A method for genotyping elite breeding stocks of leaf chicory (Cichorium intybus L.) by assaying mapped microsatellite marker loci

Abstract

BackgroundLeaf chicory (Cichorium intybus subsp. intybus var. foliosum L.) is a diploid plant species (2n = 18) of the Asteraceae family. The term “chicory” specifies at least two types of cultivated plants: a leafy vegetable, which is highly differentiated with respect to several cultural types, and a root crop, whose current industrial utilization primarily addresses the extraction of inulin or the production of a coffee substitute. The populations grown are generally represented by local varieties (i.e., landraces) with high variation and adaptation to the natural and anthropological environment where they originated, and have been yearly selected and multiplied by farmers. Currently, molecular genetics and biotechnology are widely utilized in marker-assisted breeding programs in this species. In particular, molecular markers are becoming essential tools for developing parental lines with traits of interest and for assessing the specific combining ability of these lines to breed F1 hybrids.ResultsThe present research deals with the implementation of an efficient method for genotyping elite breeding stocks developed from old landraces of leaf chicory, Radicchio of Chioggia, which are locally dominant in the Veneto region, using 27 microsatellite (SSR) marker loci scattered throughout the linkage groups. Information on the genetic diversity across molecular markers and plant accessions was successfully assessed along with descriptive statistics over all marker loci and inbred lines. Our overall data support an efficient method for assessing a multi-locus genotype of plant individuals and lineages that is useful for the selection of new varieties and the certification of local products derived from Radicchio of Chioggia.ConclusionsThis method proved to be useful for assessing the observed degree of homozygosity of the inbred lines as a measure of their genetic stability; plus it allowed an estimate of the specific combining ability (SCA) between maternal and paternal inbred lines on the basis of their genetic diversity and the predicted degree of heterozygosity of their F1 hybrids. This information could be exploited for planning crosses and predicting plant vigor traits (i.e., heterosis) of experimental F1 hybrids on the basis of the genetic distance and allelic divergence between parental inbred lines. Knowing the parental genotypes would allow us not only to protect newly registered varieties but also to assess the genetic purity and identity of the seed stocks of commercial F1 hybrids, and to certificate the origin of their food derivatives.Electronic supplementary materialThe online version of this article (doi:10.1186/s13104-015-1819-z) contains supplementary material, which is available to authorized users.

Current Advances in Genomics and Breeding of Leaf Chicory (Cichorium intybus L.)

“…A cost-and time-efficient multilocus genotyping method based on a panel of mapped SSR markers is now available for Radicchio [34]. Its application has utility for assessing the degree of homozygosity of parental inbred lines, as a measure of their genetic stability, and also for predicting the degree of heterozygosity of their F 1 hybrids, as an estimate of the specific combining ability on the basis of the genetic diversity between maternal and paternal inbred lines.…”

“…In the same year, Ghedina et al [34] published a method for genotyping elite breeding stocks of leaf chicory by assaying 27 mapped SSR markers, three per linkage group. As the plant accessions analyzed were inbred lines, the data were not comparable with the data of previous studies, in which open-pollinated varieties or wild accessions were taken into account.…”

“…Nevertheless, they also observed that inbreeding coefficients of single lines were low or negative, indicating that the observed heterozygosity is higher than expected. An interesting hypothesis is that maintenance of such levels of heterozygosity despite inbreeding reproductive strategies (i.e., selfing, full-sibling, and back-crossing) could be a consequence of the reproductive system of C. intybus, which is naturally characterized by a high frequency of allogamy as a result of self-incompatibility [34]. In addition, the authors also speculated that a fraction of the observed heterozygosity could be a consequence of phenotypic selection of morphologically superior individuals performed by breeders during inbreeding programs.…”

“…Although chicory cannot be considered as a model species, some genetic studies using molecular markers have been conducted in order to characterize commercial varieties and experimental materials [20,33,71,72]; to evaluate the genetic homogeneity and purity of inbreds and hybrids, respectively [34,73]; to investigate phylogenetic relationships between cultivars and cultivar groups of C. intybus and other species, both cultivated and wild, belonging to the same genus [12,15,18,19,74]; and to assess the degree of spontaneous gene flow between landraces, cultivars, and wild populations of chicory. Moreover, molecular markers were also applied to understand whether co-existence between transgenic varieties and conventional varieties is possible [75].…”

“…Plus, the accession used is a male-fertile inbred line that is both phenotypically and genotypically well characterized. It is permanently conserved by in vitro culture to allow high availability of clonal materials, and it is distinguished by a high degree of homozygosity, more than 80% [34]. Last but not least, it shows an excellent general combining ability, as demonstrated in trial experiments where this inbred line was used as seed parent in pairwise crosses with genetically distinct pollen donors for the development of F 1 hybrids.…”