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Redundancy and distinctness in flax germplasm as revealed by RAPD dissimilarity

Published online by Cambridge University Press:  12 February 2007

Yong-Bi Fu*
Affiliation:
Plant Gene Resources of Canada, Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
*
*Corresponding author: E-mail: fuy@agr.gc.ca

Abstract

Molecular characterization of ex situ plant germplasm, although more attainable than before, has rarely been applied to a whole germplasm collection of 2000 accessions or larger. The benefits of screening large numbers of accessions have not been well recognized for germplasm management and utilization. Challenges also exist in identifying duplicated and genetically related accessions and in validating developed core subsets. Here we show how a new approach using an average marker-based dissimilarity of an accession in a collection can be applied to identify both redundancy and distinctness in a plant germplasm collection. Application of this dissimilarity measure to 2727 flax accessions genotyped by 149 randomly amplified polymorphic DNA (RAPD) markers revealed that up to 22% of accessions could be deemed to be redundant. Up to 500 of the most distinct flax accessions were identified and these can be directly screened for traits of interest to broaden the genetic base in a flax improvement programme. These results demonstrate that molecular screening of a large number of accessions with an informative diversity analysis can facilitate the management and utilization of ex situ plant germplasm.

Type
Research Article
Copyright
Copyright © NIAB 2006

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References

Brown, AHD and Spillane, C (1999) Implementing core collections—principles, procedures, progress, problems and promise. In: Johnson, RC, Hodgkin, T (eds) Collections for Today and Tomorrow. Rome: International Plant Genetic Resources Institute, pp. 19.Google Scholar
Dean, RE, Dahlberg, JA, Hophins, MS, Mitchell, SE and Kresovich, S (1999) Genetic redundancy and diversity among ‘Orange’ accessions in the U.S. national sorghum collection as assessed with simple sequence repeat (SSR) markers. Crop Science 39, 12151221.CrossRefGoogle Scholar
Diederichsen, A, Raney, JP, Fu, YBKW (2002) Diversity in the flax collection at Plant Gene Resources of Canada. Proceedings of the Flax Institute USA 59, 138143.Google Scholar
Engels, JMM and Visser, L (2003) A Guide to Effective Management of Germplasm Collections. IPGRI Handbooks for Genebanks No. 6RomeIPGRI.Google Scholar
Excoffier, L, Smouse, PE and Quattro, JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131, 479491.CrossRefGoogle ScholarPubMed
Fu, YB (2003) Applications of bulking in molecular characterization of plant germplasm: a critical review. Plant Genetic Resources 1, 161167.CrossRefGoogle Scholar
Fu, YB (2005) Geographic patterns of RAPD variation in cultivated flax. Crop Science 45, 10841091.CrossRefGoogle Scholar
Fu, YB, Diederichsen, A, Richards, KW and Peterson, G (2002) Genetic diversity within a range of cultivars and landraces of flax ( Linus usitatissimum L.) as revealed by RAPDs. Genetic Resources and Crop Evolution 49, 167174.CrossRefGoogle Scholar
Fu, YB, Guerin, S, Peterson, GW, Carlson, JE and Richards, KW (2003 a) Assessment of bulking strategies for RAPD analyses of flax germplasm. Genetic Resources and Crop Evolution 50, 743746.CrossRefGoogle Scholar
Fu, YB, Rowland, GG, Duguid, SD and Richards, KW (2003 b) RAPD analysis of 54 North American flax cultivars. Crop Science 43, 15101515.CrossRefGoogle Scholar
Fu, YB, Peterson, GW, Williams, D, Richards, KW, Mitchell Fetch, J (2005) Patterns of AFLP variation in a core subset of cultivated hexaploid oat germplasm. Theoretical and Applied Genetics 111, 530539.CrossRefGoogle Scholar
Hintum, ThJL, van Knüpffer, H (1995) Duplication within and between germplasm collections. I. Identifying duplication and the basis of passport data. Genetic Resources and Crop Evolution 42, 127133.CrossRefGoogle Scholar
Hintum, ThJL, van Visser, DL (1995) Duplication within and between germplasm collections. II. Duplication in four European barley collections. Genetic Resources and Crop Evolution 42, 135145.CrossRefGoogle Scholar
Hodgkin, T and Rao, VR (2002) People, plants and DNA: perspectives on the scientific and technical aspects of conserving and using plant genetic resources. In: Engels, JMM, Rao, VR, Brown, AHD, Jackson, MT (eds) Managing Plant Genetic Diversity, Rome: International Plant Genetic Resources Institute, pp. 469480.Google Scholar
Karp, A (2002) The new genetic era: will it help us in managing genetic diversity? In: Engels, JMM, Rao, VR, Brown, AHD, Jackson, MT (eds) Managing Plant Genetic Diversity. Rome: International Plant Genetic Resources Institute, pp. 4356.Google Scholar
Liu, F, Sun, GL, Salomon, B, Bothmer von, R (2001) Distribution of allozymic alleles and genetic diversity in the American barley core collection. Theoretical and Applied Genetics 102, 606615.CrossRefGoogle Scholar
Lund, B, Ortiz, R, Skovgaard, IM, Waugh, R and Andersen, SB (2003) Analysis of potential duplicates in barley gene bank collections using re-sampling of microsatellite data. Theoretical and Applied Genetics 106, 11291138.CrossRefGoogle ScholarPubMed
McGregor, CE, van Treuren, R, Hoekstra, R, van Hintum, ThJL (2002) Analysis of the wild potato germplasm of the series of Acaulia with AFLPs: implications for ex situ conservation. Theoretical and Applied Genetics 104, 146156.CrossRefGoogle ScholarPubMed
Nybom, H (2004) Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Molecular Ecology 13, 11431155.CrossRefGoogle ScholarPubMed
Phippen, WB, Kresovich, S, Candelas, FG and McFerson, JR (1997) Molecular characterization can quantify and partition variation among genebank holdings: a case study with phenotypically similar accessions of Brassica oleracea var. capitata L. (cabbage) “Golden Acre”. Theoretical and Applied Genetics 94, 227234.CrossRefGoogle Scholar
Rohlf, FJ (1997) NTSYS-pc 2.1. Numerical Taxonomy and Multivariate Analysis System. Setauket, NY: Exeter Software.Google Scholar
SAS Institute (2004) The SAS System for Windows V8.02. Cary, NC: SAS Institute.Google Scholar
Sokal, RR and Michener, CD (1958) A statistical method for evaluating systematic relationships. University of Kansas Science Bulletin 38, 14091438.Google Scholar
Treuren, R, van Hintum ThJL, van (2001) Identification of intra-accession genetic diversity in selfing crop using AFLP markers: implications for collection management. Genetic Resources and Crop Evolution 48, 287295.CrossRefGoogle Scholar
Treuren, R, van Soest, LJM, van Hintum ThJL, van (2001) Marker-assisted rationalization of genetic resources collections: a case study in flax using AFLPs. Theoretical and Applied Genetics 103, 144152.CrossRefGoogle Scholar
Treuren, R, van Magda, A, Hoekstra, R, Hintum, ThJL van (2004) Genetic and economic aspects of marker-assisted reduction of redundancy from a wild potato germplasm collection. Genetic Resources and Crop Evolution 51, 277290.CrossRefGoogle Scholar
Ude, G, Pillay, M, Ogundiwin, E and Tenkouano, A (2003) Genetic diversity in an African plantain core collection using AFLP and RAPD markers. Theoretical and Applied Genetics 107, 248255.CrossRefGoogle Scholar
Virk, PS, Newbury, HJ, Jackson, MT, Ford-Lloyd, BV (1995) The identification of duplicate accessions with a rice germplasm collection using RAPD analysis. Theoretical and Applied Genetics 90, 10491055.CrossRefGoogle ScholarPubMed
Waycott, W and Fort, SB (1994) Differentiation of nearly identical germplasm accessions by a combination of molecular and morphological analyses. Genome 37, 577583.CrossRefGoogle Scholar
Williams, JKG, Kubelik, AR, Livak, KJ, Rafalski, JA and Tingey, SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research 18, 65316535.CrossRefGoogle ScholarPubMed
Zeven, AC, Dehmer, JK, Gladis, T, Hammer, K and Lux, H (1998) Are the duplicates of perennial kale ( Brassica oleracea L. var. ramosa DC.) true duplicates as determined by RAPD analysis?. Genetic Resources and Crop Evolution 45, 105111.CrossRefGoogle Scholar