Construction of an AFLP genetic map with nearly complete genome coverage in Pinus taeda

De novo construction of complete genetic linkage maps requires large mappin g populations, large numbers of genetic markers, and efficient algorithms f or ordering markers and evaluating order confidence. We constructed a compl ete genetic map of an individual loblolly pine (Pinus taeda L.) using ampli fied fragment length polymorphism (AFLP) markers segregating in haploid meg agametophytes and PGRI mapping software. We generated 521 polymorphic fragm ents from 21 AFLP primer pairs. A total of 508 fragments mapped to 12 linka ge groups, which is equal to the Pinus haploid chromosome number. Bootstrap locus order matrices and recombination matrices generated by PGRI were use d to select 184 framework markers that could be ordered confidently. Order support was also evaluated using log likelihood criteria in MAPMAKER. Optim al marker orders from PGRI and MAPMAKER were identical, but the implied rel iability of orders differed greatly. The framework map provides nearly comp lete coverage of the genome, estimated at approximately 1700 cM in length u sing a modified estimator. This map should provide a useful framework for m erging existing loblolly pine maps and adding multiallelic markers as they become available. Map coverage with dominant markers in both linkage phases will make the map useful for subsequent quantitative trait locus mapping i n families derived by self-pollination.