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

Publication Overview
TitleDevelopment of a highly efficient Axiom™ 70 K SNP array for Pyrus and evaluation for high-density mapping and germplasm characterization
AuthorsMontanari S, Bianco L, Allen BJ, Martínez-García PJ, Bassil NV, Postman J, Knäbel M, Kitson B, Deng CH, Chagné D, Crepeau MW, Langley CH, Evans K, Dhingra A, Troggio M, Neale DB
TypeJournal Article
Journal NameBMC genomics
Volume20
Issue1
Year2019
Page(s)331
CitationMontanari S, Bianco L, Allen BJ, Martínez-García PJ, Bassil NV, Postman J, Knäbel M, Kitson B, Deng CH, Chagné D, Crepeau MW, Langley CH, Evans K, Dhingra A, Troggio M, Neale DB. Development of a highly efficient Axiom™ 70 K SNP array for Pyrus and evaluation for high-density mapping and germplasm characterization. BMC genomics. 2019 May 02; 20(1):331.

Abstract

BACKGROUND
Both a source of diversity and the development of genomic tools, such as reference genomes and molecular markers, are equally important to enable faster progress in plant breeding. Pear (Pyrus spp.) lags far behind other fruit and nut crops in terms of employment of available genetic resources for new cultivar development. To address this gap, we designed a high-density, high-efficiency and robust single nucleotide polymorphism (SNP) array for pear, with the main objectives of conducting genetic diversity and genome-wide association studies.

RESULTS
By applying a two-step design process, which consisted of the construction of a first 'draft' array for the screening of a small subset of samples, we were able to identify the most robust and informative SNPs to include in the Applied Biosystems™ Axiom™ Pear 70 K Genotyping Array, currently the densest SNP array for pear. Preliminary evaluation of this 70 K array in 1416 diverse pear accessions from the USDA National Clonal Germplasm Repository (NCGR) in Corvallis, OR identified 66,616 SNPs (93% of all the tiled SNPs) as high quality and polymorphic (PolyHighResolution). We further used the Axiom Pear 70 K Genotyping Array to construct high-density linkage maps in a bi-parental population, and to make a direct comparison with available genotyping-by-sequencing (GBS) data, which suggested that the SNP array is a more robust method of screening for SNPs than restriction enzyme reduced representation sequence-based genotyping.

CONCLUSIONS
The Axiom Pear 70 K Genotyping Array, with its high efficiency in a widely diverse panel of Pyrus species and cultivars, 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 Pyrus.

Features
This publication contains information about 71,363 features:
Feature NameUniquenameType
pco_AX-115608652pco_AX-115608652genetic_marker
pco_AX-115609948pco_AX-115609948genetic_marker
pco_AX-115617399pco_AX-115617399genetic_marker
pco_AX-115626207pco_AX-115626207genetic_marker
pco_AX-115631434pco_AX-115631434genetic_marker
pco_AX-115633010pco_AX-115633010genetic_marker
pco_AX-115633197pco_AX-115633197genetic_marker
pco_AX-115633268pco_AX-115633268genetic_marker
pco_AX-115633435pco_AX-115633435genetic_marker
pco_AX-115634142pco_AX-115634142genetic_marker
pco_AX-115634620pco_AX-115634620genetic_marker
pco_AX-115635217pco_AX-115635217genetic_marker
pco_AX-115637199pco_AX-115637199genetic_marker
pco_AX-115638423pco_AX-115638423genetic_marker
pco_AX-115638547pco_AX-115638547genetic_marker
pco_AX-115640104pco_AX-115640104genetic_marker
pco_AX-115641639pco_AX-115641639genetic_marker
pco_AX-115643722pco_AX-115643722genetic_marker
pco_AX-115644369pco_AX-115644369genetic_marker
pco_AX-115644503pco_AX-115644503genetic_marker
pco_AX-115645119pco_AX-115645119genetic_marker
pco_AX-115645603pco_AX-115645603genetic_marker
pco_AX-115654260pco_AX-115654260genetic_marker
pco_AX-115660608pco_AX-115660608genetic_marker
pco_AX-123357683pco_AX-123357683genetic_marker

Pages

Libraries
This publication contains information about 1 libraries:
Library NameUnique NameOrganism
Axiom 70K Pear Genotyping ArrayAxiom 70K Pear Genotyping ArrayPyrus spp.