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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.
Highlights
Both a source of diversity and the development of genomic tools, such as reference genomes and molecular markers, are important to enable faster progress in plant breeding
Read alignment and single nucleotide polymorphism (SNP) calling by group of species Sequencing of 55 pear accessions, representing cultivars, founders and wild species, for a total of 29 different Pyrus species and interspecific hybrids (Additional file 1), resulted in an average sequencing coverage of 5.0x per sample, ranging from 3.8x (CPYR 828.001) to 6.0x (US 309), after quality and adapter-trimming
A unique set of 9.7 M variants passed the Quality filter, and they were further reduced to approximately 1 M bi-allelic SNPs (10%) after the Affymetrix filter (Fig. 1)
Summary
Both a source of diversity and the development of genomic tools, such as reference genomes and molecular markers, are 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. Despite the existence of a number of pear breeding programs internationally (for example Lespinasse et al [19], Musacchi et al [20], White and Brewer [21]), and recent progress towards the implementation of genomics into breeding [22,23,24], pear lags far behind other temperate fruit and nut crops (such as apple and peach) in terms of available genetic resources and efficiency of new cultivar development [25, 26]. New tools that enable high-density and large-scale genotyping are essential to ensure faster progress in pear breeding
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