{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Merot-L'anthoene V"],"funding":["Agropolis Fondation"],"pagination":["1418-1430"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC6576098"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["17(7)"],"pubmed_abstract":["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."],"journal":["Plant biotechnology journal"],"pubmed_title":["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."],"pmcid":["PMC6576098"],"funding_grant_id":["ID 1002‐009","ID 1402‐003"],"pubmed_authors":["Descombes P","Tournebize R","Metairon S","Crouzillat D","Kambale JL","Stoffelen P","Ferreira da Costa Neto J","de Kochko A","Bellanger L","Revel C","Pegard M","Fournier C","Kiwuka C","Musoli P","Poncet V","Legnate H","Darracq O","Coulee M","Janssens SB","Merot-L'anthoene V","Lepelley M","Tranchant-Dubreuil C","Sumirat U","Rattina V"],"additional_accession":[]},"is_claimable":false,"name":"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.","description":"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.","dates":{"release":"2019-01-01T00:00:00Z","publication":"2019 Jul","modification":"2026-03-16T14:56:42.883Z","creation":"2025-08-15T03:07:27.149Z"},"accession":"S-EPMC6576098","cross_references":{"pubmed":["30582651"],"doi":["10.1111/pbi.13066"]}}