Development of a highly efficient Axiom® 70K SNP array for Pyrus and evaluation for high-density mapping and germplasm characterization

Authors: MONTANARI, SARA - University Of California, Davis; BIANCO, LUCA - Fondazione Edmund Mach; ALLEN, BRIAN - University Of California, Davis; MARTINEZ-GARCIA, PEDRO - University Of California, Davis; Bassil, Nahla; Postman, Joseph; CHAGNE, DAVID - New Zealand Institute Of Plant & Food Research; EVANS, KATE - Washington State University; DHINGRA, AMIT - Washington State University; TROGGIO, MICHELA - Fondazione Edmund Mach; NEALE, DAVID - University Of California, Davis

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/17/2019
Publication Date: 5/2/2019
Citation: Montanari, S., Bianco, L., Allen, B., Martinez-Garcia, P., Bassil, N.V., Postman, J.D., Chagne, D., Evans, K., Dhingra, A., Troggio, M., Neale, D. 2019. Development of a highly efficient Axiom® 70K SNP array for Pyrus and evaluation for high-density mapping and germplasm. BMC Genomics. 20:331. https://doi.org/10.1186/s12864-019-5712-3.
DOI: https://doi.org/10.1186/s12864-019-5712-3

Interpretive Summary: In this study we extracted DNA from 55 highly diverse pear trees from the National Pear Collection of the USDA-ARS-NCGR housed in Corvallis Oregon and used a high density chip or "array" containing about 700,000 different DNA markers to test the ability to distinguish unique DNA sequences in the different pear trees. We evaluated this 700 K array in 288 different representative pear accessions and identified the most informative 70,000 DNA markers to place on a new more cost-efficient array. We plan on using this smaller 70 K array to genotype the entire USDA pear collection, thus generating important DNA sequence information that can be used by pear geneticists and breeders to detect DNA sequences associated with traits and optimize conservation strategies for this crop.

Technical Abstract: A source of diversity and the development of genomic tools, such as reference genomes and molecular markers, are important to ensure faster progress in plant breeding. Pear (Pyrus spp.) lags far behind other fruit and nut crops in terms of available genetic resources and new cultivar development. With this work , we designed a high-density and high-efficiency single nucleotide polymorphism (SNP) array for pear, with the double objectives of conducting genetic diversity and genome-wide association studies. A rich collection of more than 2,300 clonal pear accessions is maintained at the USDA National Clonal Germplasm Repository (NCGR) in Corvallis, OR, including nearly every known Pyrus species. We re-sequenced 55 of these accessions and designed an Affymetrix Axiom® Pear 700K Genotyping Array. By using this array to screen 288 pear samples, representing most of the diversity held at the NCGR, we were able to identify the most robust and informative SNPs to include in the commercial Axiom® Pear 70K Genotyping Array, currently the densest SNP array available for pear.Preliminary evaluation of this 70K array by genotyping the remaining NCGR pear accessions identified: 93% of the SNPs were classified as high quality and polymorphic (Poly High Resolution). The Axiom® Pear 70K Genotyping Array, with its high efficiency in a widely diverse panel of Pyrus species, represents a valuable resource for a multitude of molecular studies in pear. The characterization of the USDA-NCGR collection with this array will provide important information for pear geneticists and breeders, as well as for the optimization of conservation strategies for this genus.