Optimizing genomic diversity assessments for conservation of Bromus auleticus (Trinius ex Nees) using individual and pooled sequencing
Luciana Gillman, Federico Condón, Cesar Petroli, Mercedes Rivas
TL;DR
This study compares individual and pooled sequencing methods to assess genetic diversity in Bromus auleticus, a forage grass facing genetic erosion, to guide conservation efforts.
Contribution
The study provides optimized workflows for population genomic studies in Bromus auleticus using sequencing strategies tailored to sample size and depth.
Findings
Pooled sequencing (pool-seq) with 30–60 plants per accession and 4.8 million reads yielded the highest polymorphic sites and concordance with individual sequencing.
Pool-seq showed higher expected heterozygosity and lower allelic richness compared to individual sequencing across all accessions.
Population structure analysis confirmed the outcrossing nature of B. auleticus and its geographical origin, highlighting the need for conservation.
Abstract
Bromus auleticus, a valuable forage grass native to the Pampa biome, is currently undergoing genetic erosion. Therefore, it is essential to assess appropriate methodologies for developing population genomic studies that will contribute to the conservation of this genetic resource. In this study, we evaluated five accessions using two genotyping strategies: individual sequencing (ind-seq) and pooled sequencing (pool-seq). To assess methodologies effectiveness, the correlation between allele frequencies calculated using each approach was investigated, as well as genetic diversity and population structure. These comparisons explicitly accounted for the potential effects of factors such as sample size, missing data, sequencing depth, and minor allele frequencies. The highest values of frequencies concordance and percentage of SNPs in common between ind-seq and pool-seq were achieved using a…
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Taxonomy
TopicsGenetic and phenotypic traits in livestock · Genetic diversity and population structure · Genetic Mapping and Diversity in Plants and Animals