Open Access Research article

Genetic control of functional traits related to photosynthesis and water use efficiency in Pinus pinaster Ait. drought response: integration of genome annotation, allele association and QTL detection for candidate gene identification

Marina de Miguel12, José-Antonio Cabezas12, Nuria de María12, David Sánchez-Gómez1, María-Ángeles Guevara12, María-Dolores Vélez12, Enrique Sáez-Laguna12, Luis-Manuel Díaz12, Jose-Antonio Mancha1, María-Carmen Barbero12, Carmen Collada23, Carmen Díaz-Sala4, Ismael Aranda1 and María-Teresa Cervera12*

Author Affiliations

1 Departamento de Ecología y Genética Forestal, INIA-CIFOR. Ctra, de La Coruña Km 7.5, 28040 Madrid, Spain

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

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

4 Departamento de Ciencias de la Vida, Universidad de Alcalá, Ctra. de Barcelona Km 33.6, 28871 Alcalá de Henares, Madrid, Spain

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BMC Genomics 2014, 15:464  doi:10.1186/1471-2164-15-464

Published: 12 June 2014



Understanding molecular mechanisms that control photosynthesis and water use efficiency in response to drought is crucial for plant species from dry areas. This study aimed to identify QTL for these traits in a Mediterranean conifer and tested their stability under drought.


High density linkage maps for Pinus pinaster were used in the detection of QTL for photosynthesis and water use efficiency at three water irrigation regimes. A total of 28 significant and 27 suggestive QTL were found. QTL detected for photochemical traits accounted for the higher percentage of phenotypic variance. Functional annotation of genes within the QTL suggested 58 candidate genes for the analyzed traits. Allele association analysis in selected candidate genes showed three SNPs located in a MYB transcription factor that were significantly associated with efficiency of energy capture by open PSII reaction centers and specific leaf area.


The integration of QTL mapping of functional traits, genome annotation and allele association yielded several candidate genes involved with molecular control of photosynthesis and water use efficiency in response to drought in a conifer species. The results obtained highlight the importance of maintaining the integrity of the photochemical machinery in P. pinaster drought response.

Candidate gene; Drought; Genome annotation; Photochemistry; Photosynthesis; Pinus pinaster; QTL; Water use efficiency