Abstract
Three molecular marker protocols, chemiluminescent restriction fragment length polymorphisms (c-RFLPs), radioactivity-based restriction fragment length polymorphisms (r-RFLPs), and randomly amplified DNA polymorphisms (RAPDs) were compared in terms of cost and time efficiency. Estimates of cost of supplies and time requirements were obtained from simulations of maize (Zea mays L.) genotyping experiments utilizing protocols currently in use. The increase in total cost with increasing numbers of individuals genotyped and markers analyzed is higher for RAPDs than for RFLPs. RAPDs were generally found to be more cost and time efficient for studies involving small sample sizes, while RFLPs have the advantage for larger sample sizes. Because of the shorter exposure times involved, c-RFLPs require less time than r-RFLPs to obtain a given amount of information. Variations in the protocols, such as number of re-uses of Southern blots or cost of Taq DNA polymerase per reaction of amplification, also affect the relative merits of RAPDs and RFLPs. Two examples were analyzed where molecular markers are used: a germ plasm survey and quantitative trait loci (QTL) mapping in a segregating population. No protocol was found to be the most cost and time efficient over the entire range of sample sizes and number of marker loci studied.
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References
Asins MJ, Carbonell EA (1989) Distribution of genetic variability in a durum wheat world collection. Theor Appl Genet 77:287–294
Bassiri A, Adams MW (1978) Evaluation of bean cultivar relationships by means of isozyme electrophoretic patterns. Euphytica 27:707–720
Beckmann JS, Soller M (1983) Restriction fragment length polymorphisms in genetic improvement: methodologies, mapping and costs. Theor Appl Genet 67:35–43
Bernatzky R, Tanksley SD (1986) Toward a saturated linkage map in tomato based on isozymes and random cDNA sequences. Genetics 112:887–898
Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331
Burr B, Evola SV, Burr FA (1983) The application of restriction fragment length polymorphism to plant breeding. In: Setlow JK, Hollaender A (eds) Genetic engineering, principles and methods, Vol. 5. Plenum Press, New York, pp 45–59
Carlson JE, Tulsieram LK, Glaubitz JC, Luk VWK, Kauffeldt C, Rutledge R (1991) Segregation of random amplified DNA markers in F1 progeny of conifers. Theor Appl Genet 83:194–200
Chang C, Boowman JC, DeJohn AW, Lander ES, Meyerowitz ES (1988) Restriction fragment length polymorphism linkage map of Arabidopsis thaliana. Proc Natl Acad Sci USA 85:6856–6860
De Verna JW, Alpert KB (1990) RFLP technology. In: Proc Hortic Biotechnol Symp. University of California, Davis, Wiley-Liss, New York, pp 247–259
Devey ME, Jermstad KD, Tauer CG, Neale DB (1991) Inheritance of RFLP loci in a loblolly pine three-generation pedigree. Theor Appl Genet 83:238–242
Doebley JF, Goodman MM, Stuber CW (1984) Isoenzymatic variation in Zea (Gramineae). System Bot 9:203–218
Dudley JW (1989) Use of molecular markers in corn breeding. In: Proc 25th Annu Ill Corn Breed School. Urbana-Champaign, Illinois, pp 120–138
Fehr WR (1987) Principles of cultivar development, Vol. 1, theory and technique. McGraw-Hill, New York
Gebhardt C, Ritter E, Debener T, Schachtschabel U, Walkemeier B, Uhrig H, Salamini F (1989) RFLP analysis and linkage mapping in Solanum tuberosum. Theor Appl Genet 78:65–75
Gebhardt C, Ritter E, Barone A, Debener T, Walkemeier B, Schachtschabel U, Kaufmann H, Thompson RD, Bonierbale MW, Ganal MW, Tanksley SD, Salamini F (1991) RFLP maps of potato and their alignment with the homeologous tomato genome. Theor Appl Genet 83:49–57
Goodman MM, Stuber CW (1980) Genetic identification of lines and crosses using isoenzyme electrophoresis. In: Proc 35th Annu Corn Sorghum Industry Res Conf American Seed Trade Assoc, Vol. 35, pp 10–31
Grodzicker T, Williams J, Sharp P, Sambrook J (1974) Physical mapping of temperature-sensitive mutations of adeno viruses. Cold Spring Harbor Symp Quant Biol 39:439–446
Garner A, Jahoor A, Schondelmaier J, Siedler H, Pillen K, Fischbeck G, Wenzel G, Herrmann RG (1991) Construction of an RFLP map of barley. Theor Appl Genet 83:250–256
Helentjaris T, Slocum M, Wright S, Schaefer A, Nienhuis J (1986) Construction of genetic linkage maps in maize and tomato using restriction fragment length polymorphisms. Theor Appl Genet 72:761–769
Heun M, Kennedy AE, Anderson JA, Lapitan NLV, Sorrels ME, Tanksley SD (1991) Construction of a restriction fragment length polymorphism map for barley (Hordeum vulgare). Genome 34:437–447
Hoisington DA (1992) Laboratory protocols. CIMMYT Applied Molecular Genetics Laboratory, Mexico, D.F., CIMMYT
Hoisington DA, Coe EH (1990) Mapping in maize using RFLPs. In: Gustafson JP (ed) Gene manipulation in plant improvement II. Plenum Press, New York, pp 331–352
Keim P, Diers BW, Olson TC, Shoemaker RC (1990) RFLP mapping in soybean: association between marker loci and variation in Quantitative traits. Genetics 126:735–742
Kesseli RV, Michelmore RW (1986) Genetic analysis and phylogenies detected from isozyme markers among species of Lactuca. J Hered 77:324–331
Landry BS, Kesseli RV, Farrara B, Michelmore RW (1987) A genetic map of lettuce (Lactuca sativa L.) with restriction fragment length polymorphisms, isozyme, disease resistance and morphological markers. Genetics 116:331–337
Martin GB, Williams JGK, Tanksley SD (1991) Rapid identification of markers linked to a Pseudomonas resistance gene in tomato by using random primers and near-isogenic lines. Proc Natl Acad Sci USA 88:2336–2340
McCoucgh SR, Kochert G, Yu ZH, Wang ZY, Khush GS, Coffman WR, Tanksley SD (1988) Molecular mapping of rice chromosomes. Theor Appl Genet 76:815–829
McIntyre CL (1988) Variation at isozyme loci in Triticeae. Plant Syst Evol 160:123–142
Murray MG, Romero-Severson J, West DP, Cramer JH (1988) Restriction fragment length polymorphisms: what are they and how can breeders use them? In: Proc 43rd Annual Corn Sorghum Industry Res Conf. American Seed Trade Assoc, Vol. 43, pp 72–87
Nam H-G, Giraudat J, den Boer B, Moonan F, Loos WDB, Hauge BM, Goodman HM (1989) Restriction fragment length polymorphism linkage map of Arabidopsis thaliana. Plant Cell 1:699–705
Osborn TC, Alexander DC, Fobes JF (1987) Identification of restriction fragment length polymorphisms linked to genes controlling soluble solids content in tomato fruit. Theor Appl Genet 73:350–356
Rafalski JA, Tingey SV, Williams JGK (1991) RAPD markers — a new technology for genetic mapping and plant breeding. AgBiotech News Info 3:645–648
Sax K (1923) The association of size differences with seed-coat pattern and pigmentation in Phaseolus vulgaris. Genetics 8:552–560
Shin JS, Chao S, Corpuz L, Blake T (1990) A partial map of the barley genome incorporating restriction fragment length polymorphism, polymerase chain reaction, isozyme and morphological marker loci. Genome 33:803–810
Smith JSC, Smith OS (1989) The use of morphological, biochemical, and genetic characteristics to measure distance and to test for minimum distance between inbred lines of maize (Zea mays L.). (Paper presented at UPOV workshop, Versailles, France). Pioneer Hi-Bred Int, Johnston, Iowa
Smith JSC, Goodman MM, Stuber CW (1985a) Genetic variability within US maize germplasm. I. Historically important lines. Crop Sci 25:550–555
Smith JSC, Goodman MM, Stuber CW (1985b) Genetic variability within US maize germplasm. II. Widely-used inbred lines 1970 to 1979. Crop Sci 25:681–685
Smith JSC, Smith OS, Wall SJ (1991) Associations among widely used French and US maize hybrids as revealed by restriction fragment length polymorphisms. Euphytica 54:263–273
Soller M, Beckmann JS (1983) Genetic polymorphism in varietal identification and genetic improvement. Theor Appl Genet 67:25–33
Song KM, Suzuki JY, Slocum MK, Williams PH, Osborn TC (1991) A linkage map of Brassica rapa (syn. campestris) based on restriction fragment length polymorphism loci. Theor Appl Genet 82:296–304
Stuber CW, Edwards MD (1986) Genotypic selection for improvement of quantitative traits in corn using molecular marker loci. In: Proc 41st Annu Corn Sorghum Industry Res Conf. American Seed Trade Assoc, Vol. 41, pp 70–83
Tanksley SD, Young ND, Paterson AH, Bonierbale MW (1989) RFLP mapping in plant breeding: new tools for an old science. Bio/Technology 7:257–264
Walton M (1990) Application of RFLP technology to applied plant breeding. In: Proc Hortic Biotechnol Symp. University of California, Davis, Wiley-Liss, New York, pp 335–346
Weining S, Langridge P (1991) Identification and mapping of polymorphisms in cereals based on the polymerase chain reaction. Theor Appl Genet 82:209–216
Welsh J, McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 18:7213–7218
Welsh J, Honeycutt RJ, McClelland M, Sobral BWS (1991) Parentage determination in maize hybrids using the arbitrarily primed polymerase chain reaction (AP-PCR). Theor Appl Genet 82:473–476
Williams JGK, Kubelik AR, Livak KJ, Rafalski A, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6513–6535
Williams MNV, Pande N, Nair S, Mohan M, Bennett J (1991) Restriction fragment length polymorphism analysis of polymerase chain reaction products amplified from mapped loci of rice (Oryza sativa L.) genomic DNA. Theor Appl Genet 82:489–498
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Communicated by A. L. Kahler
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Ragot, M., Hoisington, D.A. Molecular markers for plant breeding: comparisons of RFLP and RAPD genotyping costs. Theoret. Appl. Genetics 86, 975–984 (1993). https://doi.org/10.1007/BF00211050
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DOI: https://doi.org/10.1007/BF00211050