Root system architecture in rice: impacts of genes, phytohormones and root microbiota

Abstract

To feed the continuously expanding world's population, new crop varieties have been generated, which significantly contribute to the world's food security. However, the growth of these improved plant varieties relies primarily on synthetic fertilizers, which negatively affect the environment and human health; therefore, continuous improvement is needed for sustainable agriculture. Several plants, including cereal crops, have the adaptive capability to combat adverse environmental changes by altering physiological and molecular mechanisms and modifying their root system to improve nutrient uptake efficiency. These plants operate distinct pathways at various developmental stages to optimally establish their root system. These processes include changes in the expression profile of genes, changes in phytohormone level, and microbiome-induced root system architecture (RSA) modification. Several studies have been performed to understand microbial colonization and their involvement in RSA improvement through changes in phytohormone and transcriptomic levels. This review highlights the impact of genes, phytohormones, and particularly root microbiota in influencing RSA and provides new insights resulting from recent studies on rice root as a model system and summarizes the current knowledge about biochemical and central molecular mechanisms.

Keywords: Genetic regulation; Microbiota; Phytohormone; Rice; Root growth; Root system architecture.

Fig. 1

Root architecture and the anatomy of rice. a Seedling root system (cultivar Nipponbare) after 15 days of germination, b transverse section of rice root stained with Safranin, c enlarge view of root stele. ARC, aerenchyma; CO, cortex; CR, crown root; END, endodermis; EP, epidermis; HYP, hypodermis; LR, lateral root; MX, metaxylem; PC, pericycle; PHL, phloem. Scale bars: b 50 µm, c 20 µm

Fig. 2

Impact of root microbiota on RSA in rice. Rhizospheric microbes can modulate root growth and development via the production of secondary metabolites and phytohormones. Microbes can influence plant nutrition by phosphorus solubilization, nitrogen fixation and siderophore production, and alter gene transcription and metabolite biosynthesis in plant cells that affect root physiology. CK, cytokinin; ET, ethylene; GA, gibberellic acid; IAA, indole acetic acid; NF, nitrogen fixation; PS, phosphate solubilization; SP, siderophore production