Genetic assessment of the pomological classification of plum Prunus domestica L. accessions sampled across Europe

Abstract

The genotyping of European fruit tree collections has helped to identify synonyms, determine parentage, reveal key specimens in the collections and provide information on the development of modern cultivars from one or several progenitors. However, studies on European plum Prunus domestica have been lagging behind, mainly because of the hexaploid chromosome number. In this co-operative study, 104 accessions conserved by 14 partners across Europe were phenotyped for 20 descriptors, and genotyped for 8 SSR loci together with 8 reference cultivars. Based on the descriptors as well as additional information supplied by the partners, as well as the scientific and horticultural literature, each accession was assigned to one of six pomological groups; (1) egg plums sensu lato (E), (2) prunes of the French d'Agen type (P/A), (3) prunes of the Central-Southeast European Zwetschen type (P/Z), ( 4) greengages (G), ( 5) mirabelles (M) and ( 6) bullaces, damsons and var. pomariorum (D/B). A MANOVA conducted on descriptor data revealed significant differentiation among the pomological groups as well as a ManuscriptClick here to access/download;Manuscript;Revised Manuscript 2020.docx Click here to view linked References 2 geographic impact on the differentiation of local plum accessions in Europe. SSR data showed that two trios and seven pairs of genotypes had very similar allele profiles and possibly are genetically identical in spite of different accession names. An AMOVA indicated sparse genetic differentiation when accessions were grouped according to geographic origin whereas significant differences were obtained among pomological groups. A Bayesian analysis of genetic structure, as well as a discriminant analysis of principal components (DAPC), further revealed levels of similarity among and within the different pomological groups, suggesting that egg plums sensu lato (E) and greengages (G) can be referred to subsp. domestica while damsons and bullaces (D/B) but also Central-Southeast European prunes (P/Z) show more affinity to subsp. insititia. The small and possibly heterogeneous groups with mirabelles (M) and prunes of the d'Agen type (P/A) take an intermediate position suggesting a hybridogenic origin.

ECPGR recommended SSR loci for analyses of European plum (Prunus domestica) collections

“…Detected polymorphisms were very high for the nine chosen SSR loci when a joint biostatistical analysis was performed for plum accessions previously genotyped in the above-mentioned studies (Sehic et al, 2015;Gaši et al, 2020). Although the study by Gaši et al (2020) was based on only eight of the nine recommended SSRs, all plum accessions from that study had also been genotyped for the remaining microsatellite locus (BPPCT039). Number of alleles ranged from 18 to 48, and Nei's gene diversity ranged from 0.88 to 0.93 (Table 2).…”

“…In order to facilitate harmonization between future studies, we propose a standard set of nine SSR loci, approved by the ECPGR Prunus working group, for European plum (Table 1). These loci have already been used for investigations of genetic diversity, first in plum cultivars and landraces from Norway and Sweden (Sehic et al, 2015) and subsequently in two ECPGR-funded projects with accessions sampled in a total of 14 European countries: 'PRUNDOC' (Sehic et al, 2019) and 'Prunus Alignment' (Gaši et al, 2020); reporting data from both ECPGR studies).…”

“…One locus, PacA33, is an Expressed Sequence Tag-SSR (EST-SSR) from apricot (Prunus dulcis) (Decroocq et al, 2003), while CPSCT026 originates from genomic DNA of Japanese plum (Prunus salicina) (Mnejja et al, 2004). In addition to studies based on eight or nine of these loci (Sehic et al, 2015;Gaši et al, 2020), five loci, BPPCT034, BPPCT039, BPCT040, PacA33 and UDP96-005, have also been used by Halapija Kazija et al (2013,2014) for screening of plum accessions from Croatia and neighbouring countries.…”

“…Hexaploid plum accessions are considerably more difficult to genotype compared to diploid genotypes since each locus may have up to six alleles. Overlooking a true but faint band is entirely plausible, as well as is mistakenly scoring an artefactual band as an allele (Gaši et al, 2020). Although 15 loci remained as serious candidates among a wider set of SSR loci screened initially, six of these had to be discarded due to unreliable amplification (PacA18, PacA49, PacB22, PacB26, PacB35, PacC13) (Decroocq et al, 2003), thus leaving the nine chosen loci.…”

“…Leaves of these genotypes can Table 2. Allele size range, number of alleles and gene diversity (Nei, 1978) for 9 SSR loci, calculated among 175 plum accessions investigated by Gaši et al (2020) and by Sehic et al (2015), as well as among 7 reference cultivars.…”