Core collection of Taiwanese soybeans

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 f..., 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 A260/A280 ratio of 1.8-2.0 and concentration ≥ 60 ng/μl. Genotyping employed the Axiom® SoyaSNP180K (180,961) chip array. The criteria, including a batch’s quality (Dish quality control > 0.82) and sample call rate (> 97%), led to the exclusion of 33 redundant and 191 poor-quality samples. Filtering retained single nucleotide polymorphisms (SNPs) with missing rate < 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. Prin..., , # Core collection of Taiwanese soybeans

[https://doi.org/10.5061/dryad.prr4xgxv0](https://doi.org/10.5061/dryad.prr4xgxv0)

The SNP dataset includes genetic information from 244 Taiwanese soybean accessions, comprising 192 grain soybeans and 52 vegetable soybeans.

## Description

DNA extraction utilized the DNeasy 96 Plant Kit, and genotyping employed the Axiom® SoyaSNP180K chip array, resulting in 78,189 high-quality SNPs after quality control (Dish quality control > 0.82; sample call rate > 97%; excluding unanchored scaffold SNPs; marker missing rate < 0.10; minor allele frequency < 0.05; heterozygous rate < 0.10). \
The dataset is provided in Variant Call Format (VCF) v4.2. Each line in the VCF file represents a genetic variant (SNP marker), with columns specifying information such as chromosome, position, reference allele, alternative allele, quality scores, and genotype information for each sample (accessions).

## Accessions information

Detailed information regar...