ArticleBMC genomics2019
Development of a highly efficient Axiom™ 70 K SNP array for Pyrus and evaluation for high-density mapping and germplasm characterization.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Twenty-one years of three-way hybrid breeding shaped diversity and complementarity of male and female gene pools in sugar beet.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- -Identification of QTL for steviol glycoside biosynthesis using a SNP-based genetic linkage map for Stevia rebaudiana.G3 (Bethesda, Md.) · 2026Article
- An advanced genotyping tool to inspect grapevine variability: the AxiomFrontiers in plant science · 2026Article
- AxioSAFE: an accessible, semi-automatic filtering tool for the curation of genotyping datasets.Bioinformatics advances · 2026Article
- Identification of the efficacy of parentage testing based on bi-allelic autosomal single nucleotide polymorphism markers in Taiwanese population.Forensic science, medicine, and pathology · 2024Article
- A multiplexed plant-animal SNP array for selective breeding and species conservation applications.G3 (Bethesda, Md.) · 2023Article
- Development and Evaluation of an AxiomPlants (Basel, Switzerland) · 2023Article
- Construction of a high density genetic linkage map to define the locus conferring seedlessness from Mukaku Kishu mandarin.Frontiers in plant science · 2023Article
- A high-density integrated map for grapevine based on three mapping populations genotyped by the Vitis18K SNP chip.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- QTL Analysis and CAPS Marker Development Linked with Russet in Pear (Plants (Basel, Switzerland) · 2022Article
- Genetic dissection of fruit maturity date in apricot (P. armeniaca L.) through a Single Primer Enrichment Technology (SPET) approach.BMC genomics · 2022Article
- Pear genetics: Recent advances, new prospects, and a roadmap for the future.Horticulture research · 2022Article
- Genome-wide clonal variability in European pear "Rocha" using high-throughput sequencing.Horticulture research · 2022Article
- Development of a highly efficient 50K single nucleotide polymorphism genotyping array for the large and complex genome of Norway spruce (Picea abies L. Karst) by whole genome resequencing and its transferability to other spruce species.Molecular ecology resources · 2021Article
- Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops.Plants (Basel, Switzerland) · 2021Review
- The Distribution and Origins ofFrontiers in plant science · 2021Article
- RosBREED: bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops.Horticulture research · 2020Review
- Reconstruction of the Largest Pedigree Network for Pear Cultivars and Evaluation of the Genetic Diversity of the USDA-ARS NationalG3 (Bethesda, Md.) · 2020Article
- Development and Validation of an Open Access SNP Array for Nile Tilapia (G3 (Bethesda, Md.) · 2020Article
- Genome-wide SNP identification in Prunus rootstocks germplasm collections using Genotyping-by-Sequencing: phylogenetic analysis, distribution of SNPs and prediction of their effect on gene function.Scientific reports · 2020Article
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16 authors.
Funding
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Abstract
backgroundBoth 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.
resultsBy 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.
conclusionsThe 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.
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