an annotated genetic map of loblolly pine based on microsatellite and cdna markers一个带注释的基因图谱的火炬松基于微卫星和cdna标记.pdfVIP

Echt et al. BMC Genetics 2011, 12:17 /1471-2156/12/17 RESEARCH ARTICLE Open Access An annotated genetic map of loblolly pine based on microsatellite and cDNA markers 1* 2,3 4 6 5 6 Craig S Echt , Surya Saha , Konstantin V Krutovsky , Kokulapalan Wimalanathan , John E Erpelding , Chun Liang , C Dana Nelson1 Abstract Background: Previous loblolly pine (Pinus taeda L.) genetic linkage maps have been based on a variety of DNA polymorphisms, such as AFLPs, RAPDs, RFLPs, and ESTPs, but only a few SSRs (simple sequence repeats), also known as simple tandem repeats or microsatellites, have been mapped in P. taeda. The objective of this study was to integrate a large set of SSR markers from a variety of sources and published cDNA markers into a composite P. taeda genetic map constructed from two reference mapping pedigrees. A dense genetic map that incorporates SSR loci will benefit complete pine genome sequencing, pine population genetics studies, and pine breeding programs. Careful marker annotation using a variety of references further enhances the utility of the integrated SSR map. Results: 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 m