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Genome-wide exploration of soybean domestication traits: integrating association mapping and SNP × SNP interaction analyses

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Abstract

Soybean domestication has been essential for crop evolution, adaptation, and modern breeding. Despite advancements in understanding soybean genetics, the genetic basis of DRTs has yet to be fully explored, particularly in the context of genome-wide association studies (GWASs) and gene interaction analyses (epistasis). This study evaluated 198 diverse soybean accessions using 23,574 high-quality SNPs obtained via ddRAD-seq. Nine key DRTs—including those related to seed size (length, width, and thickness), seed coat color, cotyledon color, hypocotyl color, stem growth habit, flower color, pod color, pubescence, and pod-shattering—were phenotyped in two environments. A GWASs conducted via the FarmCPU and BLINK models identified 78 significant SNPs, 14 consistently detected across both environments and models, demonstrating stability. Notably, the SNP rs.Gm16.29778273 linked to pod-shattering resistance. The functional annotation linked three known quantitative trait loci /genes and revealed 11 novel candidate genes associated with DRTs, providing insights into their roles via Gene Ontology (GO) terms. The main effect SNP × SNP interaction analysis revealed that the significant SNP rs.Gm13.16695800 exhibits a pleiotropic effect, controlling both hypocotyl and flower color. Furthermore, 324 epistatic interactions were identified, influencing the expression of DRTs, thereby highlighting the complex genetic architecture underlying these traits. These findings offer valuable insights into domestication and the traits linked to higher yield. They provide a solid foundation for developing marker-assisted selection (MAS) strategies and functional studies to improve soybean breeding for resilient, high-yielding varieties.

Key message

This study identified 78 significant single-nucleotide polymorphisms (SNPs) linked to nine domestication-related traits (DRTs) in soybean, using a diverse panel of 198 accessions and double-digest restriction site-associated DNA sequencing (ddRAD-seq). The genome-wide SNP × SNP interaction analysis uncovered one pleotropic and 324 epistatic interactions, revealing a complex genetic architecture. These findings provide valuable marker-assisted selection (MAS) resources to improve soybean breeding.

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Data availability

The datasets created and/or analyzed during the current investigation are accessible from the corresponding author upon reasonable request.

Abbreviations

BLINK:

Bayesian-information and linkage-disequilibrium iteratively nested keyway

ddRAD-seq:

Double-digest restriction site-associated DNA sequencing

DRTs:

Domestication-related traits

FarmCPU:

Fixed and random model circulating probability unification

GO:

Gene ontology

GWAS:

Genome-wide association study

HWE:

Hardy‒Weinberg equilibrium

KASP:

Kompetitive allele-specific PCR

LD:

Linkage-disequilibrium

MAS:

Marker-assisted selection

MTAs:

Marker‒trait associations

PCA:

Principal component analysis

PVE:

Phenotypic variation explained

QTL:

Quantitative trait loci

SNPs:

Single nucleotide polymorphisms

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Acknowledgements

Abhinandan S. Patil expresses gratitude for the financial support from the Ramalingaswami Re-entry Fellowship (BT/RLF/Re-entry/01/2021) provided by the Department of Biotechnology (DBT), Government of India. The authors also sincerely thank Dr Prashant Dhakephalkar, Director of the Agharkar Research Institute, Pune, for invaluable guidance and support.

Funding

This work was supported by a Ramalingaswami Re-entry Fellowship (BT/RLF/Re-entry/01/2021) provided by the Department of Biotechnology (DBT), Government of India.

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Authors

Contributions

A.S.P. acquired funding, managed the project, conceptualized the study, developed the methodology, conducted the investigation, performed formal analysis and visualization, and wrote the original draft. M.D.O. provided resources and reviewed the manuscript. S.G., A.G., and D.P. curated the data. S.J., V.D.S., S.P.G., D.S., B.N.W., and B.I. provided field resources. R.P. reviewed the manuscript.

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Correspondence to Abhinandan S. Patil.

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Patil, A.S., Oak, M.D., Gijare, S. et al. Genome-wide exploration of soybean domestication traits: integrating association mapping and SNP × SNP interaction analyses. Plant Mol Biol 115, 55 (2025). https://doi.org/10.1007/s11103-025-01583-9

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  • DOI: https://doi.org/10.1007/s11103-025-01583-9

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