A computerised algorithm for selecting a subset of multiplex molecular markers and optimising linkage map construction

A computer algorithm is presented which allows selection of a subset of mul tiplex markers based on the minimisation of an optimality criterion fora ge netic linkage map. It could be applied for choosing a subset of primers (e. g. RAPD, IMA or AFLP), each of which provides several unevenly spaced genet ic markers. The goal is to achieve a saturated map of evenly spaced markers , using as few primers as possible to minimise cost and labour. Minimising the average map distance between markers is trivial, but simply leads to se lection of those primers which provide the greatest number of markers. Howe ver, minimising the standard deviation of interval length ensures that weig ht is given both to the number of markers and to the evenness of their dist ribution on the linkage map. This criterion was found empirically to give a result fairly close to the optimum. A stepwise-like selection procedure is therefore implemented, which stops when the optimality criterion does not decrease any more. An example is given of a molecular map of perennial ryeg rass with 463 markers obtained from 17 AFLP primers. It is demonstrated tha t this can be safely reduced to a 175 marker map with only 6 primers. Genet ic diversity studies may also benefit from using such a subset of less-redu ndant markers in genetic distance estimation.