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Redjeki ES, Ho WK, Shah N, Molosiwa OO, Ardiarini NR, Kuswanto, Mayes S. Understanding the genetic relationships between Indonesian bambara groundnut landraces and investigating their origins. Genome 2020; 63:319-327. [PMID: 32097026 DOI: 10.1139/gen-2019-0137] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A total of 170 bambara groundnut (Vigna subterranea) accessions were evaluated using both simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers generated using genotyping-by-sequencing (GbS), of which 56 accessions were collected from West and East Java. Principal coordinate analysis (PCoA), population structure, and cluster analysis suggest that the East Java accessions could be a result of the introduction of selected West Java accessions. In addition, the current Indonesian accessions were likely introduced from Southern Africa, which would have produced a very marked founding effect such that these accessions present only a fraction of the genetic variability that exists within this species.
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Affiliation(s)
- E S Redjeki
- University of Muhammadiyah Gresik, Jl. Sumatera No. 101 GKB Gresik 61121, Jawa Timur, Indonesia
| | - W K Ho
- Crops For the Future, Jalan Broga, 43500 Semenyih, Selangor, Malaysia.,School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500 Semenyih, Selangor, Malaysia
| | - N Shah
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
| | - O O Molosiwa
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
| | - N R Ardiarini
- University of Brawijaya, Veteran Street, Malang, 65145, Indonesia
| | - Kuswanto
- University of Brawijaya, Veteran Street, Malang, 65145, Indonesia
| | - Sean Mayes
- Crops For the Future, Jalan Broga, 43500 Semenyih, Selangor, Malaysia.,Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
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Ellis D, Chavez O, Coombs J, Soto J, Gomez R, Douches D, Panta A, Silvestre R, Anglin NL. Genetic identity in genebanks: application of the SolCAP 12K SNP array in fingerprinting and diversity analysis in the global in trust potato collection. Genome 2018; 61:523-537. [PMID: 29792822 DOI: 10.1139/gen-2017-0201] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Breeders rely on genetic integrity of material from genebanks; however, admixture, mislabeling, and errors in original data can occur and be detrimental. Two hundred and fifty accessions, representing paired samples consisting of original mother plants and their in vitro counterparts from the cultivated potato collection at the International Potato Center (CIP) were fingerprinted using the Infinium 12K V2 Potato Array to confirm genetic identity of the accessions and evaluate genetic diversity of the potato collection. Diploid, triploid, and tetraploid accessions were included, representing seven cultivated potato taxa (based on Hawkes, 1990). Fingerprints between voucher mother plants maintained in the field and in vitro clones of the same accession were used to evaluate identity, relatedness, and ancestry using hierarchal clustering and model-based Bayesian admixture analyses. Generally, in vitro and field clones of the same accession grouped together; however, 11 (4.4%) accessions were mismatches genetically, and in some cases the SNP data revealed the identity of the mixed accession. SNP genotypes were used to assess genetic diversity and to evaluate inter- and intraspecific relationships along with determining population structure and hybrid origins. Phylogenetic analyses suggest that the triploids included in this study are genetically similar. Further, some genetic redundancies among individual accessions were also identified along with some putative misclassified accessions. Accessions generally clustered together based on taxonomic classification and ploidy level with some deviations. STRUCTURE analysis identified six populations with significant gene flow among the populations, as well as revealed hybrid taxa and accessions. Overall, the Infinium 12K V2 Potato Array proved useful in confirming identity and highlighting the diversity in this subset of the CIP collection, providing new insights into the accessions evaluated. This study provides a model for genetic identity of plant genetic resources collections as mistakes in conservation of these collections and in genebanks is a reality. For breeders and other users of these collections, confirmed identity is critical, as well as for quality management programs and to provide insights into the accessions evaluated.
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Affiliation(s)
- David Ellis
- a International Potato Center (CIP), Apartado 1558, Lima 12, Peru
| | - Oswaldo Chavez
- a International Potato Center (CIP), Apartado 1558, Lima 12, Peru
| | - Joseph Coombs
- b Michigan State University, Department of Plant, Soil and Microbial Sciences, 1066 Bogue St., Room 486, East Lansing, MI 48824, USA
| | - Julian Soto
- a International Potato Center (CIP), Apartado 1558, Lima 12, Peru
| | - Rene Gomez
- a International Potato Center (CIP), Apartado 1558, Lima 12, Peru
| | - David Douches
- b Michigan State University, Department of Plant, Soil and Microbial Sciences, 1066 Bogue St., Room 486, East Lansing, MI 48824, USA
| | - Ana Panta
- a International Potato Center (CIP), Apartado 1558, Lima 12, Peru
| | - Rocio Silvestre
- a International Potato Center (CIP), Apartado 1558, Lima 12, Peru
| | - Noelle L Anglin
- a International Potato Center (CIP), Apartado 1558, Lima 12, Peru
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Wang ML, Dzievit M, Chen Z, Morris JB, Norris JE, Barkley NA, Tonnis B, Pederson GA, Yu J. Genetic diversity and population structure of castor (Ricinus communis L.) germplasm within the US collection assessed with EST-SSR markers. Genome 2017; 60:193-200. [PMID: 28094539 DOI: 10.1139/gen-2016-0116] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Castor is an important oilseed crop and although its oil is inedible, it has multiple industrial and pharmaceutical applications. The entire US castor germplasm collection was previously screened for oil content and fatty acid composition, but its genetic diversity and population structure has not been determined. Based on the screening results of oil content, fatty acid composition, and country origins, 574 accessions were selected and genotyped with 22 polymorphic EST-SSR markers. The results from cluster analysis, population structure, and principal component analysis were consistent, and partitioned accessions into four subpopulations. Although there were certain levels of admixtures among groups, these clusters and subpopulations aligned with geographic origins. Both divergent and redundant accessions were identified in this study. The US castor germplasm collection encompasses a moderately high level of genetic diversity (pairwise dissimilarity coefficient = 0.53). The results obtained here will be useful for choosing accessions as parents to make crosses in breeding programs and prioritizing accessions for regeneration to improve germplasm management. A subset of 230 accessions was selected and will be planted in the field for establishing a core collection of the US castor germplasm. Further evaluation of the US castor germplasm collection is also discussed.
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Affiliation(s)
- M L Wang
- a USDA-ARS, Plant Genetic Resources Conservation Unit, 1109 Experiment Street, Griffin, GA 30223, USA
| | - M Dzievit
- b Department of Agronomy, Iowa State University, 2014 Agronomy Hall, Ames, IA 50011, USA
| | - Z Chen
- c Department of Crop and Soil Sciences, University of Georgia, 1109 Experiment Street, Griffin, GA 30223, USA
| | - J B Morris
- a USDA-ARS, Plant Genetic Resources Conservation Unit, 1109 Experiment Street, Griffin, GA 30223, USA
| | - J E Norris
- d Emory University Hospital, Emory University, 1364 Clifton Road, Atlanta, GA 30322, USA
| | - N A Barkley
- a USDA-ARS, Plant Genetic Resources Conservation Unit, 1109 Experiment Street, Griffin, GA 30223, USA
| | - B Tonnis
- a USDA-ARS, Plant Genetic Resources Conservation Unit, 1109 Experiment Street, Griffin, GA 30223, USA
| | - G A Pederson
- a USDA-ARS, Plant Genetic Resources Conservation Unit, 1109 Experiment Street, Griffin, GA 30223, USA
| | - J Yu
- b Department of Agronomy, Iowa State University, 2014 Agronomy Hall, Ames, IA 50011, USA
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