Evaluation of Cross-Species Transferability of SSR Markers in Foeniculum vulgare

Abstract

Fennel (Foeniculum vulgare) is a species belonging to the Apiaceae family, well known for its nutritional and pharmacological properties. Despite the economic and agricultural relevance, its genomic and transcriptomic data remain poor. Microsatellites—also known as simple sequence repeats (SSRs)—are codominant markers widely used to perform cross-amplification tests starting from markers developed in related species. SSRs represent a powerful tool, especially for those species lacking genomic information. In this study, a set of primers previously designed in Daucus carota for polymorphic SSR loci was tested in commercial varieties and breeding lines of fennel in order to: (i) test their cross-genera transferability, (ii) look at their efficiency in assessing genetic diversity, and (iii) identify their usefulness for marker-assisted selection (MAS) in breeding programs. Thirty-nine SSR markers from carrot were selected and tested for their transferability score, and only 23% of them resulted suitable for fennel. The low rate of SSR transferability between the two species evidences the difficulties of the use of genomic SSR in cross-genera transferability.

Genome-Wide Survey and Development of the First Microsatellite Markers Database (AnCorDB) in Anemone coronaria L.

“…Microsatellite—alias simple sequence repeats (SSR)-markers, are co-dominantly inherited, ubiquitous, highly polymorphic, and have found large application in plant breeding and phylogenetic studies because of their simple application through conventional PCR protocols [ 10 , 11 , 12 , 13 , 14 , 15 , 16 ]. Unlike single nucleotide polymorphisms (SNPs), which have become the gold standard among molecular markers, SSRs show the advantage of being multi-allelic and highly informative, characterized by a certain level of transferability between related specie [ 17 , 18 , 19 , 20 ], and are easily and automatically scorable.…”

Short Communication: Cross-species amplification of microsatellite markers developed for Jatropha curcas within five species of Jatropha

“…The development of species-specific SSR markers is very costly and time-consuming, so the information on SSR markers for economically less important species is still limited. A strategy that can overcome this problem is to utilize the cross-amplification ability of SSR markers to access the genetic diversity of the related species (Celiński et al 2013;Aiello et al 2020). Several studies on the SSR marker transferability were conducted among many taxonomic levels.…”

Genotyping by RAD Sequencing Analysis Assessed the Genetic Distinctiveness of Experimental Lines and Narrowed down the Genomic Region Responsible for Leaf Shape in Endive (Cichorium endivia L.)

“…However, it has been demonstrated that increasing the genetic distance among taxa may reduce the marker transfer efficiency [32,33]. For example, some recent studies aimed to test the SSR transferability among genera of the same family (e.g., Cactaceae, Arecaceae and Apiaceae) and achieved success rates of approximately 23-35% [34][35][36]. At the genus level, the percentage of SSR transferability among species rises to 80-85% [37,38] or even higher (90-98%) when EST-SSR are considered [39,40].…”