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Genetic and ploidy diversity of pear (Pyrus spp.) germplasm of Friuli Venezia Giulia, Italy

  • Irina Baccichet
  • Serena Foria
  • Rachele Messina
  • Elisabetta Peccol
  • Alessia Losa
  • Michele Fabro
  • Gianluca Gori
  • Pietro Zandigiacomo
  • Guido Cipriani
  • Raffaele TestolinEmail author
Research Article
  • 35 Downloads

Abstract

Ancient germplasm represents a reservoir of traits and genes that might maintain large the genetic diversity of a species, like pear, and help breeders to cope with climatic changes and the evolving demand of the market. This paper reports the analysis of 170 pear accessions profiled at 12 simple sequence repeat (SSR) markers. The collection was replicated in three different locations and the identification of matching profiles of duplicated genotypes reduced the dataset to 118 genotypes. Of these, 32 (27.1%) were shown to be triploid by flow cytometry, a result that was confirmed by the occurrence of triallelic profiles at molecular markers and the large leaf size. The geographic location of original plants explained very little molecular variance (2%), that was instead very high among genotypes (98%). This evidence confirms the extensive exchange of plant material among the different geographic areas of the region as well as with neighbouring countries as reported in historical documents. The analysis of synonymy revealed 38 duplicated genotypes and reduced the dataset to 80 unique genotypes, of which 12 were triploid (15.0%). The molecular metrics analysed on 70 unique diploid genotypes, including two commercial cultivars, ‘Abate Fétél’ and ‘Conference’ added as controls, revealed that the observed heterozygosity over all loci (Ho) was 0.742 (range 0.471–0.937 for individual loci), while the expected heterozygosity or gene diversity was 0.808 (range 0.534–0.912). The polymorphic information content was 0.784 on average (range 0.501–0.906 for individual loci). The probability of identity (PID) calculated for individual loci and unrelated genotypes ranged from 0.014 for the most discriminating locus, Ch01d09, to 0.250 for the least discriminating one, Ch04e03. The PID product over all loci was 2.50e−16 for unrelated genotypes and 4.86e−06 for full sibs. The analysis of data is integrated with a discussion on the use of SSR markers in pear genotyping and the origin and the frequency of triploids compared with data from the literature. Finally, a discussion on the resemblance of several groups of cultivars to those of the pomological treatises is included.

Keywords

Germplasm collection DNA fingerprinting Molecular markers Synonymy Ploidy Molecular diversity 

Notes

Acknowledgements

This study was funded by ERSA – Agenzia Regionale per lo Sviluppo Rurale (Grant Number F22I15000120002). The authors would like to thank Gianluca Bianchi, Teresa Marrazzo and Luca De Sabbata for their assistance in the identification of accessions in the field, Giorgio Comuzzo and Renato Frezza for participating to the collection of samples and to the field observations. The authors thank also Francesco Danuso for the program of conversion of the original dataset of profiles into the binary matrix of allele presence/absence. The executable program can be requested from the author (francesco.danuso@uniud.it).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Human and animal rights

The research did not involve human and animals in the experiments.

Supplementary material

10722_2019_856_MOESM1_ESM.xlsx (40 kb)
Supplementary material 1 (XLSX 40 kb)
10722_2019_856_MOESM2_ESM.xlsx (24 kb)
Supplementary material 2 (XLSX 24 kb)
10722_2019_856_MOESM3_ESM.xlsx (15 kb)
Supplementary material 3 (XLSX 15 kb)

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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Irina Baccichet
    • 1
  • Serena Foria
    • 1
  • Rachele Messina
    • 1
  • Elisabetta Peccol
    • 1
  • Alessia Losa
    • 2
  • Michele Fabro
    • 3
  • Gianluca Gori
    • 3
  • Pietro Zandigiacomo
    • 1
  • Guido Cipriani
    • 1
  • Raffaele Testolin
    • 1
    Email author
  1. 1.Department of Agricultural, Food, Environmental and Animal SciencesUniversity of UdineUdineItaly
  2. 2.Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria, Centro di Genomica e Bioinformatica (CREA - GB)Montanaso LombardoItaly
  3. 3.ERSA – Agenzia Regionale per lo Sviluppo RuralePozzuolo del FriuliItaly

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