Open Access Open Badges Research article

Annotated genetic linkage maps of Pinus pinaster Ait. from a Central Spain population using microsatellite and gene based markers

Marina de Miguel12, Nuria de Maria12, M Ángeles Guevara12, Luis Diaz12, Enrique Sáez-Laguna12, David Sánchez-Gómez1, Emilie Chancerel45, Ismael Aranda1, Carmen Collada23, Christophe Plomion45, José-Antonio Cabezas12 and María-Teresa Cervera12*

Author affiliations

1 INIA-CIFOR, Departamento de Ecología y Genética Forestal, Carretera de la Coruña Km7.5, Madrid, 28040, Spain

2 Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, Madrid, Spain

3 ETSIM, Departamento de Biotecnología, Ciudad Universitaria s/n, Madrid, 28040, Spain

4 INRA, UMR1202 BIOGECO, Cestas, F-33610, France

5 Université de Bordeaux, UMR1202 BIOGECO, Talence, 33170, France

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Citation and License

BMC Genomics 2012, 13:527  doi:10.1186/1471-2164-13-527

Published: 4 October 2012



Pinus pinaster Ait. is a major resin producing species in Spain. Genetic linkage mapping can facilitate marker-assisted selection (MAS) through the identification of Quantitative Trait Loci and selection of allelic variants of interest in breeding populations. In this study, we report annotated genetic linkage maps for two individuals (C14 and C15) belonging to a breeding program aiming to increase resin production. We use different types of DNA markers, including last-generation molecular markers.


We obtained 13 and 14 linkage groups for C14 and C15 maps, respectively. A total of 211 and 215 markers were positioned on each map and estimated genome length was between 1,870 and 2,166 cM respectively, which represents near 65% of genome coverage. Comparative mapping with previously developed genetic linkage maps for P. pinaster based on about 60 common markers enabled aligning linkage groups to this reference map. The comparison of our annotated linkage maps and linkage maps reporting QTL information revealed 11 annotated SNPs in candidate genes that co-localized with previously reported QTLs for wood properties and water use efficiency.


This study provides genetic linkage maps from a Spanish population that shows high levels of genetic divergence with French populations from which segregating progenies have been previously mapped. These genetic maps will be of interest to construct a reliable consensus linkage map for the species. The importance of developing functional genetic linkage maps is highlighted, especially when working with breeding populations for its future application in MAS for traits of interest.

Pinus pinaster; Genetic linkage map; Functional annotation; Microsatellites; SNPs