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Molecular Breeding

, Volume 18, Issue 4, pp 291–300

First Online: 03 October 2006Received: 03 November 2005Accepted: 30 March 2006

Abstract

Genetic linkage maps are often based on maximum-likelihood estimates of recombination fractions which are converted into map units by mapping functions. This paper presents a cost analysis of linkage analysis for a segregating F2␣population with codominant or dominant molecular markers and a qualitative monogenic dominant–recessive trait. For illustration, a disease-resistance trait is considered, where the susceptible allele is recessive. Three sub-populations of the F2 can be used for linkage analysis susceptible = recessive individuals, resistant = dominant individuals, complete F2. While it is well-known that recessive individuals are more informative than dominant individuals, it is not obvious a priori, which of the three sub-populations should be preferred, when costs of phenotyping and genotyping are taken into consideration. A comparative economic analysis of alternative procedures of linkage detection based on these three sub-populations does exhibit a clear economic superiority of the sub-population of susceptible = recessive individuals, when costs of genotyping are high. This cost-effectiveness is due to the higher information content of this sub-population compared to the sub-population of dominant = resistant individuals and also compared to the complete F2. Our final conclusion-recommendation is as follows: If the cost to genotype an individual is sufficiently large compared with the cost to phenotype an individual, then linkage analysis and genetic mapping should be only based on susceptible = recessive individuals. Conversely, if the cost of phenotyping exceeds that for genotyping, it may be preferable to genotype all plants. The exact conditions under which a strategy is preferable are described in the paper.

KeywordsCost analysis Economics Genetic mapping Linkage analysis Molecular marker Recombination fraction  Download to read the full article text



Author: Manfred Huehn - Hans-Peter Piepho

Source: https://link.springer.com/







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