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

Area of Science:

• Plant genetics
• Genomics
• Agricultural science

Background:

• Pear (Pyrus spp.) lags in genetic resource utilization for cultivar development compared to other crops.
• Genomic tools like reference genomes and molecular markers are crucial for plant breeding progress.
• A gap exists in available genetic resources for pear breeding.

Purpose of the Study:

• To design a high-density, high-efficiency, and robust single nucleotide polymorphism (SNP) array for pear.
• To enable genetic diversity and genome-wide association studies in pear.
• To address the limitations in current pear genetic resources.

Main Methods:

• A two-step design process was employed, starting with a 'draft' array for initial screening.
• The Applied Biosystems™ Axiom™ Pear 70K Genotyping Array was developed, representing the densest SNP array for pear.
• The array was evaluated using 1416 diverse pear accessions from the USDA National Clonal Germplasm Repository (NCGR).

Main Results:

• The 70K SNP array identified 66,616 high-quality, polymorphic SNPs (93% of tiled SNPs).
• High-density linkage maps were constructed using the Axiom Pear 70K Genotyping Array in a bi-parental population.
• Comparison with genotyping-by-sequencing (GBS) data indicated the SNP array is a more robust screening method.

Conclusions:

• The Axiom Pear 70K Genotyping Array is a valuable resource for diverse molecular studies in Pyrus species.
• Characterization of the USDA-NCGR collection using this array will benefit pear geneticists and breeders.
• The array aids in optimizing conservation strategies for Pyrus.