DOI: 10.5061/dryad.djh9w0w5d
title: Genotyping results of the FabaPanel for: Genetic erosion within the Fabada dry bean market class revealed by high-throughput genotyping

description: This dataset contains the results of the genotyping of a set of 180
 homozygous bean lines.  The dataset includes a VCF file with the
 genotypic data obtained from 'genotyping by sequencing'. The
 data set was used to perform the study 'Genetic erosion within the
 Fabada dry bean market class revealed by high-throughput genotyping.'
 ABSTRACT  The Fabada market class within the dry beans has a
 well-differentiated seed phenotype with very large white seeds. This work
 investigated the genetic diversity maintained in the seed collections
 within this market class and possible genetic erosion over the last 30
 years. A panel with 100 accessions maintained in seed collections for 30
 years, 57 accessions collected from farmers in 2021, six cultivars
 developed in SERIDA, and 16 reference cultivars were gathered and
 genotyped, revealing 108,585 SNPs using Genotyping-by-Sequencing.
 Filtering based on genotypic and phenotypic data was carried out in a
 staggered fashion to investigate the genetic diversity among populations.
 The dendrogram generated from genotyping revealed 90 lines forming 16
 groups with identical SNP profiles (redundant lines) from 159 lines
 classified as market class Fabada according to their passports. Seed
 phenotyping indicated that 19 lines were mistakenly classified as Fabada
 (homonymies), which was confirmed in the dendrogram built without
 redundant lines. This study provides evidence of genetic erosion between
 the population preserved for 30 years and the currently cultivated
 population. The conserved population contains 54.6% segregation sites and
 41 different SNP profiles, whereas the cultivated population has 19.6%
 segregation sites and 26 SNP profiles. The loss of genetic variability
 cannot be attributed to the diffusion of modern cultivars, which could
 increase the genetic diversity (six new SNP profiles). The results allow
 for the more efficient preservation of plant genetic resources in
 genebanks, minimizing redundant accessions and incorporating new
 variations based on genotypic and phenotypic data.
description: <strong>DNA isolation
 and genotyping </strong> Genomic DNA was isolated from young leaf samples
 using the SILEX method (Vilanova et al., 2020), and DNA quality was checked in agarose gels.
 The Genotyping-by-Sequencing (GBS) method was carried out in accordance
 with Elshire et al.
 (2011) and optimized by
 Schröder et al.
 (2016) using the TaqαI and
 MseI restriction enzymes. Library construction was performed following the
 protocol of Poland et al.
 (2012) with modifications
 in the adaptors for ligation. In total, 20 barcoded samples were pooled
 for PCR amplification. Sequencing was performed in the Illumina platform
 by Macrogen Inc. (Seoul, Republic of Korea). SNP calling was carried out
 by AllGenetics&Biology SL (www.allgenetics.eu) using the reference genome of Phaseolus vulgaris (Pvulgaris_442_v2.0) obtained from the JGI Data Portal (https://phytozome-next.jgi.doe.gov/info/Pvulgaris_v2_1). 
description: The
 data can be visualized in Tassel v5, for
 example.