Abstract
Exploiting the biodiversity of crops and their wild relatives is fundamental for maintaining and increasing food security. The species Cynara cardunculus includes three taxa: the globe artichoke, one of the most important Mediterranean vegetables, the leafy cardoon, and the wild cardoon. In this study, genotyping by sequencing (GBS) was successfully applied to reveal thousands of polymorphisms in a C. cardunculus germplasm collection, including 65 globe artichoke, 9 leafy cardoon, and 21 wild cardoon samples. The collection showed a strong population structure at K = 2, separating the globe artichoke from the leafy and wild cardoon. At higher K values, further substructures were observed, in which the wild cardoon was separated from the leafy cardoon, and the latter included the Spanish wild cardoons, while the wild sample from Portugal was admixed. Moreover, subpopulations within the globe artichoke set were highlighted. Structure analysis restricted to the globe artichoke dataset pointed out genetic differentiation between the ˝Catanesi˝ typology and all the other samples (K = 2). At higher values of K, the separation of the ˝Catanesi˝ group still held true, and green headed landraces from Apulia region, Italy (˝Green Apulian˝) formed a distinct subpopulation. ˝Romaneschi˝ artichoke types fell in a variable group with admixed samples, indicating that they should not be considered as a genetically uniform typology. The results of principal component analysis and Neighbor-Joining hierarchical clustering were consistent with structure results, and in addition provided a measure of genetic relationships among individual genotypes. Both analyses attributed the wild material from Spain and Portugal to the cultivated cardoon group, supporting the idea that this might be indeed a feral form of the leafy cardoon. Different reproductive habit and possibly selective pressure led to a slower LD decay in artichoke compared to cardoon. Genotyping by sequencing has proven a reliable methodology to obtain valuable SNPs and assess population genetics in C. cardunculus.
Highlights
The analysis of genetic variation of crop species and their wild relatives is a crucial aspect for biodiversity conservation and its exploitation to maintain and increase food security [1]
By surveying genotypes belonging to the three taxa of C. cardunculus species, we provide the first wide single nucleotide polymorphism (SNP) genotyping study for germplasm of this species complex, as a previous investigation based on RAD
The number of tags mapped on the globe artichoke genome was not high, and this might be due to the draft-quality of the reference genome available, which was organized in scaffolds
Summary
The analysis of genetic variation of crop species and their wild relatives is a crucial aspect for biodiversity conservation and its exploitation to maintain and increase food security [1]. The globe artichoke, a diploid plant (2n = 2x = 34) with an estimated genome size of 1.07 Gb [14], is a typical Mediterranean vegetable crop, mainly consumed for its immature flower heads and traditionally cultivated in southern Europe and Northern Africa, with a more recent diffusion in California, South America, and China. Both heads and leaves are rich in antioxidant phenolic compounds such as flavonoids, caffeic acid, chlorogenic acid and cynarin, and for this reason, artichoke plants are used in herbal and medicinal preparations [15,16,17]. Artichoke organs, including roots, contain a high amount of inulin molecules [18] with a chain length of up to 200 [19], having a marked and well tolerated prebiotic effect in humans and useful for industrial applications, e.g. for inhibiting the growth of ice crystals in frozen foodstuffs [20]
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