Rice functional genomics: decades’ efforts and roads ahead

Abstract

Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.

CG and CHG Methylation Contribute to the Transcriptional Control of OsPRR37-Output Genes in Rice

“…With the development of multi-omics technologies and related data processing pipelines ( Feng et al, 2021 ; Iqbal et al, 2021 ), the hierarchical regulation network of the circadian clock will be gradually parsed and applied to improve rice traits. Recently, the representative role of OsPRR37 in the control of photoperiodic flowering was systematically reviewed ( Chen et al, 2021 ; Zhou et al, 2021c ). However, the underlying mechanism of how OsPRR37 regulates its output genes to affect multiple agronomic traits remains unclear.…”

“…A recent study further revealed a distinct role of OsPRR37 in promoting flowering in the japonica variety Zhonghua 11 under natural long-day conditions ( Hu et al, 2021 ). Although several output genes involved in the photoperiodic flowering pathway are used to explain the trait variations ( Chen et al, 2021 ; Zhou et al, 2021c ), the underlying mechanism of how OsPRR37 regulates its output genes and multiple traits remains unclear.…”

Candidate Genes and Pathways in Rice Co-Responding to Drought and Salt Identified by gcHap Network

“…Na + , K + content, and Na + /K + ratio are important indexes for measuring rice ST [ 37 ]. High-affinity K + transporters (HKT) can effectively stabilize Na + at the cell level [ 38 ]. OsHKT1;5 excretes Na + from the roots’ xylem parenchyma cells (XPC) [ 39 ].…”

“…Increased ABA content induces stomatal closure and reduces water loss in guard cells, which has a significant impact on osmotic potential reduction [ 45 ]. The ABA signaling pathway, acting as a pivotal process in biotic and abiotic stress responses, plays an important role in drought and salt responses [ 38 , 46 ]. The main components in the core ABA signaling transduction pathway include ABA receptors PYR/PYL/RCARs, SnRK2s and ABA co-receptor branch type A 2C protein phosphatase (PP2Cs) [ 41 , 47 ].…”

“…The main components in the core ABA signaling transduction pathway include ABA receptors PYR/PYL/RCARs, SnRK2s and ABA co-receptor branch type A 2C protein phosphatase (PP2Cs) [ 41 , 47 ]. In addition, H 2 O 2 plays an important role in stomatal closure through ABA-dependent and ABA-independent pathways [ 38 ]. In the ABA signaling pathway, ROS is activated by SnRK2 in NADPH oxidase and promotes the production of H 2 O 2 [ 48 ].…”