An annotated genetic map of loblolly pine based on microsatellite and cDNA markers

The updated P. taeda genetic map, with an estimated genome coverage of 1,515 cM(KOSAMBI) across 12 linkage groups, incorporated 170 new SSR markers and 290 previously reported SSR, RFLP, and ESTP markers. The average marker interval was 3.1 cM. Of 233 mapped SSR loci, 84 were from cDNA-derived sequences (EST-SSRs) and 149 were from non-transcribed genomic sequences (genomic-SSRs). Of all 311 mapped cDNA-derived markers, 77% were associated with NCBI Pta UniGene clusters, 67% with RefSeq proteins, and 62% with functional Gene Ontology (GO) terms. Duplicate (i.e., redundant accessory) and paralogous markers were tentatively identified by evaluating marker sequences by their UniGene cluster IDs, clone IDs, and relative map positions. The average gene diversity, He, among polymorphic SSR loci, including those that were not mapped, was 0.43 for 94 EST-SSRs and 0.72 for 83 genomic-SSRs. The genetic map can be viewed and queried at http://www.conifergdb.org/pinemap webcite.Many polymorphic and genetically mapped SSR markers are now available for use in P. taeda population genetics, studies of adaptive traits, and various germplasm management applications. Annotating mapped genes with UniGene clusters and GO terms allowed assessment of redundant and paralogous EST markers and further improved the quality and utility of the genetic map for P. taeda.Loblolly pine (Pinus taeda L.) is an economically important native forest tree species in the southern United States, accounting for approximately 16% of the harvested industrial wood in the US and 5% worldwide [1,2]. Over 40% of this production occurs on 12 million hectares of sustainably managed forests, where essentially all of the planting stock is the product of genetic improvement [1,3]. In addition to its economic significance, P. taeda is ecologically important, as it is a frequent or predominant species on about 25 million hectares of non-planted forested land in the southern US [1]. Pinus taeda also is considered one of