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Research Project: Management of Temperate-Adapted Fruit, Nut, and Specialty Crop Genetic Resources and Associated Information

Location: National Clonal Germplasm Repository

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

Author
item Verma, Sujeet - University Of Florida
item Bassil, Nahla
item Van De Weg, Eric - Wageningen Ur
item Harrison, Richard - East Malling Research
item Monfort, Amparo - Institute De Recerca I Tecnologia Agroalimentaries (IRTA)
item Amaya, Iraida - Ifapa Centro Alameda Del Obispo
item Denoyes, Beatrice - Institut National De La Recherche Agronomique (INRA)
item Mahoney, Lise - University Of New Hampshire
item Davis, Tom - University Of New Hampshire
item Fan, Zhen - University Of Florida
item Knapp, Steve - University Of California
item Whitaker, Vance - University Of Florida

Submitted to: Acta Horticulturae
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/15/2016
Publication Date: 4/20/2017
Citation: Verma, S., Bassil, N.V., van de Weg, E., Harrison, R., Monfort, A., Amaya, I., Denoyes, B., Mahoney, L., Davis, T., Fan, Z., Knapp, S., Whitaker, V. 2017. Development and evaluation of the Axiom® IStraw35 384HT array for the allo-octoploid cultivated strawberry Fragaria ×ananassa. Acta Horticulturae. 1156:75-82. doi: 10.17660/ActaHortic.2017.1156.10.

Interpretive Summary: The RosBREED consortium in collaboration with the international strawberry research community have collborated on developing tools for characterizing DNA sequences. This characterization is an important step in the development of genetic tools to improve the efficiency of plant breeding. This goal was met by the public release in 2014 of a commercially available computer chip named the IStraw90 that has been used by the worldwide scientific community. To decrease the cost of this tool, we initiated an effort to identify IStraw90 DNA sequences that appeared to work well in one or more strawberry populations from seven research programs around the world. We describe the development of a cheaper version of the IStraw90 computer chip in strawberry and also report report its performance in 384 samples from the University of Florida breeding program. This array is expected to provide high-quality genotyping at a more affordable price of $50 per sample for strawberry researchers worldwide.

Technical 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 per sample) 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.