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

PLoS One. 2020 Dec 1;15(12):e0243085. doi: 10.1371/journal.pone.0243085. eCollection 2020.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Genes, Plant / genetics
  • Genetic Loci / genetics*
  • Genome-Wide Association Study*
  • Genomics*
  • Glycine
  • Glycine max / genetics*
  • Glycine max / metabolism*
  • MicroRNAs / genetics
  • Pigmentation / genetics*
  • Seeds / metabolism*

Substances

  • MicroRNAs
  • Glycine

Grants and funding

The study was supported by Rural Development Administration (PJ01313202) and The National Research Foundation of Korea (NRF) (2020R1A6A03047729) received by HKC. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.