Development and Evaluation of an Axiom<sup>TM</sup> 60K SNP Array for Almond (<i>Prunus dulcis</i>)
Henri Duval,
Eva Coindre,
Sebastian E. Ramos-Onsins,
Konstantinos G. Alexiou,
Maria J. Rubio-Cabetas,
Pedro J. Martínez-García,
Michelle Wirthensohn,
Amit Dhingra,
Anna Samarina,
Pere Arús
Affiliations
Henri Duval
Unité de Génétique et Amélioration des Fruits et Légumes (GAFL), INRAE (French National Research Institute for Agriculture, Food and Environment), 84143 Montfavet, France
Eva Coindre
Unité de Génétique et Amélioration des Fruits et Légumes (GAFL), INRAE (French National Research Institute for Agriculture, Food and Environment), 84143 Montfavet, France
Sebastian E. Ramos-Onsins
Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Carrer de la Vall Moronta, Edifici CRAG, Campus UAB, Cerdanyola del Valles, 08193 Barcelona, Spain
Konstantinos G. Alexiou
Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Carrer de la Vall Moronta, Edifici CRAG, Campus UAB, Cerdanyola del Valles, 08193 Barcelona, Spain
Maria J. Rubio-Cabetas
CITA (Agrifood Research and Technology Centre of Aragon), Department of Plant Science, Avda. Montañana 930, 50059 Zaragoza, Spain
Pedro J. Martínez-García
CEBAS (Centro de Edafología y Biología Aplicada del Segura), CSIC, Department of Plant Breeding, Campus Universitario de Espinardo, 30100 Espinardo, Spain
Michelle Wirthensohn
Waite Research Institute, University of Adelaide, PMB 1 Glen, Osmond, SA 5064, Australia
Amit Dhingra
Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
Anna Samarina
Thermo Fisher Scientific, Frankfurter Str. 129B, 64293 Darmstadt, Germany
Pere Arús
Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Carrer de la Vall Moronta, Edifici CRAG, Campus UAB, Cerdanyola del Valles, 08193 Barcelona, Spain
A high-density single nucleotide polymorphism (SNP) array is essential to enable faster progress in plant breeding for new cultivar development. In this regard, we have developed an Axiom 60K almond SNP array by resequencing 81 almond accessions. For the validation of the array, a set of 210 accessions were genotyped and 82.8% of the SNPs were classified in the best recommended SNPs. The rate of missing data was between 0.4% and 2.7% for the almond accessions and less than 15.5% for the few peach and wild accessions, suggesting that this array can be used for peach and interspecific peach × almond genetic studies. The values of the two SNPs linked to the RMja (nematode resistance) and SK (bitterness) genes were consistent. We also genotyped 49 hybrids from an almond F2 progeny and could build a genetic map with a set of 1159 SNPs. Error rates, less than 1%, were evaluated by comparing replicates and by detection of departures from Mendelian inheritance in the F2 progeny. This almond array is commercially available and should be a cost-effective genotyping tool useful in the search for new genes and quantitative traits loci (QTL) involved in the control of agronomic traits.
