1. Physiological, biochemical, and molecular
bases of low-light tolerance in rice
Dr. Lambodar Behera,
Principal Scientist(Biotechnology),
ICAR-National Rice Research Institute,
Cuttack-753006, Odisha
Lambodar Behera*1, Mirza Jaynul Baig1, Awadhesh Kumar1, Sharat Kumar Pradhan1,2,
Sangamitra Samantaray1, Rameswar Prasad Sah1, Devanna BN1, Anilkumar C1, Reshmi
Raj KR1, Darshan Panda1, Swagatika Das1, Soumya Mohanty1, Baneeta Mishra1
2. Introduction
Low light is one of the major abiotic stresses in India
(Eastern, NE-region) and Southeast Asian countries in
rainy (kharif) season.
It affects all the stages of rice growth.
It reduces tiller number, spikelet number, spikelet fertility,
reduced grain weight, and dry matter.
It causes about a 35-40% yield reduction in rice during the
kharif season.
Besides, it also reduces quality of grains.
In order to develop rice varieties with higher yield under
low light stress, understanding of physiological,
biochemical and molecular basis of low light tolerance is
needed.
3. 1400-1500 bright sunshine hours from
reproductive to grain filling stages.
Oryza sativa
Low light stress curtails yield in rice
R:FR
Normal light (1.2) Low Light (0.1)
Ballaré et al.(1990) Rice is the most
important Kharif crop
of India. Low light
stress during kharif
reduces rice grain yield
by 35%-40%.
Murty, K. S., & Sahu, G. (1987)
Normal Light = > 1000 micrpmoles/m2/sec
Low Light = < 1000 micrpmoles/m2/sec
45% Rainfed Rice Ecosystems (<750 bright sunshine
hours avaiable)
4. Simulation of Low light stress in the field condition
Study site location-ICAR-National Rice Research Institute (ICAR-
NRRI), Cuttack, Odisha, India.
Kharif-25% Shading
300 rice genotypes (landraces and HYVs) were evaluated under low light
conditions during two kharif seasons ( 2015 and 2016) at NRRI, Cuttack
5. Plant height
Flag leaf area
Chla and b
Number of tillers plant
No. of panicles/Plant
Spikelet Fertility
Grain weight
Specific leaf weight
Chla/b
Total dry weight
Grain Yield
Harvest index
Different Agronomical and Yield traits under low light stress
R
R R
R
FR
Shade -net
INCREASED
DECREASED
3 TRAITS
8 Traits
The low light tolerant and susceptible lines were selected on the basis of different
agronomic and yield traits, most significantly the yield reduction.
Yield was reduced significantly (Average: 35.13%) under low light.
Yield reduction under low light was mainly due to reduction in tiller number,
panicle number, grain number, grain fertility, grain weight and total biomass.
6. Rice Genotypes Code Tolerant/ Mod
tol. /
susceptible
Grain yield
Low Light
(g/plant)
Grain yield
under normal
light
(g/plant)
% of
reduction
SWARNAPRABHA
Tolerant Check
T 17.16 20.56 -16.52
PURNENDU CRRI24 T 11.67 12.66 -7.85
SANTHI CRRI37 T 14.13 16.01 -11.89
VLDHAN-209 CRRI60 T 15.26 16.97 -10.06
SASHI BCKV7 T 15.25 17.79 -14.37
BARHABALI DHAN BCKV11 T 14.49 16.59 -12.89
CHAMARMANI BCKV87 T 17.04 19.10 -10.81
LALDHAN BCKV28 T 14.35 17.22 -17.28
RUDRA CRRI96 T 11.18 15.09 -21.15
VAISAK CRRI38 T 12.83 16.48 -21.99
MAHANANDA BCKV91 T 12.66 16.38 -22.71
SASARANG - MT 9.66 14.51 -33.46
SWARNA - MT 14.45 20.75 -30.36
SARATHI CRRI30 S 5.59 12.96 -56.94
MAHISUGANDHA CRRI42 S 7.59 18.34 -58.65
GR-4 CRRI86 S 5.04 15.02 -66.34
IR64 CRRI3 S 5.69 12.64 -54.81
IR8
Susceptible
Check S 6.32 15.44 -59.29
SELECTION OF GENOTYPES ON THE BASIS OF GRAIN YIELD REDUCTION
These genotypes were used for physiological and biochemical basis of low light tolerance
7. Genotypes (18)
Tolerant-11, Moderately Tolerant-2,
Suscptible-5,
(Susceptible check-IR8,
Tolerant check-Swarnaprabha)
Parameters
1. PHYSIOLOGICAL:
Leaf area, Net Assimilation Rate, Stomatal conductance, Transpiration rate, CI/CA- 50%
flowering stage using LICOR 6400, Chl a and Chl b, Chl a/Chl b ratio, etc.
2. BICHEMICAL:
Total soluble sugar content(TS)-before and after 3days of flowering %, Starch-21 days
after grain filling.
Sedoheptulose-1, 7-bisphosphatase-50% flowering(0, 2, 4,6, 8hrs), other enzymes
Treatment- Normal Light (100%-open field)
Low Light (75% of normal light-Shade)
Season: Wet(Kharif) 2017, 2018
Physiological and biochemical bases
8. Most tolerant genotypes showed
lower reduction for above
parameters as compared to
susceptible genotypes.
9. Chl-a+b- Total chlorophyll content
Chl-a/b- Chlorophyll a/b ratio
CAR- Carotenoids
SPAD- Chlorophyll meter
F0 - Initial fluroscence
Fm - maximum fluroscence
Fv/Fm variance fluroscence / maximum fluroscence
ETR – electron trasnport rate
Φ – Maximum quantum yield
qP – Photochemcial quenching
NPQ – Non photochemcial quenching
PN – Photosynthesis
Gs Stomatal conductance
E Transpiration rate
WUE- Water use efficiency
10. Chl-a+b- Total chlorophyll content
Chl-a/b- Chlorophyll a/b ratio
CAR- Carotenoids
SPAD- Chlorophyll meter
F0 - Initial fluroscence
Fm - maximum fluroscence
Fv/Fm variance fluroscence / maximum fluroscence
ETR – electron trasnport rate
Φ – Maximum quantum yield
qP – Photochemcial quenching
NPQ – Non photochemcial quenching
PN – Photosynthesis
Gs Stomatal conductance
E Transpiration rate
WUE- Water use efficiency
11. Salient Findings
Physiological Bases of Low Light Tolerance:
Photosynthetic rate(Pn), stomatal conductance(gs), transpiration rate,
Carboxylation efficiency (CE), Photochemical quenching (qP) and
electron transport rate (ETR) decreased, while Ci/ Ca ratio increased
under low light as compared to normal light.
Most of tolerant genotypes showed lower reduction for above
parameters as compared to susceptible genotypes.
Leaf area increased but prominent in tolerant genotypes, and showed
correlation with yield under low light.
Total Chl content increased under low light with a parallel
enhancement in Fv/Fm ratio(maximum quantum yield of PSII). Rate of
increase was more tolerant genotypes.
Decreased of Chl(a/b) ratio was more in most of tolerant genotypes as
compared to susceptible genotypes.
Different physiological mechanisms are contributing to
tolerance/susceptibility under light.
12. Photosynthetic Rate(µmol CO2m-2 s-1)
Photosynthetic rate improvement
under low light is the selection criteria
for low light -tolerant lines.
Genotypes
Yield
Trend NL LL % Decrease
S-PRABHA TC 24.3 20.3 16.46
Barhabalidhan T 24.21 20.21 16.52
Purnendu T 22.61 18.82 16.76
Chamarmani T 23.11 19.28 16.57
VLDhan209 T 26.4 21.44 18.79
Santhi T 21.71 18.15 16.4
Sashi T 23.21 20.11 13.36
Laldhan T 24.11 20.22 16.13
Rudra T 23.82 16.89 29.09
Mahananda T 23.86 17.84 25.23
Vaisak T 23.1 16.2 29.87
Sasarang MT 24.32 17.84 26.64
Swarna MT 26.62 20.41 19.57
IR-8 SC 24.78 11.38 54.08
IR-64 S 23.21 13.42 42.18
Sarathi S 26.4 15.22 42.35
Mahisugandha S 25.8 17.55 34.22
GR4 S 22.1 14.3 36.24
0
5
10
15
20
25
30
NL LL
13. Biochemical Bases of Low Light Tolerance:
Reduction in total leaf soluble sugar content and grain Starch
content (%) were observed in all the genotypes under low light as
compared to normal light.
Tolerant genotypes showed lower reduction as compared to
susceptible genotypes.
Sucrose Synthase and AGPase showed less/no reduction under
low light in tolerant genotypes and maintain higher level than
susceptible genotypes.
Tolerant genotypes showed higher SBPase activity as compared to
susceptible genotypes, though there was reduction under LL.
SBPase activity found to correlated with photosynthesis and grain
yield under low light.
14. There is less reduction in Total
Soluble sugar content (3DBA) in most
of low light Tolerant genotypes as
compared to susceptible genotypes.
Less reduction in Total Soluble sugar
content (3DAA) under low light in
tolerant genotypes compared to
susceptible genotypes.
TOTAL SOLUBLE SUGAR(TSS) mg/g FW
Genotype
s
Yield
Trend NL LL
%
Decre
ase
S-PRABHA TC 4.01 3.69 7.98
Barhabali
dhan T 2.7 2.5 7.41
Purnendu T 4.01 3.8 5.24
Chamarm
ani T 3.85 3.5 8.73
VLDhan20
9 T 2.39 1.96 17.9
Santhi T 2.08 1.76 11.58
Sashi T 2.41 2.23 7.47
Laldhan T 2.29 1.88 15.38
Rudra T 1.98 1.56 17.99
Mahanan
da T 1.9 1.68 10.92
Vaisak T 3.9 2.99 23.33
Sasarang MT 3.7 2.37 36.92
Swarna MT 2.79 2.16 22.58
IR-8 SC 1.81 1.01 44.2
IR-64 S 2.22 1.3 48.03
Sarathi S 2.3 1.39 36.92
Mahisuga
ndha S 2.88 1.45 39.57
GR4 S 3.33 2.19 33.01
Genotypes
Yield
Tren
d NL LL
%
Decreas
e
S-PRABHA TC 3.95 3.56 9.87
Barhabalidhan T 2.6 2.37 8.85
Purnendu T 3.96 3.73 5.81
Chamarmani T 3.76 3.46 7.98
VLDhan209 T 2.33 1.96 15.88
Santhi T 1.93 1.67 13.47
Sashi T 2.35 2.21 5.96
Laldhan T 2.14 1.78 16.82
Rudra T 1.77 1.44 18.64
Mahananda T 1.76 1.48 15.91
Vaisak T 3.85 2.98 22.6
Sasarang MT 3.6 2.22 38.33
Swarna MT 2.66 2.01 24.43
IR-8 SC 1.79 0.98 45.25
IR-64 S 2.17 1.21 44.24
Sarathi S 2.19 1.31 40.18
Mahisugandha S 2.45 1.28 47.76
GR4 S 3.21 2.01 37.38
3 days before anthesis 3 days after anthesis
0
1
2
3
4
5 Swarnapra…
Barhabalid…
Purnendu
Chamarm…
VLDhan209
Santhi
Sashi
Laldhan
Rudra
Mahananda
Sasarang
Vaisak
Swarna
IR-8
IR-64
Sarathi
Mahisuga…
GR4
3 days before
NL LL
0
0.5
1
1.5
2
2.5
3
3.5
4
Swarnaprabha
Barhabalidhan
Purnendu
Chamarmani
VLDhan209
Santhi
Sashi
Laldhan
Rudra
Mahananda
Sasarang
Vaisak
Swarna
IR-8
IR-64
Sarathi
Mahisugandha
GR4
15. • Our findings indicated that LL stress results in reduction in the amylose and
resistant starch content.
• This was reflected in higher GI values of rice grains harvested from the crop
raised under LL stress.
• The rice tolerant genotypes showed comparatively lower the GI values as
compare red to susceptible varieties.
• This would help to develop better rice varieties for consumption by diabetics.
16. Carbohydrate metabolism enzymes, viz. cytosolic invertase (CI),
Sucrose synthase (SuSy), and ADP-glucose pyrophosphorylase
(ADPGPPase) activities were assessed in spikelets of tolerant and
susceptible genotypes during Rabi 2021 at 50% flowering and 10 days
after flowering (10DAF).
All the three enzyme activities decreased significantly in all the
genotypes under low light stress both at 50% flowering and 10 days
after flowering (10DAF).
Tolerant genotypes (Swarnaprabha, Purnendu and VLDhan209)
showed higher activities of all these enzymes than the susceptible
genotypes (IR8 and GR4).
Sucrose synthase and Starch synthase genes showed higher
expression levels in tolerant genotypes (Swarnaprabha, Purnendu and
VLDhan209) as compared to susceptible rice genotypes (IR8 and GR4)
under low light.
Higher carbohydrate metabolism and increased sink activity (spikelet)
in tolerant genotypes as compared to susceptible genotypes, is,
therefore, an adaptive indicator in tolerant genotypes under low light
intensity.
Analysis of carbohydrate metabolism related enzymes and genes in spikelets
18. Low
Light
Stress
Rice
Leaf
Lower
gs
CO2
Closed
stomata
CO2
Mesophyll
CO
2
Lower
gm
Calvin
Cycle
Opened
stomata
Chloroplast
3. Increased Fm results in
decreased QA re-oxidation.
Thus decrease qP.
4. Decreased qP results in lowered
electron flow( low ETR) that lowered
ΦPSII. Lowered electron flow
impaired thylakoid lumen
acidification.
5. Lowered redox effect hampered
NADPH and ATP generation.
pH distortion
pH distortion
6. Lowering of Rd-
Thx system
mediated activation
of C3 enzymes ( f-
type thioredoxin).
Lower
Hexose
1. Incoordination of
stomatal kinetics and
photosynthesis led to
low CO2 availability
for photosynthesis .
2.Lowered
Mesophyll
conductance
presents an
additional
limitation to
carbon
supply to the
chloroplast
under LL.
7. Downregulated Calvin
cycle due to;
• Low Rubisco
activation (Vcmax)
(stop and go traffic)
• Lower expression of
C3 enzymes
• Lower SBPase activity
19. Transcriptome and epigenome profiling to identify
candidate genes differentially expressing under low light.
Molecular Bases of low light tolerance
Transcriptome sequencing (Swarnaprabha-T and IR8-S):
Vegetative and reproductive stages
Epigenome sequencing (miRNA and methylation)
(Swarnaprabha and IR8): Vegetative and reproductive
stages
Identified several DEGs, DE-miRNAs and DMRs
Validated few important DEGs, DE-miRNAs and DMR
genes (T-Purnendu,Swarnaprabha, VLDhan209; S-IR8 and GR4)
20. List of DEGs photosynthesis related genes used in expression analysis
used for validation
NGS transcriptome sequencing identified several differentially
expressed genes (DEGs). Expression of 14 photosynthesis-related
genes were selected and validated in 3 tolerant (Swarnaprabha,
Purnendu, VLdhan209) and 2 susceptible (IR8 and GR4) genotypes.
SL. NO Gene ID NAME of GENE Low Light
1
OsLhcb29.1 chlorophyll a-b binding protein CP29.1,
chloroplastic
Up-regulation
2
OsPSB27-H1 photosystem II repair protein PSB27-H1,
chloroplastic
Up-regulation
3 OsPSII10 photosystem II 10 kDa polypeptide, chloroplastic Up-regulation
4 OsSBPase Sedoheptulose-1, 7-bisphosphatase Down-regulation
5 OsRCAL Rubisco activase apha subunit( large) Down-regulation
6 OsGAPA glyceraldehyde-3-phosphate dehydrogenase(A) Down-regulation
7 OsGAPB glyceraldehyde-3-phosphate dehydrogenase(B) Down-regulation
8 OsRbcS2 Rubisco small subunit -S2 Down-regulation
9 OsRbcS3 Rubisco small subunit -S3 Down-regulation
10 OsRbcS4 Rubisco small subunit -S4 Down-regulation
11 OsRbcL Rubisco Large Subunit -L Down-regulation
12 OsFBPase Fructose 1,6 bisphosphatase Down-regulation
13 OsPRK Phosphoribulokinase Down-regulation
14 OsTXF Thioredoxin F, chloroplastic Down-regulation
21. Salient Findings (Transcriptome)
Tolerant genotypes maintain higher level of expression of genes related to
photosynthesis and other metabolic pathways than susceptible genotypes
under low-light stress both at vegetative and reproductive stages, which
enable the plant to keep the photosynthetic and metabolic processes moving
at higher pace as compared to susceptible genotypes.
24. Low light tolerant: Swarnaprabha, Purnendu and VL Dhan209
Susceptible : IR8 and GR4 ; Growth Stages: vegetative and reproductive
Treatment : Veg.: T0 (Control), T1-1day LL treatment, T3 (3days), T5 (5days);
Reproductive : T0, T5, T10
Expression analysis of photoreceptor, regulatory, phytochrome, cryptochrome,
phytochrome inhibitory factor (PIF) and transcription genes.
Photoreceptor genes like Cryptochrome - CRY1 and CRY2,
Phytochrome - PHY-A, PHY-B, and PHY-C
Phytochrome interacting factors - PIF1 and PIF1-2
Regulatory genes - Constitutive photo-morphogenesis 1 (COP1),
Phototropin-2, and Rice Phytochrome-Interacting
Factor-Like genes (OsPIL1, OsPIL15)
Transcription factor - OsBBX21, HY5 (OsbZIP48)(LONG HYPOCOTYL5 ), RGB1
Other genes : OsYUC11 (Auxin gene)
Rice D1 protein (OsPsbA) and
its repair associated proteins (OsPSB27 and PSII-PSB27-H1)
25. Tolerant genotypes maintains higher levels of expressions of the
most of regulatory, phytochrome, cryptochrome and phytochrome
inhibitory factor (PIF), transcription factor genes but lower
expression of OsPIL1, OsCOP1 and OsSPA1 genes as compared to
susceptible genotypes under low light.
Higher expressions of these genes helps tolerant genotypes in the
coordination of multiple light capturing process under low light.
This process enables the tolerant genotypes to keep the
photosynthetic and metabolic processes moving at higher pace in
comparison to susceptible genotypes under low light.
Salient Findings
26. • PhytochromeA play critical role in
the expression of gibberellin genes
which promotes germination.
27. Phytochrome A plays a critical role in the low light signalling in rice that
modulates photosynthesis , growth , development and morphological
adaptations of rice necessary to optimize grain yield.
28. Expression analysis of starch biosynthesis (grain quality) related genes
in the spikelets (10 days after flowering) of tolerant and susceptible
genotypes under low light and low light conditions.
29. Expression of genes related to the Starch biosynthesis
pathway(grain quality) under low light as compared to
normal light conditions.
Starch biosynthesis-related genes significantly down-regulated in the spikelets
(10 days after flowering) under LL stress.
The rate of reduction in Starch biosynthesis pathway was lower in tolerant
varieties (Swarnaprabha, Purnendu and VLdhan209) than susceptible varieties
(IR8 and GR4) .
30. • Under LL, IAA synthesis
decreased in the
developing spikelets that
affected sucrose to
starch conversion, thus
lowering filled grains.
• LL- tolerant rice
genotypes had higher
expression of IAA in the
developing spikelets
than LL-susceptible lines.
32. Sl No. miRNA ID Mature miRNA sequences Type of miRNA Target
1
osa-miR166c-3p
UCGGACCAGGCUUCAUUCCCC Known Rolled leaf1
2 osa-miR2102-3p CGGGGCCGGUUCCGGUGUAGG
Known
Chlorophyll a-b binding protein
3 osa-miR530-3p AGGUGCAGAGGCAGAUGCAAC
Known Ubiquinone biosynthesis
protein COQ4
4 osamiR1-CRRI AGCUCGUCGGGCUUGCUGCGG Novel in rice MADS-box transcription factor
5 osa-miR2-CRRI AGCUCGUCGGGCUUGCUGCGGU Novel in rice
Myb-like DNA-binding domain
containing protein
6
osa-miR3-CRRI
UGCCGGUCAUAUGUAUCGAA Novel in rice
Granule-bound starch synthase
1
7
osa-miR4-CRRI
ACCGCUUCAUGAACUUUCAGG Novel in rice NAC domain-containing protein
8
osa-miR5-CRRI
CAAAUCCUGUCAUCCCUACC Novel in rice FAD dependent oxidoreductase
Differentially expressed miRNAs involved in photosynthesis and
related pathways (Vegetative stage)
NGS identified several DE-miRNAs. 8 miRNAs were validated in 3 tolerant
(Swarnaprabha, Purnendu, VLdhan209) and 2 susceptible (IR8 and GR4)
genotypes
33. Sl No miRNA ID
Mature miRNA
sequences
Type of
miRNA
Target
1 osa-miR2102-3p
CGGGGCCGGUUCCG
GUGUAGG
Known Chlorophyll a-b binding protein
2 osa-miR2-CRRI
AGCUCGUCGGGCUUG
CUGCGGU
Novel in
rice
Myb-like DNA-binding domain
containing protein
3 osa-miR3-CRRI
UGCCGGUCAUAUGU
AUCGAA
Novel in
rice
Granule-bound starch synthase 1
4
osa- miR531A cucgccggggcugcgugc
cgccau
Known
ATP binding protein, putative
5 osa- miR395J gugaaguguuugggggaac
uc
Known
Sulfate transporter 2.1, putative,
expressed
6 osa- miR1860 agaaaaccagcuuccagauc
u
Known DNA polymerase alpha subunit B
7 osa-miR7693 gacguccaucgaugaagagc
ga
Known
Cell division control protein 68, F-
box/LRR-repeat protein 2
8
osa- miR5161 ucuggaucagagggagua
ua
Known Senescence-associated protein
DIN1
Differentially expressed miRNAs involved in photosynthesis and
related pathways (Reproductive stage)
34. Expression of miRNAs was found to be increased/ decreased under low light.
Reverse trend was found in tolerant and susceptible genotypes in most of
miRNAs. They have important roles in regulation of gene expression, and might
be providing tolerance/ susceptibility to low light stress.
miRNAs like osa-miR166c-3p, osa-miR2102-3p and osa-miR530-3p and novel
miRNAs osa-novmiR1, osa-novmiR2, osa-novmiR3, osa-novmiR4, and osa-
novmiR5 found to involve in low light mediated signaling mechanisms in the
tolerant and susceptible rice genotypes.
Salient Findings (Epigenome-miRNA)
35. Fig.: qRT-PCR data shows that osa-miR2102-3p up-regulated in
susceptible genotypes, whereas down-regulated in tolerant genotypes.
As osa-miR2102-3p has its target of chlorophyll a-b binding protein(CAB)
involved in Light harvesting complex in photosynthesis process. CAB
has higher expression in tolerant genotypes, indicating that this
miR2102-3p play very important role in low light condition to regulate the
tolerance/ susceptible mechanism.
0
1
2
3
SW PURNENDU VLDhan-209 GR-4 IR8
T1 T3 T5
FOLD
CHANGE
(TREATED
/
CONTROL)
osa-MiR2102-3p
36. Figure: qRT-PCR data shows that osa-miR2-NRRI lower expression in susceptible
genotypes whereas upregulated in tolerant genotypes.
As osa-miR2 has its target of myb-like DNA-binding domain containing protein
involved in controlling various processes like responses to biotic and abiotic
stresses, development, differentiation, metabolism and defense through
regulation of transcription of genes. So it has indirect regulation in low light
stress
0
5
10
15
20
25
30
35
40
45
50
SW PURNENDU VLDhan-209 GR-4 IR8
T1 T3 T5
FOLD
CHANGE
(TREATED
/
CONTROL)
osa-miR2-NRRI=Novel in Oryza sativa
37. DMR genes were selected for their validation(Vegetative stage)
S No Gene id chromoso
me
Methylated Regions Gene name
1 OS04G0320100 4 exon,intron,utr3
7-hydroxymethyl chlorophyll a reductase,
chloroplastic
2 OS09G0346500 9 promoter
Chlorophyll a-b binding protein 1,
chloroplastic
3 OS09G0346500 9 exon,utr3
Chlorophyll a-b binding protein 1,
chloroplastic
4 OS09G0296800 9 intron Putative chlorophyll a/b-binding protein
5 OS08G0433350 8 promoter photosystem II reaction center protein I
6 OS08G0200300 8 promoter Putative photosystem II 10K protein
7 OS01G0246400 1 promoter Putative early light-induced protein
8 OS12G0512800 12 exon,intron,utr3 Cytochrome P450 71E1
9 OS11G0485200 11 exon,utr5,promoter E1-E2 ATPase family protein
10 OS05G0200100 5 promoter Thioredoxin-like 2, chloroplastic
38. DMR genes were selected for their validation(reproductive stage)
S No Gene id chromoso
me
Gene name
1 LOC_Os08g17980 8
PhotosystemIIP680, chlorophyll A apoprotein, putative,
expressed
2 LOC_Os01g40710 1 Light inducible protein, putative, expressed
3 LOC_Os03g30400 3
Early light-induced protein, chloroplast precursor, putative,
expressed
4 LOC_Os12g19381 12 Rubisco small chain subunit
5 LOC_Os02g18500 2 Chlorophyllase-2, chloroplast precursor, putative
6 LOC_Os10g26470 10 Sucrose transporter, putative, expressed
7 LOC_Os08g20660 8 Sucrose-phosphate synthase, putative, expressed
8 LOC_Os07g13880 7
Soluble starch synthase,2-3, chloroplast precursor, putative,
expressed
9 LOC_Os01g52250 1 Starch synthase, putative, expressed
10 LOC_Os01g22954 1 Serine carboxypeptidase, putative, expressed
39. Differential methylation was observed in different genes
related to photosynthesis and other pathways, and
difference was found between tolerant and susceptible
genotypes.
Decreased methylation regions are found in tolerant rice
genotypes as compared susceptible genotypes under low
light.
The number of decreased methylated regions leads to
increased expression of genes suppressed due to
methylation at particular site.
Salient Findings (Epigenome-melthylation)
40. Diagrammatic presentation of overall studies:
Low light stress
hv
Decreased methylation region was found more in
tolerant rice genotypes as compared to susceptible
genotypes and number of decreased Methylated
regions leads to increased expression of gene
suppressed due to methylation at particular site.
Multiple sensors
Maintained overall higher yield in tolerant rice
genotypes
Higher expressions of the most of regulatory genes,
phytochrome (PHY- A, PHY-B, and PHY-C), cryptochrome
(CRY1 and CRY2), and phytochrome inhibitory factor
(PIF1and PIF1-2) genes as compared to susceptible rice
genotypes.
Changes occur in the genome-wide expression of
different miRNAs which involve in the regulatory
pathways to regulate genes or transcript expression
during stress to cope up with it and maintained the
photosynthetic and metabolites through enhanced the
expression of positive regulators or suppression of the
genes that have a role as negative regulators mediated
through different miRNA expression.
Lower expressions of the most of regulatory genes
phytochrome, cryptochrome and phytochrome
inhibitory factor (PIF) genes as compared to tolerant
rice genotypes.
Changes occur in the genome-wide expression of
different miRNAs which involve in the regulatory
pathways to regulate genes or transcript expression
during stress and unable to maintained the
photosynthetic and metabolites pathway to cope up
with stress through decreases the expression of
positive regulators or increase of the genes that have
a role as negative regulators mediated through
different miRNA expression.
Tolerant rice genotypes (SW, Purnendu and VLdhan 209) Susceptible rice genotypes (GR4 and IR8)
Increased methylation regions was found in
sensitive rice genotypes as compared to tolerant rice
genotypes.
Decreased overall yield significantly in sensitive rice
genotypes
41. Conclusion
Low-light-tolerant genotypes showed larger foliage, greater
chlorophyll content, and a lower a/b ratio, higher activities
enzymes involved of photosynthesis and carbon metabolism, such
as SBPase and Rubisco than susceptible genotypes.
Few genes were found to regulate low-light tolerance, which are
associated with the LHC and the Calvin cycle, and produce proteins
implicated in light signalling, photosynthesis, and carbon
metabolism.
Tolerant genotypes maintains higher levels of expressions of the
most of regulatory, phytochrome, cryptochrome and
phytochrome inhibitory factor (PIF) genes as compared to
susceptible genotypes under low light.
42. Conclusion
Tolerant genotypes maintains higher levels expression of genes
related to the Starch biosynthesis pathway(grain quality) under
low light as compared to normal light conditions.
A few miRNAs were identified that play a pivotal role in
modulating gene expression, contributing to susceptibility or
tolerance to low-light stress.
Differential methylation was observed in different genes related
to photosynthesis and other pathways, and differences were
found between tolerant and susceptible cultivars.
This information would be useful in improving rice production
under low-light stress conditions, which prevail in India and
Southeast Asian countries during the wet season.
43. 1. Panda D, Dash GK, Mohanty S, Sekhar S, Roy A, Tudu C, Behera L, Tripathy BC,
Baig MJ (2023). Phytochrome A mediated modulation of photosynthesis,
development and yield in rice (Oryza sativa L.) in fluctuating light environment.
Environmental and Experimental Botany 206: 105183.
2. Panda D, Mohanty S, Das S, Mishra B, Baig MJ, Behera L (2023). Light intensity–
mediated auxin homeostasis in spikelets links carbohydrate metabolism
enzymes with grain filling rate in rice. Protoplasma 260:1233–1251.
3. Sekhar S, Das S, Panda D, Mohanty S, Mishra B, Kumar A, Navadagi DB, Sah RP,
Pradhan SK, Samantaray S, Baig MJ, Behera L, Mohapatra T (2022).
Identification of microRNAs that Provide a Low Light Stress Tolerance-Mediated
Signaling Pathway during Vegetative Growth in Rice. Plants 11: 2558.
4. Panda D,, Mohanty S, Das S, Sah RP, Kumar A, Behera L, Jaynul Baig MJ,
Tripathy BC (2022). The role of phytochrome-mediated gibberellic acid signaling
in the modulation of seed germination under low light stress in rice (O. sativa
L.). Physiology and Molecular Biology of Plants 28(3):585–605.
5. Kumar A, Panda D, Mohanty S, Biswal M, Dey P, Dash M, Sah RP, Kumar S, Baig
MJ, Behera L (2020). Role of sedoheptulose-1,7 bisphosphatase in low light
tolerance of rice (Oryza sativa L.). Physiology and Molecular Biology of
Plants 26(12):2465-2485.
List of Publications
44. 6. Panda D, Biswal M, Mohanty S, Dey P, Swain A, Behera D, Baig MJ, Kumar A, Sah
RP, Tripathy BC, Behera L (2020). Contribution of phytochromeA in the
regulation of sink capacity, starch biosynthesis, grain quality, grain yield and
related traits in rice. Plant Archives 20(1): 1179-1194.
7. Sekhar S, Panda D, Kumar J, et al. (2019). Comparative transcriptome profiling of
low light tolerant and sensitive rice varieties induced by low light stress at
active tillering stage. Scientific Reports 9:5753.
8. Panda D, Biswal M, Behera L, Baig MJ, Dey P, Nayak L, Sharma S, Samantray S,
Ngangkham U, Kumar A(2019). ). Impact of low light stress on physiological,
biochemical and agronomic attributes of rice. Journal of Pharmacognosy and
Phytochemistry 8(1) 1814-1821
9. Kumar A, Panda D, Biswal M, Dey P, Behera L, Baig MJ, Nayak L, Ngangkham U,
Sharma SG (2018). Low light stress influences resistance starch content and
glycemic index of rice (O. sativa L.). Starch, doi: 10.1002/star.201800216.
List of Publications
45. Acknowledgements
1. ICAR, New Delhi
2. Sec., DARE, DG, ICAR
3. DDG, ICAR
4. ADG, ICAR
5. Directors, ICAR-NRRI, Cuttack
7. PIs, Co-PIs and students
Editor's Notes
Photosynthesis is a multi-layered process . Imbalanced excitation of PSI and PSII.
CP12 protein , Rca activation . Rca over expression can solve the problem. Stop and go traffic
