Variation in sequences containing microsatellite motifs in the perennial biomass and forage grass, Phalaris arundinacea (Poaceae)

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.

Keywords: Microsatellite markers; Phalaris arundinacea; Poaceae; Reed canary grass; SSR.

Fig. 1

Representative image of amplified product for ten different EST-SSR markers. The samples were run on 3 % MetaPhor™ gel and three or, in one case seven different genotypes from wide geographic locations were amplified. The gel was post-stained with 3x gelRED for 1 h. Lane M—100 bp DNA ladder (New England BioLabs, Herts, United Kingdom); sample order and geographic distribution are defined in Table 1

Fig. 2

Example of motif changes, indels and SNPs in the microsatellite region of nine representative samples. a fragments amplified with primer TeaPh_nSSR49; 1 Poland (accession number KU316491); 2 Ireland (accession number KU316495); 3 Ireland (accession number KU316498). b fragments amplified with primer TeaPh_nSSR80; 4 Poland (accession number KU316501); 5 Poland (KU316502); 6 Poland (KU316514). c fragments amplified with primer TeaPh_nSSR46; 7 Germany (accession number KU316457); 8 Denmark (KU316467); 9 United Kingdom (KU316471)