from: Keygene Genetics Newsletter VI

Linkage Disequilibrium Mapping (LD Mapping), allows for testing associations between phenotype and DNA markers directly on germplasm lines (instead of segregating populations).

A prerequisite to execute this approach is the availability of a database with many thousands of genetic markers for which the precise map position is known. To date, AFLP is the only technology which can generate these numbers of marker within a reasonable amount of time and effort. Efficient mapping of the thousands of markers can be achieved using a BAC pooling strategy.

Ultra High Density Mapping using BAC Pools of Pristionchus pacificus, a free living nematode. The vast majority of bands from the parent source segregate in the BAC pools, and this segregation pattern is used to physically map the marker bands. S: size standard; P: parental source from which the BAC library is constructed.

As time goes by, the number of agronomically important species for which the complete genome is sequenced will increase. By analyzing the genome sequence, the length of AFLP fragments for each AFLP primer combination can be predicted. Vice-versa, for each band in an AFLP fingerprint of the sequenced sample, the genome position can be traced back through the genome sequence.

Keygene has built a software package called REcomb which can map AFLP bands in silico using the complete genome sequence. Together with the AFLP technology, this tool allows us to efficiently generate a germplasm dataset containing many thousands of mapped markers, the ideal start for successful LD mapping work.

Example of how our REcomb software enables the calculation of all expected AFLP fragments which will be derived from a total genome for specific Restriction Enzyme combinations (and possibly also primer extensions).