Dissecting seed pigmentation-associated genomic loci and genes by employing dual approaches of reference-based and k-mer-based GWAS with 438 Glycine accessions

• Published in: PloS one Vol. 15; no. 12; p. e0243085
• Main Authors: Kim, Jin-Hyun, Park, Joo-Seok, Lee, Chae-Young, Jeong, Min-Gyun, Xu, Jiu Liang, Choi, Yongsoo, Jung, Ho-Won, Choi, Hong-Kyu
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.12.2020; Public Library of Science (PLoS)
• Subjects: Agricultural biotechnology; Anthocyanins; Biology and Life Sciences; Breeding; Chalcone synthase; Chlorophyll; CHS gene; Color; Computer and Information Sciences; Cultivars; Cultivation; Deoxyribonucleic acid; DNA; Engineering and Technology; Flavonoids; Gene loci; Gene mapping; Gene silencing; Genes; Genes, Plant - genetics; Genetic aspects; Genetic Loci - genetics; Genome-wide association studies; Genome-Wide Association Study; Genomes; Genomics; Genotype & phenotype; Glycine; Glycine max - genetics; Glycine max - metabolism; Grain cultivation; Legumes; Mathematical analysis; Methods; MicroRNAs - genetics; miRNA; Optical properties; Physiological aspects; Phytochemicals; Pigmentation; Pigmentation - genetics; Plant breeding; Plant pigments; Production processes; Recombination; Rural development; Seed coats; Seeds; Seeds - metabolism; Soybeans; Sp1 protein; Subtilisin; Vegetable seeds; South Korea
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0243085

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.