for the degree of m.sc. (hons.) and ph.d. in soil science · ses-706 salt-affected and waterlogged...

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CURRICULUM

(Revised)

FOR THE DEGREE OF M.Sc. (HONS.) AND Ph.D. IN

SOIL SCIENCE

Implementation Session 2016-18 and onward

DEPARTMENT OF SOIL & ENVIRONMENTAL SCIENES

UNIVERSITY COLLEGE OF AGRICULTURE

UNIVERSITY OF SARGODHA

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LIST OF POST GRADUATE COURSES IN SOIL SCIENCE

Course Code Course Title Credit Hours

SES-701 Principles and Uses of Laboratory Equipment 3(0-3)

SES-702 Soil Chemistry 3(2-1)

SES-703 Soil Fertility and Plant Nutrition 3(2-1)

SES-704 Soil Microbiology and Biochemistry 3(2-1)

SES-705 Soil Classification 3(2-1)

SES-706 Salt-Affected and Waterlogged Soils 3(3-0)

SES-707 Soil Physics 3(2-1)

SES-708 Soil Mineralogy 3(3-0)

SES-709 Soil - Plant Relationship 3(3-0)

SES-710 Principles and Applications of Bioremediation 3(3-0)

SES-711 Advanced Techniques in Bioremediation 3(3-0)

SES-712 Integrated Nutrient Management 3(3-0)

SES-713 Advanced Research Methods and Technical Writing 3(3-0)

SES-714 Organic Agriculture 3(2-1)

SES-715 Advanced Soil Chemistry 3(3-0)

SES-716 Advanced Soil Fertility 3(3-0)

SES-717 Advanced Soil Microbiology 3(3-0)

SES-718 Advanced Soil Physics 3(3-0)

SES-719 Special Problem 1(1-0)

SES-720 Seminar 1(1-0)

SES-721 Soil Ecology 3(3-0)

SES-722 Soil Quality and Management 3(3-0)

SES-723 Nutrient Acquisition and Transport 3(3-0)

SES-724 Biochar: Concept and Application 3(3-0)

SES-725 Waste water impact on soil Health 3(2-1)

STAT-701 Statistical Methods for Agricultural Research-I

3(3-0)

STAT-702 Statistical Methods for Agricultural Research-II 3(3-0)

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Note: - Additional requirements, if nothing is contradictory to UOS existing rules &

regulations and amended from time to time:

1. Minimum credit hours for the completion of course work for M.Sc. (Hons.) and Ph.D.

degrees are 24 and 18 respectively. Whereas, a minimum of 16 and 12 credit hours must be

completed from the major courses for M.Sc. (Hons.) and Ph.D. degrees respectively.

2. Minor courses (if opted) can be taken from any department of the University of Sargodha.

However, the selection of minor courses will be upon the field of research as proposed by

the supervisor according to the area of specialization.

3. Courses selected/qualified for M.Sc. (Hons.) will not be permitted to take again in Ph.D.

except Special Problem and Seminar which are compulsory for both M.Sc. (Hons.) and

Ph.D. students; whereas Seminar will be enrolled twice for the completion of Ph.D. course

work.

4. STAT-701 and STAT-702 are compulsory courses for M.Sc. (Hons.) and Ph.D. degree

programs respectively.

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DETAIL OF COURSES SES-701 PRINCIPLES AND USES OF LABORATORY EQUIPMENT 3(0-3)

Objective and Learning Outcome

Principles, theory and operation of the advanced instruments used for soil and plant analyses are discussed. The students should be able to operate different laboratory instruments, control error, interpret the data and maintain quality of analyses.

Course Contents

1. Quality management, assurance and control measures 2. Analytical errors, analysis and control 3. Development of standard operating procedures 4. Use of basic laboratory equipment:

4.1 Spectrophotometer: UV and visible range 4.2 Flame photometer 4.3 Atomic absorption spectrophotometer 4.4 Ion meter: selective ion electrodes 4.5 EM-38 and EC probe

5. Introduction, principles and usage of specialized equipment: 5.1 Inductively coupled plasma meter and direct current plasma meter 5.2 Chromatography: GC and HPLC 5.3 Microscopy: Scanning and transmission 5.4 X-ray diffractometery 5.5 Mass spectrophotometery 5.6 Electro Ultra Filtration 5.7 Neutron moisture probe/time domain reflectrometery (TDR)

5.8 Oxygen diffusion rate meter 1.9 Thermocycler PCR (polymerase chain reaction) 1.10 Gel electrophoresis apparatus

6. Elements of analytical report writing

Books Recommended 1. DeLevie, R. 1997. Quantitative Chemical Analysis. McGraw-Hill Co. Inc.

New York, USA.

2. Harris, D.C. 2006. Quantitative Chemical Analysis. 7th Ed. W. H. Freeman

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& Co. NY, USA.

3. Pansu, M. and J. Gautheyrou. 2006. Handbook of Soil Analysis. Avenue de Marinville 6 94100 St. Maur des Fossés France. ISBN-10 3-540-31210-2 Springer Berlin Heidelberg New York ISBN-13 978-3-540-31210-9 Springer Berlin Heidelberg New York.

4. Smith, A. K. and M.S. Cresser. 2004. Soil and Environmental Analysis: Modern Instrumental Techniques. 3rd Ed., Marcel & Dekker, Inc., USA.

5. Spark, D.L. (ed.) 1996. Methods of Soil Analysis. Part.3. Chemical Methods. SSSA, ASA Series No.5. Madison, WI, USA.

SES-702 SOIL CHEMISTRY 3(2-1)


Principles governing ion exchange, retention, chemical equilibria for precipitation & synthesis and chemical remediation processes in soil are discussed. The students should be able to predict release of ions and fate of chemicals in soil by using models.

Course Contents

1. Chemical equilibria in soil, water and solute interactions 2. Soil solution-solid interaction 3. Mineral dissolution: congruent and incongruent 4. Neo-formation of minerals in soil 5. Thermodynamics and applications in soil 6. Organic matter: composition and fractionation 7. Surface chemistry of soil matrix 8. Sorption and desorption models 9. Ion exchange: selectivity coefficients, equivalent fraction concept

9.1 Hysteresis in ion exchange 9.2 Anion exclusion 9.3 Complementation effect 9.4 Zeta potential

10. Reactions of metal chelates in soils 11. Chemical behavior of ions / elements in aerated and submerged soils 12. Buffering reactions in soil 13. Chemical remediation of contaminated soils and water

Practical

1. Determination of CEC and base saturation

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2. Developing K vs Ca + Mg activity ratios in laboratory 3. Determination of phosphorous adsorption isotherm 4. Comparative fit (data from 3) to Freundlich and Langmuir models 5. Developing titration curves

Books Recommended 1. Bohn, H.L., B.L. McNeal and G.A.O. Connor. 2001. Soil Chemistry. 3rd Ed.

John Wiley & Sons Inc., NY, USA. 2. Essington, M. E. 2004. Soil and Water Chemistry. CRC Press, Boca Raton,

FL, USA. 3. McBride, M. 1994. Environmental Chemistry of soils. 406 pp. ISBN0-19-

507011-9. Oxford University Press. 4. Sparks, D.L. 2003. Environmental Soil Chemistry. 2nd Ed. Academic Press,

San Diego, CA, USA. 5. Sposito, G. 2008. The Chemistry of Soils. 2nd Ed. Oxford University Press,

NY, USA. 6. Sriniwas, P. 2010. Soil Chemistry. Oxford Book Company, New Delhi, India. 7. Tan, K.H. 2009. Environmental Soil Science. 3rd Ed. CRC Press,

Greenwatch Georgia, USA.

SES-703 SOIL FERTILITY AND PLANT NUTRITION 3(2-1)


Nutrient pools and dynamics in soil, uptake and translocation within the plant, their deficiencies and toxicities, interactions and fate of fertilizers are discussed. The students should be able to identify nutritional disorders, calculate fertilizer requirement and use efficiency, and understand techniques for integrated nutrient management.

Course Contents

1. Basic soil-plant-relationship in plant nutrition 2. Plant nutrient behavior in soils 3. Nutrient behavior in submerged soils 4. Soil fertility evaluation: soil test calibration and plant analysis

4.1 External and internal nutrient requirements 5. Fertilizer management strategies: nutrient availability and fertilizer

use efficiency 5.1 Fertigation and foliar fertilization 5.2 Integrated plant nutrient management (IPNM) 5.3 Variable rate fertilizer technology

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6. Nutrient-water and other interactions 7. Specific effects of fertilizers: plant, human and animal health 8. Environmental implications of fertilizer use

Practical

1. Soil and plant analysis for NPK 2. Interpretation of soil and plant analysis results 3. Create and learn deficiency symptoms of nutrients

Books Recommended 1. Ahmad, N. and M. Rashid. 2003. Fertilizers and their use in Pakistan: An

extension guide. Planning Commission, NFDC, Islamabad, Pakistan.

2. Barker A.V. and D.J. Pilbeam. 2007. Handbook of Plant Nutrition. CRC Press, Boca Raton, FL, USA.

3. Bhatti, A.U. 2005. Spatial Variability & its Management in Agriculture. Higher Education Commission, Islamabad, Pakistan.

4. Elsworth, L. and W.O. Relay (eds.). 2009. Fertilizers: Properties, Applications and Effects. Nova Science. Publ. Inc., NY, USA.

5. Havlin, J.L., S.L.Tisdale, W.L. Nelson and J.D. Beaton. 2013. Soil Fertility and Fertilizers: An Introduction to Nutrient Management. 8th ed. Pearson Education, Prentice Hall, Upper Saddle River, NJ, USA.

6. Mengel, K. and E.A. Kirkby. 2001. Principles of Plant Nutrition. 5th Ed. International Potash Inst., Bern, Switzerland.

7. Russell, E.J. 2011. The fertility of the soil. 1st Ed. Cambridge Univ. Press, UK.

SES-704 SOIL MICROBIOLOGY AND BIOCHEMISTRY 3(2-1)


Microbial mediated transformation of elements in soil, bioremediation and biotechnological approaches are discussed. The students should be able to understand and apply microbiological approaches for crop production and to safeguard the environment.

Course Contents

1. Rhizosphere: plant-microbes and microbe-microbe interactions 2. Microbial cycling of elements: macro and micronutrients and heavy metals;

agricultural and environmental significance

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3. Biochemistry and biotechnology of BNF; application in agriculture and environment

4. Mycorrhizal symbiosis 5. Plant growth regulators, phytotoxins and siderophores: microbiology and

biochemistry 6. Composting: microbiology and biotechnology; agricultural and

environmental application 7. Microbial metabolism 8. Bioremediation of contaminated soils: biodegradation and detoxification 9. Use of stable isotopes in microbiological research

10. Metabolic and nucleic acid based analysis of soil microbial diversity 11. Bio-fertilizers: present and future prospects

Practical 1. Isolation of bacteria, actinomycetes and fungi

2. Enrichment techniques 3. Organic matter decomposition rates and C:N ratio effect 4. Inoculation techniques 5. Biological N2 fixation measurement techniques

Books Recommended 1. Barton, L.L. and D.E. Northup. 2011. Microbial Ecology. John Wiley & Sons,

Inc., Hoboken, New Jersey, USA. 2. González, M.B.R. and J. González-López. 2014. Beneficial Plant-microbial

Interactions- Ecology and Applications. CRC Press, Taylor & Francis, Boca Ratoon, FL.

3. Khan, M.S., A. Zaidi, and J. Musarrat (eds.). 2009. Microbial Strategies for Crop Improvement. Springer, NY, USA.

4. Maier, R.M., I.L. Pepper and C.P. Gerba. 2009. Environmental Microbiology. 2nd Ed. Academic Press Inc., San Diego, CA, USA.

5. Paul, E.A. (ed.). 2007. Soil Microbiology, Ecology and Biochemistry. 3rd Ed. Elsevier, Oxford, UK.

6. Pommerville, J.C. 2014. Fundamentals of Microbiology. 10th Ed. Jones & Bartlett learning, Burlington, MA, USA.

7. Sylvia, D.M., J.J. Fuhrmann, P.G. Hartel, and D.V. Zuberer. 2005. Principles and Applications of Soil Microbiology. Prentice Hall International, NJ, USA.

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SES-705 SOIL CLASSIFICATION 3(2-1)


The course is aimed to develop relation among different soil categories and their importance for particular use. The students should be able to classify soils and devise strategic and efficient land use.

Course Contents

1. Concepts and importance 2. Introduction to soil taxonomy 3. Criteria of classification 4. Properties diagnostic to categories 5. Diagnostic horizons and other diagnostic properties 6. Soil moisture regimes: Classes and importance 7. Soil temperature regimes: Classes and importance 8. Categories and nomenclature 9. Keys to categories: Order, suborder, great group and sub group FAO and

other systems of classification 10. Agro ecological zones and soils of Pakistan

Practical

1. Profile description representing important soil orders

2. Classify research farm soil to sub group level.

3. Designation of genetic horizons found in Pakistan. 4. Identification of taxonomic names: orders, suborders, great groups,

subgroups, families and series

Books Recommended 1. Buol, S.W., R.J. Southard, R.C. Graham and P.A. McDaniel. 2011. Soil

Genesis and Classifications. 6th Ed. John Wiley & Sons, Inc. NY, USA

2. Eswaran, H. et al. 2003. Soil Classification: A Global Desk Reference. CRC Press. Boca Raton, FL, USA.

3. FAO. 1998. World Reference Base for Soil Resources. FAO, Rome, Italy 4. Soil Survey Division Staff. 2005. Soil Survey Manual. USDA, Washington

DC, USA. 5. Soil Survey Staff. 2010. Keys to Soil Taxonomy. 11th Ed. USDA, Washington

DC, USA. 6. USDA. 1998. Soil Taxonomy. Krieger Publishing Co., Washington DC, USA.

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SES-706 SALT-AFFECTED AND WATERLOGGED SOILS 3(3-0)


Sources, processes, accumulation and implications of excess salts and water in soil and their mitigation options are discussed in this course. The students should be able to identify sources and diagnose causes of excess salts and water, effectiveness of reclamation options and preventive measures, and select salt tolerant crops for profitable crop production.

Course Contents

1. Salt-affected and waterlogged soils in Pakistan and global perspective 2. Genesis of saline and sodic soils 3. Classification systems of salt-affected soils 4. Effects of salinity and sodicity on soil characteristics 5. Derivation and applications of Gapon equation 6. Plant responses to saline and sodic conditions 7. Amelioration strategies and economic feasibility for salt-affected soils 8. Water requirements for reclamation 9. Concept of leaching fraction and its applications 10. Soil waterlogging

10.1. Causes 10.2. Soil and plant responses 10.3. Amelioration strategies

11. Environmental and economic impacts of salinity and waterlogging

Books Recommended 1. Ghafoor, A., M. Qadir and G. Murtaza. 2004. Salt-Affected Soils: Principles

of Management. Allied Book Centre, Urdu Bazar, Lahore, Pakistan.

2. Maliwal, G.L. and L.L. Somani. 2010. Nature, Properties and Management of Saline and Alkali Soils. Agrotech Publishing Academy, Udaipur, India.

3. Pessarakli, M. (ed.). 2010. Hand Book of Plant and Crop Stress. 3rd Ed. Marcel & Dekker Inc., NY, USA.

4. Pierzynski, G.M., J.T. Sims and G.F. Vance. 2000. Soils and Environmental Quality. CRC Press. Boca Raton, FL, USA.

5. Schjonning, P., S. Elmholt and B.T. Christensen. 2004. Managing Soil Quality Challenges in Modern Agriculture. CABI Publisher Cambridge, MA, USA.

6. Singh, N.T. 2005. Irrigation and Soil Salinity in the Indian Subcontinent: Past and Present. Lehigh University Press, Bethlehem, Israel.

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SES-707 SOIL PHYSICS 3(2-1)


Physical processes of water, air, heat and pollutants movement in soil and their management are taught. The students should be able to understand soil physical conditions for optimal plant growth.

Course Contents

1. Soil physical properties and inter-relationships 2. Nature and physical behavior of clay and clay minerals 3. Properties of water: Molecular, fluid and colligative 4. Soil water potential and its components 5. Measurement of water in soil 6. Water characteristics curves: Hysteresis 7. Saturated and unsaturated water flow 8. Infiltration models: Horton, Kostiakov, Green and Ampt, and Philip’s

8.1 Flow in capillary tubes: Poiseuilles’ law 8.2 Extended Darcy’s law and its application 8.3 Richards equations for transient water flow

9. Free and artificial drainage: Drainage design equations 10. Heat flow in soil: Thermal properties; Factor affecting; heat flow equations 11. Transport of gases and water vapors through soil 12. Solute transport in soil; Solute conservation equation, convection-

dispersion equation 12.1. Miscible displacement and breakthrough curves 12.2 Transport of inert, non-adsorbing and adsorbing chemicals in soil 12.3 Volatile organic compounds transport in soil

13. Estimation of crop water requirement

Practical

1. Measurement of soil water, soil strength, particle density, soil water characteristic curves, infiltration rate and saturated hydraulic conductivity

2. Problem sets

Books Recommended 1. Hillel, D. 1998. Environmental Soil Physics. Elsevier Academic Press, San

Diego, CA, USA. 2. Hillel, D. 2004. Introduction to Environmental Soil Physics. Elsevier

Academic Press, San Diego, CA, USA. 3. Hillel, D. 2008. Soil in the Environment: Crucible of Terrestrial Life. Elsevier

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Inc., Burlington, MA, USA. 4. Jury, W.A. and R. Horton. 2004. Soil Physics. 5th Ed. John Wiley & Sons,

Inc., NY, USA. 5. Marshall, T.J., J.W. Holmes and C.W. Rose. 1996. Soil Physics. 3rd Ed.

Cambridge University Press, Cambridge, UK.

SES-708 SOIL MINERALOGY 3(3-0)


Soil minerals’ structural properties, occurrence, identification and their role in nutrient chemistry, crop production, pollutant stabilization and engineering. The students should be able to understand and interpret mineral composition and its role in nutrient availability and structural stability.

Course Contents

1. Concept and significance 2. Chemical and structural classification of soil minerals 3. Carbonate, sulphate, sulphide and phosphate minerals 4. Oxides and hydroxide of Al, Fe and Mn 5. Phyllosilicate in soils: structure and morphological characteristics 6. Kaolin, halloysite and serpentine minerals 7. Allophane and imogolite 8. Micas: structures, weathering and effect on K availability 9. Vermiculite: structure and properties in relation to K/NH4 10. Smectites: structure and properties in relation to CEC 11. Chlorites and Inter-stratification in layer silicates 12. Tectosilicates: feldspar, quartz and zeolite 13. Clay mineral economy of Pakistan 14. Impacts of soil minerals composition on environment

Books Recommended 1. Akhtar, M.S. 2001. Soil mineralogy. In: Bashir, E. and R. Bantel (eds.).

Soil Science. National Book Foundation, Islamabad, Pakistan. 2. Brindley, G.W. and G. Brown. 1984 Crystal Structures of Clay Minerals and

their X-ray Identification. Mineralogical Soc. Monograph No.5. London, U.K. 3. Dixon, J.B. and S.B. Weed (eds.), 1989. Minerals in Soil Environment. 2nd

Ed., SSSA. Madison, WI, USA. 4. Dixon, J.B. and D.G. Schulze. 2002. Soil Mineralogy with Environmental

Applications. Soil Science Society of America, Madison, WI, USA. 5. Recent literature

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SES-709 SOIL-PLANT RELATIONSHIP 3(3-0)


The course is designed to address the intricacies of soil and plant relations for crop production. The students should be able to understand hypoxia and salinity interactive effect on plant growth and importance of mycorrhizae, water and nutrient uptake and translocation to aerial parts.

Course Contents

1. Soil-plant-environment relationship

2. Plant root system: growth distribution, forms and factors affecting; Root hairs and CEC of roots; shoot-root relationship

3. Rhizosphere: root exudates and factors affecting; pH, redox potential and significance

4. Mycorrhizae: types and mechanisms for water and nutrient uptake 5. Uptake and transport of ions: movement in soil and plant 6. Mechanisms of ion transport across membranes: Ion release into xylem,

xylem and phloem transport; factors affecting ion uptake 7. Water movement from soil to plant root and within plant 8. Water use efficiency and transpiration ratio 9. Water stress, hypoxia and plant growth 10. Mechanisms of salt tolerance; salinity-hypoxia interaction 11. Plant responses and adaptation to extreme environments

Books Recommended 1. Kirkham, M.B. 2005. Principles of Soil and Plant Water Relations. Elsevier

Academic Press, San Diego, CA, USA. 2. Marschner, P. 2012. Marschner’s Mineral Nutrition of Higher Plants. 3rd Ed.

Academic Press. Inc., Orlando, FL, USA. 3. Marschner, P. 2012. Marschner’s Mineral Nutrition of Higher Plants

Academic Press is an imprint of Elsevier 32 Jamestown Road, London NW1 7BY, UK 225 Wyman Street, Waltham, MA 02451, USA 525 B Street, Suite 1800, San Diego, CA 92101-4495, USA.

4. Mengel, K. and E.A. Kirkby. 2001. Principles of Plant Nutrition. 5th Ed. Kluwer Academic Publishers, Dordrecht, The Netherlands.

5. Rendig, V.V. and H.M. Taylor. 1989. Principles of Soil–Plant Inter-relationships. McGraw Hill Publishing Co., NY, USA.

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SES-710 PRINCIPLES AND APPLICATIONS OF 3(3-0)

BIOREMEDIATION


At the completion of this course, students will be able to understand:

1. Biodegradation and bioremediation.

2. Principles and processes of bioremediation.

3. Soil and water pollution and its impact on environment.

4. Approaches for the remediation of contaminated sites.

Course Contents

1. Biodegradation: Assimilation of nutrients, lag phase, enzyme induction,

acclimation, activation and kinetics

2. Cometabolism: Substrates, enzymes and reaction; Environmental

significance

3. Factors affecting biodegradation: Biotic and Abiotic,

4. Bioremediation: Advantages/disadvantages, strategies and applications

5. In Situ Bioremediation: Land farming, prepared beds and soil piles, bioventing

& biosparging, composting, intrinsic bioremediation, phytoremediation

6. Ex Situ Bioremediation: Bioreactors, biofilters, cometabolism, anaerobic

process, biological and non-biological treatments

7. Bioremediation of inorganic pollutants: Biosorption, reduction, solubilization/

oxidation, precipitation, methylation

Books Recommended 1. Adriano, D.C., J.M. Bollag, W.T. Frankenberger Jr. and R.C. Sims (Eds.).

1999. Bioremediation of contaminated soils. SSSA, Agronomy Monograph 37, Madison, WI, USA.

2. Alexander, M. 1999. Biodegradation and bioremediation. 2nd ed. Academic Press, San Diego, CA, USA.

3. Sylvia, D. M., J.J. Fuhrmann, P.G. Hartel and D.A. Zuberer. 1998. Principles and applications of soil microbiology. Prentice Hall, Upper Saddle River, NJ, USA.

4. Hurst, C. J., R. L. Crawford, G.R. Knudsen, M.J. McInernery and L.D. Stetzenbach. 2002. Manual of environmental microbiology. American Society for Microbiology, Washington, DC, USA.

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SES-711 ADVANCED TECHNIQUES IN BIOREMEDIATION 3(3-0)

Course Contents

1. Terminology and definitions

2. Regulatory Background

3. Characteristics of wastes

4. Non-radioactive wastes

5. Inorganic wastes, Organic wastes, Mixed wastes, Radioactive wastes

6. Inorganic wastes, Organic wastes, Mixed wastes

7. Characterization and Identification of contaminated sites

8. Technologies for remediation

9. Established technologies: Principles and practices, Solidification/stabilization

(the most widely practiced)

10. On-site incineration, Off-site incineration

11. Innovative technologies: Principles and practices

12. Vacuum extraction, Ex-situ bioremediation

13. In-situ bioremediation, Soil washing

14. In-situ flushing, In-situ vitrification, Solvent extraction, Dechlorination

15. Chemical treatment

16. Ex-situ supercritical oxidation

Books Recommended 1. Chemical Fixation and Solidification of Hazardous Wastes, 1990, Printed and

produced by Penn State Copy Centers and sold at Penn State Bookstore.

2. Adriano, D.C., J.M. Bollag, W.T. Frankenberger Jr. and R.C. Sims (Eds.).

1999. Bioremediation of contaminated soils. SSSA, Agronomy Monograph

37, Madison, WI, USA.

3. Alexander, M. 1999. Biodegradation and bioremediation. 2nd ed. Academic

Press, San Diego, CA, USA.

4. Sylvia, D.M., J.J. Fuhrmann, P.G. Hartel and D.A. Zuberer. 1998. Principles

and applications of soil microbiology. Prentice Hall, Upper Saddle River, NJ,

USA.

5. Hurst, C.J., R.L. Crawford, G.R. Knudsen, M.J. McInernery and L.D.

Stetzenbach. 2002. Manual of environmental microbiology. American Society

for Microbiology, Washington, DC, USA.

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SES-712 INTEGRATED NUTRIENT MANAGEMENT 3(3-0)

Course Contents

1. Introduction, Soil-Plant Relationships

2. Nutrient forms, transformations and plant availability as influenced by

chemical and biological reactions in soils

3. Nitrogen, Phosphorus, Potassium, Sulfur, Calcium, Magnesium

4. Micronutrients

5. Soil Acidity and Alkalinity, Soil pH and management of acid and alkaline soils

6. Characteristics and use of fertilizers and soil amendments

7. Soil testing procedures, application for soil fertility management

8. Soil Fertility Evaluation

9. Fundamentals of Nutrient Management,

10. Nutrients, Water & Interactions

11. Economics of Plant-Nutrient Use

Books Recommended

1. Sylvia, D. M., J.J. Fuhrmann, P.G. Hartel and D.A. Zuberer. 1998. Principles and

applications of soil microbiology. Prentice Hall, Upper Saddle River, NJ, USA

2. Havlin, J.L., J.D. Beaton, Tisdale, S.L., and W.L. Nelson. 2005. Soil Fertility and

Fertilizers, 7th ed. Pearson

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SES-713 ADVANCED RESEARCH METHODS AND 3(3-0)

TECHNICAL WRITING

Course Contents

1. Research: Definition, types and phases

2. Inductive and deductive approaches of research

3. Literature review: Sources of scientific information and data basis

4. Hypothesis development

5. Research protocol and methodologies

6. Methods and ways to control plagiarism

7. Writing of research proposal

8. Project execution: Data collection, handling, analyzing and presentation

9. Project report writing

10. Writing scientific paper

11. Preparation of scientific presentation

12. Ethics in research and scientific writing

Books Recommended 1. Bates, D. J. 1994. Writing with precision. Acropolis Books Ltd., Washington, DC,

USA.

2. Blaxter, L., C. Hughes and M. Tight. 2002. How to research. 2nd Edition, Viva Books

Private Limited, New Delhi, India.

3. Greenfield, T. 2002. Research methods for postgraduates. Oxford Univ. Press, NY,

USA.

4. Little, M. T. and F.J. Hills. 1978. Agricultural experimentation: Design and analysis.

John Wiley and Sons, NY, USA.

5. Luellen, R.W. 2002. Fine-tuning your writing. Wise Owe Publishing Company,

Madison, WI, USA

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SES-714 ORGANIC AGRICULTURE 3(2-1)

Course Contents

1. The roots of organic agriculture,

2. Soil organic matter and plant health,

3. Nutrient management opportunities and challenges,

4. Biodynamic farming,

5. Community Supported Agriculture (CSA),

6. Growing to the market,

7. The role of research in organic agriculture,

8. Cooperative distribution and marketing of organic produce,

9. Organic Forage and Livestock Production,

10. Soils and Nutrient Cycling,

11. Organic Crop Production,

12. Organic Agriculture Case Study, Organic Agriculture Profession,

13. Organic Farming Work Placement,

14. Issues in Organic Agriculture,

15. Marketing and Business Management in the Organic Agriculture Sector

PRACTICAL 1. Comparison of organic residues,

2. Residue quality assessment on the basis of lignin content,

3. C/N ratio in relation to nutrient decomposition and mineralization

Books Recommended

1. Havlin, J.L., J.D. Beaton, Tisdale, S.L., and W.L. Nelson. 2005. Soil Fertility

and Fertilizers, 7th ed. Pearson Prentice Hall, Upper Saddle River, NJ.

2. Sylvia, D. M., J.J. Fuhrmann, P.G. Hartel and D.A. Zuberer. 1998. Principles

and applications of soil microbiology. Prentice Hall, Upper Saddle River, NJ,

USA.

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SES-715 ADVANCED SOIL CHEMISTRY 3(3-0)

Course Outline

1. Chemical thermodynamics of soils: Processes and variables 2. Chemical potentials: Metal oxides, hydroxides and silicates clays 3. Kinetics of soil chemical reactions 4. Precipitation and dissolution in soil environment 5. Surface electro-chemistry of colloids: Sorption of trace metal ions;

Selectivity and pH 6. Inter-particles attraction: Solid-solid and solid-liquid interaction 7. Chemistry of submerged soils 8. Chemical transformations of selective elements in soils 9. Contamination of soils with organic and inorganic pollutants 10. Risk assessment of trace metals in soil and water 11. Integrated management of polluted environment 12. Sorption theory: Description and application for decontamination of soils and

water 13. Recent developments in soil and environmental chemistry 14. Systems for waste water treatment: Physical, chemical and bio-chemical

Books Recommended 1. Conklin, Jr. A.R. 2005. Introduction to Soil Chemistry Analysis and

Instrumentation. John Wiley & Sons, Inc., Hoboken, NY, USA. 2. Kumar, A. 2004. Environmental Contamination and Bio-reclamation. APH

Publishing Corporation, New Delhi, India. 3. Schjonning, P., S. Elmholt and B.T. Christensen. 2004. Managing Soil

Quality Challenges in Modern Agriculture. CABI Publisher Cambridge, MA, USA.

4. Sparks, D.L. 2003. Environmental Soil Chemistry. 2nd Ed. Academic Press, Inc., San Diego, CA, USA.

5. Sposito, G. 2008. The Chemistry of Soils. Oxford University Press, NY, USA.

6. Viessman, J.W. and M.J. Hammer. 2009. Water Supply and Pollution Control. 8th Ed. Prentice Hall NY, USA.

SES-716 ADVANCED SOIL FERTILITY 3(3-0)

Course Outline

1. Growth expression: Mitscherlich and Quadratic equations

2. Plant responses to applied nitrogen: Mathematical description 2.1 Stubble management and N availability

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2.2 Effect of forms nitrogen on plant growth: Ammonia absorption, losses and toxicity

3. Phosphate phase equilibria in soils: Dissolution, precipitation, retention reaction at microsites 3.1 Reaction products and changes in applied P 3.2 Soil phosphate buffering capacity and availability

4. Potassium equilibria in soil: Quantity/intensity relationship and availability 5. Modeling nutrient uptake by plants 6. Modeling nutrient losses 7. Nutrition and plant disease interactions 8. Mineral nutrition of horticultural plants 9. Modern concept in soil fertility: Hydroponics, tunnel farming and roof top /

pot culture 10. Formulation of fertilizer recommendations 11. Integrated plant nutrient management system 12. Soil variability and its control in field experiments

Books Recommended

6. Barker A.V. and D.J. Pilbeam. 2007. Handbook of Plant Nutrition. CRC

Press, Boca Raton, FL, USA. 7. Elsworth, L. and W.O. Relay (eds.). 2009. Fertilizers: Properties,

Applications and Effects. Nova Science. Publ. Inc., NY, USA. 8. Havlin, J.L., J.D. Beaton, S.L. Tisdale and W.L. Nelson. 2005. Soil Fertility

and Fertilizers. 7th Ed. Pearson Education, Singapore. 9. Marschner, H. 1995. Mineral Nutrition of Higher Plants. Academic Press

Inc., Orlando, FL, USA. 10. Mengel, K. and E.A. Kirkby. 2001. Principles of Plant Nutrition. 5th Ed.

International Potash Inst., Bern, Switzerland. 11. Marschner, P. 2012. Marschner’s Mineral Nutrition of Higher Plants

Academic Press is an imprint of Elsevier 32 Jamestown Road, London NW1 7BY, UK 225 Wyman Street, Waltham, MA 02451, USA 525 B Street, Suite 1800, San Diego, CA 92101-4495, USA.

SES-717 ADVANCED SOIL MICROBIOLOGY 3(3-0)

Course Outline

1. Advances in soil and environmental microbiology 2. Microbiology of the terrestrial and aquatic environment 3. Organic pollutants: Sources and types, biodegradation and bioremediation

21

4. Biotransformation of metal pollutants 5. Metabolic and nucleic acid based analysis of soil microbial diversity

5.1 Extraction of bacterial DNA from soil 5.2 Recombinant DNA techniques, PCR, probes and reporter genes

used for monitoring soil microbes 6. Recent trends and approaches in soil and environmental microbiology 7. Soil enzymes and their role

Books Recommended 1. Burns, R.G. and R.P. Dik. 2002. Enzymes in the Environment. Marcel

Dekker, Inc. NY, USA. 2. Harrison, R.M. (ed.). 2001. Pollution: Causes, Effects and Control. 4th Ed.

Royal Soc. of Chem., Cambridge, UK. 3. Hurst, C.J., R.L. Crawford, G.R. Knudsen, M.J. McInernery, and L.D.

Stetzenbach. 2002. Manual of Environmental Microbiology. American Society for Microbiology, Washington DC, USA.

4. Maier, R.M., I.L. Pepper, and C.P. Gerba. 2009. Environmental Microbiology. 2nd Ed. Academic Press Inc., San Diego, CA, USA.

5. Paul, E.A. (ed.). 2007. Soil Microbiology, Ecology and Biochemistry. 3rd Ed. Elsevier, Oxford, UK.

6. Sylvia, D.M., J.J. Fuhrmann, P.G. Hartel, and D.V. Zuberer. 2005. Principles and Applications of Soil Microbiology. Prentice Hall International, NJ, USA.

SES-718 ADVANCED SOIL PHYSICS 3(3-0)

Course Outline

1. Water flow equations and their applications 2. Thermodynamic potentials and chemical potential of soil water 3. Use of models for artificial drainage

3.1 Factors influencing drainage 4. Heat flow equations: Application and calculations 5. Application of gas flow equations 6. Pollutant transport in soil environment: Analytic solutions of the CDE model 7. Mobile-immobile water flow model for solute transport 8. Behavior assessment model for pesticide and hormones transport 9. Application of soil physics for remediation of hazardous wastes 10. Spatial variability analysis of soil properties and significance 11. Analysis of frequency distribution 12. Techniques for characterizing variability 13. Irrigation water scheduling; Water balance; Old and modern concepts of

irrigation 14. Irrigation and water use efficiency

22

15. Calculation of evapo-transpiration by various methods

Books Recommended 1. Bhatti, A.U. 2005. Spatial Variability and its Management in Agriculture.

Higher Education Commission, Islamabad, Pakistan. 2. Hillel, D. 1998. Environmental Soil Physics. Academic Press Inc., San

Diego, CA, USA. 3. Hillel, D. 2004. Introduction to Environmental Soil Physics. Elsevier

Academic Press. San Diego, CA, USA. 4. Hillel, D. 2008. Soil in the Environment: Crucible of Terrestrial Life. Elsevier

Inc., Burlington, MA, USA. 5. Jury, W.A. and R. Horton. 2004. Soil Physics. 5th Ed. John Wiley & Sons,

Inc., NY, USA. 6. Marshall, T.J., J.W. Holmes and C.W. Rose. 1996. Soil Physics. 3rd Ed.,

Cambridge University Press, Cambridge, UK.

SES-719 SPECIAL PROBLEM 1(1-0)

The special problem is intended to instruct students on proper techniques for scientific

research and methodologies. The students are expected to prepare directed

assignment and collect information and material related to current research interest.

SES-720 SEMINAR 1(1-0)

The seminar is intended to instruct students on proper techniques for presentation of

scientific material. Each student is expected to prepare and present a scientific seminar

and to submit written documentation supporting that seminar.

SES-721 SOIL ECOLOGY 3(3-0)

Course Outline

1. Introduction, Viruses, Bacteria

2. Soil environment, Bacteria and archaea, Fungi, Algae

3. Soil animals, Microbial energetic

23

4. Microbial metabolism, Microbial growth and interactions

5. Environmental limits to microbial activity

6. Soil aggregates, Rhizosphere

7. Soil organic matter composition, Formation of soil organic matter

8. Decomposition and carbon mineralization

9. Composting, Xenobiotic metabolism I, Xenobiotic metabolism II, Nitrogen

fixation process

10. Symbiotic nitrogen fixation (S. Boyle)

11. Nitrogen mineralization (S. Boyle)

12. Nitrogen immobilization, Nitrification, Denitrification

13. Trace gases

14. Sulfur cycle, Phosphorus cycle

15. Mycorhizae I, Mycorrhizae II

16. Aromatic Nomenclature, Nitrogen cycle

17. Mycorrhizae

18. Metals

Books Recommended 1. Richards, 1987. The Microbiology of Terrestrial Ecosystems, Longman

Scientific & Technical.

2. Soil Microbial Ecology, Meeting, 1993, Marcel Dekker

3. Soil Ecology, Killham, 1994, Cambridge University Press

4. Biodegradation and Bioremediation, Alexander, 1994, Academic Press

5. Environmental Soil Biology, 2nd edition, Wood, 1995, Blackie A & P

6. Fundamentals of Soil Ecology, Coleman and Crossley, 2nd edition, 2004,

Academic Press

7. Modern Soil Microbiology, van Elsas et al., 1997, Marcel Dekker.

8. Soil Microbiology: An Exploratory Approach, Coyne, 1999, Delmar

9. Soil Microbiology, Tate, 2nd edition, 2000, John Wiley.

24

SES-722 SOIL QUALITY AND MANAGEMENT 3(3-0)


Soil quality is the capacity of the soil to function within the ecosystem boundaries to sustain biological productivity and maintain environmental quality. After studying this course, the student will be able to understand basic principles of soil quality and learn to assess and evaluate soil quality related to agricultural production and environmental quality including soil resilience capabilities and then its conservation.

Course Outline

1. Soil quality and its assessment: Indicators and guidelines

2. Soil management in contrasting environments

3. Maintenance of soil productivity

4. Impact of vegetation change on soils

5. Nutrient cycles in relation to soils with special reference to carbon and

nitrogen cycles

6. Soils as a source or sink of greenhouse gases

7. Soil conservation and carbon dynamics

8. Biological diversity and ecosystem function in soils

9. Soil resilience and conservation: Concept, importance, classification,

indicators and management strategies to promote soil resilience

Books Recommended

1. Blanco-Canqui, H. and R. Lal. 2008. Principles of Soil Conservation and

Management. Springer-Verlag, Berlin, Germany.

2. Frossard, E., W.E.H. Blum and B.P. Warkentin. 2006. Function of Soils for

Human Societies and the Environment. Geological Society, London, UK.

3. Fullen, M.A. and J.A. Catt. 2004. Soil Management: Problems and

Solutions. Arnold Publishers, London, UK.

4. White, R.E. 2005. Principles and Practice of Soil Science: The Soil as a

Natural Resource. 4th

25

SES-723 NUTRIENT ACQUISITION AND TRANSPORT 3(3-0)


To elaborate the molecular and morphological perspectives of nutrient acquisition

by plant roots and their transport in soil and plants

Course Outline

1. Root architecture, soil-root interaction and nutrient acquisition

2. Relation between transpiration and nutrient uptake

3. Role of cell wall in nutrient uptake

4. Nutrient transport in root and nutrient uptake mechanism

5. Membrane transport of nutrients and different ion channels; P-type, F-type

and V-type

6. ATPases; Cation and anion channels

7. Plasma membrane H+-ATPase

8. Physiology and molecular biology

9. Role of plasma membrane H+-ATPase

10. Nutrient uptake, apoplastic pH and P acquisition

11. Plant approaches to acquire macro- and micronutrients

12. Sodium acquisition and transport in plant

13. Redox potential and nutrient acquisition

14. Plant nutrient-acquisition strategies and soil aging

Books Recommended 1. Ae, N., J. Arihara, K. Okada, and A. Srinivasan. 2001. Plant Nutrient

Acquisition. New Perspectives. Springer-Verlag, Berlin, Germany.

2. Bassirad, H. 2005. Nutrient Acquisition by Plant: An Ecological

Perspective. Springer-Verlag, Berlin, Germany.

3. Marschner, P. 2011. Marschner's Mineral Nutrition of Higher Plants, 3rd

edition. Academic Press, London, UK.

4. Rengel, Z. 2002. Hand Book of Plant Growth. Marcel Dekker, Inc., New

York, USA.

26

SES-724 BIOCHAR: CONCEPT AND APPLICATION 3(3-0)


After learning this course students will be able to: 1. Biochar and biochar production technology 2. Impact of biochar on climate change 3. Economics of biochar production and utilization 4. Biochar effects on soil nutrient transformations and soil fertility

Course Outline

1. Background and introduction of biochar

2. Physical, chemical and biological properties of biochar

3. Impact of biochar on soil properties

4. Change and stability of biochar in soil

5. Biochar and soil nutrient transformations

6. Biochar and climate change

7. Biochar and emission of greenhouse gases

8. Biochar production technology

9. Economics of biochar production and utilization

10. Socio-economic assessment of biochar projects

11. Some essential concepts for commercial success of biochar

Books Recommended

1. Bates, A. 2010. The Biochar Solution: Carbon Farming and Climate

Change. New Society Publishers, Gabriola Island, Canada.

2. Lehmann, J. and S. Joseph. 2009. Biochar for Environmental

Management: Science and Technology. Earthscan, London, UK.

3. Sohi, S., E. Lopez-Capel, E. Krull and R. Bol. 2009. Biochar, Climate

Change and Soil: A review to guide future research. CSIRO Land and

Water Science Report 05/09. Centre for Bioenergy and Climate Change,

Harpenden, UK.

27

4. Verheijen, F.G.A., S. Jeffery, A.C. Bastos, M. van der Velde and I. Diafas.

2010. Biochar application to soils: A Critical Scientific Review of Effects on

Soil Properties, Processes and Functions. Official Publications, European

Communities, Luxembourg.

SES-725 WASTE WATER IMPACT ON SOIL HEALTH 3(2-1)

Course Outline

1. Definition and types of waste water

2. Sources of waste water

3. Chemical composition of waste water

4. Impact of waste water on physical properties of soil

5. Impact of waste water on chemical properties of soil

6. Impact of waste water on biological properties of soil

PRACTICAL

1. Collection of waste water from different sources

2. Analysis of waste water for heavy metals

3. Analysis of waste water for critical levels of deleterious pathogens.

Books Recommended 1. Ashfar, M. and M.A. Saleem. 2010. Environmental Pollution and Agriculture.

Pak Book Empire, Lahore.

2. Asthana, D.K. and M. Asthana. 2003. Environment Problems & Solutions. S.

Chand & Co. Ltd. New Delhi, India.

3. Cheremisioff, N.P. 2002. Handbook of Solid Waste Management and Waste

Minimization Technologies. Elsevier Science, Burlington, MA, USA.

4. Clinic, C., M. Ignazio and G.M. Lodovica. 2008. Sustainable Development

and Environmental Management: Experiences and Case Studies. 1st Ed.

28

Springer Publishers, Dordrecht, The Netherlands.

5. Cunningham, W.P., M.A. Cunningham and B.W. Saigo. 2007. Environmental

Science: A global Concern. 9th Ed. McGraw Hill, NY, USA.

6. Ghafoor, A. 2010. Environmental Pollution: Types, sources and

management. Allied Book Centre, Lahore.

7. Pepper, I.L., C.P. Gerba and M.L. Brusseu (eds.). 2006. Environmental and

Pollution Science. 2nd Ed. Elsevier / Academic Press, San Diego, CA, USA.

STAT-701 STATISTICAL METHODS FOR AGRICULTURAL RESEARCH-I 3(3-0)

Objectives of the course

1. To impart the knowledge of statistical software used to analyze the data.

2. To improve the students’ skills for selecting appropriate tools for analysis of

their research data.

Theory

Basic principles of experimental design. Layout analysis of CRD, RCBD, Latin

Square Designs. Estimation of Missing Observations in RCBD and Latin Square

Design. Split plot Designs and its variations. Multiple comparison tests. Effect of

violation of assumptions of underlying ANOVA. Simple and Multiple regression.

Logistic Regression and Odd Ratios. Survival Analysis. Dose Response Curves.

Simple correlation, Multiple Correlation and Partial Correlation. Analysis of Count

and Frequency data. Contingency Tables. Diversity Indices.

Books Recommended

1. Mead,R. The Design of Experiments. Cambridge University Press, Cambridge

(1995)

2. Steel,R.G.D., J.H. Torrie and D.A. Dicky. Principles and Procedures of Statistics: A

Biometerical Approach. Third Edition. Mc Graw Hill, New York, USA.

3. Box,G.E.P., W.G. and Hunter, J.S. Statistics for Experimenters. New York: Wiley

(1978).

29

4. Tabachnick, B. G., and Fidell, L. S. (1996). Using Multivariate Statistics. New York:

HarperCollins College Publishers.

5. Dillon, W. R. and Goldstein, M. Multivariate Analysis: Methods and Applications.

New York: Wiley. (1984)

6. Agresti. A. An Introduction to Categorical Data Analysis. New York: Wiley (2002)

7. S.Chatterjee, Ali.S.Hadi. Regression Analysis by Example. fourth Edition. l, New

York, Wiley (2004)

8. Jerrold H. Zar. Biostatistical Analysis, fourth edition ,Dorling Kindersley India,2009.

9. Cox D.R. The Theory of the Design of Experiments Chapman and Hall (2000)

10. Gomez.K.A and Gomez A.A. Statistical procedures for agricultural research. The

international Rice Research Institute (1976)

11. Richard A. Johnson, Dean W. Wichern. Applied multivariate statistical analysis. 6th

Edition. Pearson Education International (2007).

STAT-702 STATISTICAL METHODS FOR AGRICULTURAL RESEARCH-II 3(3-0)

Objectives of the course

1. To impart the knowledge of statistical software used to analyze the data

2. To improve the students’ skills for selecting appropriate tools for analysis of their

research data

Theory

Factorial Experiments, 2n, 3n… Pn and mixed levels factorial experiments.

Confounding and its types. Fractional replication. Multiple comparison tests.

Application and construction of contrasts. Analysis of Count and Frequency data.

Contingency Tables. Introduction of multivariate analysis. Principle component

analysis, Factor analysis, Cluster Analysis, Correspondence analysis, Simple

and multiple Regression and Correlation, Logistic Regression and Odd Ratios.

Survival Analysis. Diversity Indices.

30

Books Recommended

1. Kempthrone.O, Hinkelmann.K. Design and Analysis of Experiments Vol I:

Introduction to Experimental Design,second edition New York, Wiley (2005)

2. Kempthrone.O, Hinkelmann.K. Design and Analysis of Experiments Vol II:

Advanced Experimental Design,second edition New York, Wiley (2008)

3. Mead,R. The Design of Experiments. Cambridge University Press,

Cambridge (1995)

4. Steel,R.G.D., J.H. Torrie and D.A. Dicky. Principles and Procedures of

Statistics: A Biometerical Approach. Third Edition. Mc Graw Hill, New York,

USA.

5. Box,G.E.P., W.G. and Hunter, J.S. Statistics for Experimenters. New York:

Wiley (1978).

6. Tabachnick, B. G., and Fidell, L. S. (1996). Using Multivariate Statistics. New

York: HarperCollins College Publishers.

7. Dillon, W. R. and Goldstein, M. Multivariate Analysis: Methods and

Applications. New York: Wiley. (1984)

8. Agresti. A. An Introduction to Categorical Data Analysis. New York: Wiley

(2002)

9. S.Chatterjee, Ali.S.Hadi. Regression Analysis by Example. fourth Edition. l,

New York, Wiley (2004)

10. Cox D.R. The Theory of the Design of Experiments Chapman and Hall (2000)

11. Gomez.K.A and Gomez A.A. Statistical procedures for agricultural research.

The international Rice Research Institute (1976)

12. Richard A. Johnson, Dean W. Wichern. Applied multivariate statistical

analysis. 6th Edition. Pearson Education Internation (2007).

13. Jerrold H. Zar. Biostatistical Analysis, fourth edition, Dorling Kindersley

India,2009.

for the degree of m.sc. (hons.) and ph.d. in soil science · ses-706 salt-affected and waterlogged...

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