The document outlines a lecture on breeding for salt tolerance in rice. It discusses the extent of salt-affected soils globally and in Asia. It describes different types of salt stresses and complexities in breeding for tolerance. The key mechanisms of salt tolerance in plants include ion exclusion, tissue tolerance, and compartmentalization. Screening techniques are described for evaluating tolerance at seedling and adult plant stages. Breeding strategies aim to pyramid tolerance mechanisms by intermating donors with different predominant mechanisms.
Breeding for salt tolerance in rice: Phenomics and genomicsPratik Satasiya
Harmonizing the high throughput techniques for phenomics and genomics is both a challenge and opportunity.
There is no replacement of the conventional breeding, but its limitations in terms of speed and accuracy can be overcome by molecular breeding programmes.
The conventional phenotyping and breeding approaches are sound, the advantages and opportunities thrown open by automated phenotyping should be availed for faster gains.
Since modern genotyping protocols are well developed and high throughput in rice, phenotyping models need more consideration because capturing “right QTL” largely depends upon right phenotyping.
In molecular breeding for salinity tolerance, initial success has been made by the discovery of many QTLs and several rice salinity GWAS reports, but still there is a considerable gap between knowledge discovery and actual use of molecular breeding in realization of field oriented salt tolerant rice varieties.
Stage-specific and stress-specific QTLs may be identified for need based deployment for which, the screening methodology should be simple and high throughput, reproducible and representative of near-field conditions.
Breeding for salt tolerance in rice: Phenomics and genomicsPratik Satasiya
Harmonizing the high throughput techniques for phenomics and genomics is both a challenge and opportunity.
There is no replacement of the conventional breeding, but its limitations in terms of speed and accuracy can be overcome by molecular breeding programmes.
The conventional phenotyping and breeding approaches are sound, the advantages and opportunities thrown open by automated phenotyping should be availed for faster gains.
Since modern genotyping protocols are well developed and high throughput in rice, phenotyping models need more consideration because capturing “right QTL” largely depends upon right phenotyping.
In molecular breeding for salinity tolerance, initial success has been made by the discovery of many QTLs and several rice salinity GWAS reports, but still there is a considerable gap between knowledge discovery and actual use of molecular breeding in realization of field oriented salt tolerant rice varieties.
Stage-specific and stress-specific QTLs may be identified for need based deployment for which, the screening methodology should be simple and high throughput, reproducible and representative of near-field conditions.
Marker Assisted Gene Pyramiding for Disease Resistance in RiceIndrapratap1
Why marker assisted gene pyramiding?
For traits that are simply inherited, but that are difficult or expensive to measure phenotypically, and/or that do not have a consistent phenotypic expression under specific selection conditions, marker-based selection is more effective than phenotypic selection.
Traits which are traditionally regarded as quantitative and not targeted by gene pyramiding program can be improved using gene pyramiding if major genes affecting the traits are identified.
Genes with very similar phenotypic effects, which are impossible or difficult to combine in single genotype using phenotypic selection, can be pyramided through marker assisted selection.
Markers provides a more effective option to control linkage drag and make the use of genes contained in unadapted resources easier.
Pyramiding is possible through conventional breeding but is extremely difficult or impossible at early generations..
DNA markers may facilitate selection because DNA marker assays are non destructive and markers for multiple specific genes/QTLs can be tested using a single DNA sample without phenotyping.
CONCLUSION:
• Molecular marker offer great scope for improving the efficiency of conventional plant breeding.
• Gene pyramiding may not be the most suitable strategy when many QTL with small effects control the trait and other methods such as marker-assisted recurrent selection should be considered.
• With MAS based gene pyramiding, it is now possible for breeder to conduct many rounds of selections in a year.
• Gene pyramiding with marker technology can integrate into existing plant breeding program all over the world to allow researchers to access, transfer and combine genes at a rate and with precision not previously possible.
• This will help breeders get around problems related to larger breeding populations, replications in diverse environments, and speed up the development of advance lines.
For further queries please contact at isag2010@gmail.com
The nanotechnology aided applications have the potential to change agricultural production by allowing better management and conservation of inputs of plant and animal production. Several nanotechnology applications for agricultural production for developing countries within next 10 years has been predicted (Salamanca–Buentella et al., 2005).
Nanoparticles helps in Controlling the Plant Diseases, application of agricultural fertilizers, pesticides, antibiotics, and nutrients is typically by spray or drench application to soil or plants, or through feed or injection systems to animals. In this context, nanotechnologies offer a great opportunity to develop new products against pests (Caraglia et al., 2011). Nanoscale devices are envisioned that would have the capability to detect and treat an infection, nutrient deficiency, or other health problem, long before symptoms were evident at the macro-scale. The overall goal of this Nanoparticles is to reduce the number of unnecessary problems in agriculture (Thomas et al., 2011). In the management aspects, efforts are made to increase the efficiency of applied fertilizer with the help of nano clays and zeolites and restoration of soil fertility by releasing fixed nutrients (Dongling Qiao, et al., 2016). Nanoherbicides are being developed to address the problems in perennial weed management and exhausting weed seed bank. Bioanalytical Nanosensors are utilized to detect and quantify minute amounts of contaminants like viruses bacteria, toxins bio-hazardous substances etc. in agriculture and food systems (Tothill EI, 2011).
In this way, nanotechnology can be used as an innovative tool for delivering agrochemicals safely. More research should be done on the potential adverse effects of nanomaterials on human health, crops and the environmental safety. It is a challenge to Government and private sector as they have to ensure the acceptance of Nano foods. For it to flourish, continuous funding and understanding on the part of policy makers and science administrators, along with reasonable expectations, would be crucial for this promising field.
A new era of genomics for plant science research has opened due the complete genome sequencing projects of Arabidopsis thaliana and rice. The sequence information available in public database has highlighted the need to develop genome scale reverse genetic strategies for functional analysis (Till et al., 2003). As most of the phenotypes are obscure, the forward genetics can hardly meet the demand of a high throughput and large-scale survey of gene functions. Targeting Induced Local Lesions in Genome TILLING is a general reverse genetic technique that combines chemical mutagenesis with PCR based screening to identity point mutations in regions of interest (McCallum et al., 2000). This strategy works with a mismatch-specific endonuclease to detect induced or natural DNA polymorphisms in genes of interest. A newly developed general reverse genetic strategy helps to locate an allelic series of induced point mutations in genes of interest. It allows the rapid and inexpensive detection of induced point mutations in populations of physically or chemically mutagenized individuals. To create an induced population with the use of physical/chemical mutagens is the first prerequisite for TILLING approach. Most of the plant species are compatible with this technique due to their self-fertilized nature and the seeds produced by these plants can be stored for long periods of time (Borevitz et al., 2003). The seeds are treated with mutagens and raised to harvest M1 plants, which are consequently, self-fertilized to raise the M2 population. DNA extracted from M2 plants is used in mutational screening (Colbert et al., 2001). To avoid mixing of the same mutation only one M2 plant from each M1 is used for DNA extraction (Till et al., 2007). The M3 seeds produce by selfing the M2 progeny can be well preserved for long term storage. Ethyl methane sulfonate (EMS) has been extensively used as a chemical mutagen in TILLING studies in plants to generate mutant populations, although other mutagens can be effective. EMS produces transitional mutations (G/C, A/T) by alkylating G residues which pairs with T instead of the conservative base pairing with C (Nagy et al., 2003). It is a constructive approach for users to attempt a range of chemical mutagens to assess the lethality and sterility on germinal tissue before creating large mutant populations.
Salinity tolerance and breeding strategies on soybeanBishnu Adhikari
Introduction
Physiological effects
Salt tolerant varieties of different crop
Important genes mapped in soybean
Salinity condition in Korea
Breeding strategy for salinity tolerance in soybean
Marker Assisted Gene Pyramiding for Disease Resistance in RiceIndrapratap1
Why marker assisted gene pyramiding?
For traits that are simply inherited, but that are difficult or expensive to measure phenotypically, and/or that do not have a consistent phenotypic expression under specific selection conditions, marker-based selection is more effective than phenotypic selection.
Traits which are traditionally regarded as quantitative and not targeted by gene pyramiding program can be improved using gene pyramiding if major genes affecting the traits are identified.
Genes with very similar phenotypic effects, which are impossible or difficult to combine in single genotype using phenotypic selection, can be pyramided through marker assisted selection.
Markers provides a more effective option to control linkage drag and make the use of genes contained in unadapted resources easier.
Pyramiding is possible through conventional breeding but is extremely difficult or impossible at early generations..
DNA markers may facilitate selection because DNA marker assays are non destructive and markers for multiple specific genes/QTLs can be tested using a single DNA sample without phenotyping.
CONCLUSION:
• Molecular marker offer great scope for improving the efficiency of conventional plant breeding.
• Gene pyramiding may not be the most suitable strategy when many QTL with small effects control the trait and other methods such as marker-assisted recurrent selection should be considered.
• With MAS based gene pyramiding, it is now possible for breeder to conduct many rounds of selections in a year.
• Gene pyramiding with marker technology can integrate into existing plant breeding program all over the world to allow researchers to access, transfer and combine genes at a rate and with precision not previously possible.
• This will help breeders get around problems related to larger breeding populations, replications in diverse environments, and speed up the development of advance lines.
For further queries please contact at isag2010@gmail.com
The nanotechnology aided applications have the potential to change agricultural production by allowing better management and conservation of inputs of plant and animal production. Several nanotechnology applications for agricultural production for developing countries within next 10 years has been predicted (Salamanca–Buentella et al., 2005).
Nanoparticles helps in Controlling the Plant Diseases, application of agricultural fertilizers, pesticides, antibiotics, and nutrients is typically by spray or drench application to soil or plants, or through feed or injection systems to animals. In this context, nanotechnologies offer a great opportunity to develop new products against pests (Caraglia et al., 2011). Nanoscale devices are envisioned that would have the capability to detect and treat an infection, nutrient deficiency, or other health problem, long before symptoms were evident at the macro-scale. The overall goal of this Nanoparticles is to reduce the number of unnecessary problems in agriculture (Thomas et al., 2011). In the management aspects, efforts are made to increase the efficiency of applied fertilizer with the help of nano clays and zeolites and restoration of soil fertility by releasing fixed nutrients (Dongling Qiao, et al., 2016). Nanoherbicides are being developed to address the problems in perennial weed management and exhausting weed seed bank. Bioanalytical Nanosensors are utilized to detect and quantify minute amounts of contaminants like viruses bacteria, toxins bio-hazardous substances etc. in agriculture and food systems (Tothill EI, 2011).
In this way, nanotechnology can be used as an innovative tool for delivering agrochemicals safely. More research should be done on the potential adverse effects of nanomaterials on human health, crops and the environmental safety. It is a challenge to Government and private sector as they have to ensure the acceptance of Nano foods. For it to flourish, continuous funding and understanding on the part of policy makers and science administrators, along with reasonable expectations, would be crucial for this promising field.
A new era of genomics for plant science research has opened due the complete genome sequencing projects of Arabidopsis thaliana and rice. The sequence information available in public database has highlighted the need to develop genome scale reverse genetic strategies for functional analysis (Till et al., 2003). As most of the phenotypes are obscure, the forward genetics can hardly meet the demand of a high throughput and large-scale survey of gene functions. Targeting Induced Local Lesions in Genome TILLING is a general reverse genetic technique that combines chemical mutagenesis with PCR based screening to identity point mutations in regions of interest (McCallum et al., 2000). This strategy works with a mismatch-specific endonuclease to detect induced or natural DNA polymorphisms in genes of interest. A newly developed general reverse genetic strategy helps to locate an allelic series of induced point mutations in genes of interest. It allows the rapid and inexpensive detection of induced point mutations in populations of physically or chemically mutagenized individuals. To create an induced population with the use of physical/chemical mutagens is the first prerequisite for TILLING approach. Most of the plant species are compatible with this technique due to their self-fertilized nature and the seeds produced by these plants can be stored for long periods of time (Borevitz et al., 2003). The seeds are treated with mutagens and raised to harvest M1 plants, which are consequently, self-fertilized to raise the M2 population. DNA extracted from M2 plants is used in mutational screening (Colbert et al., 2001). To avoid mixing of the same mutation only one M2 plant from each M1 is used for DNA extraction (Till et al., 2007). The M3 seeds produce by selfing the M2 progeny can be well preserved for long term storage. Ethyl methane sulfonate (EMS) has been extensively used as a chemical mutagen in TILLING studies in plants to generate mutant populations, although other mutagens can be effective. EMS produces transitional mutations (G/C, A/T) by alkylating G residues which pairs with T instead of the conservative base pairing with C (Nagy et al., 2003). It is a constructive approach for users to attempt a range of chemical mutagens to assess the lethality and sterility on germinal tissue before creating large mutant populations.
Salinity tolerance and breeding strategies on soybeanBishnu Adhikari
Introduction
Physiological effects
Salt tolerant varieties of different crop
Important genes mapped in soybean
Salinity condition in Korea
Breeding strategy for salinity tolerance in soybean
Effect of salinity on seedling growth in early vegetative phase of riceSohel Rana
The aim of this investigation was to analyze genotypic variations of salt tolerance of rice varieties at germination and seedling growth of early vegetative phase of rice.
Molecular Breeding in Plants is an introduction to the fundamental techniques...UNIVERSITI MALAYSIA SABAH
This slide describe the process of molecular breeding in plants which involves the application of molecular markers for Marker Assisted Selection and Marker Assisted Breeding.
I would like to share this presentation file.
Some basics information regarding to molecular plant breeding, hope this help the beginner who start working in this field.
Thanks for many original source of information (mainly from slideshare.net, IRRI, CIMMYT and any paper received from professor and some over the internet)
Presented by Michael Dingkuhn at the CCAFS Workshop on Developing Climate-Smart Crops for a 2030 World, ILRI, Addis Ababa, Ethiopia, 6-8 December 2011.
Introgression breeding for rice submergence tolerance_geetanjaliDr. Geetanjali Baruah
Simplified way of applicability of introgression breeding for submergence tolerance in rice with special emphasis on physiology of submergence tolerance
DOI:10.21276/ijlssr.2016.2.4.3
their qualitative and quantitative distribution from eight districts of Rajasthan. A total of three species of Acaulospora, two
species of Gigaspora, fourteen species of Glomus, four species of Sclerocystis and two species of Scutellospora were
recorded. A high diversity of AM fungi was observed and it varied at different study sites. Among these five genera,
Glomus occurred most frequently. Glomus fasciculatum and G. mosseae were found to be the most predominant AM fungi
in infecting A. excelsa. G. fasciculatum, Sclerocystis was found in all the fields studied, while Gigaspora species and
Scutellospora species were found only in few sites. The maximum number (22) of AM fungal species were isolated and
identified from Sikar whereas, only ten species (10) were found from Nagaur. The spore density was varied between 195
to 682 propagules (100 g-1) soil. The percent root colonization was varied (47 to 79 %) from place to place. The pH of
study area was ranged between 7.82 to 8.79; EC was recorded from 0.13 to 0.62 (dSm-1); Percent OC ranged from 0.22 to
0.39 and available P content varied from 4.1 to 5.36 mg kg-1 for A. excelsa. A significant correlation of AM population
was observed with root colonization, percent organic carbon and pH while other variables under study had a
non-significant correlation with total AM population. Key-words- Arbuscular mycorrhizae, Arid agroecosystems, Diversity, Root colonization, Correlation, Ailanthus excelsa
Diversity of halophilic mycoflora habitat in saltpans of Tuticorin and Marakk...Open Access Research Paper
Highly diverse biological system of solar salterns with different salinities, often provide high densities of mycofloral populations, makes the salterns excellent model systems for both its diverse and activity. In this study, diversity of halophilic fungi in six stations which includes reservoir, evaporator and crystallizer pond of both Marakkanam and Tuticorin saltpans in relation to environmental parameters were carried out for a period of two years. 95 species of halophilic fungi from water and sediment samples belongs to 41 genera were recorded in both saltpans. Aspergillus and Penicillium species were recorded as dominant, vast differences in growth of each isolate at different salt concentrations in the ponds were observed. This paper also elucidated the slight fluctuations in physico-chemical parameter among the ponds with respect to seasonal variations were also recorded.
A presentation about clean water landscaping. Presented by Robert Roseen of Geosyntec Consulting during the Buzzards Bay Coalition's 2014 Decision Makers Workshop series. Learn more at www.savebuzzardsbay.org/DecisionMakers
Use of stable and radio isotopes to understand the plant physiological processRAHUL GOPALE
Introduction
what is isotope ?
Types of Isotopes
Isotopic Labelling
ADVANTAGES AND DISADVANTAGES OF ISOTOPIC STUDY
APPLICATIONS OF ISOTOPES IN AGRICULTURE
Principle isotopes used in plant-soil studies
Case studies
FUTURE THRUSTS OF ISOTOPIC STUDY
CONCLUSIONS
REFERENCES
Carbon sequestration in agricultural soils: The “4 per mil” programExternalEvents
Carbon sequestration in agricultural soils: The “4 per mil” program presented by Hervé Saint Macary, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Montpellier, France
Validation of reference genes in leaf-cutting ant Atta sexdens rubropilosa in...IJEAB
Atta sexdens rubropilosa is an important leaf-cutting ant species considered as a pest in agricultural crop or reforestation areas. Quantitative real-time reverse transcriptase-polymerase chain reaction (RT-qPCR) is a technique that can help us to understand the regulation and the function of a gene. However, its reliability depend on the data normalization. Different normalization strategies can be adopted for qPCR, reference genes has been cited as one of the most effective methods. It has not been identified a universal reference for all organism and experiment. In this way, the validation of reference gene is crucial step. This is the first study to evaluate reference genes for leaf-cutting ants. To this, we analyzed the expression levels of candidate reference genes (act, ef1-alpha, ef1-beta, GAPDH and rpl18) in different developmental stages (larva, pupa and worker) and tissues (head, mesosoma and worker without gaster) of A. sexdens rubropilosa. Four different algorithms (BestKeeper, geNorm, NormFinder and comparative ΔCt method) were used in statistical analysis of the stability of the genes and RefFinder was used to propose a consensus list for ranking the reference genes. Our results showed that the most suitable combinations of reference gene candidates were rpl18 and ef1-alpha for the different developmental stages and rpl18 and ef1-beta for the different tissues. In this work, we also report the obtaining from a putative acetylcholinesterase from A.sexdens rubropilosa (GenBank KY464935), which was used as a target gene to confirm the reliability of reference genes suggested.
Enzymes activity and content of antioxidants in leaves of halophytes from sal...Innspub Net
The purpose of the given study was to investigate characteristics of antioxidant system and other biochemical indices of some salt resistans species growing on saline soils of Georgia. Activity of antioxidant enzymes (peroxidase and catalase) and nitrate reductase, also low molecular antioxidants (proline, ascorbic acid, soluble phenols, anthocyanins and carotenoids), and of content of total proteins, chlorophylls, and soluble carbohydrates has been investigated in leaves of salt resistnt plants-Salsola soda L.-opposite-leaved saltworth, Tamarix ramosissima Ledeb.-salt cedar, Chenopodium album L.-goosefoot, Artemisia lerchiana (Web.)-sagebrush, Achillea biebersteinii (Afan.)-allheal and Adonis bienertii (Butkov ex Riedl.)-pheasant's eye-growing coastwise and in surroundings of Kumisi Lake (East Georgia, lower Kartli), in order to study the influence of salinization level on the studied parameters. Spectrophotometrical, gazometrical and titration methods has been used for investigations. Increase of salinity induced activation of peroxidase, rise of proline and total proteins content in leaves of eu-and crynohalophytes (saltworth, goosefoot, salt cedar). Activation of catalase and peroxidase, also increase of the content of anthocyanins, phenols, total proteins and soluble carbohydrates was mentioned in leaves of glyco halophytes (sagebrush, allheal, peasant's eye) under the same conditions. Activation of peroxidase and increase of the content of total proteins seemed to be the uniting mechanism for adaptation to high level salinization among the studied species..
Molecular marker analysis of A few Capsicum annum varietiesAnkitha Hirematha
The hybrid variety and parental varieties among the 3 chilly varieties were identified by finding out the genetic polymorphism between them. It helps to identify different plant varieties, disputed plant varieties, genetic polymorphism between intraspecific crosses of plants and also to protect Plant Breeder’s Rights (PBR). Based on banding pattern on gel, identification of KA, KS and HK chilly varieties using SSR & ISSR markers was successfully carried out.
Similar to R.K. Singh .Breeding for salt tolerance in rice (20)
Richard's aventures in two entangled wonderlandsRichard Gill
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DERIVATION OF MODIFIED BERNOULLI EQUATION WITH VISCOUS EFFECTS AND TERMINAL V...Wasswaderrick3
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This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
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The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
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2. R.K.Singh
Extent of the problem and
management options
Reason of Limited Success
Plant adaptation – salt
tolerant mechanisms
Morphological symptoms
Basic concepts (genotype vs.
phenotype and heritability)
Genetic Studies
Screening techniques
Breeding strategy
Physiological mechanisms
Molecular mapping
Varietal development
NRM approaches
Outlines of the Lecture
3. R.K.Singh
EXTENT OF SALT-AFFECTED SOILS
World’s Total area
12.78 b ha
340 x 106
ha (Ponamperuma, 1984)
954 x 106
ha ( Massoud, 1974)
10% area ~ 1.2 b ha (Tanji, 1991)
FAO Database
397 x 106
ha (3.1%) – Saline soils
434 x 106
ha (3.4 %)– Sodic Soils
Asia, Pacific andAsia, Pacific and
Australia (M ha)Australia (M ha)
195 249
Source : FAO database
Total : 444 M ha
5. R.K.Singh
How to Manage the Salt-affected Areas ?
1. Environment
modifying approach :
Change the
environment for the
normal growth of plants
2. Crop based
approach : Select or
develop crop variety
which can withstand
the salt stress
Do we need
ST
cultivars ?
Rice has
enormous
variability
6. R.K.Singh
Management of the Salt-affected Soils
3. Hybrid Approach
It is the combination of
environment modifying
and plant based approach.
Advantages:
• More viable
• Highly productive
• Low resource cost
Local variety without gypsum
Salt tolerant rice variety,
CSR13, with 25% Gypsum
7. R.K.Singh
Reasons of Limited Success
Salt stress seldom happen in isolation
Harsh, highly variable environment, large G/E
Lack of efficient / precise screening procedure
Lack of mechanistic understanding
Low priority and less number of researchers involved
8. R.K.Singh
Salt Stresses and Associated Complexities
S
A
L
T
S
T
R
E
S
S
E
S
Acid
SO4
Peat
S
A
L
I
N
E
ALKALINE
INLAND
SALINE
(P, Zn)
(P, Zn)
(P, Zn)
(P, Zn)
(Fe)
Fe, Al
tox
Fe, H2S
tox
Al, Organic
Acids tox
(P & Zn)
R
A
I
N
F
E
D
Sub-
merged
Deep-
water
Drought
Irrigated
G
r
a
I
n
Q
u
a
l
i
t
y
(Source: Glenn B. Gregorio)
9. R.K.Singh
Breeding
for
Salt tolerance + High productivity
• Na+
Exclusion
• Tissue tolerance
• K+
uptake
• Partitioning etc.
All are quantitative trait
Quantitative trait
Single trait
10. R.K.Singh
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
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
Na+
Cl-
11. R.K.Singh
Physiology: traits associated with
salinity tolerance
Regulation of uptake
Compartmentation
In old tissue
Upregualtion of
antioxidants
Vigorous growth
Responsive
stomata
[Na+
]
OsmoprotectantsAOSS
K+
AtNHX1
H+
Na+
Vacuolar Na+
/H+
SOS1
Na+
H+
Plasma Na+
/H+
AVP1
H+
PPiase
Compartmentation within tissue
(tissue tolerance)
Protective
metabolites
Polyamines,
dehydrins,
glyoxalates
Earliness
Source : A.M. Ismail
12. R.K.Singh
Morphological Symptoms
White leaf tip followed by tip burning (salinity)
Leaf browning & death (sodicity)
Stunted plant growth
Low tillering
Spikelet sterility
Low harvest index
Less florets per panicle
Less 1000 grain weight
Low grain yield
Change in flowering duration
Leaf rolling
White leaf blotches
Poor root growth
Patchy growth in field
Manifestation of Salt Stress
13. R.K.Singh
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
16. R.K.Singh
Physiological & Biochemical
High Na+
transport to shoot
Preferential accumulation of Na in older leaves
High Cl-
uptake
Lower K+
uptake
Lower fresh and dry weight of shoot and roots
Low P and Zn uptake
Increase of non-toxic organic compatible solutes
Increase in Polyamine levels
Manifestation of Salt Stress
Screening parameters ?
17. R.K.Singh
Which is the most reliable stage for screening ?
Association between
Correlation Coeff.
Glasshouse
studies
Field studies
Veg. stage tolerance vs. Grain yield
Rep. stage tolerance vs. Grain yield
Veg. stage vs. Rep. stage tolerance
- 0.58ns
- 0.97**
0.59ns
- 0.022ns
- 0.82**
0.34ns
Vegetative vs. Reproductive stage salt tolerance
19. R.K.Singh
Number of gene(s) responsible for a trait (n) / Genotypic classes
1 2 5 10
F2
F3
F4
F5
F6
1:2:1
3:2:3
7:2:7
15:2:15
31:2:31
1:2:1:2:4:2:1:2:1
3:2:3:6:4:6:3:2:3
7:2:7:14:4:14:7:2:7
15:2:15:30:4:30:15:2:15
31:2:31:62:4:62:31:2:31
243
classes
59,049
classes
P* 1/4 1/16 1/ 1,024 1/ 1,084,576
*: P is the probability of getting the desired homozygote at all the loci in smallest perfect
population in F2 (1/4n
)
Trait A = 5 loci -- Desired recombinant – 1/1,024
Trait B = 10 loci -- 1/1,084,576
Prob. of getting both desired one in one background = 1/1,024 x 1/1,084,576
= 1/ 1,110,605,824 (> 1b)
Probability of getting the desirable genotype
Why Recurrent selection – mating of the selected individuals ?
20. R.K.Singh
Precision vs. Resources
Precision
l
r
y
Resources
No. of
low
more
Very High
Since the salinity is highly variable in soil due to the dynamic state
of soluble salts hence one should go for more blocks at different
locations over the years (judiciously compromising the resources)
for the precise estimates
21. R.K.Singh
Based on reproductive stage tolerance
Bas. 370 / CSR10
Bas. 370 / CSR11 Pak. Bas. / CSR10
Controlled by numerous minor genes as
revealed by the normal distribution curve
with few major genes (skewness)
SALINITY
Substituted
Genetics of Salt Tolerance
Inheritance Pattern
26. R.K.Singh
Normal
Saline
1 2 3
1 2 3
FL478 / IR29 FL478 / IR29 FL478 /
IR29
FL478 / IR29 FL478 / IR29 FL478 / IR29
Performance of 1 mo-old FL478 (tolerant line) and IR29 (susceptible variety) rice seedlings
under normal and saline (14d EC12 then 14d EC18) conditions using SNAP and nutrient
solutions: (1) 100% SNAP solution in tap water, (2) 75% SNAP solution in tap water, and (3)
nutrient solution in distilled water.
(Source: Dante Adorada)
27. R.K.Singh
Comparison between 28-day old rice seedling grown for 21 days in SNAP solution (Simple
Nutrient Addition Program) with (a) 100% nitrate and (b) 90% nitrate & 10% ammonium in
their composition.
(Source: Dante Adorada)
28. R.K.Singh
Phenotyping for the Adult Plant Salinity Tolerance
Microplots with controlled salinity and sodicity
Sodic Soil Environment
Saline Soil Environment
(Rain shelter)
Automatic Circulatory Solution Culture System
29. R.K.Singh
Nais the most notorious element causing salt related
problems in plants
Its higher uptake hinders the metabolic activities in plants
Plants try to resist this element using various physiological
mechanisms
• Na+
exclusion,
• Tissue Tolerance
• Higher K+
uptake to counter Na
• Compartmention (Preferential accumulation of Na+
in stem,
leaf sheath, older leaves etc.)
• Early vigour
• …… Many more
Salinity Tolerance in Rice
30. R.K.Singh
Breeding Strategy
Identification of the genotypes based on the inherent
physiological mechanism (Na exclusion, K uptake, Tissue
tolerance and high initial vigor etc.) responsible for salinity
tolerance
Inter-mating of the genotypes with high degree of expression
of the contrasting salinity tolerance mechanism
Identifying / screening of the recombinants for pooling/
pyramiding of the mechanisms
31. R.K.Singh
Identify the donors for predominant physiological mechanisms
responsible for salt tolerance
• Na+
exclusion,
• Tissue Tolerance
• K+
uptake,
• Preferential accumulation of Na+
in stem, leaf sheath, older
leaves etc.
• Early vigour
However, none of the rice variety posses all the possible positive
mechanism conferring salinity tolerance.
Breeding Strategy
32. R.K.Singh
Grouping of the rice varieties on the basis of
Na accumulation per day
B a s .3 7 0 , C S R 1 0 , C S R 1 9
M I-4 8 , B a s .3 8 5 ,
C S R 1 8 , P R 1 0 8
L o w
< 0 .1 m m o l/g
C S R 1 1 , IR 3 6 , H B C 1 9 , C S R 2 0 , A D T 3 6
H K R 1 2 8 , C S R 1 , J a y a , C S R 1 3 , A c h h i
S u k h v e l, IR 4 2 , IR 2 4 , M a jh e ra 7 , M a n g la
S L R 5 1 2 1 4 , P ra s a d , V a n d n a , S a liv a h n a
M e d iu m
0 .1 - 0 .4 9 9 m m o l/g
S R 2 6 B , C S R 2 1 , IR 4 6 3 0 , P o k k a li, T -2 3
G R 1 1 , P a n v e l-2 , In d ra s a n , IR 5 8 , R P 1 4 4
H a th w a n , C a rp s C la rk , S w a rn d h a n , R a v i
U d a y a , T -2 1 , M a jh e ra -3 , B a rk a t, M K 4 7 -2 2
H ig h
> 0 .5 m m o l
N a a c c u m u la tio n p e r d a y
(m m o l/g d w t)
33. R.K.Singh
C S R 2 1 , IR 4 6 3 0 , H a th w a n , S w a rn d h a n
In d ra s a n , A c h h i, M u s k a n , U d a y a
R P 1 4 4 , V K L -3 9 , C a rp s C la r k
H ig h
> 0 .4 m m o l/g
C S R 1 1 , IR 3 6 , C S R 2 0 , P a n v e l-2 3 , B C 1
R a v i, S a liv a h a n a , H a s a n S a ra i, B a rk a t
P R 1 0 6 , IR 5 8 , IR 2 4 , M a jh e ra -3 , A D T 3 6
S L R 5 1 2 1 4 , IR 4 2 , M K 4 7 -2 2 , T -2 3 , M a n g la
M e d iu m
0 .2 - 0 .4 m m o l/g
S R 2 6 B , H B C 1 9 , C S R 1 , P o k k a li, T -2 3
G R 1 1 , P R 1 0 8 , C S R 1 0 , C S R 1 8 , C S R 1 9
J a y a , H K R 1 2 8 , M I-4 8 , B a s .3 7 0 , B a s .3 8 5
M a jh e ra -7 , P r a s a d , V a n d n a , V ik ra m a ry a
L o w
< 0 .2 m m o l
K a c c u m u la tio n p e r d a y
(m m o l/g d w t)
Grouping of the rice varieties on the basis of
K accumulation per day
36. R.K.Singh
Rice variety A
Good excluder
+
poor tissue tolerance
Rice variety B
Poor control at root level
+
High tissue tolerance
Dustbin
Garbage
Na+
Rice variety C
Good excluder
+
High tissue tolerance
K+
37. R.K.Singh
An Ideal High Yielding Salinity Tolerant Variety
Highly tissue tolerant
Good Excluder- Minimum per day uptake of Na+
High uptake of K+
per day
Low Cl-
uptake
Low Na+
/ K+
ratio
Good initial vigour
Agronomically superior with high yield potential (plant type
+ grain quality)
38. R.K.Singh
Breeding Strategy
Grouping of the genotypes based on the inherent
physiological mechanism responsible for salinity
tolerance
Inter-mating of the genotypes with high degree of
expression of the contrasting salinity tolerance
mechanism
Identifying / screening of the recombinants for pooling/
pyramiding of the mechanisms - MAS
41. R.K.Singh
• preprotein translocase, SecA subunit
• Sec23/Sec24 trunk domain, putative
• Ser Thr Kc
• Protein kinase domain
• S-adenosylmethionine synthetase
• chloroplast membrane protein
•Cold shock protein
• secretory peroxidase
• CBL-interacting protein kinase 19
• Peroxidase, putative
• Cell wall protein type (Extensin,
Hydorxyproline rich, glycine rich)
• phospholipid/glycerol
acyltransferase –like
• Mitochondrial carrier
protein, putative
• GDSL-like
Lipase/Acylhydrolase,
putative
• organic cation transporter
• major facilitator
superfamily protein
•Cell wall protein type
(Extensin,Hydorxyproline
rich, glycine rich)
• CP12 domain, putative
• Stress-inducible membrane pore protein
• Zinc finger, C3HC4 type (RING finger),
putative
• Universal stress protein family
• Cation-chloride co-transporter
• Receptor like protein kinase
• Myb-like DNA-binding domain, putative
• Peroxidase, putative
• Cell wall protein type
(Extensin,Hydorxyproline rich, glycine
rich)
• Cation transporter
• Phospholipase D. Active site motif,
putative
• Protein kinase domain, putative
• Dual specificity phosphatase, catalytic
domain, putative
• Pectinemethyesterase/invertase inhibitor
• Pectinesterase
Rice Chromosome 1
60.6 60.9 62.5 64.9 65.4 66.2 67.6 67.9
cM
65.8
Saltol region ( Major QTL K+
/Na+ratio )
(Source: Ellen Tumimbang)
42. R.K.Singh
11.9 Mb 12.13 Mb
12.11Mb 12.27Mb
12.25Mb 12.40Mb
12.0Mb 12.27 Mb
preprotein
translocase,
SecA subunit
Sec23/Sec2
4 trunk
WD40
Ser Thr
Kc
Receptor
like kinase
SAM
synthetase
cold
shock
protein
chloroplast
membrane
protein
secretory
peroxidase
CBL-interacting
protein kinase 19
Peroxidase,
putative
S_Tkc;
WD40
0.27 Mb
SALtol Region ( Major QTL
K+
/Na+)
(~40 genes)
11.10Mb 12.7Mb
60.6 60.9 62.5 64.9 65.4 66.2 67.6 67.9
cM
65.8
Chromosome 1 of Rice
B1135C02
OSJNBa0011P19
P0426D06
B1153f04
(Source: Ellen Tumimbang)
43. R.K.Singh
List of genes that are located in the region of QTL and up-
regulated by high salinity in rice
Gene name
Insertion
lines
Clone ID
full length
cDNA
Rice 60k chip data
under high salinity
(fold-induction)
References
0.5 h 2 h 6 h
Pectinesterase 1B-23740,
1B-23741
CG408589
Ak105998 1.1 3.3 4.9
Ser/thr kinase AK065231 2.3 2.7 Guo et al., 2001
Phospholipase D 1515 AK120868 3.5 2.6 Kacperska, 2004
Zhu, 2002
SecA/protein
transport factor
CL520490
CL520492
AK070488 3.1 1.5
Peroxidase AK099187 2.6 3.05 Pastori and Foyer, 2002
Sottosanto et al., 2004
Alkaline Invertase AK120720 4.0 2.2 4.2
Unknown cDNA AK099887 0.37 1.6 2.4
(Source: Ellen Tumimbang)
44. R.K.Singh
• Putative SecA-type
chloroplast protein
transport factor
• Serine/threonine kinase
• Peroxidase
• Pectinesterase
• Phospholipase D. Active site
motif -- putative
The position of the candidate genes in chromosome 1
60.6 60.9 62.5 64.9 65.4 66.2 67.6 67.9
cM
65.8
Saltol region ( Major QTL K+
-Na+ratio )
Plant
neutral/alkaline
invertase
(Source: Ellen Tumimbang)
45. R.K.Singh
Mapping Salinity Tolerance Genes
at Reproductive Stage
QTLs for salinity tolerance genes at seedling
stage are different from reproductive stage
• Seedling stage tolerance in chrom 1.
• Reproductive stage tolerance in chrom 3, 4, 7,
and 9
Dr. Mirza M. Islam
Ph.D.
48. R.K.Singh
Realization of the Genetic Potential
Promote the
Interdisciplinary
IRRI-NARS
collaborative
research, based
on CNRM
technology and
its validation in
the farmers
participatory
mode
49. R.K.Singh
Progress in salinity research
= completed, = fast track, = not available
/available /on-going
Saline Sodic Zn-def Acid
Donor
Screening
technique
Mechanism
Genetics ?
MAS
development
Elite lines ?
Lab.
Field
50. R.K.SinghThanks for Your Kind Attention
Glenn B. Gregorio Rafiqul Islam Mirza M. Islam Jong C. Ko
R K Singh Andy Sajise Ghasem M. Nejad Glenn Alejar
Adorada Dante Venus Elec Swe Thein Midie
Rhulyx Mendoza Jean Melgar Lorelie Ramos Venessa
Ellen Tumimbang Jaarmi Orly Kelvin
Rollin De Ocampo Angelito Francisco