Biology subjects

Loera-Sanchez, M.

Publications and source records attributed to Loera-Sanchez, M..

2 recordsLinked to original sources

bioRxiv2025

Genetic diversity unveiled: cost-effective methods for grassland species

AbstractPermanent grasslands are predominantly composed of allogamous plant species that exhibit high levels of plant genetic diversity (PGD) within their populations. Grasslands with high PGD are more resilient to environmental stress and constitute valuable reservoirs of genetic resources for plant breeding. Therefore, monitoring PGD is the basis for detecting changes in PGD and correspondingly intervening. However, PGD monitoring is often neglected in biodiversity reports due to difficulties in taking representative samples and in using standardised and affordable indicators of PGD. Here we successfully applied two common approaches, multispecies amplicon sequencing (MSAS) and genotyping-by-sequencing (GBS), to assess PGD of agronomically relevant grassland species. Using MSAS, we were able to taxonomically distinguish five species (Dactylis glomerata L., Festuca pratensis Huds., Lolium perenne L., Trifolium pratense L., Trifolium repens L.) from multispecies samples and differentiate accessions within species, with fixation index (F ST) values ranging from 0.014 for T. repens to 0.089 for L. perenne. Based on an extended L. perenne sample set containing mixtures of two cultivars at different ratios, mixtures containing both cultivars at 50% separated from the corresponding cultivars according to this ratio using MSAS and GBS. Furthermore, GBS enabled separation of samples containing two cultivars at a 75:25-ratio from the corresponding cultivars and the 50:50-ratio samples. These results indicate complementing applications of the two approaches in PGD monitoring. While we anticipate that MSAS with its cost-effectiveness could be applied to large-scale PGD monitoring, GBS with its lower detection limit could be applied to studies where cultivar composition shifts are of interest.

genetics↗

bioRxiv2021

A multispecies amplicon sequencing approach for genetic diversity assessment in grassland plant species

Grasslands are widespread and economically relevant ecosystems at the basis of sustainable roughage production. Plant genetic diversity (PGD; i.e., within-species diversity) is related to many beneficial effects to the ecosystem functioning of grasslands. The monitoring of PGD in temperate grasslands is complicated by the multiplicity of species present and by a shortage of methods for large-scale assessment. However, the continuous advancement of high-throughput DNA sequencing approaches have improved the prospects of broad, multispecies PGD monitoring. Among them, amplicon sequencing stands out as a robust and cost-effective method. Here we report a set of twelve multispecies primer pairs that can be used for high-throughput PGD assessment in multiple grassland plant species. The loci targeted by the amplicons were selected and tested in two phases: a "discovery phase" based on a sequence capture assay (611 target nuclear loci assessed in 16 grassland plant species), which resulted in the selection of eleven loci; and a "validation phase", in which the selected loci were targeted and sequenced using twelve multispecies primers in test populations of Dactylis glomerata L., Lolium perenne L., Festuca pratensis Huds., Trifolium pratense L. and T. repens L. The resulting multispecies amplicons had overall nucleotide diversities per species ranging from 5.19 x 10-3 to 1.29 x 10-2, which is in the range of flowering-related genes but slightly lower than pathogen resistance genes. We conclude that the methodology, the DNA sequence resources, and the amplicon-specific primer pairs reported in this study provide the basis for large-scale, multispecies PGD monitoring in grassland plants.

ecology↗