NDLI: 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.

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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.

Content Provider	Scilit
Author	Merot‐L'Anthoene, Virginie Tournebize, Rémi Darracq, Olivier Rattina, Vimel Lepelley, Maud Bellanger, Laurence Tranchant‐Dubreuil, Christine Coulée, Manon Pégard, Marie Metairon, Sylviane Fournier, Coralie Stoffelen, Piet Janssens, Steven B. Kiwuka, Catherine Musoli, Pascal Sumirat, Ucu Legnaté, Hyacinthe Kambale, Jean‐Léon Neto, João Ferreira Da Costa Revel, Clara de Kochko, Alexandre Descombes, Patrick Crouzillat, Dominique Poncet, Valérie
Copyright Year	2018
Description	Journal: Plant Biotechnology Journal 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 harbor 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 8,580 unique and informative SNPs were selected from C. canephora and C. arabica sequencing data, with 40% of the SNPs located in annotated genes. In particular, this array contains 227 markers associated to 149 genes and traits of agronomic importance. Among these, 7,065 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 1,307 SNP markers, while 945 SNPs were found segregating in the Arabica mapping progeny. A panel of C. canephora accessions was successfully discriminated and over 70% of the SNPs 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.
Related Links	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6576098/pdf
Ending Page	1430
Page Count	13
Starting Page	1418
e-ISSN	14677652
DOI	10.1111/pbi.13066
Journal	Plant Biotechnology Journal
Issue Number	7
Volume Number	17
Language	English
Publisher	Wiley-Blackwell
Publisher Date	2018-12-24
Access Restriction	Open
Subject Keyword	Journal: Plant Biotechnology Journal Genotyping Array Single Nucleotide Polymorphism (snp) Coffea Arabica Origin C. Canephora C. Eugenioides Coffea Diversity Genetic Map
Content Type	Text
Resource Type	Article

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