The soybean crop, Glycine max (L.) Merr., is consumed by humans, Homo sapiens, worldwide. While the respective bodies of literature and -omics data for each of these organisms are extensive, comparatively few studies investigate the molecular biological processes occurring between the two. We are interested in elucidating the network of protein–protein interactions (PPIs) involved in human–soybean allergies. To this end, we leverage state-of-the-art sequence-based PPI predictors amenable to predicting the enormous comprehensive interactome between human and soybean. A network-based analytical approach is proposed, leveraging similar interaction profiles to identify candidate allergens and proteins involved in the allergy response. Interestingly, the predicted interactome can be explored from two complementary perspectives: which soybean proteins are predicted to interact with specific human proteins and which human proteins are predicted to interact with specific soybean proteins. A total of eight proteins (six specific to the human proteome and two to the soy proteome) have been identified and supported by the literature to be involved in human health, specifically related to immunological and neurological pathways. This study, beyond generating the most comprehensive human–soybean interactome to date, elucidated a soybean seed interactome and identified several proteins putatively consequential to human health.
As the global population continues to grow, food demand will be reaching levels which current agricultural practices cannot meet. This projected demand combined with the negative impacts of climate change on crop production calls for more careful breeding efforts to develop better adapted plants more tolerant to climate fluctuations. Fortunately, the development of molecular biology techniques like genome, transcriptome and epigenome sequencing now offer new approaches to help classical breeding meet these challenges. This review focuses on the potential of epigenetic approaches, particularly the creation of epigenetic markers (epi-markers) for guiding the selection process in breeding programs. Many studies have indeed successfully linked stable epigenetic modifications to different plant traits of interest but research on the applicability of using epi-markers in breeding programs is still scarce. This review emphasises the current progress that has been made with regards to the usefulness of epi-markers in selective plant breeding programs and the gaps in knowledge that still need to be addressed. It highlights the importance of pursuing research efforts to confirm the value of epi-markers for crop development in the years to come in order to meet the agricultural challenges of the 21st century.
Over the past two decades soybeans grown in western Canada have persistently had lower seed protein than those grown in eastern Canada. To understand the discrepancy in seed protein content between eastern- and western-grown soybeans, RNA-seq and differential expression analysis have been investigated. Ten soybean genotypes, ranging from low to high in seed protein content, were grown in four locations across eastern (Ottawa) and western (Morden, Brandon, and Saskatoon) Canada. Differential expression analysis revealed 34 differentially expressed genes encoding Glycine max Sugars Will Eventually be Exported Transporters (GmSWEETs), including paralogs GmSWEET29 and GmSWEET34 (AtSWEET2 homologs) that were consistently upregulated across all ten genotypes in each of the western locations over three years. GmSWEET29 and GmSWEET34 are likely candidates underlying the lower seed protein content of western soybeans. GmSWEET20 (AtSWEET12 homolog) was downregulated in the western locations and may also play a role in lower seed protein content. These findings are valuable for improving soybean agriculture in western growing regions, establishing more strategic and efficient agricultural practices.
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