Development and evaluation of the Axiom® IStraw35 384HT array for the allo-octoploid cultivated strawberry Fragaria ×ananassa

S. Verma, N.V. Bassil, E. van de Weg, R.J. Harrison, A. Monfort, J.M. Hidalgo, I. Amaya, B. Denoyes, L.L. Mahoney, T.M. Davis, Z. Fan, S. Knapp, V.M. Whitaker

Research output: Chapter in Book/Report/Conference proceedingConference paperAcademicpeer-review

16 Citations (Scopus)

Abstract

The Axiom® IStraw90 SNP (single nucleotide polymorphism) array was developed to enable high-throughput genotyping in allo-octoploid cultivated strawberry (Fragaria ×ananassa). However, high cost ($ 80-105 sample-1) limits throughput for certain applications. On average the IStraw90 has yielded 50 to 60% usable data points, defined as PHR (Poly High Resolution) and NMH (No Minor Homozygote) marker classes. Thus, an array is needed with a higher percentage of usable data points at a lower cost. We initiated an effort to identify IStraw90 SNP markers that were genetically mapped in one or more strawberry populations from research programs around the world. Seven programs participated in this endeavor. A total of 41,183 SNP probes were submitted to Affymetrix for quality check, 38,506 of which were accommodated on the Axiom® IStraw35 384HT design. In order to assess the performance of the Axiom® IStraw35 384HT array, 384 DNA samples from the University of Florida strawberry breeding program were assayed at a cost of $ 50 per sample, all inclusive. The performance of the array met expectations. More than 87% of markers belonged to the PHR and NMH categories. This array is expected to provide high-quality genome scanning at a more affordable price for strawberry researchers worldwide.

Original languageEnglish
Title of host publication8th International Strawberry Symposium
PublisherInternational Society for Horticultural Science
Pages75-81
Volume1156
ISBN (Electronic)9789462611528
DOIs
Publication statusPublished - 20 Apr 2017
Event8th International Strawberry Symposium - Quebec, Canada
Duration: 13 Aug 201617 Aug 2016

Publication series

NameActa Horticulturae
Volume1156
ISSN (Print)0567-7572

Conference

Conference8th International Strawberry Symposium
CountryCanada
CityQuebec
Period13/08/1617/08/16

Keywords

  • Breeding
  • Genotyping
  • IStraw90
  • Single nucleotide polymorphism (SNP)

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