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Genetic mapping of EST-derived simple sequence repeats (EST-SSRs) to identify QTL for leaf morphological characters in a Quercus robur full-sib family

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Abstract

The availability of genomic resources such as expressed sequence tag-derived simple sequence repeat (EST-SSR) markers in adaptive genes with high transferability across related species allows the construction of genetic maps and the comparison of genome structure and quantitative trait loci (QTL) positions. In the present study, genetic linkage maps were constructed for both parents of a Quercus robur × Q. robur ssp. slavonica full-sib pedigree. A total of 182 markers (61 AFLPs, 23 nuclear SSRs, 98 EST-SSRs) and 172 markers (49 AFLPs, 21 nSSRs, 101 EST-SSRs, 1 isozyme) were mapped on the female and male linkage maps, respectively. The total map length and average marker spacing were 1,038 and 5.7 cM for the female map and 998.5 and 5.8 cM for the male map. A total of 68 nuclear SSRs and EST-SSRs segregating in both parents allowed to define homologous linkage groups (LG) between both parental maps. QTL for leaf morphological traits were mapped on all 12 LG at a chromosome-wide level and on 6 LG at a genome-wide level. The phenotypic effects explained by each single QTL ranged from 4.0 % for leaf area to 15.8 % for the number of intercalary veins. QTL clusters for leaf characters that discriminate between Q. robur and Quercus petraea were mapped reproducibly on three LG, and some putative candidate genes among potentially many others were identified on LG3 and LG5. Genetic linkage maps based on EST-SSRs can be valuable tools for the identification of genes involved in adaptive trait variation and for comparative mapping.

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Acknowledgments

The authors are grateful to Olga Artes, Oleksandra Dolynska, and Christine Radler for their technical support in the lab and Martha Fernandez for her help in measuring leaves. Part of the study was supported by the European Commission under the FP6 program (Network of Excellence EVOLTREE (No. 016322, Evolution of Trees as Drivers of Terrestrial Biodiversity, http://www.evoltree.eu).

Data Archiving Statement

Data used in this manuscript have been made publicly available through the Quercus Portal (https://w3.pierroton.inra.fr/QuercusPortal/index.php) and will be submitted to the TreeGenes Database.

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Authors and Affiliations

  1. Michigan Technological University, 1400 Townsend Drive, 49931, Houghton, MI, USA

    Oliver Gailing

  2. Büsgen Institute, Forest Genetic and Forest Tree Breeding, Georg-August-Universität Göttingen, Büsgenweg 2, 37077, Göttingen, Germany

    Oliver Gailing & Reiner Finkeldey

  3. UMR 1202 Biodiversité Gènes et Communautés, INRA 69, route d’Arcachon, 33612, Cestas Cedex, France

    Catherine Bodénès, Antoine Kremer & Christophe Plomion

  4. Université de Bordeaux, UMR 1202 BIOGECO, 33610, Cestas, France

    Catherine Bodénès, Antoine Kremer & Christophe Plomion

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  1. Oliver Gailing
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  2. Catherine Bodénès
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  3. Reiner Finkeldey
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  4. Antoine Kremer
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Correspondence to Oliver Gailing.

Additional information

Communicated by S. González-Martínez

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Supplementary Table 1

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Supplementary Table 2

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Supplementary Table 3

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Supplementary Table 4

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Supplementary Fig. 1

Genetic linkage maps showing 12 male (LG1m to LG12m) and 12 female (LG1f to LG12f) linkage groups. Markers that are shared between male and female linkage groups are connected by lines. Markers showing significant segregation distortion in the male or female parent are indicated by asterisks. AFLP markers are named using the nomenclature by Keygene and indicating the size of the fragment (e.g. P13/M66_112, see Gailing et al. 2008). EST-SSR markers are named according to Durand et al. (2010) using identifiers for the labs in which the markers were developed (e.g. PIE, FIR, GOT, POR). Indices a, b, etc. are added to names (e.g. POR045b) when more than one gene locus was amplified. *: 0.1 level, **: 0.05 level, ***: 0.01 level, ****: 0.005 level, *****: 0.001 level, ******: 0.0005 level (PPTX 785 kb)

Supplementary Fig. 2

QTL for leaf traits on male and female linkage groups. Arrows indicate the positions of the maximum LOD score and vertical lines show the map intervals with LOD scores above the 5 % chromosome-wide significance threshold. Frames show QTL at genome-wide significance level (p < 0.05), other QTL were significant only at the chromosome level (p < 0.05). QTL identified in at least two years on the same linkage group considering both male and female maps are labeled in bold and red. Markers showing significant segregation distortion in the male or female parent are indicated by asterisks. *: 0.1 level, **: 0.05 level, ***: 0.01 level, ****: 0.005 level, *****: 0.001 level, ******: 0.0005 level (PPTX 717 kb)

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Gailing, O., Bodénès, C., Finkeldey, R. et al. Genetic mapping of EST-derived simple sequence repeats (EST-SSRs) to identify QTL for leaf morphological characters in a Quercus robur full-sib family. Tree Genetics & Genomes 9, 1361–1367 (2013). https://doi.org/10.1007/s11295-013-0633-9

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