title: High-density SNP assay development for genetic analysis in maritime pine (Pinus pinaster).
abstract: Maritime pine provides essential ecosystem services in the south-western Mediterranean basin, where it covers around 4 million ha. Its scattered distribution over a range of environmental conditions makes it an ideal forest tree species for studies of local adaptation and evolutionary responses to climatic change. Highly multiplexed single nucleotide polymorphism (SNP) genotyping arrays are increasingly used to study genetic variation in living organisms and for practical applications in plant and animal breeding and genetic resource conservation. We developed a 9k Illumina Infinium SNP array and genotyped maritime pine trees from (i) a three-generation inbred (F2) pedigree, (ii) the French breeding population and (iii) natural populations from Portugal and the French Atlantic coast. A large proportion of the exploitable SNPs (2052/8410, i.e. 24.4%) segregated in the mapping population and could be mapped, providing the densest ever gene-based linkage map for this species. Based on 5016 SNPs, natural and breeding populations from the French gene pool exhibited similar level of genetic diversity. Population genetics and structure analyses based on 3981 SNP markers common to the Portuguese and French gene pools revealed high levels of differentiation, leading to the identification of a set of highly differentiated SNPs that could be used for seed provenance certification. Finally, we discuss how the validated SNPs could facilitate the identification of ecologically and economically relevant genes in this species, improving our understanding of the demography and selective forces shaping its natural genetic diversity, and providing support for new breeding strategies.
authors.affiliation: BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.|BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France.
authors.forename: C
authors.initials: C
authors.lastname: Plomion
authors.affiliation: BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.|BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France.
authors.forename: J
authors.initials: J
authors.lastname: Bartholomé
authors.affiliation: BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.|HelixVenture, F-33700, Mérignac, France.
authors.forename: I
authors.initials: I
authors.lastname: Lesur
authors.affiliation: BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.|BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France.
authors.forename: C
authors.initials: C
authors.lastname: Boury
authors.affiliation: Forest Research Centre, INIA, E-28040, Madrid, Spain.
authors.forename: I
authors.initials: I
authors.lastname: Rodríguez-Quilón
authors.affiliation: BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.|BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France.
authors.forename: H
authors.initials: H
authors.lastname: Lagraulet
authors.affiliation: BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.|BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France.
authors.forename: F
authors.initials: F
authors.lastname: Ehrenmann
authors.affiliation: BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.|BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France.
authors.forename: L
authors.initials: L
authors.lastname: Bouffier
authors.affiliation: BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.|UMR AGAP, CIRAD, F-33612, Cestas, France.
authors.forename: J M
authors.initials: JM
authors.lastname: Gion
authors.affiliation: Forest Research Centre, INIA, E-28040, Madrid, Spain.
authors.forename: D
authors.initials: D
authors.lastname: Grivet
authors.affiliation: BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.|BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France.
authors.forename: M
authors.initials: M
authors.lastname: de Miguel
authors.affiliation: Forest Research Centre, INIA, E-28040, Madrid, Spain.
authors.forename: N
authors.initials: N
authors.lastname: de María
authors.affiliation: Forest Research Centre, INIA, E-28040, Madrid, Spain.
authors.forename: M T
authors.initials: MT
authors.lastname: Cervera
authors.affiliation: Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino (FI), Italy.
authors.forename: F
authors.initials: F
authors.lastname: Bagnoli
authors.affiliation: Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA.
authors.forename: F
authors.initials: F
authors.lastname: Isik
authors.affiliation: Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino (FI), Italy.
authors.forename: G G
authors.initials: GG
authors.lastname: Vendramin
authors.affiliation: Forest Research Centre, INIA, E-28040, Madrid, Spain.
authors.forename: S C
authors.initials: SC
authors.lastname: González-Martínez
mesh_terms: D005602:France; D014644:Genetic Variation; D060005:Genotyping Techniques / Q000379:methods*; D019083:Mediterranean Region; D028223:Pinus / Q000145:classification* / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D011174:Portugal; D017422:Sequence Analysis, DNA
keywords: linkage mapping; maritime pine; population genetics; single nucleotide polymorphism