Integrative Identification of Chloroplast Metabolism-Related RETICULATA-RELATED Genes in Soybean

As a globally important leguminous crop, soybean (<i>Glycine max</i> L.) serves as a vital source of edible oils and proteins for humans and livestock. Oils in leaves can help crops combat fungal infections, adapt to temperature changes via fatty acid modulation, and support resource recycling during leaf senescence. However, accumulating oils in leaves is a fundamental challenge due to the need to balance the inherently competing photosynthesis and fatty acid biosynthesis processes within chloroplasts. RETICULATA-RELATED (RER), known to regulate chloroplast function and plastid metabolism in Arabidopsis, plays an essential role in leaf development. Here, 14 non-redundant <i>GmRER</i> genes were identified in soybean and phylogenetically classified into four subclades. Most Arabidopsis <i>RER</i> genes were evolutionarily preserved as gene duplicates in soybean, except for <i>GmRER5</i> and <i>GmRER6</i>. RNA secondary structures spanning the coding sequences (CDSs), the 5'- and 3'- untranslated regions (UTRs) of <i>GmRERs</i>, displayed exceptional structural plasticity in CDSs, while exhibiting limited conservation in UTRs. In contrast, protein structures retained conserved folds, underscoring evolutionary constraints on functional domains despite transcriptional plasticity. Notably, GmRER4a and GmRER4b represented an exceptional case of high similarity in both protein and RNA structures. Expression profiling across fourteen tissues and three abiotic stress conditions revealed a dynamic shift in expression levels between leaf-predominant and root-enriched <i>GmRER</i> paralogs after stress treatments. A comparative transcriptome analysis of six soybean landraces further revealed transcriptional polymorphism in the <i>GmRER</i> family, which was associated with the expression patterns of lipid biosynthesis regulators. Our comprehensive characterization of GmRERs may offer potential targets for soybean breeding optimization in overall plant oil production.