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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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Zhao C, He L, Xia H, Zhou X, Geng Y, Hou L, Li P, Li G, Zhao S, Ma C, Tang R, Pandey MK, Varshney RK, Wang X. De novo full length transcriptome analysis of Arachis glabrata provides insights into gene expression dynamics in response to biotic and abiotic stresses. Genomics 2021; 113:1579-1588. [PMID: 33819563 DOI: 10.1016/j.ygeno.2021.03.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 03/21/2021] [Accepted: 03/29/2021] [Indexed: 11/26/2022]
Abstract
The perennial ornamental peanut Arachis glabrata represents one of the most adaptable wild Arachis species. This study used PacBio combined with BGISEQ-500 RNA-seq technology to study the transcriptome and gene expression dynamics of A. glabrata. Of the total 109,747 unique transcripts obtained, >90,566 transcripts showed significant homology to known proteins and contained the complete coding sequence (CDS). RNA-seq revealed that 1229, 1039, 1671, 3923, 1521 and 1799 transcripts expressed specifically in the root, stem, leaf, flower, peg and pod, respectively. We also identified thousands of differentially expressed transcripts in response to drought, salt, cold and leaf spot disease. Furthermore, we identified 30 polyphenol oxidase encoding genes associated with the quality of forage, making A. glabrata suitable as a forage crop. Our findings presented the first transcriptome study of A. glabrata which will facilitate genetic and genomics studies and lays the groundwork for a deeper understanding of the A. glabrata genome.
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Affiliation(s)
- Chuanzhi Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, People's Republic of China; College of Life Sciences, Shandong Normal University, Jinan 250014, People's Republic of China.
| | - Liangqiong He
- Cash Crop Research Institute, Guangxi Academy of Agricultural Sciences, 530007 Nanning, People's Republic of China
| | - Han Xia
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, People's Republic of China; College of Life Sciences, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Ximeng Zhou
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, People's Republic of China; College of Life Sciences, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Yun Geng
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, People's Republic of China
| | - Lei Hou
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, People's Republic of China
| | - Pengcheng Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, People's Republic of China; College of Life Sciences, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Guanghui Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, People's Republic of China
| | - Shuzhen Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, People's Republic of China
| | - Changle Ma
- College of Life Sciences, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Ronghua Tang
- Cash Crop Research Institute, Guangxi Academy of Agricultural Sciences, 530007 Nanning, People's Republic of China
| | - Manish K Pandey
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Xingjun Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, People's Republic of China; College of Life Sciences, Shandong Normal University, Jinan 250014, People's Republic of China.
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4
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Ortiz AM, Robledo G, Seijo G, Valls JFM, Lavia GI. Cytogenetic evidences on the evolutionary relationships between the tetraploids of the section Rhizomatosae and related diploid species (Arachis, Leguminosae). JOURNAL OF PLANT RESEARCH 2017; 130:791-807. [PMID: 28536982 DOI: 10.1007/s10265-017-0949-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 03/22/2017] [Indexed: 05/17/2023]
Abstract
Rhizomatosae is a taxonomic section of the South American genus Arachis, whose diagnostic character is the presence of rhizomes in all its species. This section is of particular evolutionary interest because it has three polyploid (A. pseudovillosa, A. nitida and A. glabrata, 2n = 4x = 40) and only one diploid (A. burkartii, 2n = 2x = 20) species. The phylogenetic relationships of these species as well as the polyploidy nature and the origin of the tetraploids are still controversial. The present study provides an exhaustive analysis of the karyotypes of all rhizomatous species and six closely related diploid species of the sections Erectoides and Procumbentes by cytogenetic mapping of DAPI/CMA heterochromatin bands and 5S and 18-26S rDNA loci. Chromosome banding showed variation in the DAPI heterochromatin distribution pattern, which, together with the number and distribution of rDNA loci, allowed the characterization of all species studied here. The bulk of chromosomal markers suggest that the three rhizomatous tetraploid species constitute a natural group and may have at least one common diploid ancestor. The cytogenetic data of the diploid species analyzed evidenced that the only rhizomatous diploid species-A. burkartii-has a karyotype pattern different from those of the rhizomatous tetraploids, showing that it is not likely the genome donor of the tetraploids and the non-monophyletic nature of the section Rhizomatosae. Thus, the tetraploid species should be excluded from the R genome, which should remain exclusively for A. burkartii. Instead, the karyotype features of these tetraploids are compatible with those of different species of the sections Erectoides and Procumbentes (E genome species), suggesting the hypothesis of multiple origins of these tetraploids. In addition, the polyploid nature and the group of diploid species closer to the tetraploids are discussed.
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Affiliation(s)
- Alejandra Marcela Ortiz
- Instituto de Botánica del Nordeste (CONICET-UNNE), CC 209, Sargento Juan Bautista Cabral 2131, 3402BKG, Corrientes, Argentina.
- Facultad de Ciencias Exactas y Naturales y Agrimensura (UNNE), Av. Libertad 5000, 3402BKG, Corrientes, Argentina.
| | - Germán Robledo
- Instituto de Botánica del Nordeste (CONICET-UNNE), CC 209, Sargento Juan Bautista Cabral 2131, 3402BKG, Corrientes, Argentina
- Facultad de Ciencias Exactas y Naturales y Agrimensura (UNNE), Av. Libertad 5000, 3402BKG, Corrientes, Argentina
| | - Guillermo Seijo
- Instituto de Botánica del Nordeste (CONICET-UNNE), CC 209, Sargento Juan Bautista Cabral 2131, 3402BKG, Corrientes, Argentina
- Facultad de Ciencias Exactas y Naturales y Agrimensura (UNNE), Av. Libertad 5000, 3402BKG, Corrientes, Argentina
| | | | - Graciela Inés Lavia
- Instituto de Botánica del Nordeste (CONICET-UNNE), CC 209, Sargento Juan Bautista Cabral 2131, 3402BKG, Corrientes, Argentina
- Facultad de Ciencias Exactas y Naturales y Agrimensura (UNNE), Av. Libertad 5000, 3402BKG, Corrientes, Argentina
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Vishwakarma MK, Kale SM, Sriswathi M, Naresh T, Shasidhar Y, Garg V, Pandey MK, Varshney RK. Genome-Wide Discovery and Deployment of Insertions and Deletions Markers Provided Greater Insights on Species, Genomes, and Sections Relationships in the Genus Arachis. FRONTIERS IN PLANT SCIENCE 2017; 8:2064. [PMID: 29312366 PMCID: PMC5742254 DOI: 10.3389/fpls.2017.02064] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 11/17/2017] [Indexed: 05/04/2023]
Abstract
Small insertions and deletions (InDels) are the second most prevalent and the most abundant structural variations in plant genomes. In order to deploy these genetic variations for genetic analysis in genus Arachis, we conducted comparative analysis of the draft genome assemblies of both the diploid progenitor species of cultivated tetraploid groundnut (Arachis hypogaea L.) i.e., Arachis duranensis (A subgenome) and Arachis ipaënsis (B subgenome) and identified 515,223 InDels. These InDels include 269,973 insertions identified in A. ipaënsis against A. duranensis while 245,250 deletions in A. duranensis against A. ipaënsis. The majority of the InDels were of single bp (43.7%) and 2-10 bp (39.9%) while the remaining were >10 bp (16.4%). Phylogenetic analysis using genotyping data for 86 (40.19%) polymorphic markers grouped 96 diverse Arachis accessions into eight clusters mostly by the affinity of their genome. This study also provided evidence for the existence of "K" genome, although distinct from both the "A" and "B" genomes, but more similar to "B" genome. The complete homology between A. monticola and A. hypogaea tetraploid taxa showed a very similar genome composition. The above analysis has provided greater insights into the phylogenetic relationship among accessions, genomes, sub species and sections. These InDel markers are very useful resource for groundnut research community for genetic analysis and breeding applications.
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Affiliation(s)
| | - Sandip M. Kale
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Manda Sriswathi
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Talari Naresh
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Yaduru Shasidhar
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Vanika Garg
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Manish K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
- *Correspondence: Manish K. Pandey
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
- The University of Western Australia, Crawley, WA, Australia
- Rajeev K. Varshney
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6
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Seijo G, Samoluk SS, Ortiz AM, Silvestri MC, Chalup L, Robledo G, Lavia GI. Cytological Features of Peanut Genome. COMPENDIUM OF PLANT GENOMES 2017. [DOI: 10.1007/978-3-319-63935-2_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Huang L, Jiang H, Ren X, Chen Y, Xiao Y, Zhao X, Tang M, Huang J, Upadhyaya HD, Liao B. Abundant microsatellite diversity and oil content in wild Arachis species. PLoS One 2012; 7:e50002. [PMID: 23185514 PMCID: PMC3502184 DOI: 10.1371/journal.pone.0050002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Accepted: 10/15/2012] [Indexed: 01/05/2023] Open
Abstract
The peanut (Arachis hypogaea) is an important oil crop. Breeding for high oil content is becoming increasingly important. Wild Arachis species have been reported to harbor genes for many valuable traits that may enable the improvement of cultivated Arachis hypogaea, such as resistance to pests and disease. However, only limited information is available on variation in oil content. In the present study, a collection of 72 wild Arachis accessions representing 19 species and 3 cultivated peanut accessions were genotyped using 136 genome-wide SSR markers and phenotyped for oil content over three growing seasons. The wild Arachis accessions showed abundant diversity across the 19 species. A. duranensis exhibited the highest diversity, with a Shannon-Weaver diversity index of 0.35. A total of 129 unique alleles were detected in the species studied. A. rigonii exhibited the largest number of unique alleles (75), indicating that this species is highly differentiated. AMOVA and genetic distance analyses confirmed the genetic differentiation between the wild Arachis species. The majority of SSR alleles were detected exclusively in the wild species and not in A. hypogaea, indicating that directional selection or the hitchhiking effect has played an important role in the domestication of the cultivated peanut. The 75 accessions were grouped into three clusters based on population structure and phylogenic analysis, consistent with their taxonomic sections, species and genome types. A. villosa and A. batizocoi were grouped with A. hypogaea, suggesting the close relationship between these two diploid wild species and the cultivated peanut. Considerable phenotypic variation in oil content was observed among different sections and species. Nine alleles were identified as associated with oil content based on association analysis, of these, three alleles were associated with higher oil content but were absent in the cultivated peanut. The results demonstrated that there is great potential to increase the oil content in A. hypogaea by using the wild Arachis germplasm.
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Affiliation(s)
- Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaoping Ren
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Xinyan Zhao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Mei Tang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jiaquan Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Hari D. Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Andhra Pradesh, India
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
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Bechara MD, Moretzsohn MC, Palmieri DA, Monteiro JP, Bacci M, Martins J, Valls JFM, Lopes CR, Gimenes MA. Phylogenetic relationships in genus Arachis based on ITS and 5.8S rDNA sequences. BMC PLANT BIOLOGY 2010; 10:255. [PMID: 21092103 PMCID: PMC3095334 DOI: 10.1186/1471-2229-10-255] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Accepted: 11/19/2010] [Indexed: 05/20/2023]
Abstract
BACKGROUND The genus Arachis comprises 80 species and it is subdivided into nine taxonomic sections (Arachis, Caulorrhizae, Erectoides, Extranervosae, Heteranthae, Procumbentes, Rhizomatosae, Trierectoides, and Triseminatae). This genus is naturally confined to South America and most of its species are native to Brazil. In order to provide a better understanding of the evolution of the genus, we reconstructed the phylogeny of 45 species using the variation observed on nucleotide sequences in internal transcribed spacer regions (ITS1 and ITS2) and 5.8 S of nuclear ribosomal DNA. RESULTS Intraspecific variation was detected, but in general it was not enough to place accessions of the same species in different clades. Our data support the view that Arachis is a monophyletic group and suggested Heteranthae as the most primitive section of genus Arachis. The results confirmed the circumscriptions of some sections (Caulorrhizae, Extranervosae), but raised questions about others. Sections Erectoides, Trierectoides and Procumbentes were not well defined, while sections Arachis and Rhizomatosae seem to include species that could be moved to different sections. The division of section Arachis into A and B genome species was also observed in the phylogenetic tree and these two groups of species may not have a monophyletic origin. The 2n = 2x = 18 species of section Arachis (A. praecox, A. palustris and A. decora) were all placed in the same clade, indicating they are closely related to each other, and their genomes are more related to B genome than to the A genome. Data also allowed insights on the origin of tetraploid A. glabrata, suggesting rhizome appeared twice within the genus and raising questions about the placement of that species in section Rhizomatosae. CONCLUSION The main clades established in this study in general agreed with many other studies that have used other types of evidences and sets of species, being some of them included in our study and some not. Thus, the relationships established can be a useful framework for future systematic reviews of genus Arachis and for the selection of species to pre-breeding programs.
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Affiliation(s)
| | - Márcio C Moretzsohn
- Embrapa Recursos Genéticos e Biotecnologia, C.P. 02372, 70770-917, Brasília, DF, Brazil
| | - Darío A Palmieri
- Departamento de Ciências Biológicas, Faculdade de Ciências e Letras, UNESP - Universidade Estadual Paulista, 19806-900, Assis, SP, Brazil
| | - Jomar P Monteiro
- Departamento de Genética, Instituto de Biociências, UNESP - Universidade Estadual Paulista, 18618-000, Botucatu, SP, Brazil
| | - Maurício Bacci
- Departamento de Bioquímica e Microbiologia, Instituto de Biociências, UNESP - Universidade Estadual Paulista, 13506-900, Rio Claro, SP, Brazil
| | - Joaquim Martins
- Centro de Estudos de Insetos Sociais, Instituto de Biociências, UNESP - Universidade Estadual Paulista, 13506-900, Rio Claro, SP, Brasil
| | - José FM Valls
- Embrapa Recursos Genéticos e Biotecnologia, C.P. 02372, 70770-917, Brasília, DF, Brazil
| | - Catalina R Lopes
- Departamento de Genética, Instituto de Biociências, UNESP - Universidade Estadual Paulista, 18618-000, Botucatu, SP, Brazil
| | - Marcos A Gimenes
- Embrapa Recursos Genéticos e Biotecnologia, C.P. 02372, 70770-917, Brasília, DF, Brazil
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Palmieri DA, Bechara MD, Curi RA, Monteiro JP, Valente SES, Gimenes MA, Lopes CR. Genetic diversity analysis in the section Caulorrhizae (genus Arachis) using microsatellite markers. Genet Mol Biol 2010; 33:109-18. [PMID: 21637613 PMCID: PMC3036074 DOI: 10.1590/s1415-47572010005000001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Accepted: 10/07/2009] [Indexed: 11/25/2022] Open
Abstract
Diversity in 26 microsatellite loci from section Caulorrhizae germplasm was evaluated by using 33 accessions of A. pintoi Krapov. & W.C. Gregory and ten accessions of Arachis repens Handro. Twenty loci proved to be polymorphic and a total of 196 alleles were detected with an average of 9.8 alleles per locus. The variability found in those loci was greater than the variability found using morphological characters, seed storage proteins and RAPD markers previously used in this germplasm. The high potential of these markers to detect species-specific alleles and discriminate among accessions was demonstrated. The set of microsatellite primer pairs developed by our group for A. pintoi are useful molecular tools for evaluating Section Caulorrhizae germplasm, as well as that of species belonging to other Arachis sections.
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Affiliation(s)
- Darío A Palmieri
- Departamento de Ciências Biológicas, Faculdade de Ciências e Letras de Assis, Universidade Estadual Paulista, UNESP, Assis, SP Brazil
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