ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2021
Whole-genome sequence diversity and association analysis of 198 soybean accessions in mini-core collections.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
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- Integration of proxy intermediate omics traits into a nonlinear two-step model for accurate phenotypic prediction.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Tocopherol Profile Variations of Soybean World Mini-Core Collection Accessions Grown in Hokkaido.microPublication biology · 2026Article
- Reciprocal BLUP: A Predictability-Guided Multi-Omics Framework for Plant Phenotype Prediction.Plants (Basel, Switzerland) · 2025Article
- LAYLA: development of a comprehensive and cross-sample program for detecting structural variants and its application to citrus cultivars.Breeding science · 2025Article
- Inhibition of DCL4 activity by maternally supplied flavonoid aglycons induces a bicolor pattern in the saddle soybean seed coat.The Plant journal : for cell and molecular biology · 2025Article
- Genetic design of soybean hosts and bradyrhizobial endosymbionts reduces NNature communications · 2025Article
- Landscape of rare-allele variants in cultivated and wild soybean genomes.The plant genome · 2025Article
- The genomic landscape of gene-level structural variations in Japanese and global soybean Glycine max cultivars.Nature genetics · 2025Article
- Article
- Cross potential selection: a proposal for optimizing crossing combinations in recurrent selection using the usefulness criterion of future inbred lines.G3 (Bethesda, Md.) · 2024Article
- Whole-genome sequencing analysis of soybean diversity across different countries and selection signature of Korean soybean accession.G3 (Bethesda, Md.) · 2024Article
- Modeling soybean growth: A mixed model approach.PLoS computational biology · 2024Article
- Assessing genetic diversity and geographical differentiation in a global collection of wild soybean (Glycine soja Sieb. et Zucc.) and assigning a mini-core collection.DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- Reaction norm for genomic prediction of plant growth: modeling drought stress response in soybean.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- A high-performance computational workflow to accelerate GATK SNP detection across a 25-genome dataset.BMC biology · 2024Article
- Novel Soybean Variety Lacking Raffinose Synthase 2 Activity.ACS omega · 2024Article
- High-Throughput Phenotyping of Soybean Biomass: Conventional Trait Estimation and Novel Latent Feature Extraction Using UAV Remote Sensing and Deep Learning Models.Plant phenomics (Washington, D.C.) · 2024Article
- Random regression for modeling soybean plant response to irrigation changes using time-series multispectral data.Frontiers in plant science · 2023Article
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Authors and funding
13 authors.
Funding
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Abstract
We performed whole-genome Illumina resequencing of 198 accessions to examine the genetic diversity and facilitate the use of soybean genetic resources and identified 10 million single nucleotide polymorphisms and 2.8 million small indels. Furthermore, PacBio resequencing of 10 accessions was performed, and a total of 2,033 structure variants were identified. Genetic diversity and structure analysis congregated the 198 accessions into three subgroups (Primitive, World, and Japan) and showed the possibility of a long and relatively isolated history of cultivated soybean in Japan. Additionally, the skewed regional distribution of variants in the genome, such as higher structural variations on the R gene clusters in the Japan group, suggested the possibility of selective sweeps during domestication or breeding. A genome-wide association study identified both known and novel causal variants on the genes controlling the flowering period. Novel candidate causal variants were also found on genes related to the seed coat colour by aligning together with Illumina and PacBio reads. The genomic sequences and variants obtained in this study have immense potential to provide information for soybean breeding and genetic studies that may uncover novel alleles or genes involved in agronomically important traits.
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