title: Nucleotide polymorphisms in a pine ortholog of the Arabidopsis degrading enzyme cellulase KORRIGAN are associated with early growth performance in Pinus pinaster.
abstract: We have carried out a candidate-gene-based association genetic study in Pinus pinaster Aiton and evaluated the predictive performance for genetic merit gain of the most significantly associated genes and single nucleotide polymorphisms (SNPs). We used a second generation 384-SNP array enriched with candidate genes for growth and wood properties to genotype mother trees collected in 20 natural populations covering most of the European distribution of the species. Phenotypic data for total height, polycyclism, root-collar diameter and biomass were obtained from a replicated provenance-progeny trial located in two sites with contrasting environments (Atlantic vs Mediterranean climate). General linear models identified strong associations between growth traits (total height and polycyclism) and four SNPs from the korrigan candidate gene, after multiple testing corrections using false discovery rate. The combined genomic breeding value predictions assessed for the four associated korrigan SNPs by ridge regression-best linear unbiased prediction (RR-BLUP) and cross-validation accounted for up to 8 and 15% of the phenotypic variance for height and polycyclic growth, respectively, and did not improve adding SNPs from other growth-related candidate genes. For root-collar diameter and total biomass, they accounted for 1.6 and 1.1% of the phenotypic variance, respectively, but increased to 15 and 4.1% when other SNPs from lp3.1, lp3.3 and cad were included in RR-BLUP models. These results point towards a desirable integration of candidate-gene studies as a means to pre-select relevant markers, and aid genomic selection in maritime pine breeding programs.
authors.affiliation: Department of Forest Ecology and Genetics, INIA-CIFOR, 28040 Madrid, Spain Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, 28040 Madrid, Spain.
authors.forename: José Antonio
authors.initials: JA
authors.lastname: Cabezas
authors.affiliation: Department of Forest Ecology and Genetics, INIA-CIFOR, 28040 Madrid, Spain INRA, UMR1202 BIOGECO, F-33610 Cestas, France University of Bordeaux, UMR1202 BIOGECO, F-33170 Talence, France.
authors.forename: Santiago C
authors.initials: SC
authors.lastname: González-Martínez
authors.affiliation: Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, 28040 Madrid, Spain Departamento de Biotecnología, ETSIM, Ciudad Universitaria s/n 28040 Madrid, Spain.
authors.forename: Carmen
authors.initials: C
authors.lastname: Collada
authors.affiliation: Department of Forest Ecology and Genetics, INIA-CIFOR, 28040 Madrid, Spain Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, 28040 Madrid, Spain.
authors.forename: María Angeles
authors.initials: MA
authors.lastname: Guevara
authors.affiliation: INRA, UMR1202 BIOGECO, F-33610 Cestas, France University of Bordeaux, UMR1202 BIOGECO, F-33170 Talence, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Boury
authors.affiliation: Department of Forest Ecology and Genetics, INIA-CIFOR, 28040 Madrid, Spain Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, 28040 Madrid, Spain.
authors.forename: Nuria
authors.initials: N
authors.lastname: de María
authors.affiliation: INRA, UMR1202 BIOGECO, F-33610 Cestas, France University of Bordeaux, UMR1202 BIOGECO, F-33170 Talence, France.
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Eveno
authors.affiliation: Department of Forest Ecology and Genetics, INIA-CIFOR, 28040 Madrid, Spain Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, 28040 Madrid, Spain.
authors.forename: Ismael
authors.initials: I
authors.lastname: Aranda
authors.affiliation: INRA, UMR1202 BIOGECO, F-33610 Cestas, France University of Bordeaux, UMR1202 BIOGECO, F-33170 Talence, France.
authors.forename: Pauline H
authors.initials: PH
authors.lastname: Garnier-Géré
authors.affiliation: INRA, UMR1202 BIOGECO, F-33610 Cestas, France University of Bordeaux, UMR1202 BIOGECO, F-33170 Talence, France.
authors.forename: Jean
authors.initials: J
authors.lastname: Brach
authors.affiliation: Department of Forest Ecology and Genetics, INIA-CIFOR, 28040 Madrid, Spain Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, 28040 Madrid, Spain.
authors.forename: Ricardo
authors.initials: R
authors.lastname: Alía
authors.affiliation: INRA, UMR1202 BIOGECO, F-33610 Cestas, France University of Bordeaux, UMR1202 BIOGECO, F-33170 Talence, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Plomion
authors.affiliation: Department of Forest Ecology and Genetics, INIA-CIFOR, 28040 Madrid, Spain Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, 28040 Madrid, Spain cervera@inia.es.
authors.forename: María Teresa
authors.initials: MT
authors.lastname: Cervera
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics; D001483:Base Sequence; D001947:Breeding; D002480:Cellulase / Q000235:genetics*; D018745:Genome, Plant; D006239:Haplotypes / Q000235:genetics; D008565:Membrane Proteins / Q000235:genetics; D008969:Molecular Sequence Data; D028223:Pinus / Q000201:enzymology* / Q000235:genetics / Q000254:growth & development*; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017386:Sequence Homology, Amino Acid
chemical_list: D029681:Arabidopsis Proteins; C429844:KOR1 protein, Arabidopsis; D008565:Membrane Proteins; D010940:Plant Proteins; D002480:Cellulase
keywords: SNP; association genetics; candidate gene; genomic selection; maritime pine; wood formation