title: A Consensus Genetic Map for Pinus taeda and Pinus elliottii and Extent of Linkage Disequilibrium in Two Genotype-Phenotype Discovery Populations of Pinus taeda.
abstract: A consensus genetic map for Pinus taeda (loblolly pine) and Pinus elliottii (slash pine) was constructed by merging three previously published P. taeda maps with a map from a pseudo-backcross between P. elliottii and P. taeda. The consensus map positioned 3856 markers via genotyping of 1251 individuals from four pedigrees. It is the densest linkage map for a conifer to date. Average marker spacing was 0.6 cM and total map length was 2305 cM. Functional predictions of mapped genes were improved by aligning expressed sequence tags used for marker discovery to full-length P. taeda transcripts. Alignments to the P. taeda genome mapped 3305 scaffold sequences onto 12 linkage groups. The consensus genetic map was used to compare the genome-wide linkage disequilibrium in a population of distantly related P. taeda individuals (ADEPT2) used for association genetic studies and a multiple-family pedigree used for genomic selection (CCLONES). The prevalence and extent of LD was greater in CCLONES as compared to ADEPT2; however, extended LD with LGs or between LGs was rare in both populations. The average squared correlations, r(2), between SNP alleles less than 1 cM apart were less than 0.05 in both populations and r(2) did not decay substantially with genetic distance. The consensus map and analysis of linkage disequilibrium establish a foundation for comparative association mapping and genomic selection in P. taeda and P. elliottii.
authors.affiliation: School of Forest Resources and Conservation, University of Florida, Gainesville, Florida, 32611-0410.
authors.forename: Jared W
authors.initials: JW
authors.lastname: Westbrook
authors.affiliation: Southern Research Station, USDA Forest Service, Saucier, Mississippi, 39574.
authors.forename: Vikram E
authors.identifier: http://orcid.org/0000-0001-6627-2832
authors.initials: VE
authors.lastname: Chhatre
authors.affiliation: National Center for Genome Analysis Support, Indiana University, Bloomington, Indiana 47408.
authors.forename: Le-Shin
authors.initials: LS
authors.lastname: Wu
authors.affiliation: Department of Biology, University of Florida, Gainesville, Florida 32611 Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida 32603 Genetics Institute, University of Florida, Gainesville, Florida 32608.
authors.forename: Srikar
authors.initials: S
authors.lastname: Chamala
authors.affiliation: RAPiD Genomics LLC, Gainesville, Florida 32601.
authors.forename: Leandro Gomide
authors.initials: LG
authors.lastname: Neves
authors.affiliation: Department of Agronomy, University of Florida, Gainesville, Florida 32608.
authors.forename: Patricio
authors.initials: P
authors.lastname: Muñoz
authors.affiliation: Department of Plant Sciences, University of California, Davis, Davis, California, 95616.
authors.forename: Pedro J
authors.initials: PJ
authors.lastname: Martínez-García
authors.affiliation: Department of Plant Sciences, University of California, Davis, Davis, California, 95616.
authors.forename: David B
authors.initials: DB
authors.lastname: Neale
authors.affiliation: School of Forest Resources and Conservation, University of Florida, Gainesville, Florida, 32611-0410.
authors.forename: Matias
authors.initials: M
authors.lastname: Kirst
authors.affiliation: Pervasive Technology Institute, Indiana University, Bloomington, Indiana 47408.
authors.forename: Keithanne
authors.initials: K
authors.lastname: Mockaitis
authors.affiliation: Southern Research Station, USDA Forest Service, Saucier, Mississippi, 39574.
authors.forename: C Dana
authors.initials: CD
authors.lastname: Nelson
authors.affiliation: School of Forest Resources and Conservation, University of Florida, Gainesville, Florida, 32611-0410.
authors.forename: Gary F
authors.initials: GF
authors.lastname: Peter
authors.affiliation: School of Forest Resources and Conservation, University of Florida, Gainesville, Florida, 32611-0410 cecht@fs.fed.us.
authors.forename: John M
authors.initials: JM
authors.lastname: Davis
authors.affiliation: Southern Research Station, USDA Forest Service, Saucier, Mississippi, 39574 cecht@fs.fed.us.
authors.forename: Craig S
authors.identifier: http://orcid.org/0000-0001-9330-4051
authors.initials: CS
authors.lastname: Echt
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping; D020224:Expressed Sequence Tags; D005819:Genetic Markers; D018745:Genome, Plant; D005838:Genotype; D015810:Linkage Disequilibrium / Q000235:genetics*; D010375:Pedigree; D010641:Phenotype; D028223:Pinus / Q000235:genetics*; D041603:Pinus taeda / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D059467:Transcriptome
chemical_list: D005819:Genetic Markers
keywords: linkage disequilibrium; linkage mapping; pine; population structure