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High‐density SNP assay development for genetic analysis in maritime pine ( P inus pinaster )
Author(s) -
Plomion C.,
Bartholomé J.,
Lesur I.,
Boury C.,
RodríguezQuilón I.,
Lagraulet H.,
Ehrenmann F.,
Bouffier L.,
Gion J. M.,
Grivet D.,
Miguel M.,
María N.,
Cervera M. T.,
Bagnoli F.,
Isik F.,
Vendramin G. G.,
GonzálezMartínez S. C.
Publication year - 2016
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12464
Subject(s) - biology , snp genotyping , genetic diversity , single nucleotide polymorphism , population , linkage disequilibrium , population genetics , genetic variation , evolutionary biology , genetics , gene , genotype , demography , sociology
Maritime pine provides essential ecosystem services in the south‐western M editerranean 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 ( F 2) pedigree, (ii) the F rench breeding population and (iii) natural populations from P ortugal and the F rench A tlantic coast. A large proportion of the exploitable SNP s (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 SNP s, natural and breeding populations from the F rench gene pool exhibited similar level of genetic diversity. Population genetics and structure analyses based on 3981 SNP markers common to the P ortuguese and F rench gene pools revealed high levels of differentiation, leading to the identification of a set of highly differentiated SNP s that could be used for seed provenance certification. Finally, we discuss how the validated SNP s 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.