Genetic characterization of worldwide Prunus domestica (plum) germplasm using sequence-based genotyping

Tetyana Zhebentyayeva,Christopher A Saski,Ann Callahan,Michel Ravelonandro,Sarah Castro,Theodore Dejong,Ralph Scorza,Vijay Shankar,Chris Dardick

doi:10.1038/s41438-018-0090-6

Abstract

Prunus domestica commonly known as European plum is a hexaploid fruit tree species cultivated around the world. Locally it is used for fresh consumption, in jams or jellies, and the production of spirits while commercially the fruit is primarily sold dried (prunes). Despite its agricultural importance and long history of cultivation, many questions remain about the origin of this species, the relationships among its many pomological types, and its underlying genetics. Here, we used a sequence-based genotyping approach to characterize worldwide plum germplasm including the potential progenitor Eurasian plum species. Analysis of 405 DNA samples established a set of four clades consistent with the pomological groups Greengages, Mirabelles, European plums, and d’Agen (French) prune plums. A number of cultivars from each clade were identified as likely clonal selections, particularly among the “French” type prune germplasm that is widely cultivated today. Overall, there was relatively low genetic diversity across all cultivated plums suggesting they have been largely inbred and/or derived from a limited number of founders. The results agree with P. domestica having originated as an interspecific hybrid of a diploid P. cerasifera and a tetraploid P. spinosa that itself may have been an interspecific hybrid of P. cerasifera and an unknown Eurasian plum species. The low genetic diversity and lack of true wild-types coupled with the known cultivation history of Eurasian plums imply that P. domestica may have been a product of inter-specific cross breeding and artificial selection by early agrarian Eurasian societies.

Highlights

Introduction European plum Prunus domesticaL. is a polymorphic allopolyploid species (2n = 6x = 48) commercially grown worldwide for a variety of uses including fresh fruit, prunes, distilling, and as processed additive ingredients
Genetic diversity and phylogenetic analysis We investigated genetic relationships among all 405 plum accessions by performing a hierarchical clustering analysis on a dissimilarity matrix calculated in R
The results show that the subset of 161 markers may have prediction value for classification of plum germplasm by fruit type (GRG vs. d’Agen prune plums (DAP) vs. European plums (EUP) vs. MIR) as well as for possible genomic selection for fruit type in plum breeding programs

Summary

Introduction

L. is a polymorphic allopolyploid (hexaploid) species (2n = 6x = 48) commercially grown worldwide for a variety of uses including fresh fruit, prunes, distilling, and as processed additive ingredients. This plum species, commonly referred to as “European plums” or “prune plums”, is distinct from the large round diploid “Japanese plums” (Prunus salicina) which are widely grown for fresh market consumption. Historical evidence suggests P. domestica and other Eurasian plum species including Prunus cerasifera (Cherry plum) and Prunus spinosa (“Sloe” or “Blackthorn” plum) were important to the development of early European societies. The propensity of P. domestica to form root suckers would have provided a simple and efficient way to distribute clonal material across long distances even before grafting techniques had been developed

Methods

Results

Conclusion