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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETIC AND CULTURAL METHODS TO MANAGE RENIFORM NEMATODE IN COTTON

Location: Crop Genetics Research Unit

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

Authors
item Echt, Craig -
item Saha, Surya -
item Krutovsky, Konstantin -
item Wimalanathan, Kokulpalan -
item Erpelding, John
item Liang, Chun -
item Nelson, C -

Submitted to: BioMed Central (BMC) Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 26, 2011
Publication Date: January 26, 2011
Citation: Echt, C.S., Saha, S., Krutovsky, K., Wimalanathan, K., Erpelding, J.E., Liang, C., Nelson, C.D. 2011. An annotated genetic map of loblolly pine based on microsatellite and cDNA markers. BioMed Central (BMC) Genetics. 12:17.

Interpretive Summary: Loblolly pine 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. The development of improved varieties is hindered by a long juvenile growth stage; however, selection of individual trees with desirable genetic traits can be conducted during this growth stage if DNA markers linked to these traits can be identified. Genetic linkage maps where DNA markers are arranged on specific chromosomes are important tools in mapping desirable traits to specific chromosomes and for the identification of DNA markers to select individuals with these traits. One hundred-seventy DNA markers were developed and a genetic linkage map for loblolly pine was constructed incorporating these markers plus 290 previously reported markers. This genetic map will benefit the sequencing of the loblolly pine genome, population genetics studies to identify important traits and pine breeding programs to develop improved varieties.

Technical Abstract: 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 recently published markers and a large set of SSR markers newly developed from cDNA and genomic DNA sequences into a composite loblolly pine genetic map using two reference mapping pedigrees. A dense reference 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. The updated loblolly pine genetic map, covering 1,415 cM across 12 linkage groups, was constructed from 170 new SSR markers and 290 previously reported SSR, RFLP, and ESTP markers that segregated in one or both reference pedigrees. Of 233 mapped SSR loci, 84 were from cDNA-derived sequences (EST-SSRs) and 149 were from non-transcribed genomic sequences. Of 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 SSR marker gene diversity estimated as expected heterozygosity, He, was 0.43 for 95 EST-SSRs and at 0.72 for 83 genomic SSRs. The genetic map, with an average marker spacing of 3.1 cM, can be viewed and queried at http://www.conifergdb.org/pinemap. Many polymorphic and genetically mapped SSR markers are now available for use in loblolly pine 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.

Last Modified: 7/25/2014
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