Cultivated apple (Malus × domestica Borkh.) is one of the most important fruit crops in temperate regions, and has great economic and cultural value. The apple genome is highly heterozygous and has undergone a recent duplication which, combined with a rapid linkage disequilibrium decay, makes it difficult to perform genome-wide association (GWA) studies. Single nucleotide polymorphism arrays offer highly multiplexed assays at a relatively low cost per data point and can be a valid tool for the identification of the markers associated with traits of interest. Here, we describe the development and validation of a 487K SNP Affymetrix Axiom® genotyping array for apple and discuss its potential applications. The array has been built from the high-depth resequencing of 63 different cultivars covering most of the genetic diversity in cultivated apple. The SNPs were chosen by applying a focal points approach to enrich genic regions, but also to reach a uniform coverage of non-genic regions. A total of 1324 apple accessions, including the 92 progenies of two mapping populations, have been genotyped with the Axiom®Apple480K to assess the effectiveness of the array. A large majority of SNPs (359 994 or 74%) fell in the stringent class of poly high resolution polymorphisms. We also devised a filtering procedure to identify a subset of 275K very robust markers that can be safely used for germplasm surveys in apple. The Axiom®Apple480K has now been commercially released both for public and proprietary use and will likely be a reference tool for GWA studies in apple.

Bianco, L.; Cestaro, A.; Linsmith, G.; Muranty, H.; Denance, C.; Théron, A.; Poncet, C.; Micheletti, D.; Kerschbamer, E.; Di Pierro, E.A.; Larger, S.; Pindo, M.; van de Weg, E.; Davassi, A.; Laurens, F.; Velasco, R.; Durel, C.; Troggio, M. (2016). Development and validation of the Axiom®Apple480K SNP genotyping array. PLANT JOURNAL, 86 (1): 62-74. doi: 10.1111/tpj.13145 handle: http://hdl.handle.net/10449/29460

Development and validation of the Axiom®Apple480K SNP genotyping array

Bianco, Luca;Cestaro, Alessandro;Linsmith, Gareth;Micheletti, Diego;Kerschbamer, Emanuela;Di Pierro, E. A.;Larger, Simone;Pindo, Massimo;Velasco, Riccardo;Troggio, Michela
2016-01-01

Abstract

Cultivated apple (Malus × domestica Borkh.) is one of the most important fruit crops in temperate regions, and has great economic and cultural value. The apple genome is highly heterozygous and has undergone a recent duplication which, combined with a rapid linkage disequilibrium decay, makes it difficult to perform genome-wide association (GWA) studies. Single nucleotide polymorphism arrays offer highly multiplexed assays at a relatively low cost per data point and can be a valid tool for the identification of the markers associated with traits of interest. Here, we describe the development and validation of a 487K SNP Affymetrix Axiom® genotyping array for apple and discuss its potential applications. The array has been built from the high-depth resequencing of 63 different cultivars covering most of the genetic diversity in cultivated apple. The SNPs were chosen by applying a focal points approach to enrich genic regions, but also to reach a uniform coverage of non-genic regions. A total of 1324 apple accessions, including the 92 progenies of two mapping populations, have been genotyped with the Axiom®Apple480K to assess the effectiveness of the array. A large majority of SNPs (359 994 or 74%) fell in the stringent class of poly high resolution polymorphisms. We also devised a filtering procedure to identify a subset of 275K very robust markers that can be safely used for germplasm surveys in apple. The Axiom®Apple480K has now been commercially released both for public and proprietary use and will likely be a reference tool for GWA studies in apple.
SNP chip
Malus 3 domestica Borkh.
Genotyping
Genome-wide association study
Validation
Linkage mapping
Settore AGR/07 - GENETICA AGRARIA
2016
Bianco, L.; Cestaro, A.; Linsmith, G.; Muranty, H.; Denance, C.; Théron, A.; Poncet, C.; Micheletti, D.; Kerschbamer, E.; Di Pierro, E.A.; Larger, S.; Pindo, M.; van de Weg, E.; Davassi, A.; Laurens, F.; Velasco, R.; Durel, C.; Troggio, M. (2016). Development and validation of the Axiom®Apple480K SNP genotyping array. PLANT JOURNAL, 86 (1): 62-74. doi: 10.1111/tpj.13145 handle: http://hdl.handle.net/10449/29460
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10449/29460
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