Abstract
Ensuring the clonal identity of accessions within a germplasm repository, such as the US National Pyrus collection, is critical. Additionally, pedigree confirmation and understanding population structure is an important part of breeding and managing genetic resources. The ability to validate pedigree and identity is challenging and inconclusive through morphology alone. DNA information can be used to confirm parentage and identity by descent. A Pyrus fingerprinting set was previously developed by the European Cooperative Program for Plant Genetic Resources (ECPGR) and consists of 12 dinucleotide-containing simple sequence repeats (SSRs) markers that are amplified in two PCR reactions. The ECPGR set is difficult to use because dinucleotide-containing SSRs often exhibit a number of amplification artifacts such as stutters, split peaks, and binning errors. High-core repeat (3–6 bp motifs) SSRs do not exhibit many of the artifacts displayed by dinucleotide-containing SSRs. Therefore, an easy-to-use 10-SSR fingerprint set containing high-core repeat SSRs that can be evaluated in a single reaction was developed. This fingerprinting set, known as the US Pyrus Genetic Resources (USPGR) set, was compared with the ECPGR set and to single nucleotide polymorphism (SNP) markers found on the new 70K pear Axiom™ array for its ability to assess diversity, population structure, pedigree, and identity. The USPGR set performed similarly to both genotyping platforms while being easier to use. Additionally, the present study demonstrates the usefulness of SSRs in the age of high-throughput genotyping and sequencing platforms.
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Acknowledgments
The authors would like to thank Mandie Driskill and Barb Gilmore for their technical support.
Data Archiving Statement
SSR data for the 237 accessions genotyped with the USPGR set as well as the 152 accessions genotyped with the ECPGR set are available in GRIN-GLOBAL at https://npgsweb.ars-grin.gov/gringlobal/method.aspx?id=496471. Accession numbers (PI numbers) and USDA-ARS-NCGR local numbers (CPYR) are included at the GRIN-GLOBAL site and in Supplementary Table S1. SNP data are archived at the Genome Database for the Rosaceae website at https://www.rosaceae.org/publication_datasets, accession number tfGDR1042.
Funding
This research was funded through the USDA National Institute of Food and Agriculture Specialty Crop Research Initiative project “RosBREED: Combining Disease Resistance and Horticultural Quality in New Rosaceous Cultivars” (2014-51181-22378), the California Pear Advisory Board, and the USDA-ARS CRIS project 2072-21000-049-00D.
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Zurn, J.D., Nyberg, A., Montanari, S. et al. A new SSR fingerprinting set and its comparison to existing SSR- and SNP-based genotyping platforms to manage Pyrus germplasm resources. Tree Genetics & Genomes 16, 72 (2020). https://doi.org/10.1007/s11295-020-01467-7
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DOI: https://doi.org/10.1007/s11295-020-01467-7