This document discusses the physiology of submergence tolerance in rice. It describes how flooding can damage rice plants by restricting gas exchange and causing mechanical damage. Tolerant rice varieties exhibit traits like restricted shoot elongation, maintenance of carbohydrate levels, and efficient fermentation during submergence. The Sub1 gene from FR13A rice confers tolerance by suppressing elongation and carbohydrate breakdown. Introducing Sub1 into high-yielding rice with good carbohydrate accumulation could provide greater submergence tolerance.

1. Physiology ofPhysiology of
Submergence ToleranceSubmergence Tolerance
and Prospects forand Prospects for
BreedingBreeding
Prabhasmita ShatpathyPrabhasmita Shatpathy
Adm. No.: 02PP/Ph.D./13Adm. No.: 02PP/Ph.D./13
Dept. of Plant PhysiologyDept. of Plant Physiology

2. Flooding is one of the most important environmental stressesFlooding is one of the most important environmental stresses
worldwideworldwide
Flash flooding adversely affects at least 16 % of the rice lands of theFlash flooding adversely affects at least 16 % of the rice lands of the
world (Khush, 1984)world (Khush, 1984)
In the rainfed lowland areas of eastern India, submergence is the thirdIn the rainfed lowland areas of eastern India, submergence is the third
most important limitation to rice production (Widawsky and O'Toole,most important limitation to rice production (Widawsky and O'Toole,
1990)1990)
Complete submergence due to frequent flooding adversely affectsComplete submergence due to frequent flooding adversely affects
plant growth and yieldplant growth and yield
The problemThe problem

3.  Rice is the only crop plant adapted to aquatic environmentsRice is the only crop plant adapted to aquatic environments
because of its well-developed aerenchyma tissuesbecause of its well-developed aerenchyma tissues
 However, complete submergence due to frequent flooding canHowever, complete submergence due to frequent flooding can
adversely affect plant growth and yieldadversely affect plant growth and yield
 Two types of flooding cause damages to rice:Two types of flooding cause damages to rice:
 Flash floodingFlash flooding
 Deepwater floodingDeepwater flooding
The problemThe problem

5. *Imposition of slow rates of gas exchange: due toImposition of slow rates of gas exchange: due to
development of unstirred boundary layer arounddevelopment of unstirred boundary layer around
tissues.tissues.
*Severe shadingSevere shading
*Mechanical damage: from strong flow rates or fromMechanical damage: from strong flow rates or from
abrasion caused by suspended particles.abrasion caused by suspended particles.
*Flowing water bring inorganic nutrients or pollutantsFlowing water bring inorganic nutrients or pollutants
into contact with flooded plants.into contact with flooded plants.
DAMAGE CAUSED BY SUBMERGEDDAMAGE CAUSED BY SUBMERGED
ENVIRONMENTENVIRONMENT

6. 1.1. Turbidity: greater the turbid is the floodwater, the chancesTurbidity: greater the turbid is the floodwater, the chances
of survival is lower.of survival is lower.
2.2. Temperature: greater the temperature of the floodwaterTemperature: greater the temperature of the floodwater
lower is the chances of survival.lower is the chances of survival.
3.3. Light intensity: Threshold light intensity (200Light intensity: Threshold light intensity (200 ++ 25 µmol m25 µmol m−2−2
ss−1−1
).).
4.4. pH: greater the pH (> 7.0) of the floodwater lower is thepH: greater the pH (> 7.0) of the floodwater lower is the
chances of survival.chances of survival.
5.5. Oxygen: 0.098-0.163 mol mOxygen: 0.098-0.163 mol m-3-3
is the optimum.is the optimum.
6.6. Carbon dioxide-greater concentration during day help inCarbon dioxide-greater concentration during day help in
survival.survival.
(Ramakrishnayya(Ramakrishnayya et al.(1998).et al.(1998). Exp. Agric.Exp. Agric. 3535: 167-180.: 167-180. DasDas et al.et al.
(2009).(2009). Environ. Exp. BotEnviron. Exp. Bot.,., 66:66: 425–434.425–434. Sarkar et alSarkar et al. (2009).. (2009). Func.Func.
Plant PhysiolPlant Physiol.,., 3636: 1-12.): 1-12.)

7. TT SS
• Minimum elongationMinimum elongation
• Maintenance ofMaintenance of
Carbohydrate level inCarbohydrate level in
stemstem
• Optimum fermentationOptimum fermentation
• UnderwaterUnderwater
photosynthesisphotosynthesis
• Efficient ROSEfficient ROS
scavengingscavenging
• Low ethyleneLow ethylene
synthesis orsynthesis or
sensitivitysensitivity
The traits associated with toleranceThe traits associated with tolerance
ProtectionProtection
EnergyEnergy
maintenancemaintenance

8. Photoperiod sensitivityPhotoperiod sensitivity
• Due to photosensitivity, traditional cultivars adapted to deep waterDue to photosensitivity, traditional cultivars adapted to deep water
ecosystems avoid submergence stress at the time of flowering.ecosystems avoid submergence stress at the time of flowering.
• Photoperiod-sensitive cultivars possess high plasticity and can bePhotoperiod-sensitive cultivars possess high plasticity and can be
planted at different ages without much loss in grain yield.planted at different ages without much loss in grain yield.
Carbohydrate statusCarbohydrate status
• A strong positive correlationA strong positive correlation
• Non-structural carbohydrate content before and after submergenceNon-structural carbohydrate content before and after submergence
is important for maintenance of vital metabolic processes duringis important for maintenance of vital metabolic processes during
submergence and for regeneration & recovery after submergencesubmergence and for regeneration & recovery after submergence
(Sarkar et al., 1996).(Sarkar et al., 1996).
PHYSIOLOGY OF SUBMERGENCEPHYSIOLOGY OF SUBMERGENCE
TOLERANCETOLERANCE

9. Elongation ability and survivalElongation ability and survival
•A strong negative correlationA strong negative correlation is found. Fast under water extension isis found. Fast under water extension is
linked with more injury and poor tolerance.linked with more injury and poor tolerance.
Reason:Reason: Tolerant genotypes use only a small quantity of availableTolerant genotypes use only a small quantity of available
carbohydrates for elongation growth, leaving enough reserve forcarbohydrates for elongation growth, leaving enough reserve for
survival during submergence (Sarkar et al., 1996).survival during submergence (Sarkar et al., 1996).
•Sensitive cultivars survived on application of a gibberellinsSensitive cultivars survived on application of a gibberellins
biosynthesis inhibitor, paclobutrazolbiosynthesis inhibitor, paclobutrazol
• Addition of GA reduced survival of submergence tolerant linesAddition of GA reduced survival of submergence tolerant lines
Chloroplast’s structural and functional integrity during and afterChloroplast’s structural and functional integrity during and after
the submergencethe submergence
•As this is directly related with photosynthetic abilityAs this is directly related with photosynthetic ability
PHYSIOLOGY OF SUBMERGENCEPHYSIOLOGY OF SUBMERGENCE
TOLERANCETOLERANCE

10. Anaerobic respiration/Anaerobic respiration/Alcoholic fermentation (AF)Alcoholic fermentation (AF)
* Essential for survival under anaerobiosis as this producesEssential for survival under anaerobiosis as this produces
energy in the form of ATP.energy in the form of ATP.
* Recent studies showed that AF decreased progressivelyRecent studies showed that AF decreased progressively
with time in tolerant lineswith time in tolerant lines
* Evidence also suggested that down regulation of AF mayEvidence also suggested that down regulation of AF may
be adaptive to conserve energy.be adaptive to conserve energy.
PHYSIOLOGY OF SUBMERGENCEPHYSIOLOGY OF SUBMERGENCE
TOLERANCETOLERANCE

11. Role of Ethylene generated duringRole of Ethylene generated during
submergencesubmergence
• Ethylene produced during submergence trigger leafEthylene produced during submergence trigger leaf
senescencesenescence
• This was proved by using an ethylene inhibitor, 1-methylThis was proved by using an ethylene inhibitor, 1-methyl
cyclopropene (MCP)cyclopropene (MCP)
* Blocking ethylene perceptionBlocking ethylene perception
Decreased chlorophyll degradation,Decreased chlorophyll degradation,
Maintained sugar and starch contentMaintained sugar and starch content
Improved survivalImproved survival
PHYSIOLOGY OF SUBMERGENCEPHYSIOLOGY OF SUBMERGENCE
TOLERANCETOLERANCE

12. Aerenchyma FormationAerenchyma Formation
PHYSIOLOGY OF SUBMERGENCEPHYSIOLOGY OF SUBMERGENCE
TOLERANCETOLERANCE
Fig. 2: Diffrences in formation of lysigenous aerenchyma and patterns ofFig. 2: Diffrences in formation of lysigenous aerenchyma and patterns of radial O2radial O2
loss (ROL)loss (ROL) in rice roots under drained soil conditions & waterlogged soilin rice roots under drained soil conditions & waterlogged soil
conditions, Nishiuchiconditions, Nishiuchi etet al., 2012al., 2012

13. Post Submergence EventsPost Submergence Events
• High light intensity and higher oxygen levelsHigh light intensity and higher oxygen levels
• Generation of reactive oxygen species (ROS) and toxic oxidativeGeneration of reactive oxygen species (ROS) and toxic oxidative
products as acetaldehydeproducts as acetaldehyde
Antioxidant enzymesAntioxidant enzymes
• Higher activity of antioxidants like CAT, APX, DHAR and GR in tolerantHigher activity of antioxidants like CAT, APX, DHAR and GR in tolerant
cultivars helped in better physiological adaptation to hypoxic conditioncultivars helped in better physiological adaptation to hypoxic condition
and maintain the structural integrity of enzymes by detoxifying the ROS.and maintain the structural integrity of enzymes by detoxifying the ROS.
• Catalase activity was found to be higher in tolerant rice cultivars (SarkarCatalase activity was found to be higher in tolerant rice cultivars (Sarkar
et alet al., 2001). This produce., 2001). This produce OO22 fromfrom HH22OO22 and improveand improve OO22 supplysupply
PHYSIOLOGY OF SUBMERGENCEPHYSIOLOGY OF SUBMERGENCE
TOLERANCETOLERANCE

14. Regeneration capacityRegeneration capacity
• Total non-structural carbohydrate content after submergenceTotal non-structural carbohydrate content after submergence
showed significant positive association with survival percentage andshowed significant positive association with survival percentage and
regeneration growth as these helped in developing new leavesregeneration growth as these helped in developing new leaves
quickly (Pandaquickly (Panda et alet al., 2008).., 2008).
• Tolerant cultivars maintained higher chlorophyll content, greaterTolerant cultivars maintained higher chlorophyll content, greater
photosynthetic and rubisco activities post submergence.photosynthetic and rubisco activities post submergence.
PHYSIOLOGY OF SUBMERGENCEPHYSIOLOGY OF SUBMERGENCE
TOLERANCETOLERANCE

15. Some management options canSome management options can
enhance performance of tolerantenhance performance of tolerant
genotypesgenotypes
Enriching nursery with N, P, Zn & FYMEnriching nursery with N, P, Zn & FYM
can result in more robust and taller seedlingscan result in more robust and taller seedlings
can increase CHO content of seedlingcan increase CHO content of seedling
Improve seedling establishment and plant survivalImprove seedling establishment and plant survival
Increase yield substantiallyIncrease yield substantially
 Even susceptible cultivars can perform well, if they can accumulate higherEven susceptible cultivars can perform well, if they can accumulate higher
carbohydrate content.carbohydrate content.
Application of N:P:K @ 15:40:20 kg per ha in seed bed helped inApplication of N:P:K @ 15:40:20 kg per ha in seed bed helped in
raising robust seedlings which can withstand submergenceraising robust seedlings which can withstand submergence
Older seedlings widely spaced in the nursery (75 g mOlder seedlings widely spaced in the nursery (75 g m-2-2
instead ofinstead of
>150 g m>150 g m-2-2
) perform better) perform better
Nutrient supply after water recedes enhances rate of recovery andNutrient supply after water recedes enhances rate of recovery and
yieldyield

16. Proper nutrient management in the nurseryProper nutrient management in the nursery
resulted in more robust seedlingsresulted in more robust seedlings

17. Screening for submergenceScreening for submergence
tolerancetolerance
The period of submergence variesThe period of submergence varies
and oftenand often not under full experimentalnot under full experimental
controlcontrol

18. SowingSowing
14-3014-30 d oldd old
SubmergeSubmerge
6-6-1414 dd (age)(age)
10 to 20 d10 to 20 d
DesubmergeDesubmerge
ScoreScore

19. ScaleScale forfor scoring submergencescoring submergence
tolerance of ricetolerance of rice in the field.in the field.
IndexIndex DDscriptionscription Scale (%)Scale (%)
11 MinorMinor visible symptom of injuryvisible symptom of injury 100%100%
33 Some vSome visible symptom of injuryisible symptom of injury 95-9995-99
55 MModerate injuryoderate injury 75-9475-94
77 SeverSeveree injuryinjury 50-7550-75
99 Partial to cPartial to complete deaomplete deathth 0-490-49
Adopted from SESAdopted from SES

20. Scoring for submergence toleranceScoring for submergence tolerance

21. SUB1A gene was discovered from FR13ASUB1A gene was discovered from FR13A (IR49830-7),(IR49830-7), anan
IndicaIndica rice cultivar, cultivated in Odisha as “Dhallaputia”.rice cultivar, cultivated in Odisha as “Dhallaputia”.
SUB 1 A confers flash flood toleranceSUB 1 A confers flash flood tolerance
Reason:Reason:
Restricts shoot elongationRestricts shoot elongation
Supresses expression ofSupresses expression of αα-amylase & sucrose synthase and-amylase & sucrose synthase and
regulates alcohol fermentation (Fukao et al., 2006)regulates alcohol fermentation (Fukao et al., 2006)
Enhances expression of genes involved in ABA-mediatedEnhances expression of genes involved in ABA-mediated
acclimationacclimation
Reduces accumulation of ROSReduces accumulation of ROS
Sub1A gene and how it worksSub1A gene and how it works

22. Sub 1 conferred tolerance to M2O2, a submergence intolerantSub 1 conferred tolerance to M2O2, a submergence intolerant
japonica rice variety ( Septiningsihjaponica rice variety ( Septiningsih et al.et al., 2009), 2009)

23. More submergence tolerantMore submergence tolerant
No negative side effect in terms of yield and grain quality whenNo negative side effect in terms of yield and grain quality when
grown under controlgrown under control ConditionsConditions
Starch and soluble carbohydrate levels declined more slowlyStarch and soluble carbohydrate levels declined more slowly
mRNA levels coding formRNA levels coding for αα-amylases and sucrose synthases were-amylases and sucrose synthases were
lowerlower
Pyruvate decarboxylase (PDC) and alcohol dehydrogenasePyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH)(ADH)
activity was increasedactivity was increased
Ethylene production was lowerEthylene production was lower

24. *Probability to get new major submergence tolerant geneProbability to get new major submergence tolerant gene
is less, yet the chance is greater for us as we haveis less, yet the chance is greater for us as we have
numbers of submergence tolerant rice cultivars differentnumbers of submergence tolerant rice cultivars different
from FR 13A morphologically, physiologically and levelsfrom FR 13A morphologically, physiologically and levels
of tolerance.of tolerance.
*Introgression of Sub1 in high yielding rice cultivars withIntrogression of Sub1 in high yielding rice cultivars with
greater carbohydrate accumulation capacity (e.g. Sabitagreater carbohydrate accumulation capacity (e.g. Sabita
etc) would give greater degree of tolerance compared toetc) would give greater degree of tolerance compared to
cultivars with less carbohydrate accumulation capacitycultivars with less carbohydrate accumulation capacity
like Swarna, IR 64 and SambaMahsuri.like Swarna, IR 64 and SambaMahsuri.
*High yielding cultivars with Sub1 have less regenerationHigh yielding cultivars with Sub1 have less regeneration
capacity: molecular and physiological mechanismcapacity: molecular and physiological mechanism
associated with the trait would be unravel.associated with the trait would be unravel.
*Knowledge on nutrient management and submergenceKnowledge on nutrient management and submergence
tolerance is scanty, needs attention.tolerance is scanty, needs attention.
Future ThrustFuture Thrust

25. RefRef::
1.1.PandaPanda et al. (2008).et al. (2008). Aquatic BotanyAquatic Botany 8888: 127-133.: 127-133.
2.2.BaliyarsinghBaliyarsingh et al. (2007).et al. (2007). J. Plant BiolJ. Plant Biol.. 3434: 193-198.: 193-198.
3.3.SarkarSarkar et al. (et al. (20062006)).. Current ScienceCurrent Science 9191: 899-906.: 899-906.
4.4.Panda et al. (2006).Panda et al. (2006). PhotosyntheticaPhotosynthetica 4444: 69-75.: 69-75.
5.5.DasDas et al. (2005).et al. (2005). PlantPlant Sci.,Sci., 168168: 131-136.: 131-136.
6.6.DasDas et al. (2004).et al. (2004). Bulgarian J. Plant Physiol.,Bulgarian J. Plant Physiol., 30(1-2)30(1-2): 34-44.: 34-44.
7.7.Sarkar et al.Sarkar et al. (2001).(2001). J. Agro. Crop SciJ. Agro. Crop Sci.. 187187: 69-74.: 69-74.
8.8.Sarkar et al.Sarkar et al. (2000).(2000). J. Plant Biol.J. Plant Biol. 2727: 307-311.: 307-311.
9.9.SarkarSarkar (1998).(1998). Biol. Plant.Biol. Plant. 4040: 597-603.: 597-603.
10.10.Sarkar et al.Sarkar et al.(1996).(1996). J. Plant PhysiolJ. Plant Physiol.. 149149: 623-625.: 623-625.

26. THANK YOUTHANK YOU
FOR YOUR ATTENTIONFOR YOUR ATTENTION