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Redundancy and distinctness in flax germplasm as revealed by RAPD dissimilarity

  • Yong-Bi Fu (a1)

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.

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Corresponding author

*Corresponding author: E-mail: fuy@agr.gc.ca

References

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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.
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.
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.
Engels, JMM and Visser, L (2003) A Guide to Effective Management of Germplasm Collections. IPGRI Handbooks for Genebanks No. 6RomeIPGRI.
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.
Fu, YB (2003) Applications of bulking in molecular characterization of plant germplasm: a critical review. Plant Genetic Resources 1, 161167.
Fu, YB (2005) Geographic patterns of RAPD variation in cultivated flax. Crop Science 45, 10841091.
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.
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.
Fu, YB, Rowland, GG, Duguid, SD and Richards, KW (2003 b) RAPD analysis of 54 North American flax cultivars. Crop Science 43, 15101515.
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.
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.
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.
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.
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.
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.
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.
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.
Nybom, H (2004) Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Molecular Ecology 13, 11431155.
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.
Rohlf, FJ (1997) NTSYS-pc 2.1. Numerical Taxonomy and Multivariate Analysis System. Setauket, NY: Exeter Software.
SAS Institute (2004) The SAS System for Windows V8.02. Cary, NC: SAS Institute.
Sokal, RR and Michener, CD (1958) A statistical method for evaluating systematic relationships. University of Kansas Science Bulletin 38, 14091438.
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.
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.
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.
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.
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.
Waycott, W and Fort, SB (1994) Differentiation of nearly identical germplasm accessions by a combination of molecular and morphological analyses. Genome 37, 577583.
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.
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.

Keywords

Redundancy and distinctness in flax germplasm as revealed by RAPD dissimilarity

  • Yong-Bi Fu (a1)

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