Molecular markers for plant breeding: comparisons of RFLP and RAPD genotyping costs

Ragot, M and Hoisington, D A (1993) Molecular markers for plant breeding: comparisons of RFLP and RAPD genotyping costs. TAG Theoretical and Applied Genetics, 86 (8). pp. 975-984. ISSN 1432-2242

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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.

Item Type: Article
Uncontrolled Keywords: Chemiluminescence, Genotyping costs, RAPD, RFLP, Zea mays
Subjects: Others > Maize
Depositing User: Mr Siva Shankar
Date Deposited: 20 Mar 2012 04:51
Last Modified: 20 Mar 2012 04:51
Official URL:
Acknowledgement: [NOTE: D. A. Hoisington is presently with ICRISAT (Patancheru)]---This study was made possible in part by a fellowship from Ciba-Geigy to MR.
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