Testing a set of SSR markers to obtain the genetic profiles of common plum and cherry plum varieties and to assess the genetic similarity between hybrids obtained in remote crossing

Abstract

Common plum (Prunus domestica L.) is one of the fruit crops that are particularly difficult to study genetically. Unlike most other species of the genus Prunus, it is a hexaploid species (2n=48) originating from complex interspecific hybridization, and the question of its origin is yet to be conclusively resolved. Presently, several studies are available that examine the phylogeny and systematics of the genus Prunus in general and specifically the speciation of Prunus domestica L., with the use of molecular genetics methods. Although the SSR marker method is widely adopted in the practice of studying the most important stone fruit crops, the polymorphism of SSR loci in Prunus domestica L. is rarely studied in the gene pool. The present study examined the effectiveness of 22 microsatellite (SSR) markers using common plum and cherry plum varieties bred at the Federal Horticultural Center for Breeding, Agrotechnology, and Nursery in order to obtain the genetic profiles of these varieties and develop a variety passport. In addition, this set of markers was used to evaluate the genetic diversity and genetic similarity between the varieties of common plum and cherry plum, as well as remote hybrids obtained using embryo rescue, from the collection of the Federal Horticultural Center for Breeding, Agrotechnology, and Nursery. The screening results obtained for a set of 22 SSR markers using 10 varieties and 19 hybrid specimens revealed a low level of polymorphism detected by this set and a small number of shared alleles. This set of markers was found to be inadequate to fully evaluate our sample in terms of allelic diversity, as well as genetic similarity between parental and hybrid forms. The proportion of unique genotypes that can be identified using these markers amounts to less than 50 %. The large number of overlapping fragment sizes prevents the generation of individual genetic profiles for the varieties. It was found necessary to apply and test additional markers, as well as to develop multiplex sets on their basis, which will form the basis for routine genotyping of varieties. For a more accurate and reliable estimation of fragment lengths and allele sharing, further analysis should be performed using capillary electrophoresis. The work was carried out at the Laboratory of Reproductive Biotechnology of the Federal Horticultural Center for Breeding, Agrotechnology and Nursery in 2022.