Gene regulatory networks and key genes for source and sink strength unveiled by comparison of cultivated and wild rice

Targeting source and sink strength for crop yield increases requires an extensive genetic and metabolic understanding of desirable source and sink features. We performed comprehensive metabolite and transcriptomic comparisons of the photosynthetic flag leaves and developing grains of two cultivated rice varieties (Oryza sativa L. ssp. Indica cv. IR64 and Oryza sativa L. ssp. Japonica cv. Nipponbare) and two wild rice species (Oryza rufipogon and Oryza australiensis) that exhibit remarkable differences in their source and sink features. Metabolic, along with physiological, comparisons showed stronger source in photosynthetically efficient wild rice accessions and efficient sink in cultivated rice varieties. Transcriptomic analyses identified genes, enriched for biological pathways related to photosynthesis, carbohydrate metabolism, and transport, associated with the efficient source in wild rice. Genes enriched for starch biosynthesis and lipid metabolism were significant for the efficient sink strength in the cultivated varieties. Gene co-expression network analysis identified the key transcription factors and phytohormone-related genes driving the source and sink strength in rice. In summary, the study provides comprehensive metabolic and genetic underpinnings, including gene regulatory networks and regulators, for source and sink strength in rice that can be used for optimizing source-sink dynamics in crop improvement programs.