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

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.

Effect of five desiccants applied alone and in combination with glyphosate in dry edible bean (Phaseolus vulgaris L.)

McNaughton, K. E., Blackshaw, R. E., Waddell, K. A., Gulden, R. H., Sikkema, P. H. and Gillard, C. L. 2015. Effect of five desiccants applied alone and in combination with glyphosate in dry edible bean (Phaseolus vulgaris L.). Can. J. Plant Sci. 95: 1235–1242. Application of dry bean desiccants just prior to crop maturity is common practice by Canadian producers. As dry beans are grown for human consumption it is critical that producers pick desiccants that do not affect crop yield, seed quality, or result in desiccant seed residue levels above accepted levels. In this study the efficacy of glyphosate, diquat, glufosinate, carfentrazone, flumioxazin, and saflufenacil as desiccants was examined for navy, cranberry, pinto, and great northern dry bean. Seed herbicide residues were also tested for each of the dry bean classes tested. Navy, cranberry, pinto, and great northern dry bean yields were not impacted by use of the desiccants diquat, carfentrazone, flumioxazin, or saflufenacil when applied at labelled rates and application timings. Additionally, herbicide residues in seed following application remained lower than maximum residue limits (MRL) established by primary Canadian dry bean export partners. Generally, dry bean colour, irrespective of class, was not altered by desiccant use; diquat and flumioxazin caused minor increases in the degree of red and yellow seed pigmentation for cranberry bean only. Although colour differences were noted using a Chroma meter the differences were slight and would not likely be of economic importance. Application of glyphosate did not affect crop yield, and seed residue levels were below MRLs for navy, pinto, and great northern bean. However, seed glyphosate residue levels were above the MRL for cranberry bean when glyphosate was applied alone or tankmixed with carfentrazone, flumioxazin, or saflufenacil. Seed residue levels were also above listed MRLs for some export countries when glufosinate was applied to navy, cranberry, and pinto bean, although crop yield and seed quality remained unaffected. These findings suggest that growers and contractors should avoid using glufosinate as a dry bean desiccant at least for some markets and that care should be taken when selecting glyphosate as a desiccant, especially for cranberry bean. Across all market classes desiccation progress of bean leaf, stem, and pod tissue was slowest when glyphosate and carfentrazone were used.