3. •White leaf tip followed by tip burning (salinity)
•Stunted plant growth
•Low tillering ability
•Spikelet sterility and poor seed setting
•Poor grain filling
•Low harvest index
•Lesser florets per panicle
Salinity morphological symptoms observed in natural sites/salinity hot spots
•Lesser florets per panicle
•Lesser 1000 grain weight
•Lower grain yield
•Change in flowering duration
•Leaf rolling
•White leaf blotches
•Poor root growth
•Patchy growth in field
RK Singh PBC 2006
4. First symptom
“Leaf tip
burning”
“Leaf tip burning
extends toward
base through
Lamina”
“Ultimate death
of leaf – always
from oldest to
youngest”
Salinity symptoms at the vegetative stage
RK Singh PBC 2006
5. Effect of salinity at reproductive stage – papery sterile spikelets
RK Singh PBC 2006
6. Effect of salinity at Reproductive stage – Spikelet Sterility
RK Singh PBC 2006
7. 4. Sequestration of the toxic ions
to vacuole or cell wall – cell level
compartmentation
3. Excretion of salt through salt
glands, salt-hairs or bladders – in
most halophytes
Predominant salt-tolerance mechanisms operating in plant
R.K.Singh
Plant Breeding Course, April 06
1. Restricting the entry of toxic
ions at root level - Exclusion
2. Transporting the toxic ions to
stem, leaf sheath or older leaves –
plant level compartmentation
Na+ Cl-
8. Physiology: traits associated with
salinity tolerance
Regulation of uptake
Compartmentation
In old tissue
Upregualtion of
antioxidants
Responsive
stomata
Protective
metabolites
Polyamines,
dehydrins,
Earliness
R.K.Singh
Plant Breeding Course, April 06
antioxidants
Vigorous growth
[Na+
]
OsmoprotectantsAOSS
K+
AtNHX1
H+
Na+
Vacuolar Na+
/H+
SOS1
Na+ H+
Plasma Na+
/H+
AVP1
H+
PPiase
Compartmentation within tissue
(tissue tolerance)
glyoxalates
Source : A.M. Ismail
9. Salinity screeningSalinity screeningSalinity screeningSalinity screening
• GSR salinity screening was
previously done in greenhouse
under salinized SNAP nutrient
solution
• For 2 seasons now, salinity
screening moved saline prone on-
farm site (Infanta, Quezon,
Philippines).Philippines).
10. Salinity Screening: salinized nutrient solutionSalinity Screening: salinized nutrient solutionSalinity Screening: salinized nutrient solutionSalinity Screening: salinized nutrient solution
Populations (BC1F2)
Single plant selections (BC1F3-5)
Day 0: Soaking
(pre-germinate seeds at 35OC
for 2 days & Room Temp. for 1 day)
Day 21: 2nd Salinization
(to EC 18 dS/m by adding NaCl,
pH5.0)
(Score for EC 12 using SES)
(maintain EC & pH level daily)
Day 35: Conditioning
Day 3: Sowing
(3 seeds/hole in styro-seedling floats)
(over the SNAP nutrient solution
1% SNAP A + 1% SNAP B, pH 5.0)
Day 7: 1st Salinization
(to EC 12 dS/m by adding NaCl,
pH5.0)
(maintain EC & pH level daily)
Day 35: Conditioning
(Change SNAP solution with fresh
water)
(Score for EC 18 using SES)
Day 37: Transplanting
(of surviving seedlings)
(Single seedling per hill)
Maturity: Harvesting
(Single plant harvesting)
11.
12.
13. Populations (BC1F2)
Single plant selections (BC1F3-4)
Seeding
(on-farm salinity site)
Seedling stage salinity
Salinity Screening: OnSalinity Screening: OnSalinity Screening: OnSalinity Screening: On----farm saline prone sitefarm saline prone sitefarm saline prone sitefarm saline prone site
Promising populations and lines
from seedling stage screening.
Transplanting
(21 day-old seedlings)
(Single seedling per hill)
Seedling stage salinity
treatment
(10-21 DAS)
(seedbeds are irrigated with sea
water)
(EC level is monitored using data
logger)
Scoring & Selection
(21 DAS)
(promising populations and lines are
EC level monitoring
(EC reading varies from 6 to 15
mS/cm)
(Sea water is irrigated on to the field
when field EC level is low)
Selection & harvesting of
survivals
(Maturity)
16. Objectives
• To understand the salinity tolerance in relation
to drought tolerance
• To identify & map the salinity tolerance QTLs
using DT selected ILs from varied donorusing DT selected ILs from varied donor
sources
• To find ST mechanistic pathways adopting
time related mapping approach.
17. Materials & methods
• DT selected material under lowland drought conditions
during DS2000-non target trait mapping
• 150 ILs BC2F4 population of 16 crosses, RP(IR64,
Teqing & NPT); tolerant(Pokkali), susceptible check
(IR29) 2 replications
• Controlled growth conditions (29oC/21oC day /night
temperature & 75% RH) immediately after 2 days of
germination (30oc)in distilled water in petri plates, to
initial salinization in plastic tubs with styrofoam floats
• 3days at EC of 6 dSm-1increased to EC 12 dSm-1 and
maintained upto 23 days with NaCl into Yoshida(1976)
nutrient solution with pH 5.0
• 23 DAIS salinised nutrient solution with 150 ILs PA• 23 DAIS salinised nutrient solution with 150 ILs PA
score at 10, 16, 23 DAIS and survival %
• Tissue extracted in 10ml of 0.1N acetic acid & Na, K
measured in atomic absorption spectrophotometer
• QTL mapping using145 well distributed SSR markers
and phenotypic scores with PROC GLM –ANOVA using
SAS
• Normalised LD coefficient and GGT was used to find
close associations of the introgressions for DT and
related to ST
19. Results & Discussion
• Salinity and drought share certain common regions for tolerance
• Identified closely associated QTL bins over different chromosomes
related to salinity
• Is there any role of such strongly associated bins in the developmental
response to salinity stress?
• Time related mapping of ST: switching on & off of genes/QTLs against• Time related mapping of ST: switching on & off of genes/QTLs against
salinity stress over a given time frame. QTLs for Na-K uptake
identified.
• ILs identified with enhanced salinity tolerance over check variety
Pokkali in elite IR64 & Teqing background and currently being field
tested.
• Closely related non target traits such as salinity can be mapped using
such an approach
20. Relative salinity tolerance of introgression lines at 10,16
and 23DAIS
60
80
100
Frequency
highly tolerant
tolerant
moderately tolerant
0
20
40
10DAIS 16DAIS 23DAIS
Days after initial salinisation
Frequency
moderately tolerant
susceptible
highly susceptible
21. IL 62
Pokkali
Highly tolerant IL 62 (Teqing x Type 3) in the
foreground of Tolerant check Pokkali & susceptible
check IR29
After 23 days in EC12.0 dSm-1
IR29
26. Salinity tolerance QTLs
• 23 QTL segments identified governing salinity tolerance out of which 19 were
common for both the crosses
• Na-K relationship with salinity tolerance fitted well with PA scores & survival
%.
• Chromosome 1,2,6,8,10,11 showed major salinity QTL segments with• Chromosome 1,2,6,8,10,11 showed major salinity QTL segments with
improved salinity tolerance.
• 17 QTL segment introgressions from Binam donor improved tolerance in
Teqing background while only 7 in case of IR64 RP.
• Na- exclusion mechanism in both root & shoot was introgressed from Binam
donor into Teqing background primarily responsible for improved salinity
tolerance.
28. IR64/Binam Teqing/Binam
chromosome 1 chromosome 1
QTL detected
Common QTL detected
Additive effects direction
14(4,4,5,82.5% );6(4,3,4,95%);3(3,3,3,95%);8(5,6,6,80%); 7(5,5,4,90%) 2(1,4,5,80% );5(1,3,7,42.5%);7(1,1,3,92.5%);9(3,3,2,95%)
Individual No.( PA score on 10,16,23d,sur%)
29. IR64/Binam Teqing/Binam
chromosome 11 chromosome 11
QTL detected
Common QTL detectedAdditive effects direction
14(4,4,5,82.5% );6(4,3,4,95%); 2(5,5,4,82.5%); 9(7,7,7,62.5%) 9(3,3,2,95%) 7(1,1,3,92.5%); 5(1,3,7,42.5%)
Individual No.( PA score on 10,16,23d,sur%)
30. Salinity in relation to drought tolerance
• A separate group of closely associated Bins for DT was identified
and was distinctively different from Salinity tolerance for both the
crosses.
• Up regulated Bins seems to be quite strongly associated with both
DT & ST and were common for both the crosses.
• Down regulated Bins showed many putative ST QTLs for
TeqingxBinam cross improving ST in comparison to IR64xBinam
cross.
• 40% of DT Bins coincided with ST in IR64xBinam while 31.3% for
TeqingxBinam cross.
32. What ?
• Salinity tolerance is a complex trait and needs to be understood in
a wholistic manner.
• Molecular QTL pyramiding of ST & DT in select ILs was feasible.
• Salinity and drought has relatively similar pathways for tolerance
mechanisms and needs to be addressed together to achieve
success in breeding superior stress tolerant rice varieties.
• Dissection of salinity tolerance QTLs from drought tolerant
material will open up new research avenues in the future.
