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1.  Gas film retention and underwater photosynthesis during field submergence of four contrasting rice genotypes 
Journal of Experimental Botany  2014;65(12):3225-3233.
Summary
The flood-tolerant genotype FR13A retains leaf gas films and its capacity for underwater net photosynthesis, whereas gas films are lost faster and photosynthesis declines markedly in sensitive genotypes.
Floods can completely submerge some rice (Oryza sativa L.) fields. Leaves of rice have gas films that aid O2 and CO2 exchange under water. The present study explored the relationship between gas film persistence and underwater net photosynthesis (PN) as influenced by genotype and submergence duration. Four contrasting genotypes (FR13A, IR42, Swarna, and Swarna-Sub1) were submerged for 13 days in the field and leaf gas films, chlorophyll, and the capacity for underwater PN at near ambient and high CO2 were assessed with time of submergence. At high CO2 during the PN assay, all genotypes initially showed high rates of underwater PN, and this rate was not affected by time of submergence in FR13A. This superior photosynthetic performance of FR13A was not evident in Swarna-Sub1 (carrying the SUB1 QTL) and the declines in underwater PN in both Swarna-Sub1 and Swarna were equal to that in IR42. At near ambient CO2 concentration, underwater PN declined in all four genotypes and this corresponded with loss of leaf gas films with time of submergence. FR13A retained leaf gas films moderately longer than the other genotypes, but gas film retention was not linked to SUB1. Diverse rice germplasm should be screened for gas film persistence during submergence, as this trait could potentially increase carbohydrate status and internal aeration owing to increased underwater PN, which contributes to submergence tolerance in rice.
doi:10.1093/jxb/eru166
PMCID: PMC4071835  PMID: 24759881
Aerenchyma; flooding stress; leaf gas films; leaf air layer; leaf hydrophobicity; Oryza sativa; submergence tolerance; SUB1; leaf chlorophyll; survival; FR13A; IR42; Swarna; Swarna-Sub1.
2.  Adaptation to flooding during emergence and seedling growth in rice and weeds, and implications for crop establishment 
AoB Plants  2012;2012:pls019.
Direct seeding is replacing transplanting in rice. Early flooding suppresses weeds but selective action is compromised by the sharing of flood-tolerance traits. Understanding adaptive traits in both species is therefore a prerequisite for developing direct seeding systems that control weeds while leaving rice seedlings relatively unharmed.
Background and aims
Direct seeding of rice is being adopted in rainfed and irrigated lowland ecosystems because it reduces labour costs in addition to other benefits. However, early flooding due to uneven fields or rainfall slows down seed germination and hinders crop establishment. Conversely, early flooding helps suppress weeds and reduces the costs of manual weeding and/or dependence on herbicides; however, numerous weed species are adapted to lowlands and present challenges for the use of flooding to control weeds. Advancing knowledge on the mechanisms of tolerance of flooding during germination and early growth in rice and weeds could facilitate the development of improved rice varieties and effective weed management practices for direct-seeded rice.
Principal results
Rice genotypes with a greater ability to germinate and establish in flooded soils were identified, providing opportunities to develop varieties suitable for direct seeding in flooded soils. Tolerance of flooding in these genotypes was mostly attributed to traits associated with better ability to mobilize stored carbohydrates and anaerobic metabolism. Limited studies were undertaken in weeds associated with lowland rice systems. Remaining studies compared rice and weeds and related weed species such as Echinochloa crus-galli and E. colona or compared ecotypes of the same species of Cyperus rotundus adapted to either aerobic or flooded soils.
Conclusions
Tolerant weeds and rice genotypes mostly developed similar adaptive traits that allow them to establish in flooded fields, including the ability to germinate and elongate faster under hypoxia, mobilize stored starch reserves and generate energy through fermentation pathways. Remarkably, some weeds developed additional traits such as larger storage tubers that enlarge further in deeper flooded soils (C. rotundus). Unravelling the mechanisms involved in adaptation to flooding will help design management options that will allow tolerant rice genotypes to adequately establish in flooded soils while simultaneously suppressing weeds.
doi:10.1093/aobpla/pls019
PMCID: PMC3434364  PMID: 22957137
3.  Seed pre-treatment in rice reduces damage, enhances carbohydrate mobilization and improves emergence and seedling establishment under flooded conditions 
AoB Plants  2011;2011:plr007.
Priming rice seeds (soaking followed by drying) or soaking just before sowing improved emergence from flooded soil, reduced membrane damage from ROS and hastened carbohydrate mobilization. Most benefit was to lines with a superior ability to germinate in flooded soil even when untreated.
Background and aims
Early flooding helps control weeds but reduces seedling establishment in direct-seeded rice (Oryza sativa). When combined with appropriate management practices, the use of genotypes that better tolerate flooding during emergence can enhance crop establishment in flood-prone areas. Management options include seed pre-treatment and we tested the influence of pre-soaking for 24 h prior to sowing or of priming (soaking for 24 or 48 h followed by drying).
Methodology
The effects on seedling establishment after 21-day flooding of pre-soaking seeds for 24 h before sowing and/or of priming seeds were examined together with physiological responses connected with reactive oxygen scavenging. Seeds of four lines with contrasting abilities to tolerate flooding at the germination stage were compared. Seeds were primed using KCl solutions (48 h) or water (24 h) and pre-soaked using water. Lipid peroxidation and activities of reactive oxygen-scavenging enzymes were measured in seeds before sowing. Carbohydrate mobilization in germinating seeds and seedling growth were also monitored at intervals.
Principal results
Seed pre-treatment by pre-soaking or by priming increased survival of flooding and accelerated and improved seedling establishment, especially in tolerant genotypes. Primed seeds had less lipid peroxidation and higher superoxide dismutase (SOD) and catalase (CAT) activities than non-primed seeds. Amylase activities and starch breakdown were also hastened in primed seeds. Survival after flooding was positively correlated with amylase activity but negatively correlated with the extent of lipid peroxidation.
Conclusions
Pre-soaking and priming improved seedling establishment in flooded soil, enhanced the capacity to scavenge reactive oxygen species in seeds by increasing SOD and CAT activities, and hastened carbohydrate mobilization. Tolerant genotypes responded better to these treatments, emphasizing the effectiveness of combining genetic tolerance with appropriate seed pre-treatment to improve seedling establishment of rice sown in flooded soils.
doi:10.1093/aobpla/plr007
PMCID: PMC3072768  PMID: 22476478
4.  Mechanisms associated with tolerance to flooding during germination and early seedling growth in rice (Oryza sativa) 
Annals of Botany  2008;103(2):197-209.
Background and Aims
Flooding slows seed germination, imposes fatalities and delays seedling establishment in direct-seeded rice. This study describes responses of contrasting rice genotypes subjected to flooding or low oxygen stress during germination and discusses the basis of tolerance shown by certain cultivars.
Methods
In one set of experiments, dry seeds were sown in soil and either watered normally or flooded with 10 cm of water. Seedling survival and shoot and root growth were assessed and seed portions of germinating seedlings were assayed for soluble sugars and starch concentrations. The whole germinating seedlings were assayed for amylase and peroxidase activities and for ethylene production. Activities of enzymes associated with anaerobic respiration were examined and gene expression was analysed separately with seeds germinating under different amounts of dissolved oxygen in dilute agar.
Key Results
Flooding during germination reduced survival but to a lesser extent in tolerant genotypes. Starch concentration in germinating seeds decreased while sugar concentration increased under flooding, but more so in tolerant genotypes. Amylase activity correlated positively with elongation (r = 0·85 for shoot and 0·83 for root length) and with plant survival (r = 0·92). Tolerant genotypes had higher amylase activity and higher RAmy3D gene expression. Ethylene was not detected in seeds within 2 d after sowing, but increased thereafter, with a greater increase in tolerant genotypes starting 3 d after sowing. Peroxidase activity was higher in germinating seeds of sensitive genotypes and correlated negatively with survival.
Conclusions
Under low oxygen stress, tolerant genotypes germinate, grow faster and more seedlings survive. They maintain their ability to use stored starch reserves through higher amylase activity and anaerobic respiration, have higher rates of ethylene production and lower peroxidase activity as germinating seeds and as seedlings. Relevance of these traits to tolerance of flooding during germination and early growth is discussed.
doi:10.1093/aob/mcn211
PMCID: PMC2707318  PMID: 19001425
Amylase; anoxia; crop establishment; direct-seeded rice; ethylene; flooding; germination; hypoxia; Oryza sativa

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