ArticlePloS one2020
Dissecting seed pigmentation-associated genomic loci and genes by employing dual approaches of reference-based and k-mer-based GWAS with 438 Glycine accessions.
Article in PloS one, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 20 citations in OpenAlex.
- mirtronDB 2.0: enhanced database with novel mirtron discoveries.Bioinformatics (Oxford, England) · 2026Article
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- Genome-wide exploration of soybean domestication traits: integrating association mapping and SNP × SNP interaction analyses.Plant molecular biology · 2025Article
- K-mer-based Approaches to Bridging Pangenomics and Population Genetics.Molecular biology and evolution · 2025Review
- Mem-based pangenome indexing for k-mer queries.Algorithms for molecular biology : AMB · 2025Article
- k-mer genome-wide association study for anthracnose and BCMV resistance in a Phaseolus vulgaris Andean Diversity Panel.The plant genome · 2024Article
- Previously unmeasured genetic diversity explains part of Lewontin's paradox in abioRxiv : the preprint server for biology · 2024Article
- Effect of Origin, Seed Coat Color, and Maturity Group on Seed Isoflavones in Diverse Soybean Germplasm.Plants (Basel, Switzerland) · 2024Article
- MEM-based pangenome indexing forbioRxiv : the preprint server for biology · 2024Article
- A k-mer-based bulked segregant analysis approach to map seed traits in unphased heterozygous potato genomes.G3 (Bethesda, Md.) · 2024Article
- An omics strategy increasingly improves the discovery of genetic loci and genes for seed-coat color formation in soybean.Molecular breeding : new strategies in plant improvement · 2023Article
- Review
- Two decades of association mapping: Insights on disease resistance in major crops.Frontiers in plant science · 2022Review
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8 authors at 3 institutions in 1 country.
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Abstract
The soybean is agro-economically the most important among all cultivated legume crops, and its seed color is considered one of the most attractive factors in the selection-by-breeders. Thus, genome-wide identification of genes and loci associated with seed colors is critical for the precision breeding of crop soybeans. To dissect seed pigmentation-associated genomic loci and genes, we employed dual approaches by combining reference-based genome-wide association study (rbGWAS) and k-mer-based reference-free GWAS (rfGWAS) with 438 Glycine accessions. The dual analytical strategy allowed us to identify four major genomic loci (designated as SP1-SP4 in this study) associated with the seed colors of soybeans. The k-mer analysis enabled us to find an important recombination event that occurred between subtilisin and I-cluster B in the soybean genome, which could describe a special structural feature of ii allele within the I locus (SP3). Importantly, mapping analyses of both mRNAs and small RNAs allowed us to reveal that the subtilisin-CHS1/CHS3 chimeric transcripts generate and act as an initiator towards 'mirtron (i.e., intron-harboring miRNA precursor)'-triggered silencing of chalcone synthase (CHS) genes. Consequently, the results led us to propose a working model of 'mirtron-triggered gene silencing (MTGS)' to elucidate a long-standing puzzle in the genome-wide CHS gene silencing mechanism. In summary, our study reports four major genomic loci, lists of key genes and genome-wide variations that are associated with seed pigmentation in soybeans. In addition, we propose that the MTGS mechanism plays a crucial role in the genome-wide silencing of CHS genes, thereby suggesting a clue to currently predominant soybean cultivars with the yellow seed coat. Finally, this study will provide a broad insight into the interactions and correlations among seed color-associated genes and loci within the context of anthocyanin biosynthetic pathways.
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