DOI: 10.5061/dryad.prr4xgxv0
title: Core collection of Taiwanese soybeans

description: NOTICE At the authors' request, the data files for this submission
 have been removed from public view due to concerns regarding compliance
 with data usage agreements. (June 2024) Vegetable soybean (Glycine max L.)
 stands as a significant crop in East Asia, distinguished by unique
 phenotypic traits such as seed size, coat color, and sweetness, setting it
 apart from grain soybeans. These traits are likely attributed to
 intensive, extensive, and long-term selection processes, yet the genomic
 alterations underlying these variations remain inadequately elucidated.
 Here, we established a core collection panel comprising 52 vegetable
 soybean and 192 grain soybean samples, selected from a pool of 2,394
 Taiwanese accessions. Through population structure, genetic diversity, and
 differentiation analyses, we observed reduced genetic variability in
 vegetable soybeans compared to grain soybeans, with significant
 differentiation between the two types. Our investigation identified 159
 significant signatures within 67 putative regions linked to selective
 breeding in vegetable soybeans, many of which overlap with previously
 identified genomic loci, indicating selective breeding footprints.
 Phenotypic variation patterns suggest that improved productivity in
 vegetable soybeans may be achieved by pyramiding specific favorable
 alleles. Furthermore, we pinpointed two promising genes, GmAP2-2 and
 GmTFL1b (Dt1), as potential focal points for future vegetable soybean
 breeding, given their roles in flowering time and seed development. This
 comprehensive study underscores the utility of core collection panels and
 provides valuable insights into soybean genetics, laying the groundwork
 for future breeding endeavors and research in vegetable soybeans.
description: A total of 2,618 Taiwanese soybean accessions from the National
 Plant Genetic Resources Center at the Taiwan Agricultural Research
 Institute were classified into 2,511 grain soybeans and 107 vegetable
 soybeans. DNA extraction and purification from 2,618 soybean accessions
 utilized the DNeasy 96 Plant Kit (QIAGEN) system, ensuring an
 A<sub>260</sub>/A<sub>280</sub> ratio of 1.8-2.0
 and concentration ≥ 60 ng/μl. Genotyping employed the
 Axiom<sup>®</sup> SoyaSNP180K (180,961) chip array. The
 criteria, including a batch’s quality (Dish quality control &gt; 0.82)
 and sample call rate (&gt; 97%), led to the exclusion of 33 redundant
 and 191 poor-quality samples. Filtering retained single nucleotide
 polymorphisms (SNPs) with missing rate &lt; 0.10, excluding 366
 unanchored scaffold SNPs and chloroplast genome SNPs. The quality-filtered
 SNP dataset comprised 147,560 SNPs, with a call rate of 99.78%. The core
 collection of Taiwanese vegetable and grain soybeans was constructed to
 minimize redundancy within germplasm pools. Principal coordinate analysis
 (PCoA) was executed on the quality-filtered 147k SNP dataset using Tassel
 v.5.0 software, enabling the identification of principal components (PCs)
 capturing 80% of the total genetic variation. Subsequently, the PowerCore
 program v.1.0 systematically facilitated the selection of core accessions
 based on phenotypic traits and the PCs derived from genotypic data,
 resulting in a core collection comprising 192 accessions for grain
 soybeans and 52 accessions for vegetable soybeans. Further SNP data
 refinement using the command --maf 0.05 --hardy on PLINK v.1.9 filtered
 out SNPs with rare variants (i.e., minor allele frequency (MAF) &lt;
 0.05) and heterozygous rate &lt; 0.10, resulting in a final dataset of
 78,189 SNPs.
description: At the authors' request, the data files for this submission have been
 removed from public view due to concerns regarding compliance with data
 usage agreements. (June 2024)