Data from: Genetic diversity unveiled: Cost-effective methods for grassland species

Permanent grasslands are the basis for sustainable ruminant livestock
production and provide various ecosystem services. They are mainly
composed of outcrossing plant species, leading to populations with high
genetic diversity (i.e., intraspecific diversity). Grasslands of high
plant genetic diversity (PGD) can better cope with environmental stress
and have stabilised biomass productivity. Additionally, they are valuable
reservoirs of genetic resources used for forage plant breeding. To detect
undesired changes and intervene accordingly, monitoring PGD in these
grasslands is key. Despite the availability of various molecular genetic
approaches, PGD monitoring is often neglected in biodiversity reports,
which is attributed to a lack of standardised and affordable indicators of
genetic diversity in natural populations. To assess PGD of agronomically
relevant grassland species, we applied multispecies amplicon sequencing
(MSAS) and genotyping-by-sequencing (GBS), resulting in three data sets.
Using MSAS, we analysed 39 samples based on five species (Dactylis
glomerata L., Festuca pratensis Huds., Lolium perenne L., Trifolium
pratense L., Trifolium repens L.). The sample set contains 30
single-accession (SA) seedling samples (five species, two accessions (A
and B) per species, three replicates) and nine mixed-species (MS) seedling
samples (three compositions, three replicates). The latter were prepared
by pooling DNA from SA samples for three different compositions: 1)
MS-A100, containing accession A of each species at equal amounts, 2)
MS-B100, containing accession B of each species at equal amounts, and 3)
MS-AB50, for equal amounts of MS-A100 and MS-B100.  Furthermore,
we prepared an extended L. perenne sample set consisting of 42 samples
based on six cultivars. This sample set contained 18 single-cultivar
samples (six cultivars, three replicates) and 18 mixtures of two cultivars
(three mixtures, two mixing ratios (50:50 and 75:25), three replicates).
In addition to these samples, which were based on a greenhouse experiment,
the sample set contained six 50:50-ratio mixtures based on a field
experiement (one mixture, two locations, three replicates). Subsequently,
the sample set was analysed using MSAS and GBS.