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

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.