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Genome-wide association mapping of sexual incompatibility genes in cacao (Theobroma cacao L.)

da Silva Marcos Ramos, Clément Didier, Gramacho Karina Peres, Monteiro Wilson Reis, Argout Xavier, Lanaud Claire, Lopes Uilson Vanderlei. 2016. Genome-wide association mapping of sexual incompatibility genes in cacao (Theobroma cacao L.). Tree Genetics and Genomes, 12 (3):62, 13 p.

Journal article ; Article de revue à facteur d'impact
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DOI-10-1007s11295-016-1012-0.pdf

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Quartile : Q1, Sujet : HORTICULTURE / Quartile : Q2, Sujet : FORESTRY / Quartile : Q3, Sujet : GENETICS & HEREDITY

Abstract : Sexual compatibility limits the production of cacao plantations, being an important selection criterion in breeding programs. However, the current method for characterizing compatibility, based on the frequency of flower setting after controlled pollination, is time consuming, requiring a long time to identify self-compatible individuals. The identification of molecular markers in genomic regions can be an alternative to allow early selection of self-compatible plants. The present study aimed to identify SNP markers associated with sexual compatibility in cacao, by utilizing genome-wide association (GWAS) mapping. A population of 295 individuals mostly from third-generation breeding populations, but also founder clones, was used. This population was phenotypically characterized by hand pollinating 8199 flowers and evaluating the flower retention 15 days after pollination. In addition, leaf samples of each individual were collected and DNA extracted for genotyping by sequencing, generating 5301 SNP markers after cleaning. Genome-wide association mapping analysis was performed using Synbreed, GCTA, and TASSEL softwares. Significant markers associated to incompatibility, likely in strong linkage disequilibrium, were found within a region of 196 kb, in the proximal end of chromosome 4, suggesting the existence of a major gene in that region. However, this result should be validated in a larger population, considering that only 295 trees were used here. When the SNP effects were treated as random in the estimation process, many other regions in the genome appears to be involved with sexual incompatibility in cacao. Candidate genes were found not only in the proximal end of chromosome 4 but also spread in several other regions of the genome. (Résumé d'auteur)

Mots-clés Agrovoc : Theobroma cacao, Reproduction sexuée, Sélection précoce, Marqueur génétique, Génotype, Carte génétique, Autocompatibilité, Gène, Phénotype, Génétique des populations, Génie génétique, Pollinisation, Incompatibilité pollinique

Mots-clés géographiques Agrovoc : Brésil, Bahia

Mots-clés complémentaires : Séquencage

Classification Agris : F30 - Plant genetics and breeding
F63 - Plant physiology - Reproduction
U30 - Research methods

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

Auteurs et affiliations

Source : Cirad-Agritrop (https://agritrop.cirad.fr/580962/)

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