Differential gene expression offers insights into the environmentally regulated protein content of soybean seeds, with emphasis on Asparagine synthesis pathway

Soybean plays a crucial global role as a source of plant-based protein. Over the last two decades, a consistent pattern has emerged, indicating that soybeans cultivated in western Canada tend to have lower seed protein levels compared to those grown in eastern Canada. This research project involved the cultivation of ten soybean genotypes, each characterized by varying average seed protein content. These genotypes were planted in an eastern location (used as a control) and three experimental western locations in Canada. Subsequently, seed protein and oil contents were quantified for all genotypes at each location. To elucidate the factors contributing to the relatively lower protein content in soybeans from western Canada, RNA-sequencing and differential gene expression analysis were employed. This approach helped identify genes with significantly varied expression and that might be responsible for the observed protein content differences between the two regions. Differentially expressed genes were found to be associated with critical biological processes and pathways, including amino acid biosynthesis, circadian rhythm regulation, starch metabolism, and lipid biosynthesis. Through gene ontology, pathway mapping, and quantitative trait locus (QTL) mapping, we gained in-depth insights into the mechanisms underlying nitrogen assimilation and amino acid biosynthesis disparities between eastern and western-grown soybeans. Notably, our research revealed a persistent upregulation of asparaginase (an asparagine hydrolase) and a consistent downregulation of asparagine synthetase in western-grown soybeans across 30 individual differential expression datasets. This specific distinction in asparagine metabolism between growing environments is highly likely to be linked to the observed differences in seed protein content, supported by the positive correlation found between seed protein content at maturity and the levels of free asparagine in developing seeds. These findings offer valuable insights into the genetic underpinnings of seed protein content influenced by environmental factors. Such information holds significance for breeding programs and genetic engineering endeavors aimed at optimizing soybean varieties for specific geographic regions.