Genebank Management Through Microsatellite Markers: A Case Study in Two Italian Peach Germplasm Collections

TL;DR

This study uses microsatellite markers to analyze peach germplasm collections in Italy, identifying mislabeled accessions and revealing population structure to improve genebank management.

Contribution

The study introduces a detailed microsatellite-based analysis to identify mislabeling and population structure in peach germplasm collections.

Findings

DNA fingerprinting data distinguished 80.95% of peach accessions.

161 accessions were found to be mislabeled, with a 16.56% error rate.

Three subpopulations were identified: modern peaches, modern nectarines, and traditional peaches.

Abstract

Two germplasm collections, comprising 1026 peach accessions located in Italy, were analyzed with 12 simple sequence repeat (SSR) markers. SSR reactions were performed using the multiplex-ready PCR protocol, and 147 alleles were amplified with an average of 12 alleles per locus. BPPCT001 was the most informative marker displaying the highest discrimination power (0.734). The observed heterozygosity showed an average of 0.45 alleles per locus, lower than expected (0.61). The fixation index (F) values were positive in all loci, with an average of 0.27 alleles per locus, suggesting the presence of endogamy. The DNA fingerprinting data allowed the discrimination of 80.95% of the analyzed accessions. If we exclude known sport mutations, known synonymies, and cultivars with the same pedigree, 161 accessions are mislabeled, with an error rate of 16.56% within or between collections. Population structure analysis revealed three subpopulations: modern peach cultivars, modern nectarine cultivars, and a third group mainly comprising traditional peach cultivars. The results obtained in this work will be useful to efficiently manage Genebank, reducing unwanted redundancy, synonyms and homonyms, mislabeling, and spelling errors, as well as identifying parents in controlled crosses.

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