Comparative assessment of SSR and SNP markers for inferring the population genetic structure of the common fungus Armillaria cepistipes

Abstract

During the last years, simple sequence repeats (SSRs, also known as microsatellites) and single-nucleotide polymorphisms (SNPs) have become the most popular molecular markers for describing neutral genetic variation in populations of a wide range of organisms. However, only a limited number of studies has focused on comparing the performance of these two types of markers for describing the underlying genetic structure of wild populations. Moreover, none of these studies targeted fungi, the group of organisms with one of the most complex reproductive strategies. We evaluated the utility of SSRs and SNPs for inferring the neutral genetic structure of Armillaria cepistipes (basidiomycetes) at different spatial scales. For that, 407 samples were collected across a small (150 km) area in the Ukrainian Carpathians and a large (41 000 km) area in the Swiss Alps. All isolates were analyzed at 17 SSR loci distributed throughout the whole genome and at 24 SNP loci located in different single-copy conserved genes. The two markers showed different patterns of structure within the two spatial scales studied. The multi-allelic SSR markers seemed to be best suited for detecting genetic structure in indigenous fungal populations at a rather small spatial scale (radius of ~50-100 km). The pattern observed at SNP markers rather reflected ancient divergence of distant (~1000 km) populations that in addition are separated by mountain ranges. Despite these differences, both marker types were suitable for detecting the weak genetic structure of the two A. cepistipes populations investigated.

Comparison of structure analyses and core collections for the management of walnut genetic resources

“…As a result, it is fair to wonder how to conduct the tasks related to germplasm management, such as core collections construction, and the choice of the type of marker to be used is one of the first questions. Neutral SSR loci, due to slippage during replication, usually mutate much more frequently than SNP loci, leading to population-specific alleles that are useful for revealing population structure (Tsykun et al 2017). On the other hand, since they are usually developed in small numbers for one species, they therefore may not reflect genome-wide genetic diversity contrary to SNP loci that are much more frequent in the genome of most species (Ljungqvist et al 2010).…”

Development, characterization, and cross-amplification of polymorphic microsatellite markers for North American Trachymyrmex and Mycetomoellerius ants

“…Conversely, microsatellite markers, once developed, can be used repeatedly in multiple studies, which may reduce their overall expense on a per-project basis [22]. Moreover, recent comparative studies in insects, fungi, and birds reported no major population genetic structural differences between these two approaches [23][24][25][26], or that more SNPs were required to produce the same information as a single microsatellite marker [27].…”

Deciphering the SSR incidences across viral members of Coronaviridae family

“…SSRs have been widely exploited as neutral markers in multitudes of studies such as ecology and evolutionary genetics, genome mapping, etc. irrespective of their hypermutablility [ 37 , 39 ]. SSRs are characterized by their inherent ability to cause frameshift mutations in genomic regions encoding phenotypic changes and therefore, confer an adaptive advantage in the course ofviral mutations [ 1 ]; Y.…”