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

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.

Defining the‘HoneySweet’insertion event utilizing NextGen sequencing and a de novo genome assembly of plum(Prunus domestica)

HoneySweet’plum(Prunus domestica)is resistant to Plum pox potyvirus,through an RNAi-triggered mechanism.Determining the precise nature of the transgene insertion event has been complicated due to the hexaploid genome of plum.DNA blots previously indicated an unintended hairpin arrangement of the Plum pox potyvirus coat protein gene as well as a multicopy insertion event.To confirm the transgene arrangement of the insertion event,‘HoneySweet’DNA was subjected to whole genome sequencing using Illumina short-read technology.Results indicated two different insertion events,one containing seven partial copies flanked by putative plum DNA sequence and a second with the predicted inverted repeat of the coat protein gene driven by a double 35S promoter on each side,flanked by plum DNA.To determine the locations of the two transgene insertions,a phased plum genome assembly was developed from the commercial plum‘Improved French’.A subset of the scaffolds(2447)that were>10 kb in length and representing,>95%of the genome were annotated and used for alignment against the‘HoneySweet’transgene reads.Four of eight matching scaffolds spanned both insertion sites ranging from 157,704 to 654,883 bp apart,however we were unable to identify which scaffold(s)represented the actual location of the insertion sites due to potential sequence differences between the two plum cultivars.Regardless,there was no evidence of any gene(s)being interrupted as a result of the insertions.Furthermore,RNA-seq data verified that the insertions created no new transcriptional units and no dramatic expression changes of neighboring genes.