2016
Genomics and Forest Tree Genetics Conference (2016-05-30-2016-06-03) Arcachon (FRA). In : Book of abstracts. 2016. 134 p.
30 May 2016 Detection of WUE positional candidate genes by combining QTL maps and BAC sequencing with the annotated oak genome sequenceFrancillonne, N. ; Bodénès, C. ; Ehrenmann, F. ; Michotey, C. ; Kremer, A. ; Brendel, O. ; Amselem, J. ; Plomion, C. ; Faivre-Rampant, P.
Water use efficiency, estimated using carbon isotope composition (δ13C), represents the balance between carbon acquisition and water loss. It is an important trait affecting tree growth and economical use of water. Mapping of quantitative trait loci related to δ13C in a Quercus robur full-sib family revealed one major QTL stable across 3 years of measurement. This QTL is located on linkage group (LG) #11 of the male and female parental genotypes of this progeny (Brendel et al, 2008, Trees Genet Genomes 4: 263).
The phenotypic variance explained by the QTL across different years varies between 21% and 31% on the male and between 3% and 5% on the female LG, respectively. More recently, EST-SSR and SNP markers were added to the maps (Bodénès et al, 2012, BMC Plant Biol 12:153, Bodénès et al, 2016, DNA Res In press). On the composite linkage map, the QTL interval was found to be flanked by one SSR marker and one SNP marker. This interval spans 1.8 cM and comprises 3 other SNP markers. These markers were used to screen 2 BAC libraries constructed for the female parent (selected as a reference genotype for WGS) and arranged in 3D pools to identify BAC inserts corresponding to the genome region covered by the QTL confidence interval (Faivre Rampant et al, 2011, BMC Plant Biol 12:153). Five positive BAC clones were selected for insert sequencing. Both markers and BAC insert-sequences were aligned on the Q. robur genome assembly (Plomion et al, 2015, Mol Ecol Res 16: 254). Two scaffolds were identified and annotated using Eugene to integrate ab initio and similarity gene finding software (Sallet et al, 2014, Bioinformatics 30:2659), and FunAnnotPipe an in-house pipeline mainly based on InterproScan to search for patterns/motifs and Blast based comparative genomics.
Annotation identified 30 gene models including 17 known protein-coding genes, providing a first list of positional candidate genes to be further validated by functional genomics and association study.This research was supported by the ANR project H2Oak, ANR-14-CE02-0013.
Creation date: 30 Sep 2016
eZ PublishPublication supervisor: A-F. Adam-Blondon
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