Abstract
Crocus sativus, the saffron crocus, is the source of saffron, which is made from the dried stigmas of the plant. It is a male-sterile triploid lineage that ever since its origin has been propagated vegetatively. Its mode of evolution and area of origin are matters of long-lasting debates. Here we analyzed chloroplast genomes and genome-wide DNA polymorphisms obtained through genotyping-by-sequencing (GBS) to infer the parent and area of origin of C. sativus. These data were complemented by genome size measurements and analyses of nuclear single-copy genes. We could place 99.3% of saffron GBS alleles in Crocus cartwrightianus, a species occurring in southeastern mainland Greece and on Aegean islands, identifying it as the sole progenitor of the saffron crocus. Phylogenetic and population assignment analyses together with chloroplast polymorphisms indicated the C. cartwrightianus population in the vicinity of Athens as most similar to C. sativus. We conclude that the crop is an autotriploid that evolved in Attica by combining two different genotypes of C. cartwrightianus. Triploid sterility and vegetative propagation prevented afterwards segregation of the favorable traits of saffron, resulting in worldwide cultivation of a unique clonal lineage.
Highlights
*&" To see if alleles present in C. sativus can all be traced back to its putative progenitor C. *'" cartwrightianus and to infer the geographic location of the origin of saffron, we analyzed *(" genome-wide SNP data obtained via genotyping-by-sequencing (GBS; Elshire et al, 2011). *)" We first processed 22 saffron individuals within the IPYRAD analysis pipeline (Eaton, 2014) to **" detect the loci common for 85% of the individuals, i.e. assembling a GBS reference of saffron
In a recent study inferring ('" phylogenetic relationships of the species of Crocus series Crocus, that is the taxonomic ((" group to which C. sativus belongs, we found that C. cartwrightianus is the closest relative of ()" the saffron crocus and hypothesized that no other species might have contributed to the (*" formation of the triploid (Nemati et al, 2018)
GBS-based genetic distances in C. cartwrightianus are an order of magnitude higher than in saffron, and within the C. cartwrightianus populations genetic diversity is comparatively high, This is reflected in the respective branch lengths of the phylogenetic trees (Figure S1 and S2)
Summary
&%" Saffron is the most expensive spice worldwide and is used since ancient times for its aroma &&" and the ability to give dishes and textiles a golden-yellow hue (Negbi, 1999). &*" sativus but belonged to wild saffron, C. cartwrightianus (Negbi and Negbi, 2002). In a recent study inferring ('" phylogenetic relationships of the species of Crocus series Crocus, that is the taxonomic ((" group to which C. sativus belongs, we found that C. cartwrightianus is the closest relative of ()" the saffron crocus and hypothesized that no other species might have contributed to the (*" formation of the triploid (Nemati et al, 2018). (iv) To understand why analyses of potential progenitor species of the )*" saffron crocus resulted up to now in widely contradicting results we analyze allele diversity at *+" five nuclear single-copy genes in a group of species closely related to C. sativus Depending on the species’ genetic structure, this should allow )'" identifying the region where C. sativus originated. (iii) We test the results of SNP data by )(" analyzing diversity of chloroplast genomes, which provide an independent source of ))" population data. (iv) To understand why analyses of potential progenitor species of the )*" saffron crocus resulted up to now in widely contradicting results we analyze allele diversity at *+" five nuclear single-copy genes in a group of species closely related to C. sativus
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