title: A high-resolution reference genetic map positioning 8.8 K genes for the conifer white spruce: structural genomics implications and correspondence with physical distance.
abstract: Over the last decade, extensive genetic and genomic resources have been developed for the conifer white spruce (Picea glauca, Pinaceae), which has one of the largest plant genomes (20 Gbp). Draft genome sequences of white spruce and other conifers have recently been produced, but dense genetic maps are needed to comprehend genome macrostructure, delineate regions involved in quantitative traits, complement functional genomic investigations, and assist the assembly of fragmented genomic sequences. A greatly expanded P. glauca composite linkage map was generated from a set of 1976 full-sib progeny, with the positioning of 8793 expressed genes. Regions with significant low or high gene density were identified. Gene family members tended to be mapped on the same chromosomes, with tandemly arrayed genes significantly biased towards specific functional classes. The map was integrated with transcriptome data surveyed across eight tissues. In total, 69 clusters of co-expressed and co-localising genes were identified. A high level of synteny was found with pine genetic maps, which should facilitate the transfer of structural information in the Pinaceae. Although the current white spruce genome sequence remains highly fragmented, dozens of scaffolds encompassing more than one mapped gene were identified. From these, the relationship between genetic and physical distances was examined and the genome-wide recombination rate was found to be much smaller than most estimates reported for angiosperm genomes. This gene linkage map shall assist the large-scale assembly of the next-generation white spruce genome sequence and provide a reference resource for the conifer genomics community.
authors.affiliation: Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Pavy
authors.affiliation: Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380, Stn. Sainte-Foy, Québec, QC, G1V 4C7, Canada.
authors.forename: Manuel
authors.initials: M
authors.lastname: Lamothe
authors.affiliation: Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada.|Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380, Stn. Sainte-Foy, Québec, QC, G1V 4C7, Canada.
authors.forename: Betty
authors.initials: B
authors.lastname: Pelgas
authors.affiliation: Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada.
authors.forename: France
authors.initials: F
authors.lastname: Gagnon
authors.affiliation: Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.
authors.forename: Inanç
authors.initials: I
authors.lastname: Birol
authors.affiliation: Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
authors.forename: Joerg
authors.initials: J
authors.lastname: Bohlmann
authors.affiliation: Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada.|Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, 0X1 3RB, UK.
authors.forename: John
authors.initials: J
authors.lastname: Mackay
authors.affiliation: Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada.|Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380, Stn. Sainte-Foy, Québec, QC, G1V 4C7, Canada.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Isabel
authors.affiliation: Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada.
authors.forename: Jean
authors.initials: J
authors.lastname: Bousquet
mesh_terms: D002874:Chromosome Mapping / Q000379:methods; D019295:Computational Biology / Q000379:methods; D018744:DNA, Plant / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics / Q000379:methods; D028222:Picea / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D026801:Synteny
chemical_list: D018744:DNA, Plant
keywords: Picea glauca [Moench] Voss; conifer genome; expression clusters; gene density; linkage maps; recombination rate; scaffolds; single nucleotide polymorphisms; synteny; tandemly arrayed genes