Anchored reference loci in loblolly pine (Pinus taeda L.) for integrating pine genomics

Anchored reference loci provide a framework for comparative mapping. They a re landmarks to denote conserved chromosomal segments,, allowing the synthe sis of genetic maps from multiple sources. We evaluated 90 expressed sequen ce tag polymorphisms (ESTPs) from loblolly pine (Pinus taeda L.) for this f unction. Primer sets were assayed for amplification and polymorphism in six pedigrees, representing two subgenera of Pinus and a distant member of the Pinaceae, Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco). On average, 89% of primer sets amplified in four species of subgenus Pinus, 49% in one species of subgenus Strobus, and 22% in Douglas-fir. Polymorphisms were det ected for 37-61% of the ESTPs within each pedigree. Comparative mapping in loblolly and slash pine (P. elliottii Englm.) revealed that ESTPs mapped to the same location, Disrupted synteny or significant disruptions in colinea rity were not detected. Thirty-five ESTPs met criteria established for anch or loci. The majority of those that did not meet these criteria were exclud ed when map location was known in only a single species. Anchor loci provid e a unifying tool for the community, facilitating the creation of a "generi c" pine map and serving as a foundation for studies on genome organization and evolution.