Salinity tolerance and breeding strategies on

soybean

Presented by:Bishnu Adhikari

Student Id: 2016226596Plant Resources Development Lab

7 June 2016

Outlines

• 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• Conclusion

What is soil salinity?

Introduction

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

Salt-affected soils can be divided into saline, saline-sodic and sodic, depending in salt amounts, type of salts, amount of sodium present and soil alkalinity.

Each type of salt-affected soil will have different characteristics.

Soil salinity is one of the important abiotic components that frequently have critical effects on crop growth, productivity and quality

Iran salt affected soil

China salt affected soil

What are the salt-affected soils?

Salt-affected types

Electrical Conductivity (dS/m)

Exchangeable Sodium Percentage (ESP)

Sodium Adsorption Ratio(SAR)

pH

Saline >4 <15 <13 <8.8

Sodic <4 >15 >13 8.5-10.5

Why does soil become salinity?

1.Semiarid and arid regions Annual precipitation< evapotranspiration

2.Natural sources of soil salinity a) Mineral weathering b) Fossil salts c) Atmospheric precipitation

Introduction (contd…….)

3.Local salt accumulation Soils in low-lying areas

4.Human Activitiesa. Salts from areas of over-irrigation accumulate in

poorly drained areas.b. Relatively saline irrigation water are used.c. Oil-field development, waste-spreading operation,

and crop fertilization

Evaporation

Capillary rise

water table

Extent of Salt affected land

• As agricultural land is increasingly salinized throughinefficient fertilizer practices, salt-water intrusion, and useof poor quality irrigation water (Abel and MacKenzie,1964).

• 50% of the arable land will be affected by salt stress by 2050

(Blumwald and Grover,2006).

• Ocean contain 97% of total water supply in the world with major component of NaCl (500 molm-3) which is highly toxic to normal plants.

• Globally the total area of saline soils is 397 million ha and sodic soils 434 million ha. Out of 230 million ha irrigated land, 45 million ha (19.5 %) were salt-affected soils and almost 1500 million ha of dryland agriculture, 32 million (2.1 %) were salt-affected soils (FAO, 2016).

• The regional impact of salinity is much serious than the average value. For e.g. Pakistan, Australia(Ahmad, 1990; Northcote & Skene, 1972)  

Physiological effects of Salt Stress Germination• Increased osmotic pressure of the soil solution which restricts the absorption

and entry of water into the seeds.• Certain salt constituents like CO3

-2, NO3-,Cl-, SO4

-2 are more harmful to seed germination.

• Hampers the metabolism of stored materials

Vegetative growth• Closure of stomata leads to reduction in CO2 assimilation and

transpiration.• Reduced turgor potential affects the leaf expansion. • Decreased rate of leaf growth due to osmotic effect of salt around

roots,• Leaf cells loose water• Reductions in cell elongation and cell division

Total 444 M ha

Photosynthesis• Accumulation of high concentration of Na+ and Cl- in chloroplast,

photosynthesis is inhibited• Photosynthetic enzyme for carbon assimilation are very sensitive to the

presence of NaCl

Nitrogen Metabolism• The key enzyme, nitrate reductase is very sensitive to NaCl .

Reproductive growth and yield• Onset of flowering is delayed due to the limitations of source size.• Quantum of reproductive structure such as number of flowers is very much

reduced. • Affects the mobility of metabolites. • Hormone synthesis is hampered• Seed oil content decreases

Effect of salt stress on crop growth & development

MorphologicallyStuntedChlorosisWiltedSenescence

Physiologically Lowering of osmotic pressure,Lowering antioxidants

Genetically by biosynthesis of specific proteins for salt stress

Salt tolerance degree of some important crops

Crop Threshold salinity level (EC ds/m)

Tolerant crops

Barley 8.0

Sugar beet 7.0

Moderately tolerant crops

Soybean 5.0

Cowpea 4.9

Moderately sensitive crops

Rice 3.0

Tomato 2.5

Sensitive crops

Orange 1.7

Bean 1.0

(Ashraf & Wu, 1994)

A soybean salt-tolerant plant compared to a non-tolerant variety

(Guan et al. 2014)

Important genes mapped in soybean

Trait GeneAphid Resistance Rag1Bacterial Blight Rpg1,Rpg4 Salt tolerance GmDREBa, GmDREBb,

GmDREBc, GmSALT3 ,Ncl2Fatty acid(Linolenic acid) GmFAD3,Fan FasFlower color W1,Wp,gmfls1Salt stress GmPAP3,GmCAX1Soybean mosaic virus Rsv1,Rsv4Soybean rust Rpp1

Some of the salt tolerant varieties /lines of different crops

Crops Salt tolerant varieties/linesBarley Selection from composite cross XXI

Rice Pokkali, Johna 349, Kala rata, Damodar, Benisail, Nonabokra

Sorghum Double TX

Tomato Selection line from the cross L. esculentum × L. cheesmanii

Wheat Kharchia, LU-26S Accessions 178704,178012,180988

Soybean S-100, Lee, Tiefeng 8, Wenfeng 7, Jindou, Wild Soybean Accession PI483463

Salinity condition in Korea Why salinity tolerant soybean in Korea?

• Reclaimed tidal lands that locate mainly in west and south coastal areas of Korean peninsula are approximately 350,000 ha, which occupy about 21% of arable lands for crop production (Lee et. al., 2013).

• The importance of reclaimed tidal lands is gradually increasing in Korea because stable food production is fundamental in response to increasing world population and improvement of living standard (UN, 2013).

• Reclamation and preventable measures for transforming salt affected lands into arable land are very expensive.

• Breeding approach to overcome salinity problems seems to be the only economic and efficient alternative.

Breeding Strategies for salinity tolerance in soybean Conventional Breeding• Introduction• Selection(Mass

selection/Pure line Selection) • Hybridization

Pedigree Bulk method SSD method Back cross Multiple crossing

Molecular Breeding• Marker Assisted Selection

(MAS)• Marker Assisted Backcross

(MABC)• Marker Assisted Pyramiding• Marker Assisted Recurrent

Selection (MARS)• Quantitative Trait Loci (QTL)• Genomic Selection

What is Marker Assisted Selection (MAS)?

A process whereby a marker is used for selection of a genetic determinants of a trait of interest like disease resistance, tolerance to abiotic stresses and quality traits.

First direct benefit that breeders obtained from genomics and being applied successfully in molecular breeding for genetic improvements of many major crops including soybean.

MAS can enhance conventional breeding in early selection of traits independent to season and location for the trait gene pyramiding recovery of recurrent parent selection of parental lines with wider genetic base monitoring seed purity and germplasm identity

Types of markers: RFLPs, SCARs, STS, SSRs & more recently SNPs .

• There is complex polygenic trait controlling stress tolerance, however salt tolerance in soybean is a single dominant gene.

• Abel (1969) reported that a single dominant gene controlled salt tolerance in the soybean cultivar Lee which is derived from S-100 × CNS with S-100.

• Lee JD et al. (2009)  identified one major QTL Ncl2 in G. soja line PI483463 for salt tolerance, which was associated with markers sat_091, satt237 and satt339 on linkage group N (Chr. 3).

Breeding Strategies contd….

• For hybridisation, modest resistance species closer to the cultivated crops should be chosen in the context of stress tolerance (not only salinity tolerance) as ecological adaptations and agronomic objectives need to be mutually inclusive.

• For breeding of soybean salinity tolerant ‘Daepung2ho’ and ‘Uram’ cultivars are taken as recurrent parent and Wild Soybean (Glycine soja Sieb. and Zucc.) Accession PI483463 is taken as donor parent.

• Daepung2ho is a cultivar of the highest yield (3450 Kg/ha) in Korea which is tolerant to lodging, fire blight and seed shattering.

• Uram is another high yield cultivar (3270 Kg/ha) and has merits of suitability to mechanized farming and fire blight resistance (RDA 2011).

Breeding Strategies contd….

Bulk method

Line PI483463 Daepung2ho/Uram (Donor parent) (Recurrent parent)

F2

F3

F1

F4……

….…

..

F7 (Preliminary Yield Trials)

Multi location trial and yield and other traits evaluation

Release new salinity tolerant line/variety

(Reclaimed tidal lands)

Grown in naturally saline field conditions

Backcross method Salt tolerant Line PI483463(P1 ) X Daepung2ho/Uram (P2)

1st Backcross( 50% genes from P2)

F1 X Daepung2ho/Uram

2nd Backcross( 75% genes from P2)

BC1 X Daepung2ho/Uram

3rd Backcross( 87.5% genes from P2)

BC2X Daepung2ho/Uram

4th Backcross( 93.75% genes from P2)

BC3X Daepung2ho/Uram

5th Backross(96.875% genes from P2)

BC4

Self replication(Homogygous with P2)

BC4F2

Preliminary trial BC4F2 lines are evaluated for important characters in comparison with the recurrent parent(P2)

Multi-location trial Grow in different reclaimed tidal lands that locate mainly in west and south coastal areas of Korea

Grown in naturally saline field conditions

(High yielding cultivars in korea)

Backcrossing by molecular marker

DNAMarker

PI483463 Daepung2ho/Uram

F1

NCL2 ncl2F1

PI483463 (P1) X Daepung2ho/Uram (P2)(Non-recurrent parent) (Recurrent parent)

BC1F1

P2X

P2X

BC2F1 P2X

BCnF1Segregation in BCnF2 line

NCL2NCL2 NCL2ncl2 ncl2ncl2 NCL2NCL2 NCL2NCL2 NCL2ncl2 ncl2ncl2 NCL2NCL2 NCL2NCL2 NCL2ncl2Test for the presence of the homozygosis alleles from the donor

In each BC generation test whether the parents are true BC or maternal self

In each BC generation test presence of the desirable alleles of the parents.

single dominant gene Ncl2

NCL2ncl2

Grown in naturally saline field conditions

Multi-location trials in reclaimed tidal land

• Reclaimed tidal lands of South Korea are Hwaseong, Saemangeum and Yongsan-gang area. (Lee et al., 2014)

Hwaseong Saemangeum Yongsan gang

• Many arable land are being lost from crop production due to increasing soil salinity.

• Genes for salt tolerance of plant have been identified by molecular analysis.

• Development of salt tolerant cultivars becomes increasingly important as a means of combating salt-related yield losses.

• The greatest advancement in the genomic tools is the use of molecular markers for MAS

• In addition to conventional breeding techniques various modern genetic engineering techniques and recombinant DNA techniques may have role in the crop salinity tolerance.

Conclusion

ReferencesAbel GH. Inheritance of the capacity for chloride inclusion and chloride exclusion by soybeans. Crop Sci 1969;9:697-

698.Abel GH, MacKenzie AJ (1964) Salt tolerance of soybean varieties (Glycine max L. Merrill) during germination and later growth.

Crop Sci 14:157–161Ahmad S. (1990). Soil salinity and water management. In proceedings of the Indo-Pak workshop on soil salinity and

water management. pp.3-18 (PARC:Islamabad)Ashraf M (1994). Breeding for salinity tolerance in plants. Crit. Rev. Plant Sci. 13, 17–42.Blumwald E., Grover, A., 2006, Salt tolerance, in: Plant Biotechnology: Current and future uses of genetically modified

crops, Nigel G. Halford, eds., John Wiley and Sons Ltd, UK, pp. 206–224.Food and Agriculture Organization 2016Lee JD, Shannon JG, Vuong TD, Nguyen HT (2009) Inheritance of salt tolerance in wild soybean (Glycine soja Sieb.

and Zucc.) Accession PI483463. Journal of Heredity 100: 798–801.Lee, K.B., Hwang, S.W., Kim, H.K., Kang, J.G., Bae, H.S., Lee, S.H and Park, K.H. (2013) Soil Characteristic

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Northcote,K.h., and Skene, J.K.M. (1972). Australian soils with saline and sodic properties. Soil publication No. 27. CSIRO Australia, Melbourne.

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Guan R., Qu, Y. Guo Y, Yu L., Liu Y., Jiang J, Chen J., Ren Y, Liu G., Tian L, Jin L., Liu Z., Hong H., Chang R. , Gilliham M., Qiu L. 2014. Salinity tolerance in soybean is modulated by natural variation in GmSALT3.

United Nations (2013) World Population Prospects.Wen-Jie Zhang , Yuan Niu , Su-Hong Bu , Meng Li , Jian-Ying Feng, Jin Zhang, Sheng-Xian Yang 2014,Epistatic

Association Mapping for Alkaline and Salinity Tolerance Traits in the Soybean Germination Stage.

Thank you all for your Kind attention