AUTHOR=Correa Abondano Miguel , Ospina Jessica Alejandra , Wenzl Peter , Carvajal-Yepes Monica 

TITLE=Sampling strategies for genotyping common bean (Phaseolus vulgaris L.) Genebank accessions with DArTseq: a comparison of single plants, multiple plants, and DNA pools

JOURNAL=Frontiers in Plant Science

VOLUME=15

YEAR=2024

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1338332

DOI=10.3389/fpls.2024.1338332

ISSN=1664-462X

ABSTRACT=<sec><title>Introduction</title><p>Genotyping large-scale gene bank collections requires an appropriate sampling strategy to represent the diversity within and between accessions.</p></sec><sec><title>Methods</title><p>A panel of 44 common bean (<italic>Phaseolus vulgaris</italic> L.) landraces from the Alliance Bioversity and The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT) gene bank was genotyped with DArTseq using three sampling strategies: a single plant per accession, 25 individual plants per accession jointly analyzed after genotyping (<italic>in silico–pool</italic>), and by pooling tissue from 25 individual plants per accession (<italic>seq-pool</italic>). Sampling strategies were compared to assess the technical aspects of the samples, the marker information content, and the genetic composition of the panel.</p></sec><sec><title>Results</title><p>The <italic>seq-pool</italic> strategy resulted in more consistent DNA libraries for quality and call rate, although with fewer polymorphic markers (6,142 single-nucleotide polymorphisms) than the <italic>in silico–pool</italic> (14,074) or the single plant sets (6,555). Estimates of allele frequencies by <italic>seq-pool</italic> and <italic>in silico–pool</italic> genotyping were consistent, but the results suggest that the difference between pools depends on population heterogeneity. Principal coordinate analysis, hierarchical clustering, and the estimation of admixture coefficients derived from a single plant, <italic>in silico</italic>–<italic>pool</italic>, and <italic>seq-pool</italic> successfully identified the well-known structure of Andean and Mesoamerican gene pools of <italic>P. vulgaris</italic> across all datasets.</p></sec><sec><title>Conclusion</title><p>In conclusion, <italic>seq-pool</italic> proved to be a viable approach for characterizing common bean germplasm compared to genotyping individual plants separately by balancing genotyping effort and costs. This study provides insights and serves as a valuable guide for gene bank researchers embarking on genotyping initiatives to characterize their collections. It aids curators in effectively managing the collections and facilitates marker-trait association studies, enabling the identification of candidate markers for key traits.</p></sec>