Assessment of genetic diversity in Nordic timothy (Phleum pratense L.)

Abstract

BackgroundTimothy (Phleum pratense L.), a cool-season hexaploid perennial, is the most important forage grass species in Nordic countries. Earlier analyses of genetic diversity in a collection of 96 genebank accessions of timothy with SSR markers demonstrated high levels of diversity but could not resolve population structure. Therefore, we examined a subset of 51 accessions with REMAP markers, which are based on retrotransposons, and compared the diversity results with those obtained with SSR markers.ResultsUsing four primer combinations, 533 REMAP markers were analyzed, compared with 464 polymorphic alleles in the 13 SSR loci previously. The average marker index, which describes information obtained per experiment (per primer combination or locus) was over six times higher with REMAPs. Most of the variation found was within accessions, with somewhat less, 89 %, for REMAPs, than for SSR, with 93 %.ConclusionsSSRs revealed differences in the level of diversity slightly better than REMAPs but neither marker type could reveal any clear clustering of accessions based on countries, vegetation zones, or different cultivar types. In our study, reliable evaluation of SSR allele dosages was not possible, so each allele had to be handled as a dominant marker. SSR and REMAP, which report from different mechanisms of generating genetic diversity and from different genomic regions, together indicate a lack of population structure. Taken together, this likely reflects the outcrossing and hexaploid nature of timothy rather than failures of either marker system.

Use of retrotransposon-derived genetic markers to analyse genomic variability in plants

“…Completely different RTE amplification banding patterns are obtained if the same LTR primers are used alone or in combinations indicating that the majority of IRAP bands are derived from sequences bordered by one LTR or a microsatellite on one side, and by another LTR on the other side (Leigh et al 2003;Kalendar and Schulman 2006;Boronnikova and Kalendar 2010;Hosid et al 2012;Abdollahi Mandoulakani et al 2015;Tanhuanpää et al 2016).…”

DNA markers for Typhula resistance in timothy (Phleum pratense L.)

“…REMAP markers were amplified in a reaction volume of 20 µl, using 1U Biotools DNA polymerase (Biotools B&M Labs, S.A., Madrid, Spain), with the buffer containing 2 mM MgCl 2 supplied by the enzyme manufacturer, 200 µM each dNTP, 500 nM each primer, and 25 ng DNA. The PCR program used is described in Tanhuanpää et al (2016). Amplification products were resolved on a 1.4% agarose gel (GellyPhor® LE, Euroclone S.p.A, Pero, Italy).…”

Assessment of Anthropogenic Impacts on the Genetic Diversity of Phragmites australis in Small-River Habitats

“…In this study, we analyzed a larger sample set and other regions of the Phragmites genome to assess the anthropogenic factors that can impact the genetic diversity of the populations of this species. Here, we employed intersimple sequence repeats (ISSRs), dominant molecular markers that are highly polymorphic, sufficiently reliable, inexpensive and, as some other dominant markers, equally informative as SSRs in the analysis of polyploid genotypes [56]. The application of the ISSR technique enabled the investigation of DNA polymorphisms between adjacent, inverted microsatellite loci, located at suitable distances for PCR amplification, and produced reproducible multilocus band patterns [38,[57][58][59][60][61][62][63].…”