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A note on the bias of genetic distances in linkage maps based on small samples for backcrosses and intercrosses with complete dominance

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Abstract:

This paper investigates the bias (the difference between the expectation (mean) of an estimator and its true value) of genetic distances for small samples. Exact results on this bias have not received much attention in genetic mapping literature. We show that bias drops quickly with increasing sample size for both a backcross population and an F2 in coupling. By contrast, bias may be substantial even for larger sample size for an F2 when markers are in repulsion. It is concluded that Karlin’s map function should be used with care when mapping is done using an F2 population. The same note of caution applies to other map functions such as Haldane’s and Kosambi’s. Finite-sample bias of these latter functions cannot be assessed because of the nonexistence of an expected value, but their median bias is similar to that of Karlin’s function.

Ce travail examine le biais (i.e., la différence entre la valeur attendue (moyenne) d’un estimateur et sa vraie valeur) dans la mesure de distances génétiques au moyen de petits effectifs. Des résultats exacts concernant ce biais n’ont pas reçu beaucoup d’attention dans la littérature portant sur la cartographie génétique. Les auteurs montrent que le biais diminue rapidement avec l’accroissement de la taille de l’effectif, tant chez des populations issues d’un rétrocroisement que chez une F2 en couplage. Par contre, ce biais peut être substantiel, même avec de grands effectifs, pour une F2 lorsque les marqueurs sont en répulsion. Les auteurs en concluent qu’il faut être prudent lorsqu’on utilise la fonction de Karlin sur une population F2. La même prudence est de mise lorsqu’on utilise d’autres fonctions comme celles de Haldane ou de Kosambi. Dans ces derniers cas, le biais occasionné par la taille finie de l’effectif ne peut être mesuré en raison de l’absence d’une valeur attendue, mais leur biais médian est semblable à celui obtenu avec la fonction de Karlin.

Document Type: Research Article

Publication date: December 1, 2008

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  • From its inception in 1957, this international cytogenetics journal has catered to the research areas of the members of the Genetics Society of Canada; traditionally, these have included agriculture, entomology, genetics/cytogenetics, and evolutionary mechanisms. The contents of the journal have evolved as contributors developed new technologies and interests. A 20-member Editorial Board is composed of scientists from around the world. Reviews and commentary from respected experts are often featured.
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