Seminar on Molecular studies and

breeding approaches of salt tolerance in rice

(Oryza sativa)

Presented by:Nushrat Jahan Moon

Reg no: 05-01837Department of Genetics & Plant Breeding

What is soil salinity?

Soil containing enough soluble salts to reduce its fertility and interfere with crop growth.

These soils are two types:

Saline soil and Sodic soil(or alkali)

Introduction

What are the salt-affected soils ?

Salt-affected types

Electrical Conductivity ECe (dS/m)

Exchangable Sodium PercentageESP (%)

Sodium Absorption Ration (SAR)

pHs

Saline >4 <15 <13 <8.8

Sodic <4 >15 >13 8.5-10.5

Introduction (continued)

Source: http://www.knowledgebank.irri.org/ricebreedingcourse/breeding_for_salt_tolerance.htm

Extent of salt affected soils

Sodic

Saline

Asia, Pacific and Asia, Pacific and Australia (M ha)Australia (M ha)

Source : FAO database

195 249

Total 444 M ha

Introduction (continued)

Objectives To get an idea about advanced research works on salt tolerance of rice.

To exploit different molecular breeding strategies for the development of salt tolerant rice varieties.

Expression of salt stress on rice

Stress status Soil pH Electrical conductivity

Salinity status

Non-stress pH 8.8 - 9.2 Beyond ECe ~ 4 dS/m

Moderate

Moderate 9.3 – 9.7 More than 8 dS/m

High

Higher Equal or > 9.8 -- Very high

Source: http://www.knowledgebank.irri.org/ricebreedingcourse/breeding_for_salt_tolerance.htm

Physiology: Traits associated with salinity tolerance

Degree of salt stress can affect the different crops differently

Modified standard evaluation score (SES) of visual salt injury at seedling stage

Observation Tolerance

Normal growth, no leaf symptoms Highly tolerant

Nearly normal growth, but leaf tips

Or few leaves whitish and rolled

tolerant

Growth severely retarded; most leaves

rolled; only a few are elongating

Moderately tolerant

Complete cessation of growth; most

leaves dry; some plants dying

Susceptible

Almost all plants dead or dying Highly susceptible

Source: http://www.knowledgebank.irri.org/ricebreedingcourse/breeding_for_salt_tolerance.htm

Manifestation of Salt Stress

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

“Ultimate death of leaf – always from oldest to

youngest”

Salinity symptoms at the vegetative stage

Effect of salinity at Reproductive stage – Spikelet Sterility

Effect of salinity at Reproductive stage – papery sterile spikelets

Manifestation of Salt Stress

Physiological & Biochemicalv     High Na+ transport to shootv     Preferential accumulation of Na in older leavesv     High Cl- uptake v     Lower K+ uptake v     Lower fresh and dry weight of shoot and rootsv     Low P and Zn uptakev     Increase of non-toxic organic compatible solutesv     Increase in Polyamine levels

Basic Concepts – Genotype vs. phenotype

Plant breeding is based upon most basic yet most important genotype and phenotype relationship (William Johannsen, 1903)

Genes cannot push a trait to develop unless appropriate environment is provided

No amount of manipulation can cause a phenotype to develop unless necessary genes(s) are present

Breeding Strategy

Conventionalbreeding• Introduction• Selection • Hybridization• Pedigree• Bulk• SSD method

Molecular breeding

• MAS

• QTLs

• Somaclonal approach

• Anther culture

• Genetic transformation

What is MAS?

Marker assisted selection  (MAS) is a process whereby a marker is used for selection of a genetic determinant or determinants of a trait of interest.

Progress of Saltol locus

• Saturated map of the Chromosome 1 (Saltol segment) is developed

• Closely linked markers linked to the saltol locus identified

• MAS is being validated in 3 breeding

populations

AP3206

RM3412CP03970

RM8094RM493CP6224

RM140

(Source: Glenn B. Gregorio,2002)

RM283

R844S2139

RM246

RM237

RM23RM140

C17RM113S1715

S13994RM9

R2374BRM5

C1456

0.0

27.4

129.9

60.6

123.5

119.5

103.1

99.1

98.291.9

40.0

28.4

64.9

66.271.2

75.377.2

Short arm of chromosome 1

C52903S

A

What is QTLs?

Quantitative Trait Loci (QTLs) is a

location on a chromosome

which regulate phenotype for

quantitative trait and is determined by a

number of genes.

List of genes that are located in the region of QTL and up-regulated by high salinity in rice

Gene name Insertion linesClone ID full length cDNA

References

Pectinesterase 1B-23740,

1B-23741

CG408589

Ak105998

Ser/thr kinase AK065231 Guo et al., 2001

Phospholipase D 1515 AK120868 Kacperska, 2004

Zhu, 2002

SecA/protein transport factor

CL520490

CL520492

AK070488

Peroxidase AK099187 Pastori and Foyer, 2002

Sottosanto et al., 2004

Alkaline Invertase AK120720

Unknown cDNA AK099887

Source: http://www.knowledgebank.irri.org/ricebreedingcourse/breeding_for_salt_tolerance.htm

• Agrobacterium mediated transformation• Particle bombardment (gun)• PEG-mediated• Electroporation• Silicon carbide fibers

Methods of genetic transformation

Agrobacterium mediated method

Partical bombardment method

PEG-method

Electroporation method

Progress in salinity researchSaline Sodic Zn-def Acid

Donor Screening technique

Mechanism Genetics ? MAS development

Elite lines ?

= completed, = fast track, = not available /available /on-going

Lab.

Field

Salt tolerant rice varieties developed by IRRI and released in Philippines

IRRI 112 - PSBRc48 (Hagonoy) IRRI 113 - PSBRc50 (Bicol) IRRI 124 - PSBRc84 (Sipocot) IRRI 125 - PSBRc86 (Matnog) IRRI 126 - PSBRc88 (Naga) IRRI 128 - NSICRc106

Other salt-tolerant rice varieties

CSR10, CSR13, CSR23, CSR27, CSR30, CSR36 and Lunishree, Vytilla 1, Vytilla 2, Vytilla 3, Vytilla 4, Panvel 1, Panvel 2, Sumati, Usar dhan 1, 2 & 3 (India); BRRI dhan-40, BRRI dhan-41 (Bangladesh); OM2717, OM2517, OM3242 (Vietnam)

• Salt tolerance in rice is polygenic • Genes for salt tolerence have been

identified by molecular analysis• Molecular breeding strategies utilizing

these genes have been initiated to develop transgenic salt tolerant rice varieties.

Conclusion

Thank you all for your Kind attention