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

Käch, Damian12; Loera-Sánchez, Miguel13; Reidy, Beat2; Studer, Bruno1; Kölliker, Roland1

Published Mar 13, 2026 on Dryad. https://doi.org/10.5061/dryad.2rbnzs82f

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Abstract

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.