A new SSR fingerprinting set and its comparison to existing SSR and SNP based genotyping platforms to manage pyrus germplasm resources

Authors: Zurn, Jason; Nyberg, April; MONTANARI, SARA - University Of California, Davis; POSTMAN, JOSEPH - Former ARS Employee; NEALE, DAVID - University Of California, Davis; Bassil, Nahla

Submitted to: Tree Genetics and Genomes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/28/2020
Publication Date: 9/9/2020
Publication URL: https://handle.nal.usda.gov/10113/7104805
Citation: Zurn, J.D., Nyberg, A.M., Montanari, S., Postman, J., Neale, D., Bassil, N.V. 2020. A new SSR fingerprinting set and its comparison to existing SSR and SNP based genotyping platforms to manage pyrus germplasm resources. Tree Genetics and Genomes. 16. Article 72. https://doi.org/10.1007/s11295-020-01467-7.
DOI: https://doi.org/10.1007/s11295-020-01467-7

Interpretive Summary: The ability to distiguish individuals and confirm pedigrees is an important aspect of maintaining germplasm collections for clonally propigated plants such as pear. In the past, pedigree and identity confirmasion was conducted using morphological observations. This approach is not ideal because fruit is often needed for confirmation, which may not be available, particularly if the variety is being used as a rootstock. To overcome the limitations of using morphology, a DNA fingerprinting set was developed by the European Cooperative Program fro Plant Genetic Resources (ECPGR). This fingerprinting set consists of 12 markers and is conducted in three reactions. The ECPGR DNA fingerprinting set is difficult to use due to the nature of the markers chosen. As such, we created a new SSR DNA fingerprinting set called the U.S. Pyrus Genetic Resources (USPGR) set that can be performed in a single reaction. The USPGR ses was compared against to ECPGR set and data from the Axiom SNP array. The USPGR was found to be easier to use than the ECPGR set and came to the same conclusions as data generated using the ECPGR set and Axiom data.

Technical Abstract: Ensuring the identity of individuals within a germplasm repository, such as the United States 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, single reaction, 10-SSR fingerprint set containing high-core repeat SSRs was developed and compared to 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 new fingerprinting set, known as the U.S. Pyrus Genetic Resources (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.