Genetic diversity and accession structure in European Cynara cardunculus collections

Abstract

Understanding the distribution of genetic variations and accession structures is an important factor for managing genetic resources, but also for using proper germplasm in association map analyses and breeding programs. The globe artichoke is the fourth most important horticultural crop in Europe. Here, we report the results of a molecular analysis of a collection including globe artichoke and leafy cardoon germplasm present in the Italian, French and Spanish gene banks. The aims of this study were to: (i) assess the diversity present in European collections, (ii) determine the population structure, (iii) measure the genetic distance between accessions; (iv) cluster the accessions; (v) properly distinguish accessions present in the different national collections carrying the same name; and (vi) understand the diversity distribution in relation to the gene bank and the geographic origin of the germplasm. A total of 556 individuals grouped into 174 accessions of distinct typologies were analyzed by different types of molecular markers, i.e. dominant (ISSR and AFLP) and co-dominant (SSR). The data of the two crops (globe artichoke and leafy cardoon) were analyzed jointly and separately to compute, among other aims, the gene diversity, heterozygosity (He, Ho), fixation indexes, AMOVA, genetic distance and structure. The findings underline the huge diversity present in the analyzed material, and the existence of alleles that are able to discriminate among accessions. The accessions were clustered not only on the basis of their typology, but also on the basis of the gene bank they come from. Probably, the environmental conditions of the different field gene banks affected germplasm conservation. These outcomes will be useful in plant breeding to select accessions and to fingerprint varieties. Moreover, the results highlight the particular attention that should be paid to the method used to conserve the Cynara cardunculus germplasm and suggest to the preference of using accessions from different gene banks to run an association map.

How extraction method affects yield, fatty acids composition and bioactive properties of cardoon seed oil?

“…altilis DC) and wild cardoon (C. cardunculus var. sylvestris (Lamk) Fiori) (Pagnotta et al, 2017;Raccuia et al, 2011). Cultivated and wild cardoon have been traditionally used for its edible leaf stems (Renna et al, 2018), while in many regions of the Mediterranean plant immature inflorescences are also consumed in various gourmet dishes (Christaki et al, 2012;Fernández et al, 2006), or in the cheese-making industry (Almeida and Simões, 2018).…”

Phenotyping, Genotyping, and Selections within Italian Local Landraces of Romanesco Globe Artichoke

“…Profiles were converted to a 1/0 matrix for statistical analyses, while band dimensions were considered for SSR markers. Statistics of the molecular data, such as number of polymorphic bands (NPB), expected heterozygosity (He), observed heterozygosity (Ho), and polymorphic information content (PIC), were computed for each clone, in accordance with Pagnotta et al [29], utilizing GenAlEx [30] or Power Marker [31]. The marker matrix was also used to compute Nei's genetic distances [32] between clones, and then used to conduct a cluster analysis and to draw an UPGMA diagram.…”

Comparison among Methods and Statistical Software Packages to Analyze Germplasm Genetic Diversity by Means of Codominant Markers

“…Structure can provide the histograms of Fst, alpha, and likelihood for each cluster, as well as a tree plot of the distance among clusters. It is also possible to plot the average proportion of the Q values directly on a geographic map [30]. In Structure, the analysis should be set in agreement with the populations' information and the procedures used in the population sampling.…”