AFLP marker-assisted characterization of mulberry (Morus spp.) cultivars for the setting up of a haplotype-based identification method

Mulberries are members of the genus Morus L., a widespread taxonomic group showing a great genetic variability and adaptability to different environmental conditions. In addition to a confused and often misleading nomenclature, the lack of a modern monograph makes a univocal classification far from easy and the precise identification of genotypes is very difficult because of the influence of environmental variation on the morphological characteristics used by taxonomists. This study deals with the use of AFLP-based fingerprints as a tool for the setting up of an identification method based on accession-specific markers able to discriminate 40 mulberry accessions belonging to three main species (i.e., M. alba L., M. latifolia Poir. and M. bombycis Koidz.). Nine combination of primers have been shown to be the most discriminant and chosen for the identification and isolation of key amplicons. Unique haplotypes were found for 34 accession and the specific bands were sequenced and characterized by means of bioinformatics analyses. According to BlastX analyses, the majority of the accession-specific markers show significant similarity with sequences encoding known proteins, a moderate number of markers are quite similar to retrotransposon sequences, whereas few sequences encode unknown proteins or give no results. The specific markers isolated in this research will allow the setting up of a high reproducible identification method to be used in simple PCR-based haplotyping.