High-density SNP assay development for genetic analysis in maritime pine (Pinus pinaster)

Molecular Ecology Resources

Volume 16, Issue 2, 1 March 2016, Pages 574-587

Plomion, C.^ab , 

Bartholomé, J.^ab, 

Lesur, I.^ac, 

Boury, C.^ab, 

Rodríguez-Quilón, I.^d, 

Lagraulet, H.^ab, 

Ehrenmann, F.^ab, 

Bouffier, L.^ab, 

Gion, J.M.^ae, 

Grivet, D.^d, 

de Miguel, M.^ab, 

de María, N.^d, 

Cervera, M.T.^d, 

Bagnoli, F.^f, 

Isik, F.^g, 

Vendramin, G.G.^f, 

González-Martínez, S.C.^d

 

^a  BIOGECO, UMR 1202, INRA, Cestas, France
^b  BIOGECO, UMR 1202, University of Bordeaux, Talence,

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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. © 2016 John Wiley & Sons Ltd.

Author keywords

Linkage mapping; Maritime pine; Population genetics; Single nucleotide polymorphism

ISSN: 1755098XSource Type: Journal Original language: English

DOI: 10.1111/1755-0998.12464Document Type: Article

Publisher: Blackwell Publishing Ltd