Epigenetic Variability Among Saffron Crocus (Crocus sativus L.) Accessions Characterized by Different Phenotypes

This work represents the first epigenomic study carried out on saffron crocus. Five\r\naccessions of saffron, showing differences in tepal pigmentation, yield of saffron\r\nand flowering time, were analyzed at the epigenetic level by applying a methylationsensitive\r\nrestriction enzyme-sequencing (MRE-seq) approach. Five accession-specific\r\nhypomethylomes plus a reference hypomethylome, generated by combining the\r\nsequence data from the single accessions, were obtained. Assembled sequences\r\nwere annotated against existing online databases. In the absence of the Crocus\r\ngenome, the rice genome was mainly used as the reference as it is the best annotated\r\ngenome among monocot plants. Comparison of the hypomethylomes revealed many\r\ndifferentially methylated regions, confirming the high epigenetic variability present among\r\nsaffron accessions, including sequences encoding for proteins that could be good\r\ncandidates to explain the accessions’ alternative phenotypes. In particular, transcription\r\nfactors involved in flowering process (MADS-box and TFL) and for the production of\r\npigments (MYB) were detected. Finally, by comparing the generated sequences of the\r\ndifferent accessions, a high number of SNPs, likely having arisen as a consequence\r\nof the prolonged vegetative propagation, were detected, demonstrating surprisingly\r\nhigh genetic variability. Gene ontology (GO) was performed to map and visualize\r\nsequence polymorphisms located within the GOs and to compare their distributions\r\namong different accessions. As well as suggesting the possible existence of alternative\r\nphenotypes with a genetic basis, a clear difference in polymorphic GO is present\r\namong accessions based on their geographic origin, supporting a possible signature\r\nof selection in the Indian accession with respect to the Spanish ones.