Abstract
Forty three microsatellite markers were developed for further genetic characterisation of a forage and biomass grass crop, for which genomic resources are currently scarce. The microsatellite markers were developed from a normalized EST-SSR library. All of the 43 markers gave a clear banding pattern on 3 % Metaphor agarose gels. Eight selected SSR markers were tested in detail for polymorphism across eleven DNA samples of large geographic distribution across Europe. The new set of 43 SSR markers will help future research to characterise the genetic structure and diversity of Phalaris arundinacea, with a potential to further understand its invasive character in North American wetlands, as well as aid in breeding work for desired biomass and forage traits. P. arundinacea is particularly valued in the northern latitude as a crop with high biomass potential, even more so on marginal lands.
Highlights
Slight changes in the genetic code, such as single nucleotide polymorphisms (SNPs) and single sequence repeats (SSRs) can be directly linked to phenotype differences
The eleven genotypes are grouped by six European countries with latitude and longitude coordinates of their origin and cross-amplification with other important and closely related forage grass species like P. aquatica [16]
Total genomic DNA was extracted from eleven genotypes which were collected as part of the European Grass Margins project (Table 1) by either fresh extraction in liquid nitrogen or freeze-drying prior to extraction following a standard cetyltrimethylammonium bromide (CTAB) method [18]
Summary
Slight changes in the genetic code, such as single nucleotide polymorphisms (SNPs) and single sequence repeats (SSRs) can be directly linked to phenotype differences. Single sequence repeats are abundant in the genome, multi-allelic and polymorphic and often can be cross-amplified on related species [3]. Next-generation sequencing can provide large numbers of SSRs as demonstrated in this study and is even more useful once converted into routinely applicable genetic markers.
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