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-172385842pco_AX-172385842genetic_marker
pco_AX-172385843pco_AX-172385843genetic_marker
pco_AX-172385850pco_AX-172385850genetic_marker
pco_AX-172385856pco_AX-172385856genetic_marker
pco_AX-172385857pco_AX-172385857genetic_marker
pco_AX-172385865pco_AX-172385865genetic_marker
pco_AX-172385872pco_AX-172385872genetic_marker
pco_AX-172385899pco_AX-172385899genetic_marker
pco_AX-172385908pco_AX-172385908genetic_marker
pco_AX-172385925pco_AX-172385925genetic_marker
pco_AX-172385927pco_AX-172385927genetic_marker
pco_AX-172385948pco_AX-172385948genetic_marker
pco_AX-172385979pco_AX-172385979genetic_marker
pco_AX-172385985pco_AX-172385985genetic_marker
pco_AX-172385986pco_AX-172385986genetic_marker
pco_AX-172385991pco_AX-172385991genetic_marker
pco_AX-172386003pco_AX-172386003genetic_marker
pco_AX-172386016pco_AX-172386016genetic_marker
pco_AX-172386022pco_AX-172386022genetic_marker
pco_AX-172386052pco_AX-172386052genetic_marker
pco_AX-172386081pco_AX-172386081genetic_marker
pco_AX-172386116pco_AX-172386116genetic_marker
pco_AX-172386119pco_AX-172386119genetic_marker
pco_AX-172386123pco_AX-172386123genetic_marker
pco_AX-172386157pco_AX-172386157genetic_marker

Pages

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