Detection of SNP and validation of a SFP InDel (deletion) in inverted repeat region of the Prunus species chloroplast genome

• We discover an InDel in the ycf1 gene in the IRB region of chloroplast genome.
• We develop an intraspecific DNA marker to characterize the maternal parent in Prunus.
• This InDel indicates a point of divergence within the Prunophora subgenus.

In order to control tree size, disease, precocity and stress most Prunus varieties are cultivated as composite plants grafted onto desirable rootstocks that impart all the afore-mentioned traits. Several Prunus rootstock breeding programs have been focused on the production of interspecific hybrids. The pedigree of most of these rootstocks remains unknown due to the lack of parental information necessitating the application of DNA-based knowledge in breeding programs. The amplification and sequencing of the chloroplast inverted repeat B (IRB) region spanning 25,960 bp from P. cerasifera (myrobalan plum) Ehrh., P. amygdalus (almond) and P. persica (peach) using the ASAP method revealed a single nucleotide polymorphisms (SNP) in the rps19-rpl2 IRB region in myrobalan when compared to almond and peach. In addition, a prominent and an easily identifiable single feature polymorphism (SFP-InDel (deletion)) of 18 nucleotides was discovered in reference to the peach chloroplast genome in the ycf1 gene in the IRB region. In this work, it has been developed a highly useful polymorphic molecular marker to characterize the maternal parent in interspecific hybrids of Prunus rootstocks as a first step toward developing pedigree information. The ycf1 SFP-InDel (deletion) has been successfully used in several 3-way hybrids generated in the stone fruit rootstock breeding program for the characterization of new interspecific plant material. This SFP is expected to be highly utile in characterizing the maternal lineage of Prunus hybrids in other breeding programs.