Optimizing parental selection for genetic linkage maps

TLDR

RFLP‑based linkage maps are valuable, but different populations are required for distinct objectives, and clones from these maps are subsequently probed onto specialized populations for gene tagging. The study aimed to compute polymorphism information content for 51 low‑copy DNA clones and use those values to select optimal mapping parents. PIC values were derived from gene‑diversity analyses of restriction fragment patterns across 18 wheat genotypes, and parent combinations were evaluated by the proportion of polymorphic clones and the probability of generating polymorphism in other populations. The authors identified genotype pairs that would map more informative DNA clones than a population built from the most polymorphic parents, and the approach is generalizable to other species and marker types.

Abstract

Genetic linkage maps based on restriction fragment length polymorphisms are useful for many purposes; however, different populations are required to fulfill different objectives. Clones from the linkage map(s) are subsequently probed onto populations developed for special purposes such as gene tagging. Therefore, clones contained on the initial map(s) must be polymorphic on a wide range of genotypes to have maximum utility. The objectives of this research were to (i) calculate polymorphism information content values of 51 low-copy DNA clones and (ii) use the resulting values to choose potential mapping parents. Polymorphism information content was calculated using gene diversity by classifying restriction fragment patterns on a diverse set of 18 wheat genotypes. Combinations of potential parents were then compared by examining both the proportion of polymorphic clones and the likelihood that those mapped clones would give a polymorphism when used on other populations. Genotype pairs were identified that would map more highly informative DNA clones compared with a population derived from the most polymorphic potential parents. The methodologies used to characterize clones and rank potential parents should be applicable to other species and types of markers as well.