Monilinia spp. SSR markers distributed genomic-wide

Abstract

The biggest damage to Rosaceae family stone and pome fruit plants is caused by brown rot disease (Monilinia spp.). There are four main world widespread Monilinia spp. pathogens: M. laxa and M. fructigena – commonly found in Europe; M. polystroma spread in Japan, expanding in Europe and USA; M. fructicola is indigenous in the USA and Australia, already found in Europe, where this pathogen is assigned to quarantine pathogens list. Simple sequence repeats (SSR) are a suitable tool for discovering genetic diversity and for tracking the epidemic of this disease, but it requires priori knowledge about genomic data. Therefore, up until now only four SSR markers are available for M. fructicola and one for M. laxa. Since 2019, all Monilinia spp. genomes are available in the National Center for Biotechnology Information (NCBI) GenBank database at scaffold or contigs level, it is possible to develop genome-wide SSR markers. During this study M. fructicola, M. fructigena, and M. laxa reference genomes were analysed using Genome-wide Microsatellite Analyzing Tool Package (GMATA) for the development of SSR markers. In total 15 788 SSR motifs of the whole M. fructicola genome were found, 11 091 and 12 337 of M. fructigena and of M. laxa genome, respectively. In total 81.7% of them were assigned as markers and the primers as well melting temperatures for them were provided. For identification of the species-specific markers in silico polymerase chain reaction was conducted. The structure of SSR motives were analyzed – in all three species dimers are dominating (more than 41.5%). The most abundant SSR motives for all the species are TA and AT; in M. fructicola they comprise 28.6 % of all motives, in M. fructigena – 22.1%, and M. laxa – 33.3%. Such markers would be useful for the intraspecific and interspecific genetic diversity studies of Monilinia spp.