Department of Soil, Plant and Food Science, University of Bari ˝Aldo Moro˝, Bari, Italy.
Institute of Biomedical Technologies, National Research Council (CNR), Bari, Italy.
PLoS One. 2018 Oct 23;13(10):e0205988. doi: 10.1371/journal.pone.0205988. eCollection 2018.
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.
利用作物及其野生亲缘物种的生物多样性对于维护和增加粮食安全至关重要。Cynara cardunculus 物种包括三个分类群：球茎洋蓟，一种最重要的地中海蔬菜，叶用洋蓟和野生洋蓟。在这项研究中，测序基因型分析（GBS）成功地应用于揭示包括 65 个球茎洋蓟、9 个叶用洋蓟和 21 个野生洋蓟样本在内的 C. cardunculus 种质资源收集的数千个多态性。该收集在 K = 2 时表现出强烈的群体结构，将球茎洋蓟与叶用和野生洋蓟分开。在更高的 K 值时，观察到进一步的亚结构，其中野生洋蓟与叶用洋蓟分离，后者包括西班牙野生洋蓟，而来自葡萄牙的野生样本则是混合的。此外，还突出了球茎洋蓟内部的亚种群。将结构分析限制在球茎洋蓟数据集内，指出了“Catanesi”分类与所有其他样本之间的遗传分化（K = 2）。在更高的 K 值时，“Catanesi”组的分离仍然成立，意大利普利亚地区的绿头陆地品种（“Green Apulian”）形成了一个独特的亚种群。“Romaneschi”洋蓟类型落在一个混合样本的可变群体中，表明它们不应该被视为遗传上统一的分类。主成分分析和邻接法层次聚类的结果与结构结果一致，此外还提供了个体基因型之间遗传关系的度量。两种分析都将西班牙和葡萄牙的野生材料归为栽培洋蓟组，支持这种野生形式可能确实是叶用洋蓟的野生物种的观点。不同的繁殖习性和可能的选择压力导致洋蓟的 LD 衰减速度比洋蓟慢。测序基因型分析已被证明是一种可靠的方法，可以获得有价值的 SNPs 并评估 C. cardunculus 的群体遗传学。
