Summary: Seed germination is a complex trait determined by both quantitative trait loci (QTLs) and environmental factors and also their interactions. In this study, we mapped one majorQTLqSE3for seed germination and seedling establishment under salinity stress in rice. To understand the molecular basis of thisQTL, we isolatedqSE3by map‐based cloning and found that it encodes a K⁺transporter gene,OsHAK21. The expression ofqSE3was significantly upregulated by salinity stress in germinating seeds. Physiological analysis suggested thatqSE3significantly increased K⁺and Na⁺uptake in germinating seeds under salinity stress, resulting in increased abscisic acid (ABA) biosynthesis and activatedABAsignaling responses. Furthermore,qSE3significantly decreased the H₂O₂level in germinating seeds under salinity stress. All of these seed physiological changes modulated byqSE3might contribute to seed germination and seedling establishment under salinity stress. Based on analysis of single‐nucleotide polymorphism data of rice accessions, we identified aHAP3 haplotype ofqSE3that was positively correlated with seed germination under salinity stress. This study provides important insights into the roles ofqSE3in seed germination and seedling establishment under salinity stress and facilitates the practical use ofqSE3in rice breeding.

Submergence stress represents a major obstacle limiting the application of direct seeding in rice cultivation. Under flooding conditions, coleoptile elongation can function as an escape strategy that contributes to submergence tolerance during seed germination in rice; however, the underlying molecular bases have yet to be fully determined. Herein, we report that natural variation of rice coleoptile length subjected to submergence is determined by the glucosyltransferase encoding gene OsUGT75A. OsUGT75A regulates coleoptile length via decreasing free abscisic acid (ABA) and jasmonic acid (JA) levels by promoting glycosylation of these two phytohormones under submergence. Moreover, we find that OsUGT75A accelerates coleoptile length through mediating the interactions between JASMONATE ZIMDOMAIN (OsJAZ) and ABSCISIC ACID-INSENSITIVE (OsABI) proteins. Last, we reveal the origin of the haplotype that contributes to coleoptile length in response to submergence and transferring this haplotype to indica rice can enhance coleoptile length in submergence conditions. Thus, we propose that OsUGT75A is a useful target in breeding of rice varieties suitable for direct seeding cultivation.

Summary: Seed vigour is an imperative trait for the direct seeding of rice. Isopropylmalate synthase (IPMS) catalyses the committed step of leucine (Leu) biosynthesis, but its effect on seed vigour remains unclear. In this study, rice OsIPMS1 and OsIPMS2 was cloned, and the roles of OsIPMS1 in seed vigour were mainly investigated. OsIPMS1 and OsIPMS2 catalyse Leu biosynthesis, and Leu feedback inhibits their IPMS activities. Disruption of OsIPMS1 resulted in low seed vigour under various conditions, which might be tightly associated with the reduction of amino acids in germinating seeds. Eleven amino acids that associated with stress tolerance, GA biosynthesis and tricarboxylic acid (TCA) cycle were significantly reduced in osipms1 mutants compared with those in wide type (WT) during seed germination. Transcriptome analysis indicated that a total of 1209 differentially expressed genes (DEGs) were altered in osipms1a mutant compared with WT at the early germination stage, wherein most of the genes were involved in glycolysis/gluconeogenesis, protein processing, pyruvate, carbon, fructose and mannose metabolism. Further analysis confirmed that the regulation of OsIPMS1 in seed vigour involved in starch hydrolysis, glycolytic activity and energy levels in germinating seeds. The effects of seed priming were tightly associated with the mRNA levels of OsIPMS1 in priming seeds. The OsIPMS1 might be used as a biomarker to determine the best stop time‐point of seed priming in rice. This study provides novel insights into the function of OsIPMS1 on seed vigour and should have practical applications in seed priming of rice.

Reactive oxygen species (ROS) play an essential role in the regulation of seed dormancy, germination, and deterioration in plants. The low level of ROS as signaling particles promotes dormancy release and triggers seed germination. Excessive ROS accumulation causes seed deterioration during seed storage. Maintaining ROS homeostasis plays a central role in the regulation of seed dormancy, germination, and deterioration in crops. This study highlights the current advances in the regulation of ROS homeostasis in dry and hydrated seeds of crops. The research progress in the crosstalk between ROS and hormones involved in the regulation of seed dormancy and germination in crops is mainly summarized. The current understandings of ROS-induced seed deterioration are reviewed. These understandings of ROS-dependent regulation on seed dormancy, germination, and deterioration contribute to the improvement of seed quality of crops in the future.

Summary: Seed vigour is an important trait for direct seeding in rice. In this study, indole‐3‐acetate beta‐glucosyltransferase OsIAGLU was cloned in rice, and its roles on seed vigour were mainly investigated. Disruption of OsIAGLU resulted in low seed vigour in rice. Quantitative RT‐PCR analysis showed that the expressions of OsIAGLU were relatively higher in the late developing and the early germinating seeds and were significantly induced by indole‐3‐acetic acid (IAA) and abscisic acid (ABA). Transcriptome analysis revealed that the IAA‐ and ABA‐related genes were involved in the OsIAGLU regulation of seed vigour in rice. The higher levels of free IAA and ABA were identified in germinating seeds of osiaglu mutants compared to wild‐type (WT) plants. When treated with exogenous IAA and ABA, the osiaglu mutants and WT plants showed sensitivity to ABA while not IAA, but the exogenous IAA amplified ABA‐induced reduction of seed vigour in rice. The continuously higher expressions of ABA‐INSENSITIVE 3 (OsABI3) and OsABI5 occurred in germinating seeds of osiaglu mutants compared to WT plants. The regulation of seed vigour by OsIAGLU might be through modulating IAA and ABA levels to alert OsABIs expression in germinating seeds in rice. Based on analysis of single‐nucleotide polymorphism data of rice accessions, two haplotypes of OsIAGLU that positively correlated with seed vigour were identified in indica accessions. This study provides important insights into the roles of OsIAGLU on seed vigour and facilitates the practical use of OsIAGLU in rice breeding.

Seed vigor is a complex trait, including the seed germination, seedling emergence, and growth, as well as seed storability and stress tolerance, which is important for direct seeding in rice. Seed vigor is established during seed development, and its level is decreased during seed storage. Seed vigor is influenced by genetic and environmental factors during seed development, storage, and germination stages. A lot of factors, such as nutrient reserves, seed dying, seed dormancy, seed deterioration, stress conditions, and seed treatments, will influence seed vigor during seed development to germination stages. This review highlights the current advances on the identification of quantitative trait loci (QTLs) and regulatory genes involved in seed vigor at seed development, storage, and germination stages in rice. These identified QTLs and regulatory genes will contribute to the improvement of seed vigor by breeding, biotechnological, and treatment approaches.