Hostname: page-component-cd9895bd7-gxg78 Total loading time: 0 Render date: 2024-12-26T04:36:57.308Z Has data issue: false hasContentIssue false
  • English
  • Français

Applications of bulking in molecular characterization of plant germplasm: a critical review

Published online by Cambridge University Press:  27 June 2007

Yong-Bi Fu
Yong-Bi Fu*
Affiliation:
Plant Gene Resources of Canada, AAFC Saskatoon Research Centre, 107 Science Place, Saskatoon, SK S7N0X2, Canada
*
*Corresponding author. E-mail: [email protected]
Get access Rights & Permissions [Opens in a new window]

Abstract

Characterization of plant germplasm using molecular techniques is playing an increasingly important role in the management and utilization of plant genetic resources, but has its limitations in the screening of large numbers of accessions held in seed genebanks worldwide. Bulking individual plants from one accession or group to form a representative sample is a promising approach to widening the scope of a characterization, but it is not without technical problems in detecting genetic variation. This review was conducted to assess the technical pitfalls of bulking, and to evaluate the effectiveness of various bulking methods in the assessment of genetic variation and genetic relationships, and in the identification of plant germplasm. Clearly, some alleles, particularly those occurring at low frequency, may go undetected in a bulked sample, depending on the bulking methods and the molecular techniques used. As a result, genetic diversity estimates and genetic relationship inferences can be significantly biased. Germplasm identification may not be always reliable. Thus, it is imperative that the detection limit imposed by bulking be assessed for a newly initiated molecular germplasm characterization and bias be considered in interpretation of the resulting characterization data. Equally imperative is the need for continuous efforts of exploring efficient bulking procedures for the screening of large germplasm collections, particularly by the newly developed marker systems.

Keywords

bulkingmolecular markersgermplasm characterizationgenetic diversitygenetic relationshipgermplasm identification
Type
Research Article
Information
Plant Genetic Resources , Volume 1 , Issue 2-3 , August 2003 , pp. 161 - 167
Copyright
Copyright © NIAB 2003

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Arnheim, N, Strange, C and Erlich, H (1985) Use of pooled DNA samples to detect linkage disequilibrium of polymorphic restriction fragments and human disease: studies of the HLA class II loci. Proceedings of the National Academy of Sciences USA 82: 6970–6974.Google Scholar
Ayad, WG, Hodgkin, T, Jaradat, A and Rao, VR (1997) Molecular Genetic Techniques for Plant Genetic Resources. Report of an IPGRI Workshop, 9–11 October 1995, Rome, Italy. Rome: International Plant Genetic Resources Institute.Google Scholar
Barcellos, LF, Klitz, W, Field, L, Tobias, R, Bowcock, AM, Wilson, R, Nelson, MP, Nagatomi, J and Thomson, G (1997) Association mapping of disease loci by use of a pooled DNA genomic screen. American Journal of Human Genetics 61: 734–747.Google Scholar
Breen, G, Sham, P, Li, T, Shaw, D, Collier, DA and St. Clair, D (1999) Accuracy and sensitivity of DNA pooling with microsatellite repeats using capillary electrophoresis. Molecular and Cellular Probes 13: 359–365.Google Scholar
Bretting, PK and Widrlechner, MP (1995) Genetic markers and plant genetic resource management. Plant Breeding Reviews 13: 11–86.Google Scholar
Churchill, GA, Giovannoni, JJ and Tanksley, SD (1993) Pooledsampling makes high resolution mapping practical with DNA markers. Proceedings of the National Academy of Sciences USA 90: 16–20.Google Scholar
Divaret, I, Margale, E and Thomas, G (1999) RAPD markers on seed bulks efficiently assess the genetic diversity of a Brassica oleracea L collection. Theoretical and Applied Genetics 98: 1029–1035.Google Scholar
Dubreuil, P, Rebourg, C, Merlino, M and Charcosset, A (1999) Evaluation of a DNA pooled-sampling strategy for estimating the RFLP diversity of maize populations. Plant Molecular Biology Reporter 17: 123–138.Google Scholar
Dulson, J, Kott, LS and Ripley, VL (1998) Efficacy of bulked DNA samples for RAPD DNA fingerprinting of genetically complex Brassica napus cultivars. Euphytica 102: 65–70.Google Scholar
FAO (Food and Agriculture Organization) (1998) Report on the State of the World's Plant Genetic Resources for Food and Agriculture. Rome: Food and Agriculture Organization.Google Scholar
Fu, YB (2000) Effectiveness of bulking procedures in measuring population-pairwise similarity with dominant and co-dominant genetic markers. Theoretical and Applied Genetics 100: 1284–1289.Google Scholar
Fu, YB, Diederichsen, A, Richards, KW and Peterson, GW (2002) Genetic diversity of a range of flax (Linum usitatissimum L.) cultivars and landraces revealed by RAPDs. Genetic Resources and Crop Evolution 49: 167–174.Google Scholar
Fu, YB, Guerin, S, Peterson, GW, Carlson, JE and Richards, KW (2003a) Assessment of bulking strategies for RAPD analyses of flax germplasm. Genetic Resources and Crop Evolution 50: 743–746.Google Scholar
Fu, YB, Whitwill, S, Ferdinandez, YSN, Coulman, BE and Richards, KW (2003b) Bulking generated considerable bias in detection of AFLP variations in oat, fringed brome and smooth bromegrass. Molecular Ecology Notes 3: 476–478.Google Scholar
Gilbert, JE, Lewis, EV, Wilkinson, MJ and Caligari, PDS (1999) Developing an appropriate strategy to assess genetic variability in plant germplasm collections. Theoretical and Applied Genetics 98: 1125–1131.Google 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 and Jackson, MT (eds) Managing Plant Genetic Diversity. Rome: International Plant Genetic Resources Institute, pp. 469–480.Google Scholar
Karp, A (2002) The new genetic era: will it help us in managing genetic diversity? In: Engels, JMM, Rao, VR, Brown, AHD and Jackson, MT (eds) Managing Plant Genetic Diversity. Rome: International Plant Genetic Resources Institute, pp. 43–56.Google Scholar
Karp, A, Kresovich, S, Bhat, KV, Ayad, WG and Hodgkin, T (1997) Molecular Tools in Plant Genetic Resources Conservation: A Guide to the Technologies. IPGRI Technical Bulletin No. 2. Rome: International Plant Genetic Resources Institute.Google Scholar
Khatib, H, Darvasi, A, Plotski, Y and Soller, M (1994) Determining relative microsatellite allele frequencies in pooled DNA samples. PCR Methods and Applications 4: 13–18.Google Scholar
Kolliker, R, Jones, ES, Jahufer, MZZ and Forster, JW (2001) Bulked AFLP analysis for the assessment of genetic diversity in white clover. Euphytica 121: 305–315.Google Scholar
Kraft, T and Sall, T (1999) An evaluation of the use of pooled samples in studies of genetic variation. Heredity 82: 488–494.Google Scholar
Kraft, T, Fridlund, B, Hjerdin, A, Sall, T, Tuvesson, S and Hallden, C (1997) Estimating genetic variation in sugar beets and wild beets using pools of individuals. Genome 40: 527–533.Google Scholar
LeDuc, C, Miller, P, Lichter, J and Parry, P (1995) Batched analysis of genotypes. PCR Methods and Applications 4: 331–336.CrossRefGoogle ScholarPubMed
Mailer, RJ and May, CE (1999) Heterogeneity of random amplified polymorphic DNA sequences in individual seedlings and bulk samples of four cultivars of Brassica napus. Plant Breeding 118: 465–470.CrossRefGoogle Scholar
McGregor, CE, van Treuren, R, Hoekstra, R and van Hintum, TJL (2002) Analysis of the wild potato germplasm of the series Acaulia with AFLPs: implications for ex situ conservation. Theoretical and Applied Genetics 104: 146–156.Google Scholar
Mellish, A, Coulman, B and Ferdinandez, Y (2002) Genetic relationships among selected crested wheatgrass cultivars and species determined on the basis of AFLP markers. Crop Science 42: 1662–1668.CrossRefGoogle Scholar
Michelmore, RW, Paran, I and Kesseli, RV (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proceedings of the National Academy of Sciences USA 88: 9828–9832.CrossRefGoogle ScholarPubMed
Mitchell, SE, Kresovich, S, Jester, CA, Hernandez, CJand, Szwec- McFadden, AK (1997) Application of multiplex PCR and fluorescence- based, semi-automated allele sizing technology for genotyping plant genetic resources. Crop Science 37: 617–624.CrossRefGoogle Scholar
Pacek, P, Sajantila, A and Syvanen, AC (1993) Determination of allele frequencies at loci with length polymorphism by quantitative analysis of DNA amplified from pooled samples. PCR Methods and Applications 2: 313–317.CrossRefGoogle ScholarPubMed
Perlin, MW, Lancia, G and Ng, SK (1995) Toward fully automated genotyping: genotyping microsatellite markers by deconvolution. American Journal of Human Genetics 57: 1199–1210.Google ScholarPubMed
Rafalski, A (2002) Applications of single nucleotide polymorphisms in crop genetics. Current Opinion in Plant Biology 5: 94–100.Google Scholar
Ritland, K (2002) Estimation of gene frequency and heterozygosity from pooled samples. Molecular Ecology Notes 2: 370–372.Google Scholar
Sweeney, PM and Danneberger, TK (1994) Random amplified polymorphic DNA in perennial ryegrass: a comparison of bulk samples vs. individuals. HortScience 29: 624–626.Google Scholar
van Treuren, R (2001) Efficiency of reduced primer selectivity and bulked DNA analysis for the rapid detection of AFLP polymorphism in a range of crop species. Euphytica 117: 27–37.CrossRefGoogle Scholar
Virk, PS, Newbury, HJ, Jackson, MT and Ford-Lloyd, BV (1995) The identification of duplicate accessions within a rice germplasm collection using RAPD analysis. Theoretical and Applied Genetics 90: 1049–1055.Google Scholar
Warburton, ML, Hoisington, DA, Xia, XC and Charcosset, A (2000) Fingerprinting maize populations using a bulking strategy. In: 2000 Annual Meeting Abstracts of Crop Science Society ofAmerica,5–9 November 2000,Minneapolis, MN, USA, pp. 191–192.Google Scholar
Wolford, JK, Blunt, D, Ballecer, C and Prochazka, M (2000) Highthroughput SNP detection by using DNA pooling and denaturing high performance liquid chromatography (DNPLC). Human Genetics 107: 483–487.CrossRefGoogle Scholar
Yu, K and Pauls, KP (1993) Rapid estimation of genetic relatedness among heterogeneous populations of alfalfa by random amplification of bulked genomic DNA samples. Theoretical and Applied Genetics 86: 788–794.Google Scholar
Zhu, J, Gale, MD, Quarrie, S, Jackson, MT and Bryan, GJ (1998) AFLP markers for the study of rice biodiversity. Theoretical and Applied Genetics 96: 602–611.Google Scholar