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.

Pedigrees of crop species reflect genealogical relationships among bred lines and are important resources for breeding design. Recently, as more genomic and phenomic data are being accumulated at an astonishing rate, well‐organized pedigrees and database‐linked systems have become ever more important. To cope with the prospective future of breeding science, this study aimed to develop a pedigree‐centered web interface called SoyPedi for the purpose of searching the phenotypic information of soybean [Glycine max (L.) Merr.] cultivars. SoyPedi employed an integrated pedigree composed of 178 well‐defined soybean cultivars and phenotype data. The system was constructed using various bioinformatic tools, such as SQLite3, PHP, and JavaScript. SoyPedi consists largely of three submodules, including a pedigree map, a tabular format database, and single cultivar‐dedicated web pages. The pedigree and tabular databases are interconnected by a single page application system, so that users can promptly switch between these two modules. In addition, comparative analysis of whole genome resequencing‐derived phylogeny and pedigrees implicated some extent of parallel correlation between these two. SoyPedi was developed with the intention of serving breeders for selecting parental lines in hybridization planning, which will be readily operable and intuitive for users. This system will be potentially expandable by integrating more data in the future and is available at https://tgil.donga.ac.kr/SoyPedi/index.html.

Callus, a valuable tool in plant genetic engineering, originates from dedifferentiated cells. While transcriptional reprogramming during callus formation has been extensively studied in Arabidopsis thaliana, our knowledge of this process in other species, such as Glycine max, remains limited. To bridge this gap, our study focused on conducting a time-series transcriptome analysis of soybean callus cultured for various durations (0, 1, 7, 14, 28, and 42 days) on a callus induction medium following wounding with the attempt of identifying genes that play key roles during callus formation. As the result, we detected a total of 27,639 alterations in gene expression during callus formation, which could be categorized into eight distinct clusters. Gene ontology analysis revealed that genes associated with hormones, cell wall modification, and cell cycle underwent transcriptional reprogramming throughout callus formation. Furthermore, by scrutinizing the expression patterns of genes related to hormones, cell cycle, cell wall, and transcription factors, we discovered that auxin, cytokinin, and brassinosteroid signaling pathways activate genes involved in both root and shoot meristem development during callus formation. In summary, our transcriptome analysis provides significant insights into the molecular mechanisms governing callus formation in soybean. The information obtained from this study contributes to a deeper understanding of this intricate process and paves the way for further investigation in the field.