**Table 3.** *List of traits, donors, QTLs/genes, and markers associated used in crossing program for the development of climate resilient lines at IRRI, Philippines.*

**379**

*Advances in Developing Multigene Abiotic and Biotic Stress-Tolerant Rice Varieties*

inferior plant type can be rejected for further advancement.

**6. Role of genomic selection in multiple-trait breeding**

of introgression lines pyramided with various drought grain yield QTLs in rice [128–131]. In some cases, epistatic interactions between different loci can enhance or reduce the effect of some of the genes/QTLs. Under such a situation, as an alternative strategy of identifying and advancing lines with different combinations of genes/QTLs- six, seven, or eight for different stresses and showing higher grain yield under nonstress conditions will also be selected and the best combinations that will show tolerance of a maximum number of abiotic and biotic stresses and the highest yield advantage will be advanced for testing. Plants carrying maximum number QTLs/gene but having negative interaction with grain yield and showing

Maintenance of larger population size could also be a feasible strategy which can allow to select rare recombinants having maximum number of targeted QTLs/genes and also free from undesirable linkages. In previous studies, drought tolerant rice lines were developed through successful breakage of the linkages between loci for tolerance to drought and undesirable traits by fine mapping and maintain huge population

Genomic selection (GS) in crop plants facilitates the rapid selection of superior accessions/genotypes and accelerate the breeding cycle targeted for higher genetic gain. It aims to use the genome-wide markers to predict the effects of all associated loci. The developed best prediction model is applied to the tested breeding material which has been charactized only genotypically but not phenotypically. The breeding estimated value called as GEBV (genomic estimated breeding value). The parental lines with higher GEBV can be selected as the candidate lines for future breeding programs. Most of the previous studied in cereal crops has shown great potential for GS to enhance the selection for grain yield and yield related traits [133, 134]. Multi trait genomic selection can be also implemented on phenotypic data of multiple traits *viz.* grain quality traits, grain yield and yield components, and reaction to the biotic and abiotic stresses, however it is important that a favorable genetic correlation exists

between traits to implement genomic prediction model effectively [135, 136].

To solve the global issue of food security in the era of changing climate, novel approaches involving successful stacking of multiple genes/QTLs in a single rice line utilizing strategic phenotypic-genotypic selection could provide opportunity targeting genetic gain in rice. New advances in hybridization stratgies, genom

ics, marker development, and sequencing permitted the opportunity to create muti-gene carrying high-yielding rice varieties to combat multiple stresses. The development of rice varieties carrying multiple QTLs/genes in homozygous conditions can address the production constraints faced due to both biotic and abiotic stresses simultaneously. These stress-tolerant rice varieties with desired grain quality can greatly help farmers in improving productivity under multiple

The authors declare that they have no conflict of interest.


*DOI: http://dx.doi.org/10.5772/intechopen.93751*

size [132].

**7. Conclusions**

stress conditions.

**Conflict of interest**

#### *Advances in Developing Multigene Abiotic and Biotic Stress-Tolerant Rice Varieties DOI: http://dx.doi.org/10.5772/intechopen.93751*

of introgression lines pyramided with various drought grain yield QTLs in rice [128–131]. In some cases, epistatic interactions between different loci can enhance or reduce the effect of some of the genes/QTLs. Under such a situation, as an alternative strategy of identifying and advancing lines with different combinations of genes/QTLs- six, seven, or eight for different stresses and showing higher grain yield under nonstress conditions will also be selected and the best combinations that will show tolerance of a maximum number of abiotic and biotic stresses and the highest yield advantage will be advanced for testing. Plants carrying maximum number QTLs/gene but having negative interaction with grain yield and showing inferior plant type can be rejected for further advancement.

Maintenance of larger population size could also be a feasible strategy which can allow to select rare recombinants having maximum number of targeted QTLs/genes and also free from undesirable linkages. In previous studies, drought tolerant rice lines were developed through successful breakage of the linkages between loci for tolerance to drought and undesirable traits by fine mapping and maintain huge population size [132].

#### **6. Role of genomic selection in multiple-trait breeding**

Genomic selection (GS) in crop plants facilitates the rapid selection of superior accessions/genotypes and accelerate the breeding cycle targeted for higher genetic gain. It aims to use the genome-wide markers to predict the effects of all associated loci. The developed best prediction model is applied to the tested breeding material which has been charactized only genotypically but not phenotypically. The breeding estimated value called as GEBV (genomic estimated breeding value). The parental lines with higher GEBV can be selected as the candidate lines for future breeding programs. Most of the previous studied in cereal crops has shown great potential for GS to enhance the selection for grain yield and yield related traits [133, 134]. Multi trait genomic selection can be also implemented on phenotypic data of multiple traits *viz.* grain quality traits, grain yield and yield components, and reaction to the biotic and abiotic stresses, however it is important that a favorable genetic correlation exists between traits to implement genomic prediction model effectively [135, 136].

#### **7. Conclusions**

*Abiotic Stress in Plants*

[40, 117,

121]

[117, 122]

**378**

**Trait** Biotic stress

Blast Bacterial leaf

IRBB60,

*Xa4, xa5, xa13, Xa21, Xa23*

blight

Brown plant

Rathu Heenati

*Bph3, Bph17*

*Gm4*

hopper

Gall midge Abiotic stress

Drought +

IR96322-34-223-B

*qDTY*1.1 *+ qDTY*2.1 *+ qDTY*3.1 *+ Sub1*

snpOS0074 (G)

*qDTY*1.1: RM431, RM11943, RM12233(linked markers), snpOS0071 (A),

[19, 117]

*qDTY*2.1: RM324, RM3549, RM12868, RM12987, RM12995(linked

markers), snpOS0078 (A), snpOS0079 (A)

*qDTY*3.1: RM520, RM16030, RM416(linked markers), snpOS0085 (G),

snpOS0089 (C)

*Sub1:* ART5, snpOS0040 (T)

RM28099, RM28166, Indel 8, SnpOS00483(G), SnpOS00484(A)

*qCTS4a:* RM349, RM17604, RM17623, RM3648, RM2799

*qCTS11:* RM26889, RM21, RM206

id4005120, id4011562

G11A, AP3206, RM3412, RM493

[77, 117]

[125, 126]

[104]

[110, 127]

submergence

Drought

Cold Heat Salinity

**Table 3.**

IR74371-46-1-1

IR 83222-8-1-1-1-1-1-1-1, IR 66160-

121-4-4-2, HGKN

N22/IR64 Pokkali/IR29

*qDTY*12.1 *qCTS4a, qCTS11.1*

*qHTSF4.1, qHTSF4.2*,

*Saltol* *List of traits, donors, QTLs/genes, and markers associated used in crossing program for the development of climate resilient lines at IRRI, Philippines.*

Abhaya

WHD-1S-75-1-127, Tadukan, IRBL9

*Pi9*, *Pita2*

**Donor**

**QTLs/genes**

**Markers (SNPs/Indels/SSRs/gene based markers)**

*Pi9: Pi9*STS2, Pi9-659T, Pi9-1477G, MSU7\_6\_10381500 (M492 + M493),

M891 (C), Pi9-659T, Pi9-1477G

YL87, YL153/YL154

*Xa4:* snpOS0054 (AG), RM224, MP1 + MP2

*xa5: xa5S*, *xa5R, xa5*DRR

147/*xa13* R\_1678-1662

pTA248

*xa13: xa13*-promoter (M478Lm + M479Lm + M480Lm), *xa13*F\_130-

*Xa21:* Xa21s\_exon (M769 + M770), snpOS0061 (C), U1/I1, M1207 (T),

RM589,RM586,RM190, RM8213, RM16556, RM586, RM589, RM190,

[14, 117,

123]

[49, 117,

124]

RM7639, RM19311(linked markers)

GM4\_LRR-del\_F, GM4\_LRR-del\_R

*Pita2:* MSU7\_12\_9177624 (M535 + M536), SnpOS00488(G), YL155/

**Reference**

To solve the global issue of food security in the era of changing climate, novel approaches involving successful stacking of multiple genes/QTLs in a single rice line utilizing strategic phenotypic-genotypic selection could provide opportunity targeting genetic gain in rice. New advances in hybridization stratgies, genomics, marker development, and sequencing permitted the opportunity to create muti-gene carrying high-yielding rice varieties to combat multiple stresses. The development of rice varieties carrying multiple QTLs/genes in homozygous conditions can address the production constraints faced due to both biotic and abiotic stresses simultaneously. These stress-tolerant rice varieties with desired grain quality can greatly help farmers in improving productivity under multiple stress conditions.

#### **Conflict of interest**

The authors declare that they have no conflict of interest.

*Abiotic Stress in Plants*

#### **Author details**

Nitika Sandhu1,2, Shailesh Yadav2,3 and Arvind Kumar2,3\*

1 Punjab Agricultural University, Ludhiana, Punjab, India

2 International Rice Research Institute, Philippines

3 IRRI South Asia Regional Centre (ISARC), Varanasi, Uttar Pradesh, India

\*Address all correspondence to: a.kumar@irri.org

© 2020 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/ by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

**381**

*Advances in Developing Multigene Abiotic and Biotic Stress-Tolerant Rice Varieties*

agriculture: A review. Agronomy for Sustainable Development. 2014;**34**:707- 721. DOI: 10.1007/s13593-014-0245-2

[8] McDonald A, Riha S, DiTommaso A, DeGaetano A. Climate change and the geography of weed damage: Analysis of US maize systems suggests the potential for significant range transformations.

Environment. 2009;**130**(3-4):131-140. DOI: 10.1016/j.agee.2008.12.007

[9] Jedmowski C, Ashoub A, Momtaz O, Brüggemann W. Impact of drought, heat, and their combination on chlorophyll fluorescence and yield of wild barley (*Hordeum spontaneum*). Journal of Botany. 2015;**9**:120868. DOI:

[10] Duveiller E, Singh RP, Nicol JM. The challenges of maintaining wheat productivity: Pests, diseases, and potential epidemics. Euphytica. 2007;**157**(3):417-430. DOI: 10.1007/

[11] Khush GS. Strategies for increasing the yield potential of cereals: Case of rice as an example. Plant Breeding. 2013;**132**(5):433-436. DOI: 10.1111/

[12] Sasaki T, Burr B. International Rice genome sequencing project: The effort to completely sequence the rice genome. Current Opinion in Plant Biology. 2000;**3**(2):138-142. DOI: 10.1016/

[13] Thirze H. Modelling grain surplus and deficit in Cameroon for 2030 [Master's thesis]. Lund, Sweden: Lund

[14] Dixit S, Singh UM, Singh AK, Alam S, Venkateshwarlu C,

Nachimuthu VV, et al. Marker assisted forward breeding to combine multiple biotic-abiotic stress resistance/tolerance

Agriculture, Ecosystems and

10.1155/2015/120868

s10681-007-9380-z

S1369-5266(99)00047-3

University; 2016. p. 59

pbr.1991

*DOI: http://dx.doi.org/10.5772/intechopen.93751*

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*Advances in Developing Multigene Abiotic and Biotic Stress-Tolerant Rice Varieties DOI: http://dx.doi.org/10.5772/intechopen.93751*

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*Abiotic Stress in Plants*

**380**

**Author details**

Nitika Sandhu1,2, Shailesh Yadav2,3 and Arvind Kumar2,3\*

1 Punjab Agricultural University, Ludhiana, Punjab, India

3 IRRI South Asia Regional Centre (ISARC), Varanasi, Uttar Pradesh, India

© 2020 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/ by/3.0), which permits unrestricted use, distribution, and reproduction in any medium,

2 International Rice Research Institute, Philippines

\*Address all correspondence to: a.kumar@irri.org

provided the original work is properly cited.

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[7] Peters K, Breitsameter L, Gerowitt B. Impact of climate change on weeds in

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[12] Sasaki T, Burr B. International Rice genome sequencing project: The effort to completely sequence the rice genome. Current Opinion in Plant Biology. 2000;**3**(2):138-142. DOI: 10.1016/ S1369-5266(99)00047-3

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[18] Das G, Rao GJ, Varier M, Prakash A, Prasad D. Improved Tapaswini having four BB resistance genes pyramided with six genes/QTLs, resistance/ tolerance to biotic and abiotic stresses in rice. Scientific Reports. 2018;**8**:2413. DOI: 10.1038/s41598-018-20495-x

[19] Sandhu N, Dixit S, Swamy BP, Raman A, Kumar S, Singh SP, et al. Marker assisted breeding to develop multiple stress tolerant varieties for flood and drought prone areas. Rice. 2019;**12**:8. DOI: 10.1186/

[20] Muthu V, Abbai R, Nallathambi J, Rahman H, Ramasamy S, Kambale R, et al. Pyramiding QTLs controlling tolerance against drought, salinity, and submergence in rice through marker assisted breeding. PLoS One. 2020;**15**:1- 18. DOI: 10.1371/journal.pone.0227421

[21] Mew TW, Vera Cruz CM,

Medalla ES. Changes in race frequency of Xanthomonas oryzae pv. Oryzae in response to rice cultivars planted

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in the Philippines. Plant Disease.

[23] Ou SH. Rice Diseases. 2nd ed. Kew, Surrey (GB): Commonwealth

[24] Neelam K, Mahajan R, Gupta V, Bhatia D, Gill BK, Komal R, et al. Highresolution genetic mapping of a novel bacterial blight resistance gene xa-45 (t) identified from *Oryza glaberrima* and transferred to *Oryza sativa*. Theoretical and Applied Genetics. 2020;**133**(3):689- 705. DOI: 10.1007/s00122-019-03501-2

[25] Cheema KK, Grewal NK, Vikal Y, Sharma R, Lore JS, Das A, et al. A novel bacterial blight resistance gene from *Oryza nivara* mapped to 38 kb region on chromosome 4L and transferred to *Oryza sativa* L. Genetics Research. 2008;**90**(5):397-407. DOI: 10.1017/

[26] Sun X, Yang Z, Wang S, Zhang Q. Identification of a 47-kb DNA fragment containing Xa4, a locus for bacterial blight resistance in rice. Theoretical and Applied Genetics. 2003;**106**(4):683-687.

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[112] Septiningsih EM, Pamplona AM, Sanchez DL, Neeraja CN, Vergara GV, Heuer S, et al. Development of submergence-tolerant rice cultivars: The Sub1 locus and beyond. Annals of Botany. 2009;**103**(2):151-160. DOI:

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conventional and molecular approaches.

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*Abiotic Stress in Plants*

QTL to variety-harnessing the benefits of QTLs for drought, flood and salt tolerance in mega rice varieties of India through a multi-institutional network. Plant Science. 2016;**242**:278-287. DOI:

[103] Ye C, Argayoso MA, Redoña ED, Sierra SN, Laza MA, Dilla CJ, et al. Mapping QTL for heat tolerance at flowering stage in rice using SNP markers. Plant Breeding. 2012;**131**(1):33-41. DOI:

10.1111/j.1439-0523.2011.01924.x

s00122-015-2526-9

s12284-017-0167-0

s00122-006-0311-5

s11032-007-9096-8

BF00564199

[104] Ye C, Tenorio FA, Redoña ED, Morales-Cortezano PS, Cabrega GA, Jagadish KS, et al. Fine-mapping and validating qHTSF4. 1 to increase spikelet fertility under heat stress at flowering in rice. Theoretical and Applied Genetics. 2015;**128**(8):1507-1517. DOI: 10.1007/

[105] Shanmugavadivel PS, Sv AM, Prakash C, Ramkumar MK, Tiwari R, Mohapatra T, et al. High resolution mapping of QTLs for heat tolerance in rice using a 5K SNP array. Rice. 2017;**10**(1):28. DOI: 10.1186/

[106] Andaya VC, Tai TH. Fine mapping of the qCTS12 locus, a major QTL for seedling cold tolerance in rice. Theoretical and Applied Genetics. 2006;**113**(3):467-475. DOI: 10.1007/

[107] Andaya VC, Tai TH. Fine mapping of the qCTS4 locus associated with seedling cold tolerance in rice (*Oryza sativa* L.). Molecular Breeding. 2007;**20**(4):349-358. DOI: 10.1007/

[108] Xu K, Mackill DJ. A major locus for submergence tolerance mapped on rice chromosome 9. Molecular Breeding.

1996;**2**(3):219-224. DOI: 10.1007/

[109] Neeraja CN, Maghirang-Rodriguez R, Pamplona A, Heuer S, Collard BC, Septiningsih EM, et al. A marker-assisted backcross approach for developing submergence-tolerant rice cultivars. Theoretical and Applied Genetics. 2007;**115**(6):767-776. DOI:

10.1007/s00122-007-0607-0

10.1016/j.plantsci.2015.08.008

10.1155/2018/8319879

[99] Babu NN, Vinod KK,

[100] Bhandari A, Jayaswal P, Yadav N, Singh R, Singh Y, Singh B, et al. Genomics-assisted backcross breeding for infusing climate resilience in high-yielding green revolution varieties of rice. Indian Journal of Genetics and Plant Breeding. 2019;**79**(1):160-170. DOI: 10.31742/

[101] Stocker TF, Qin D, Plattner GK, Tignor M, Allen SK, Boschung J, et al. Climate change 2013: The physical science basis. In: Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate

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IJGPB.79S.1.5

Change. 2013. p. 1535

2008;**36**:15811-15813

Krishnamurthy SL, Krishnan SG, Yadav A, Bhowmick PK, et al. Microsatellite based linkage

disequilibrium analyses reveal Saltol haplotype fragmentation and identify novel QTLs for seedling stage salinity tolerance in rice (*Oryza sativa* L.). Journal of Plant Biochemistry and Biotechnology. 2017;**26**(3):310-320. DOI: 10.1007/s13562-016-0393-3

[98] Singh VK, Singh BD, Kumar A, Maurya S, Krishnan SG, Vinod KK, et al. Marker-assisted introgression of Saltol QTL enhances seedling stage salt tolerance in the rice variety "Pusa Basmati 1". International Journal of Genomics. 2018;**2018**:1-12. DOI:

**388**

[111] Gregorio GB, Senadhira D, Mendoza RD, Manigbas NL, Roxas JP, Guerta CQ. Progress in breeding for salinity tolerance and associated abiotic stresses in rice. Field Crops Research. 2002;**76**(2-3):91-101. DOI: 10.1016/ S0378-4290(02)00031-X

[112] Septiningsih EM, Pamplona AM, Sanchez DL, Neeraja CN, Vergara GV, Heuer S, et al. Development of submergence-tolerant rice cultivars: The Sub1 locus and beyond. Annals of Botany. 2009;**103**(2):151-160. DOI: 10.1093/aob/mcn206

[113] Kumar A, Dixit S, Ram T, Yadaw RB, Mishra KK, Mandal NP. Breeding high yielding drought-tolerant rice: Genetic variations and conventional and molecular approaches. Journal of Experimental Botany. 2014;**65**(21):6265-6278. DOI: 10.1093/ jxb/eru363

[114] Thomson MJ, Ocampo D, Egdane J, Katimbang M, Singh R, Gregorio G, et al. QTL mapping and marker-assisted backcrossing for improved salinity tolerance in rice. BioAsia. 2007;(Supplement Papers):6-12

[115] Collard BCY, Mackill DJ. Markerassisted selection: An approach for precision plant breeding in the 21st century. Philosophical Transactions of the Royal Society, B: Biological Sciences. 2008;**363**(1491):557-572. DOI: 10.1098/ rstb.2007.2170

[116] Khanna A, Sharma V, Ellur RK, Shikari AB, Krishnan SG, Singh UD, et al. Development and evaluation of near-isogenic lines for major blast resistance gene (s) in basmati rice.

Theoretical and Applied Genetics. 2015;**128**(7):1243-1259. DOI: 10.1007/ s00122-015-2502-4

[117] Yadav S, Sandhu N, Dixit S, Singh VK, Catolos M, Mazumder RR, Rahman MA, Kumar A. 2020. Genomics-Assisted Breeding Enables Successful Development of Multiple Stress Tolerant Climate Smart Rice for South and South East Asia. Communicated

[118] Bandillo N, Raghavan C, Muyco PA, Sevilla MA, Lobina IT, Dilla-Ermita CJ, et al. Multi-parent advanced generation inter-cross (MAGIC) populations in rice: Progress and potential for genetics research and breeding. Rice. 2013;**6**(1):11. DOI: 10.1186/1939-8433-6-11

[119] Sandhu N, Yadav S, Catolos M, Cruz MTS, Kumar A. Developing Climate-Resilient, Direct-Seeded Adapted Multiple-Stress Tolerant Rice Applying Genomic Assisted Breeding. 2020

[120] Sagare DB, Abbai R, Jain A, Kj P, Dixit S, Singh AK, et al. More and more of less and less: Is genomics based-breeding of dry direct seeded rice (DDSR) varieties the need of hour? Plant Biotechnology Journal. 2020;**18**:2173-2186. DOI: 10.1111/ pbi.13454

[121] Koide Y, Kobayashi N, Xu D, Fukuta Y. Resistance genes and selection DNA markers for blast disease in rice (*Oryza sativa* L.). Japan Agricultural Research Quarterly. 2009;**43**(4):255-280

[122] Song WY, Pi LY, Wang GL, Gardner J, Holsten T, Ronald PC. Evolution of the rice *Xa21* disease resistance gene family. The Plant Cell. 1997;**9**(8):1279-1287

[123] Jairin J, Phengrat K, Teangdeerith S, Vanavichit A, Toojinda T. Mapping of a broad-spectrum brown planthopper

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**391**

salinity, sodicity

**Chapter 19**

Review

**Abstract**

Salt Stress in Plants and

*Sajal Roy and Nasrin Chowdhury*

Amelioration Strategies: A Critical

High salt concentration in soil is a major abiotic stress, which adversely influences the growth, overall development, and productivity of crops. More than 20% of the land of the world used for crop production is adversely affected by high salt concentration. The problem of salt stress becomes a major concern when previously fertile, productive agricultural lands are salinized more profoundly as a result of anthropogenic activities along with natural causes. Therefore, this review is focused on various aspects of salt-affected soils (SAS), their effects on plants, and different approaches for reclamation of SAS to enhance the potentiality for crop production. Salt-affected soils are categorized into saline, saline-sodic, and sodic soils based on the amount of total soluble salts as expressed by electrical conductivity (EC), sodium adsorption ratio (SAR), exchangeable sodium percentage (ESP), and soil pH. The inhibition of plant growth in saline soils is mainly induced by osmotic stress; reduced uptake of essential macro- and micronutrients, including nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), iron (Fe), manganese (Mn), zinc (Zn), and copper (Cu); and specific toxicities of sodium (Na) and chloride (Cl). Sodic soils adversely affect the plant through high soil pH and poor physical condition resulting from an excessive amount of exchangeable Na. Different plants respond to salt stress in different extents. Saltaffected soils must be reclaimed to restore their productivity for increasing food production. The approaches for the management of SAS include leaching, incorporation of different organic and inorganic amendments, mulching, and development of salt-tolerant crops. The suitability of approaches depends on several considerations such as cost of reclamation, the time required, the extent of the salt stress, soil properties, availability of technology, and other environmental factors. Among different strategies, the incorporation of organic amendments is beneficial, costeffective, environment friendly, and sustainable for amelioration of salt stress and enhancement of crop production due to the extensive roles of organic amendments in improving the soil's physical (structural stability, porosity, and permeability), chemical [pH, EC, ESP, organic matter, cation exchange capacity (CEC), and Na leaching], and biological and/or biochemical (microbial abundance, microbial

activity, biomass carbon, and enzymatic activities) properties.

**Keywords:** abiotic stress, nutrient uptake, organic amendments, reclamation,

#### **Chapter 19**

*Abiotic Stress in Plants*

2007;**19**(1):35-44

2012;**184**(1):101-108

2014;**28**(6):989-998

2020;**11**:833

Warraich AS, Rathor S,

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