The Multisite PeachRefPop Collection: A True Cultural Heritage and International Scientific Tool for Fruit Trees

Abstract

Plants have evolved a range of adaptive mechanisms that adjust their development and physiology to variable external conditions, particularly in perennial species subjected to long-term interplay with the environment. Exploiting the allelic diversity within available germplasm and leveraging the knowledge of the mechanisms regulating genotype interaction with the environment are crucial to address climatic challenges and assist the breeding of novel cultivars with improved resilience. The development of multisite collections is of utmost importance for the conservation and utilization of genetic materials and will greatly facilitate the dissection of genotype-by-environment interaction. Such resources are still lacking for perennial trees, especially with the intrinsic difficulties of successful propagation, material exchange, and living collection maintenance. This work describes the concept, design, and realization of the first multisite peach (Prunus persica) reference collection (PeachRefPop) located across different European countries and sharing the same experimental design. Other than an invaluable tool for scientific studies in perennial species, PeachRefPop provides a milestone in an international collaborative project for the conservation and exploitation of European peach germplasm resources and, ultimately, as a true heritage for future generations.

Figure 1.

Overview of the range of phenotypic diversity in the PRP. Images are as follows: columnar and standard tree growth habit (top left and right images, respectively); heart-shaped, round, and flat fruit (top and third rows); range of fruit flesh, skin color, and overcolor (second and bottom rows); variation in flower morphology and color (third and fourth rows); and fruit size variation (fourth row, first and last images).

Figure 2.

Graphical summary of the overall scheme followed for selecting the PRP collection. From the starting panel of 1,262 accessions, 169 accessions were selected combining two sets: 69 accessions extracted from genetic and phenotypic diversity analyses and taking into account the availability of whole-genome resequencing (WGRS) data; and 100 accessions selected by an empirical strategy from an experts panel considering breeding and traditional value along with genetic structure. These were supplemented with 214 seedlings from crossing populations of scientific importance and their respective 20 parents. The total number of entries in the PRP amounts to 403.

Figure 3.

Assessment of allelic redundancy observed at marker loci in the starting panel (FB_1262). Core collections of incremental size were generated, based on the maximization (OPT) and random sampling (RAN) methods in MSTRAT software, using a set of 445 SNPs. Data points represent averaged values over five independent repetitions for each size.

Figure 4.

Genetic structure and phylogenetic analysis of PRP accessions. A, Population structure estimated in the whole panel (FB_1262) and PRP accessions (PRP_X), as estimated for K (number of a priori cluster) equal to 4. OC_B, Occidental breeding; OC_T, o_{ccidental traditional;} OR_T, oriental traditional, respectively. B, PCA analysis of the subsets with a core size of 169 entries. Scores for each accession were obtained from the work of Micheletti et al. (2015). The 95% confidence ellipses in the scatterplot were estimated using PAST software. C, NJ phylogenetic tree. Blue squares indicate accessions with traditional and historical value, violet circles indicate the other PRP accessions, and colors reflect the population structure.

Figure 5.

Distribution of main phenotypic traits in the PRP accessions. In the maturity date plot, UE, E, M, L, and VL indicate ultra-early, early, medium, late, and very late ripening accessions, respectively. SSC, Soluble solids content. In the fruit texture plot, four major texture groups are shown: nonmelting (NM), melting (M), slow softening (SwS), and stony hard (SH).

Figure 6.

Experimental design and PRP orchards layout. A, Google Maps satellite images of the established PRP orchards across the different European sites. B, Experimental design of multisite PRP. A schematic example is provided for the Gimenells location. Accessions (A) and seedlings (S) in each block and subblock were completely randomized. The M1.1 and M1.2 subblocks each include a full copy of the collection (189 accessions, 214 seedlings) plus replicate checks (C) of the accessions cv Big Top, cv Nectaross, and cv Springcrest (five additional trees for each subblock). The M2.1 and M2.2 subblocks include half of the PRP collection and each site has a different half, chosen according to a pairwise design scheme. To this end, accessions (excluding control checks) and seedlings were randomly assigned to eight disjoint subgroups (A1–A4 and S1–S4) of approximately equal size and four of them assigned so that each site shares at least one A or one S group with the other sites. In the example, each M2 subblock at Gimenells is composed of A1 and A2 (46 and 46 accessions, respectively, plus the three checks for a total of 95), S1 and S2 (54 and 54 seedlings, respectively, for a total of 108), and three other additional replicates for each check (nine trees). Gimenells shares the A1 and S1 groups with Mula, S2 with Imola, and A2 with Naoussa.

Figure 7.

Climatic profiles of PRP sites. A, Trend of minimum and maximum daily air temperatures at the five PRP locations (averaged from the 1999–2018 time series). Thick lines show smoothed mean temperatures. B, Average monthly precipitation (in millimeters).