Identical genomes but different properties – saffron as a model for epigenetics of quality traits and environmental adaptation

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Saffron, the most expensive spice of the world, is produced from the stigmas of the saffron crocus, Crocus sativus. This species is a male sterile autotriploid (2n = 3x = 24, 1C = 3.45 Gbp), propagated only vegetatively through daughter corms. Saffron crocus emerged only once in Greece, and was cultivated for about 3000 years as a single clonal lineage in many countries under different climate conditions. Adaptation to different environments and spice quality differences seem mainly based on epigenetic differences. Thus, today’s saffron cultivation is essentially a unique long-term experiment in epigenetic differentiation, adaptation, and human-driven selection. We want to take advantage of this finding by analyzing the triploid genome of saffron crocus in comparison to its diploid progenitor and the differences in DNA methylation of saffron cultivars from diverse cultivation areas. Moreover, we want to estimate how far the effects of vegetative propagation regarding the accumulation of detrimental mutations (Muller’s ratchet) are already influencing the genome of saffron. The working groups of the three PIs already work on saffron biology: Prof. Björn Usadel (RWTH Aachen) is interested in saffron’s secondary metabolites and the genetics of their pathways as well as plant genome assembly and analysis, Dr. Tony Heitkam (TU Dresden) in the cytogenetic and evolutionary analysis of saffron using its repeat fraction, and Dr. Frank Blattner (IPK Gatersleben) in the evolution of Crocus and domestication of saffron, also providing a large collection of wild and cultivated Crocus individuals. Very recently, the latter two showed that saffron originated as an autotriploid from Crocus cartwrightianus in southern Greece. In contrast to saffron crocus, wild C. cartwrightianus is diploid, and characterized by very high genetic diversity within and among its populations. We propose to generate high quality reference genome sequences for C. cartwrightianus and C. sativus with comprehensive gene and repeat annotations, physically anchored to the plants’ chromosomes. The diploid C. cartwrightianus genome will be assembled first, providing a reference for the assembly of the heterozygous triploid saffron genome. We will target the differences in phenotypes and metabolites, and characterize the underlying epigenetic variation between saffron accessions. As outcome of our work we expect (i) the saffron and C. cartwrightianus reference genome sequences as the basis for comparative and epigenetic analysis; (ii) the annotated gene and repeat fractions of C. cartwrightianus and C. sativus to anchor our epigenetic analysis; (iii) a clear definition of genome-wide differences between the di- and triploid genomes, particularly with respect to homoeologous loci and the effects of Muller’s ratchet in the vegetatively propagated cultivars; (iv) the clear determination of DNA methylation differences between the genomes of several saffron ecotypes.