Development and evaluation of a genome‐wide Coffee 8.5K SNP array and its application for high‐density genetic mapping and for investigating the origin of Coffea arabica L. - Archive ouverte HAL Accéder directement au contenu
Article Dans Une Revue Plant Biotechnology Journal Année : 2019

Development and evaluation of a genome‐wide Coffee 8.5K SNP array and its application for high‐density genetic mapping and for investigating the origin of Coffea arabica L.

Virginie Merot‐l'Anthoene
  • Fonction : Auteur
Olivier Darracq
  • Fonction : Auteur
Vimel Rattina
  • Fonction : Auteur
Maud Lepelley
  • Fonction : Auteur
Laurence Bellanger
  • Fonction : Auteur
Pascal Musoli
  • Fonction : Auteur
Ucu Sumirat
  • Fonction : Auteur
João Ferreira da Costa Neto
  • Fonction : Auteur
Clara Revel
  • Fonction : Auteur
Dominique Crouzillat
  • Fonction : Auteur

Résumé

Coffee species such as Coffea canephora P. (Robusta) and C. arabica L. (Arabica) are important cash crops in tropical regions around the world. C. arabica is an allotetraploid (2n = 4x = 44) originating from a hybridization event of the two diploid species C. canephora and C. eugenioides (2n = 2x = 22). Interestingly, these progenitor species harbour a greater level of genetic variability and are an important source of genes to broaden the narrow Arabica genetic base. Here, we describe the development, evaluation and use of a single-nucleotide polymorphism (SNP) array for coffee trees. A total of 8580 unique and informative SNPs were selected from C. canephora and C. arabica sequencing data, with 40% of the SNP located in annotated genes. In particular, this array contains 227 markers associated to 149 genes and traits of agronomic importance. Among these, 7065 SNPs (~82.3%) were scorable and evenly distributed over the genome with a mean distance of 54.4 Kb between markers. With this array, we improved the Robusta high-density genetic map by adding 1307 SNP markers, whereas 945 SNPs were found segregating in the Arabica mapping progeny. A panel of C. canephora accessions was successfully discriminated and over 70% of the SNP markers were transferable across the three species. Furthermore, the canephora-derived subgenome of C. arabica was shown to be more closely related to C. canephora accessions from northern Uganda than to other current populations. These validated SNP markers and high-density genetic maps will be useful to molecular genetics and for innovative approaches in coffee breeding.
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hal-03211173 , version 1 (28-04-2021)

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Virginie Merot‐l'Anthoene, Rémi Tournebize, Olivier Darracq, Vimel Rattina, Maud Lepelley, et al.. Development and evaluation of a genome‐wide Coffee 8.5K SNP array and its application for high‐density genetic mapping and for investigating the origin of Coffea arabica L.. Plant Biotechnology Journal, 2019, 17 (7), pp.1418-1430. ⟨10.1111/pbi.13066⟩. ⟨hal-03211173⟩
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