University, Stephenville, 76401, TX, USA
| | - José F M Valls
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, Brasília, DF 70.770-917, Brazil
| | - Shyam P Tallury
- USDA-Agricultural Research Service, Plant Genetic Resources Conservation Unit, Griffin, 30223, GA, USA
| | - Márcio C Moretzsohn
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, Brasília, DF 70.770-917, Brazil
| | - Adriana R Custodio
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, Brasília, DF 70.770-917, Brazil
| | - H Thomas Stalker
- Department of Crop and Soil Sciences North Carolina State University, Raleigh, 27695, NC, USA
| | - Guillermo Seijo
- Botanical Institute of the Northeast (IBONE), CC 209, Corrientes, W3402, Argentina
- Faculty of Exact and Natural Sciences, National University of Northeast, Libertad 5470, Corrientes, W3402, Argentina
| | - David J Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, 30602, GA, USA
- Department of Crop and Soil Science, University of Georgia, Athens, 30602, GA, USA
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Ortiz AM, Chalup L, Silvestri MC, Seijo G, Lavia GI. Genomic relationships of the polyploid rhizoma peanut (Arachis glabrata Benth.) inferred by genomic in situ hybridization (GISH). AN ACAD BRAS CIENC 2023; 95:e20210162. [PMID: 37075375 DOI: 10.1590/0001-3765202320210162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/11/2021] [Indexed: 04/21/2023] Open
Abstract
The rhizoma peanut (Arachis glabrata Benth., section Rhizomatosae) is a tetraploid perennial legume. Although several A. glabrata cultivars have been developed as forage and ornamental turf, the origin and genomic constitution of this species are still unknown. In this study, we evaluated the affinity between the genomes of A. glabrata and the probable diploid donors of the sections Rhizomatosae, Arachis, Erectoides and Procumbentes by genomic in situ hybridization (GISH). Single GISH analyses detected that species of the sections Erectoides (E2 subgenome) and Procumbentes (E3 subgenome) were the diploid species with the highest degree of genomic affinity with A. glabrata. Based on single GISH experiments and DNA sequence similarity, three species -A. duranensis, A. paraguariensis subsp. capibarensis, and A. rigonii-, which showed the most uniform and brightest hybridization patterns and lowest genetic distance, were selected as probes for double GISH experiments. Double GISH experiments showed that A. glabrata is constituted by four identical or very similar chromosome complements. In these assays, A. paraguariensis subsp. capibarensis showed the highest brightness onto A. glabrata chromosomes. Thus, our results support the autopolyploid origin of A. glabrata and show that the species with E2 subgenome are the most probable ancestors of this polyploid legume forage.
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Affiliation(s)
- Alejandra Marcela Ortiz
- CONICET-UNNE, Fac. Cs. Agrarias, Instituto de Botánica del Nordeste, Sargento Cabral 2131, C.C. 209, 3400 Corrientes, Argentina
| | - Laura Chalup
- CONICET-UNNE, Fac. Cs. Agrarias, Instituto de Botánica del Nordeste, Sargento Cabral 2131, C.C. 209, 3400 Corrientes, Argentina
- Universidad Nacional del Chaco Austral, UNCAUS, Comandante Fernandez 755, 3700, Pcia. Roque Sáenz Peña, Chaco, Argentina
| | - María Celeste Silvestri
- CONICET-UNNE, Fac. Cs. Agrarias, Instituto de Botánica del Nordeste, Sargento Cabral 2131, C.C. 209, 3400 Corrientes, Argentina
| | - Guillermo Seijo
- CONICET-UNNE, Fac. Cs. Agrarias, Instituto de Botánica del Nordeste, Sargento Cabral 2131, C.C. 209, 3400 Corrientes, Argentina
- Universidad Nacional del Nordeste (UNNE), Facultad de Ciencias Exactas y Naturales y Agrimensura, Av. Libertad 5460, 3400, Corrientes, Argentina
| | - Graciela Inés Lavia
- CONICET-UNNE, Fac. Cs. Agrarias, Instituto de Botánica del Nordeste, Sargento Cabral 2131, C.C. 209, 3400 Corrientes, Argentina
- Universidad Nacional del Nordeste (UNNE), Facultad de Ciencias Exactas y Naturales y Agrimensura, Av. Libertad 5460, 3400, Corrientes, Argentina
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