A new SSR fingerprinting set and its comparison to existing SSR- and SNP-based genotyping platforms to manage Pyrus germ
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ORIGINAL ARTICLE
A new SSR fingerprinting set and its comparison to existing SSR- and SNP-based genotyping platforms to manage Pyrus germplasm resources Jason D. Zurn 1 & April Nyberg 1 & Sara Montanari 2 & Joseph Postman 1 & David Neale 2 & Nahla Bassil 1 Received: 11 May 2020 / Revised: 20 August 2020 / Accepted: 28 August 2020 # This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply 2020
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. Keywords RosBREED . Genebank management . Conservation . Microsatellite . Pear
Introduction The confirmation of germplasm identity and pedigrees is a critical aspect of managing germplasm collections and maintaining genetic diversity within the collection (Gilbert et al. 1999; Peace 2017; Postman 2008). The US national Pyrus (pear) collection, housed at the USDA-ARS
Communicated by M. Troggio Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11295-020-01467-7) contains supplementary material, which is available to authorized users. * Nahla Bassil [email protected] 1
USDA-ARS National Clonal Germplasm Repository, Corvallis, OR, USA
2
Department of Plant Science, University of California Davis, Davis, CA, USA
National Clonal Germplasm Repository (NCGR) in Corvallis, OR, consists of 2378 accessions from 35 species and hybrids, representing 58 countries (Hummer 1994; Postman 2008; USDA-NPGS 2020). Of the
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