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

Abstract

BackgroundUnderstanding 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.ResultsHigh 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-464) contains supplementary material, which is available to authorized users.

Haploids in Conifer Species: Characterization and Chromosomal Integrity of a Maritime Pine Cell Line

“…In addition, a set of 64 SNPs located on the 23 remaining chromosome arms of the Oria 6 genetic map [28] was selected to further analyze chromosome integrity. Thus, new primers were designed flanking these selected 64 SNPs.…”

“…SNP and SSR molecular markers covering all chromosome arms were identified based on their positions on the Oria 6 genetic map [28] (Figure 2). Allelic composition of the SSR loci was determined by electrophoresis in acrylamide gels according to de Miguel et al [28]. SNPs were genotyped by sequencing a region of 200-400 bp flanking each targeted site amplified by PCR using specific primers.…”

“…Pinus pinaster (maritime pine) is an important conifer in Mediterranean regions with a high ecological and socio-economical value [28], but is also one of the most advanced models for conifer research. As a result, several collaborative initiatives to sequence the genome of this species have been launched in the last few years [29].…”

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“…Moreover, since the pioneering work of Lepoittevin et al (2010), describing the design of the first multiplex single nucleotide polymorphism (SNP) genotyping assay in maritime pine, medium-scale SNP arrays have been developed (Tables S1 and S2, Supporting information). These assays have made it possible to characterize hundreds of trees, at hundreds of loci, for various applications: nucleotide diversity analysis , QTL detection (de Miguel et al 2014), association mapping , environmental association and linkage map construction .…”