MS Program


Bangladesh Agricultural University, Mymensingh

Department of Genetics and Plant Breeding

MS in Genetics and Plant Breeding

Curricula and Syllabi

Effective from January-June 2019

 

                                                      

                                                         Footnotes: Odd number = Theory        Even number = Practical            S = Satisfactory                  U = Unsatisfactory

 

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Bangladesh Agricultural University, Mymensingh

Department of Genetics and Plant Breeding

Syllabus for MS in Genetics and Plant Breeding

Course: GPB 501 Molecular Genetics (Compulsory)

Credit hours: 2

 

 

  1. Genetic material: a) DNA as the genetic material – indirect and direct evidences.b) RNA as the genetic material – evidences.
  2. Replication of DNA: Models of DNA replication – evidence of semi conservative replication of DNA, Generalized DNA replication in prokaryotes, Properties of important enzymes involved in DNA replication, Replication of DNA in eukaryotes.
  3. Protein synthesis: apparatus, Transfer RNA and ribosomes, gene directed synthesis of protein, transfer and translation of genetic information, genetic code.
  4. Regulation of gene action at transcriptional and translational levels. 
  5. Genetic recombination in microorganisms: Transduction, transformation and conjugation.
  6. Transposable genetic elements, definition, occurrence in both prokaryote and eukaryote, genetic and evolutionary significance.
  7. Endonuclease: Definition, classification, characteristics used in construction of restriction map, restriction fragment length polymorphism (RFLP), RFLP map and its significance.
  8. DNA sequencing and synthesis of gene, DNA amplification by polymerase chain reaction.
  9. Gene: Classical and modern concept, fine structure of gene.
  10. Epigenetics: Paramutation; DNA methylation and histone modification; histone code.
  11. Signal perception and transduction: Cell receptors and signaling molecules e.g. ethylene signaling pathway, salicylic acid pathway and jasmonate signaling pathway.

 

 References: 

  1. Burns, G.W. 1980. The Science of Genetics, Macmillan Publishing Co., Inc. New York.
  2. Corn, R.E., P.K. Stumpf, G. Bruening and R.H. Doy. 1987. Outlines of Biochemistry. 5th John Wiley and Sons. New York.
  3. Gardner, E.J.; M.J. Simmons and B.D.P Srustad. 1991. Principles of Genetics. John Wiley and Sens, Inc. New York.
  4. Goodenough, U. 1984. Genetics. Third edition. Saunders College Publishing. New York.
  5. Lewin, B. 1983. Genes. John Wiley & Sons, New York.
  6. Lewin, B. 1997 Genes VI. Oxford University Press. Oxford.
  7. Old, R.W. and S.B. Primerose (ed.) 1994. Principles of Gene Manipulation. An introduction to Genetic engineering. 5th Blackwell Scientific Publications. Oxford. London.
  8. Singer, M. and P. Berg. 1991. Genes and Genomes. Blackwell Scientific Publications. Oxford.
  9. Skoda, J. and H. Skodova. 1987. Molecular Genetics. Elsevier Amsterdam.
  10. Srb, A.M., R. Owen and R.S. Edgar. 1965. General Genetics. Second edition. W.H. Freeman Company, San Francisco and London.

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 Bangladesh Agricultural University, Mymensingh

Department of Genetics and Plant Breeding

Syllabus for MS in Genetics and Plant Breeding

Course: GPB 503 Molecular Plant Breeding (Compulsory)

Credit hours: 2

 

  1. Introduction to Molecular Plant Breeding. Molecular plant breeding tools: markers and maps.
  2. Structural and functional genomics.
  3. Phenomics, comparative phenomics and array technologies in omics.
  4. Molecular dissection of complex traits: single marker based approaches, interval mapping, composite interval mapping, multiple interval mapping, multiple quantitative trait loci, Bayesian mapping, linkage disequilibrium and association mapping in plants.
  5. Mapping populations: F2, backcross (BC), doubled haploid (DH) and recombinant inbred line (RIL) populations.
  6. Quantitative trait loci (QTL): requisites for QTL mapping, molecular linkage maps, data for QTL mapping (marker data and phenotype data).
  7. QTL mapping: Quantitative genetic models (single QTL model, multiple locus model), mixture model. Epistatic QTLs and QTL × environment interaction. Genomics and e-QTLs.
  8. Statistics for QTL mapping: Softwares for QTL interval mapping, softwares for linkage analysis and map construction, softwares for QTL mapping.
  9. Molecular marker-assisted breeding: Marker-assisted selection (MAS), marker-assisted gene introgression, gene pyramiding and selection for QTL; opportunities and challenges.
  10. Molecular breeding strategies for improving nutritional quality of crop plants, abiotic and biotic stresses, nitrogen fixation and transfer of NIF genes and wide adaptation.

 References: 

  1. Chahal, G. S. and Gosal, S. S. (2003). Principles and Procedures of Plant Breeding: Biotechnological and Conventional Approaches. Narosa Publishing House, New Delhi.
  2. Flint-Garcia, S. A., Thornsberry J. M. and Buckler, E. S. (2003). Structure of linkage disequilibrium in plants. Ann Rev Plant Biol 54:357-374.
  3. Gupta, P. K. and Varshney, R. K. (eds.) (2004). Cereal Genomics. Kluwer Academic Publishers, Dordrecht.
  4. Jain, H. K. and Kharkwal, M. C. (ed.) (2004). Plant Breeding: Mendelian to molecular approaches. Kluwer Academic Publishers, New York.
  5. Liu, B. H. (1998). Statistical Genomics: Linkage, Mapping, and QTL Analysis. CRC Press, Boca Raton, New York, USA.
  6. Lorz, H. and Wenzel, G. (ed.) (2004). Molecular marker systems in plant breeding and crop improvement. Springer, London.
  7. Paterson, A. H. (ed.) (1998). Molecular Dissection of Complex Traits. CRC Press, Boca Raton, New York, USA.
  8. Phillips, R. L. and Vasil, I. K. (eds.) (1994). DNA Based Markers in Plants. Kluwer Academic Publishers, Dordrecht.
  9. Xu, Y. (2010). Molecular Plant Breeding. CABI North American Office, Cambridge, MA.

 

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Bangladesh Agricultural University, Mymensingh

Department of Genetics and Plant Breeding

Syllabus for MS in Genetics and Plant Breeding

Course: GPB 505 Biometrical and Population Genetics (Theory-Compulsory)

Credit hours: 3

 

  1. Quantitative genetic analysis and biometrical approach.
  2. Additive and dominance effects of gene– Components of mean, components of Variation, testing the additive dominance model.
  3. Non-allelic interaction and genetic analysis; biometrical basis of heterosis.
  4. Heritability, co-heritability and expected genetic advance; maximizing genetic advance for a polygenic character.
  5. Diallel analysis and combing ability: Hayman and Giffing approaches.
  6. G × E interaction and stability: Genetic and statistical approaches.
  7. Correlated response and selection index (simultaneous selection of multiple characters).
  8. Gene in populations; frequency of gene and genotype; Algebraic proof of the maintenance of genetic equilibrium; factors changing gene frequencies.
  9. Population and gene pools; divergence of gene pools; genetic similarity and genetic distance.
  10. Polymorphism –Transient, balanced, geographic, and chromosomal polymorphisms.
  11. Homeostasis –Physiological, developmental and population homeostasis.
  12. Plant character association: multivariate correlation, regression (multivariate regression coefficients, interpreting coefficients, F-tests and R-squared, and multiple sets of dummy variables) and path coefficient analysis.

 

References

  1. Beeker, W.A. 1984. Manual of Quantitative Genetics, Pullman, WA Academic Enterprises, USA.
  2. Bulmer, M.G. 1980. The Mathematical theory of Quantitative Genetics, Oxford: Claredon, UK.
  3. Crow, J.F. 1987. Population genetics history: A personal view. Ann.  Genet. 21: 1-22.
  4. Dabholkar, A.R. 1992. Elements of Biometrical Genetics. Concept Pub. Comp., New Delhi, India.
  5. Fa1coner, D.S. and Mackay, T.F.C. 1996. Introduction to Quantitative Genetics. Longman Essex, UK.
  6. Hartl, D.L. and Clark, A.G. 1997. Principles of Population Genetics. Sinauer Associates, Inc, Massachusetts, USA.
  7. Ignacimuthu, S. 2005. Basic bioinformatics. Alpha Science International, Harrow, UK.
  8. Lin, C.S. and Binnas, M.R. 1991. Genetic Properties of four types of stability parameter. Theor. Appl. Genet.:32 505-9.
  9. Lynch, M and Walsh, B. 1998. Genetics and Analysis of Quantitative Traits. Sinauer Associates, Inc. Massachusetts, USA.
  10. Mather, K. and Jinks, J.L. 1987. Biometrical Genetics. Chapman & Hall London.
  11. Mather, K. 1973. Genetic structure of Population. Chapman & Hall London.
  12. Narain, P. 1993. Statistical Genetics. Wiley Eastern Ltd. New Delhi, India.
  13. Rastogi, S.C., Mendiratta, N., Rastogi, P. 2003. Bioinformatics: Concepts, Skills and Applications. CBS Publishers, New Delhi.
  14. Singh, R.K. and Chawdhary, R.D. 1985. Biometrical Methods in Quantitative Genetic Analysis. Kalyani Pub. Ludhiana, India.
  15. Species, E.B. 1977. Genes in Population. John Wiley & Sons, NY.

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Bangladesh Agricultural University, Mymensingh

Department of Genetics and Plant Breeding

Syllabus for MS in Genetics and Plant Breeding

Course: GPB 507 Biotechnology & Genetic Engineering &

                                                   GPB 502 Biotechnology and Molecular Genetics-Practical (Compulsory)

 

GPB 507: Biotechnology & Genetic Engineering (2 credits)

  1. Biotechnology ­– Concept, scope and application in biological sciences.
  2.  Prerequisites for cell and tissue culture. Media and its preparation. Culturing explants: Cell, Tissue, Anther, Pollen, Ovary and Embryo culture.
  3. Somatic hybridization and cybridization: Protoplast isolation, culture, fusion and regeneration of plants; Application of somatic hybridization, strategies and methods for producing somatic hybrids. Cryopreservation and germplasm storage.
  4. Somaclonal & gametoclonal variation: Causes of somaclonal and gametoclonal variation, methods of creation of artificial somaclones and gametoclones; and their detection, Practical application of variability in tissue cultures. 
  5. Haploid Production: Haploid production and its significance, monoploid production through chromosome elimination, production of triploids through endosperm culture, role of haploids, monoploids and triploids in agriculture.
  6. Genetic engineering: Introduction to recombinant DNA Technology, Basic Techniques, Electrophoresis, Nucleic acid blotting. Isolation and purification of DNA from various sources.
  7. Restriction endonuclcases: Their host, restriction types, purification, termination of reaction and generating new restriction enzyme. Cutting and joining of DNA molecules.
  8. Recombinant selection and screening: Genetic, Immunochemical and Nucleic Acid hybridization methods.
  9. Cloning: Plant virus and plasmid cloning vectors. Fragmentation of DNA, Joining of foreign DNA to the vector, introduction of artificial recombinant into host cells, Selection and screening of clone of recipient cells.
  10. Gene transfer to plants; Direct and vector mediated gene transfer.
  11. The impact of recombinant DNA technology: The generation of novel plants and foods; and related regulatory aspects.

 

GPB 502: Biotechnology & Molecular Genetics Practical (1 credit)

  1. Basic techniques in plant cell, tissue and organ culture; Excised embryo culture; Organogenesis and somatic embryogenesis; Stages of micropropagation ; Callus and cell suspension culture; isolation and culture of protoplasts; basic techniques in genetic transformation in plants; transformation with wild type and disarmed strains of Agrobacterium.
  2. Isolation of Genomic DNA from plant tissues; isolation of RNA; Agarose Gel Electrophoresis; isolation of protein from different sources, analysis of proteins by SDS-PAGE, native PAGE, gel staining, western blotting, gel filtration, protein electrophoresis and protein expression analysis.
  3. Visit to national institute of biotechnology and other biotechnology research laboratories in Bangladesh.

  

References: 

  1. Bajaj, Y.P.S. (Ed.) 1989. Plant Protoplasts and Genetic Engineering I. Springer -Verlag, Berlin.
  2. Bhojwani, S.S and M.K. Razdan, 1983. Plant Tissue Culture: Theory and Practice. Elservier Science: Publishers, Amsterdam.
  3. Chawla, M.A. 2009. Introduction to Plant Biotechnology. Enfield, N.H.: Science, Plymouth.
  4. Dixon, R.A. (Ed.) 1985. Plant Cell Culture, A practical Approach. IRL. Press, Oxford, Washington D.C.
  5. Dodds, J.W. (Ed.) 1985. Plant Genetic Engineering. Cambridge University Press, Cambridge. 
  6. Dodds, J.H. and L.W. Roberts, 1988. Experiments in plant Tissue Culture. 2nd Ed., Cambridge.  
  7. Natesh, S., V.I. Chopra and S. Ramachandran, (Ed.) 1985. Biotechnology in Agriculture. Oxford & IBH Publishing Co. Pvt. Ltd. New Delhi.
  8. Old, R.W. and S.B. Primrose, (Ed.) 1994. Principles of Gene manipulation: An introduction to    Genetic Engineering.  5th Edition, Blackwell Scientific Publications, Oxford, London.    
  9. Pierik, R.L.M. 1987. In vitro culture of higher p1ants.  Martinus Nijoff Publishers, Dordrecht.
  10. Perbal, B. 1988. A Practical Guide to Molecular Cloning (2nd Edition). John Wiley and Sons. New York. 
  11. Rodriguez, R.L. and R. C. Tait, 1983. Recombinant DNA Techniques: An Introduction. The Benjamin/Cummings Publishing Co. Inc. USA. 
  12. Razdan, M.K. 1994. An Introduction to Plant Tissue Culture. Oxford and IBM Publishing Co. London.
  13. Semal. J. (Ed.) 1986. Somaclonal Variation and Crop Improvement. Nartinus Nijhoff Publishers,     Dordrecht. 
  14. Thorpe, T.A. (Ed.) 1981. Plant Tissue Culture: Methods and Applications in Agriculture. Academic Press, INC. Ltd. London.
  15. Torres, K.C. (Ed.) 1989. Tissue Culture Techniques for Horticultural Crops, Van Nostrand Reinhold   Pubs. New York University Press, Cambridge. 
  16. Zimmerman, R.H., R.J. Griesbach, F.A. Hammerschlay and  Lawson, R.H. (Ed.) 1986. Tissue Culture as a Plant Production system for Horticultural Crops. Martinus Nijhoff Publishers, Dordrecht. The Netharlands.

 

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Bangladesh Agricultural University, Mymensingh

Department of Genetics and Plant Breeding

Syllabus for MS in Genetics and Plant Breeding

Course: GPB 517: Developmental and Physiological Genetics (Elective)

Credit hour: 2 credits

 

  1. Introduction to the subject of Developmental Genetics: Theories of development; Mosaic theory, Driesch experiments.
  2. Role of Nucleus and cytoplasm in development. : Nucleus-Cytoplasm Interaction, Nuclear transplantation.
  3. Differentiation and development: Nuclear differentiation, Chromosomal differentiation, Genic control of development.
  4. Genic control of morphogenetic process: Genic control of hormonal coordination, Genic control of growth.
  5. Totipotency-Switch on Switch off Mechanism of differentiation and its use in tissue culture.
  6. Genetics of abnormal growth and cancer development.
  7. Introduction to the subject of physiological genetics: Cytoplasm in heredity and development.
  8. Effects of genes on characters at different levels. 
  9. Genic control of Pigments, Proteins and Antigens.

 

References

  1. Altenburg, E. 1970. Genetics, Revised Edition, Mohan primlani, Oxford & IBH Publishing Co., 66. Janpath, New Delhi 110001. 
  2. Islam, A.S. 1973. Fundamentals of Genetics. Humaria Islam, Ehram Corporation, 69-70, Motijheel Commercial Area, Dhaka-2.
  3. King, R.C. 1965. Genetics. Oxford University Press.
  4. Levine, L. 1973. Biology of the Gene, 2nd Edition. The C. V. Mosby Company.
  5. Muntzing, A. 1973. Biology of the Gene, 2nd Edition. The C.V. Mosby Company.
  6. Sinnott, E.W., Dunn, I.C. and Dobshansky T. 1958. Principles of Genetics. T.M.H. Edition, Tata Mcgraw Hill Publishing Co. Ltd.
  7. Srb, A.M., Owen, R.D. and Edgar, R.S. 1965. General Genetics W.H.  Freeman and Company, San Francisco & London.
  8. Winchester, A.M. 1977. Genetics, Fifth Edition, Houghton Mifflin Company, Boston.  

 

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Bangladesh Agricultural University, Mymensingh

Department of Genetics and Plant Breeding

Syllabus for MS in Genetics and Plant Breeding

Course: GPB 519 Stress Breeding (Elective)

Credit hour: 2 credits

 

  1. The scope and practical dimension of stress factors of crop production. Types of stress-their importance in Bangladesh and the need for breeding crop varieties tolerant to these stresses.
  2. Responses of growth phases, grain development. Yield components and yield of crops to different abiotic and biotic stresses.
  3. Mechanism of plant’s resistance to abiotic stresses. Oxidative stress and antioxidant defense system in plants in abiotic stress response.
  4. Plant genes for abiotic stresses. Contribution of proteomics studies to understand plant stress response.
  5. Techniques and methodology of breeding for the development of drought and heat tolerant crop varieties.
  6. Soil salinity and its effect on root and shoot characters of crop plants, screening tool and breeding strategy for development of salt tolerant crop variety. Physiological and molecular mechanism of salinity tolerance in plants.
  7. Genetic variation for nitrogen, phosphorus and potassium use efficiency under low input conditions and their relationships with yield and yield components.
  8. Genetics of micro-nutrient efficiency in crop plants and the breeding procedure for micronutrient deficiency tolerant variety. Plant responses to heavy metals and enriched atmospheric CO2.
  9. Mechanism and genetic basis of disease resistance.
  10. Testing factors affecting expression and measurement of disease resistance.
  11. Methods of breeding for disease resistance.
  12. Nature of insect resistance and plant characters affecting the same. Genetics of insect resistance and breeding techniques for the development of insect resistant varieties.

 

References

  1. Abraham Blum. 2011. Plant Breeding for Water-Limited Environments. Springer Science Business Media, LLC, 233 Spring Street, New York, NY 10013, USA
  2. Baligar, V.C. and Duncan R.R. (eds.) 1990. Crops as enhancers of nutrient use. Academic press.
  3. Chopra, V.I. and Paroda, D.S. (eds.) 1996. Approaches for incorporating drought and salinity resistance in crop plants, Oxford and IBH publishing Co. Ltd., New Delhi.
  4. Chopra, V.L. 1989. Plant Breeding: Theory and practices, Oxford and IBH publishing Co. Pt. Ltd., New Delhi.
  5. Ciarmiello, L.F., Woodrow, P., Fuggi, A., Pontecorvo, G., Carillo, P. 2011. Plant genes for abiotic stress. In Abiotic stress in plants-mechanisms and adaptations, Shanker, A.K. and Venkateswarlu, B (eds.), pp. 283-308, INTECH-Open Access Publisher, Rijeka, Croatia.
  6. David Raper, C., Jr., Kramer and Paul J. 1983. Crop reactions to water and temperature stresses in humid, temperate climates. West view press, Colorado.
  7. Dell, B. 1981. Male sterility and anther wall structure in copper –deficient plant. Ann. Bot. 48: 599-608.
  8. Gorhan, J., Wyne-Jones, R.G. and McDonald, E. 1985. Some mechanism of salt tolerance in plants. Plant and Soil, 89: 15-40.
  9. Graham, R.D. 1991. Breeding wheats for tolerance to micronutrient deficient soils: Present status and priorities. In pages 315-331. Saunders, D.A. (ed) 1991. Wheat for the non-traditional warm areas, Mexico D.F., CIMMYT.
  10. Gupta, U.S. (ed) 1972. Physiological principles of dryland farming. Oxford and IBH publishing Co., New Delhi.
  11. Hasanuzzaman, M., Hossain, M.A., da Silva, J.A.T. and Fujita,M. 2012. Plant response and tolerance to abiotic oxidative stress: antioxidant defense is a key factor. In: Crop stress management: Perspective and Strategies, Venkateshwarlu B., Shanker A.K., Shanker C. and Maheswari M. (eds.), pp. 261-315, Springer, Heidelberg, Germany.
  12. Hossain, M.A., da Silva, J.A.T. and Fujita, M. 2011. Glyoxalase system and reactive oxygen species detoxification system in plant abiotic stress response and tolerance: An intimate relationship. In Abiotic stress in plants-mechanisms and adaptations, Shanker, A.K. and Venkateswarlu, B. (eds.), pp. 235-266, INTECH-Open Access Publisher, Rijeka, Croatia.
  13. Hossain, M.A. ,da Silva, J.A.T., Piyatida, P. and Fujita, M. 2012. Molecular mechanism of heavy metal toxicity and tolerance in plants: central role of glutathione in detoxification of reactive oxygen species and methylglyoxal and in heavy metal chelation. Journal of Botany, vol. 2012, Article ID 872875, 37 pages, 2012.
  14. Kosova, K.,Vıtamvas, P., Prasil, I.T. and Renaut, J. 2011. Plantproteome changes under abiotic stress-contribution of proteomics studies to understanding plant stress response. Journal of Proteomics, vol. 74, no. 8, pp. 1301–1322, 2011.
  15. Roso, O.S. and Camargo, C.E.O. 1991. Wheat breeding for better efficiency in phosphorus use. In pages 333-351 Saunders, D.A. (ed.) 1991. Wheat for the non- traditional warm areas. Mexico. D.F., CIMMYT. San Diego, C.A.
  16. Sharma, J.R. 1994. Principles and practices of plant breeding. Tatta McGraw-Hill publishing company Limited, New Delhi.
  17. Singh, B.D. 1986. Plant Breeding: Principles and methods. Kalyani publishers, New Delhi.
  18. Yoshida, S. 1972. Physiological aspects of grain yield. Ann. Rev. Plant Physiol. 23: 447-464.

 

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Bangladesh Agricultural University, Mymensingh

Department of Genetics and Plant Breeding

Syllabus for MS in Genetics and Plant Breeding

Course: GPB 521 Distant Hybridization and Chromosome Manipulation (Elective)

Credit hours: 2 

 

  1. Definition, importance and scope of distant hybridization. 
  2. Evaluation and utilization of wild germplasms of wheat, Rice, Brassica, Cotton and Tomato.
  3. Methods of distant hybridization.
  4. Barriers of distant hybridization: Pre-fertilization barriers and Post fertilization barriers.
  5. Overcoming the problems of pre- and post-fertilization of interspecific and intergeneric hybridization. 
  6. Production of alien addition, Substitution and translocation lines, their behaviour and uses in plant transformation.
  7. Uses of chromosome pairing mutants in alien gene transfer in allopolyploid species. Process of shorting alien DNA segments by various methods.
  8. Markers-assisted introgression of alien genetic materials in recipient species with special emphasis on commercially cultivated allopolyploid crop plants.

 

Text books

  1. Fehr, W.R, and H.H. Hadley, 1980. Hybridization of Crop Plants. American. Soc. Agron and crop science Soc. America Pubs. Madison.
  1. Kush, G.S.1973. Cytogenetics of Aneuploidy. Academic Press, New York
  2. Rilcy, R. and  K.R. Lewis, 1966. Chromosome Manipulations and Plant Genetics. Oliver, Edinburgh.

Reference books

  1. Ayala, F. J. and I. A. Kiger, 1980. Modem Genetics. The Benjamia Cummings Pub. Co. Carolina.
  2. Chang, T. T. 1976. Manual on Genetic Conservation of Rice Germplasm for Evaluation and Utilization. IRRI. Manila.
  3. Feuillet, C. G. J. Muehlbauer (eds.) 2009. Genetics and Genomics of the Triticeae. Plant Genetics and Genomics: Crops and Models 7, Springer Science+Business Media, LLC.
  4. Gupta, A.K., (Ed.) 1977. Genetics and Wheat improvement. Ford & I8- Pub. Co. New- Delhi.
  5. Kihara, H. 1982. Wheat Studies: Retrospect and Prospects. Elsevier Sci. Pub. Co., Amsterdam, Tokyo.
  6. Kole C. (ed.), Wild Crop Relatives: Genomic and Breeding Resources, Cereals. Springer-Verlag Berlin Heidelberg.
  7. Leaver C.S. (Ed.) 1980. Genome Organization and Expression in Plants. Plenum Press, New York.
  8. Seeberg, E. and K. Kleppe, 1981. Chromosome damage and Repair, Plenum Press, New York.
  9. Singh B.D. 1986. Plant Breeding, Kalayani Pubs., New Delhi.

 

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Bangladesh Agricultural University, Mymensingh

Department of Genetics and Plant Breeding

Syllabus for MS in Genetics and Plant Breeding

Course: GPB 523 Multivariate Statistics for Researchers (Elective)

Credit hours: 2

 

GPB 523: Multivariate Statistics for Researchers

  1. Introduction to multivariate statistics: Example data sets, Graphical methods for multivariate data, classification techniques, methods for multivariate statistics, data reduction techniques
  2. Principal component analysis (PCA): co-variance matrix, matrix algebra, dimensionality reduction, eigenvectors, eigenvalues, properties and assumption of PCA, derivation of PCA using co-variance method, PC scores, limits of dimensional reduction. Principal component analysis with Minitab/SAS/R software
  3. Discriminant analysis: Purposes of discriminant analysis, assumptions of discriminant analysis, linear discriminant analysis: Fisher’s discriminant, Bayesian discriminant; Canonical dicriminant analysis (CDA): canonical co-efficients, canonical components. Canonical discriminant analysis with Minitab/SAS/R software
  4. The multivariate normal distribution: sampling from a multivariate normal distribution and maximum likelihood estimation, outlier detection.
  5. Data transformation techniques: transformations to near normality, log, logit, square root, cube root, square and cube transformations.
  6. Multivariate Analysis of Variance (MANOVA): review of univariate ANOVA, properties of multivariate analysis of variance. MNOVA with Minitab/SAS/R software
  7. Cluster analysis and multidimensional scaling. Cluster analysis and multidimensional scaling with Minitab/SAS/R software
  8. Project report preparation demonstrating various multivariate analyses on plant breeding experiments.

 

References:

  1. Bilodeau, M., Brenner, D. 1999. Theory of multivariate statistics. Springer, New York.
  2. Flury, B.D. 1997. A first course in multivariate statistics. Springer, New York.
  3. Hardle, W., Hlavka, Z. 2007. Multivariate statistics: exercises and solutions. Springer, New York.
  4. Khattree, R., Naik, D.N. 1999. Applied multivariate statistics with SAS software. SAS Institute, J. Wiley and Sons, Cary, New York.
  5. Srivatava, M.S. 2002. Methods of multivariate statistics. Wiley-Interscience, New York.
  6. Tabachnick, B. G., Fidell, L.S. 2000. Using multivariate statistics. Allyn and Bacon (4th eds.), Boston.

 

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Bangladesh Agricultural University, Mymensingh

Department of Genetics and Plant Breeding

Syllabus for MS in Genetics and Plant Breeding

Course: GPB 509 Cytology & Cytogenetics

Credit hour: 2 credits

 

  1. Mitotic cycle: Cell doubling time, mitotic index, estimation of duration of different component phases of mitotic cycle.
  2. Karyotypic analysis and evolution of karyotype.
  3. Factors affecting embryo abnormalities and degeneration. Polyembryony.
  4. Applications of cytogenetics in crop improvement.
  5. Structural changes of chromosomes: meiotic behaviour and cytogenetic consequences.
  6. Permanent inversion and translocation heterozygosity; their role in speciation.
  7. Haploids: Spontaneous and induced haploids. Mechanisms of haploid induction. Meiotic behaviour and application of haploids in crop improvement.
  8. Chromosome pairing behaviour and cytogenetic consequences of euploids and aneuploids.
  9. Genetics of Chromosome pairing.
  10. Physical mapping of genes on chromosomes: In situ hybridization with DNA probes (FISH, McFISH, GISH, fibre fish); deletion mapping.
  11. Cytogenetic basis of apomixis: Definition, classification, detection of apomixis, cytology of apomixis, molecular basis of apomixis, apomixis hybridization and polyploidy, importance of apomixis in plant breeding. 

Text books

  1. Gupta, P.K. 1995. Cytogenetics. Rastogi and Co.
  2. Maheswari, P. 1950. An Introduction to the Embryology of Angiosperms New York: McGraw-Hill.
  3. Roy, D. 2009. Cytogenetics. Alpha Science International, Oxford, UK.
  4. Singh, R.J. 2002. Plant Cytogenetics. Boca Raton, FL.
  5. Sybenga, J. 1972. General Cytogenetics. North Holland Publishing Co., Amsterdam & London.

References: 

  1. Burnham, C.R. 1962. Discussions of Cytogenetics. Minneapelia, Burress Pub. Co.
  2. Burns, G. W. 1980. The Science of Genetics, 4th Macmillan Publishing Co. Inc. New York.
  3. Dawson, C.W.F. 1962. An Introduction to Cytogenetics of Polylploids, Oxford, Blackwell.
  4. Garber, E.D. 1972. Cytogenetics: An Introduction. Tata Mcgraw Hill, New Delhi.
  5. Khokhlov, S.S. 1976. Apomixis in Breeding. Amerind Publishing Co. Pvt. Ltd. New Delhi.
  6. Lewis, W.H. (Ed) 1980. Polyploidy. Proceedings of Internal Conference on Polyploidy, Biological Science relevance, Washington University.
  7. Sinha, U. and Sinha, S. 1976. Cytogenetics, Plant Breeding and Evolution. Jones and Barlett Publishers; Boston, London.
  8. Swanson, C.P., Merz, T. and Young, W.J. 1990. Cytogenetics. Prentice-Hall of India Private Limited, New Delhi, India.

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Bangladesh Agricultural University, Mymensingh

Department of Genetics and Plant Breeding

Syllabus for MS in Genetics and Plant Breeding

Course: GPB 511 Principles of Genetics (Compulsory)

Credit hours: 2

 

  1. Introduction: Pre-Mendelian views–Vapour and fluid theories, Pre formation theory, Epigenetic theory and Particulate theories. Critical review of Mendelism, Development of the subject.
  2. Linkage and crossing over: Mechanism of crossing over at molecular level. Evidence of linkage and crossing over, detection of linkage, factors affecting recombination frequencies measurement of crossing over in eukaryotes using F2 and 3 - point test cross data, and chromosome mapping.
  3. Gene expression: Effect of external and internal environments, penitrance and expressivity, phenocopies and pleiotropism.
  4. Multiple alleles: Test of allelism, inheritance of multiple alleles, self-incompatibility in flowering plants, pseudoalleles and isoalleles.
  5. Mutation: Definition, classification, induction and detection of mutation, classification of mutagenes, and action mechanism of mutagens at molecular level, DNA damage and repair, significance of mutation.
  6. Extranuclear inheritance: Features of extranuclear inheritance, maternal effect, mitochondrial and chloroplast genome in higher eukaryotes, male sterility and its types in flowering plants, use of male sterility in Plant Breeding.
  7. Genetic basis of Apomixis.
  8. Genetics of race and species formation: Change in natural population, mutation, recombination, selection, genetic drift, gene migration and adaptiveness. Reproductive isolation, role of hybridization and polyploidy in speciation. 

References

  1. Beale, G. and J. Knowles 1978. Extra-nuclear Genetics. First edition. Edward Arnalol, London.
  2. Burns, G.W. 1980. The Science of Genetics, Macmillan Publishing Co., Inc. New York.
  3. Fehr, W.R. and H.H. Hadley 1980. Hybridization of Crop Plants. American Society of Agronomy & Crop Science Society of America, Mandison, Wisconsin.
  4. Gardner, E.J., M.J. Simmons and D.P Snustad 1991. Principles of Genetics. John Wiley and Sens, Inc. New York.
  5. Goodenough, U. 1984. Genetics. Third edition, Saunders College Publishing, New York.
  6. Sinnott, E.W., L.C. Dunn and T. Dobzhansky 1958. Principles of Genetics. McGrew Hill Company, Inc. New York.
  7. Srb, A.M., R. Owen and R.S. Edgar 1965. General Genetics. Second edition. W.H. Freeman Company, San Franciseo and London.
  8. Strickberger, M.W. 1990. Genetic. 3rd Edition, Macmillan Publishing Co. Inc., New York, Collier MacMillan Publishers, London.
  9. Verma P.S. and V.K. Agarwal 1983. Cell Biology genetics Evolution & Ecology, S. Chand & Co Ltd. Ram Nagar, New Delhi- 110055.
  10. Verma P.S. and V.K. Agarwal 1983. Genetics, S. Chand & Co. Ltd. Ram Nagar, New Delhi.

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Bangladesh Agricultural University, Mymensingh

Department of Genetics and Plant Breeding

Syllabus for MS in Genetics and Plant Breeding

GPB 504 Applications of Bioinformatics in Plant Breeding (Practical- Compulsory)

Credit hour: 1

 

  1. Introduction and objectives of bioinformatics. Applications of bioinformatics in plant breeding and molecular biology.
  2. Tools and softwares: FASTA, BLAST, BLAT, RASMOL, GENBANK, Pubmed. PDB, RASMOL, Genetyx, Mega.
  3. Introduction of Biological databases:
  4. Nucleic acid databases: NCBI, DDBJ, and EMBL
  5. Specialized Genome databases: SGD and TIGR
  6. Protein structure databases: CATH, SCOP and SMART
  7. Protein function database: PROSITE, ENZYME and BioLip
  8. Data storage and retrieval: Retrieval methods for DNA sequence, protein sequence and protein structure information. File Formatting for Genbank, DDBJ, FASTA, PDB, SwissProt.
  9. Sequence alignments and database search: Introduction to Sequences alignments and Dynamic Programming; Local alignment and Global alignment (algorithm and example), Pairwise alignment (BLAST and FASTA Algorithm) and multiple sequence alignment (Clustal W algorithm).
  10. Gene expression and representations: General introduction to Gene expression in prokaryotes and eukaryotes, transcription factors binding sites, ORF finding.
  11. Primer designing for gene specific expression.
  12. Phylogenetic analysis: comparative genomics, orthologs, paralogs, methods of phylogenetic analysis (UPGMA, WPGMA, maximum-likelihood and neighbor-joining)
  13. Protein folding and structure modeling: Motif databases and analysis tools. Domain databases (CDD, SMART, ProDom) and Analysis tools. Protein structure prediction, protein-protein interaction.

References:

  1. Ignacimuthu, S. 2005. Basic bioinformatics. Alpha Science International, Harrow, UK.
  2. Draghici, S. 2010. Bioinformatics Databases: Design, Implementation, and Usage. CRC Press, Inc.
  3. Lesk, A. M. (Ed.) Database Annotation in Molecular Biology: Principles and Practice. John Wiley & Sons.
  4. Jiang, T., Xu, Y., & Zhang, M. Q. (Eds.) 2002. Current topics in computational molecular biology. MIT Press.
  1. Letovsky, Stanley I., ed. 2006. Bioinformatics: databases and systems. Springer Science & Business Media.

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Bangladesh Agricultural University, Mymensingh

Department of Genetics and Plant Breeding

Syllabus for MS in Genetics and Plant Breeding

Course: GPB 513 Advanced Plant Breeding & GPB 506 Practical Plant Breeding (Compulsory)

  

GPB 513: Advanced Plant Breeding (2 credits)

  1. Sources of variation, the genetic basis of selection based on breeding behaviour.
  2. Breeding strategies in respect of the crop and crop products.
  3. Problems of Plant Breeding: Breeding behaviour, gene pattern of the traits, breeding methods. Factors limiting genetic improvement of crop plants.
  4. Barriers of plant breeding behaviour and methods. System of pollination control and their role in breeding. Selection response –types and measurement.
  5. Genetic principles and methods of breeding self and cross-pollinated crops.
  6. Concept of plant ideotype and breeding varieties using morphological, physiological and economical traits together.
  7. Mutation and polyploid breeding –types, uses, consequences and screening methods.
  8. Breeding strategies for horticultural crops.
  9. Distinctiveness, Uniformity and Stability (DUS) and Value for Cultivation and Use (VCU) Tests, plant descriptors and identification of crop varieties, plant variety protection act of Bangladesh.

 

GPB 506: Practical Plant Breeding (1 credit)

  1. Demonstration of hybridization program of different field crops.
  2. Demonstration of observational yield trial and preliminary yield trials.
  3. Visiting seed certification agency to discuss with plant variety release procedure.
  4. Visiting crop germplasm collection centers in Bangladesh.
  5. Visit to relevant NARS research institutions.
  6. Report preparation and submission on all research visits.

 

Books and Journals Recommended

  1. Chopra, V.L. (ed.) 1989. Plant Breeding: Theory and practice, Oxford and IBH publishing Co., New Delhi.
  2. Donald, G.M. 1968. The breeding of crop ideotypes. Euphytica, 17: 383-403.
  3. Graham, R.D. 1984. Breeding nutritional characteristics in cereals. Adv. Plant Nutri. 1 : 57- 107.
  4. Mayo, O. 1984. The theory of plant breeding. Clarendor press, Oxford.
  5. Sharma, J.R. 1994. Principles and practices of plant breeding. Tata McGraw–Hill Publishing Company-Limited, New Delhi.
  6. Simonds, N.W. 1962. Variability in crop plants, its use and conservation. Biol. Rev. 37: 422- 465.
  7. Simonds, N.W. 1981. Principles of crop improvement, ELBS edition, Longman, U.K.
  8. Singh, B.D. 1999 Plant Breeding. Kalyania Publishers. Ludhiana, India. 107.
  9. Sneep, J., Hendrikson, A.J.T. and Holbek, O. (eds). 1979. Plant breeding perspectives. Centennial Publication of D.J. van der Have seeds, the Netherlands.

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Bangladesh Agricultural University, Mymensingh

Department of Genetics and Plant Breeding

Syllabus for MS in Genetics and Plant Breeding 

Course: GPB 515 Research Methodology and Scientific Writing (Compulsory)

Credit hours: 2

 

  1. Research Methodology

a) Research: types, processes and steps in it.

b) Hypothesis.

c) Determining research problem: Need; problem identification: originality, literature survey and review, research proposal preparation.

d) Design of experiments: Choice of design and layout randomization.

e) Data management through spreadsheet tools (MS Excel, OpenOffice) for computational data analysis (MSTATC, Minitab, Genstat, R).

 

  1. Academic Writing

a) Criteria of a good academic essay, Plagiarism and ways to avoid plagiarism, Organizational patterns and topic development of an essay: keeping chronological order, coherence, strategies for gathering information (literature search, brainstorming); Paragraph structuring, transition and linking, Punctuation uses, stating opposing arguments and quotations, giving credit to other people’s information.

b) Types of scientific writing: Journal articles: publishing journal articles, reviewing process, authorship Issue. Thesis: types of thesis, different parts of a standard thesis, contents and criteria, citation, how to make your thesis better.

 

  1. Presentations skill development: Concepts and need of presenting data or research works, types of presentation, basic rules of poster and oral presentation, academic presentations through MS Office PowerPoint.

 

References: 

  1. Coffey, Margaret P. 1987. Communication through Writing. Prentice Hall Regents, Englewood Cliffs, NJ 07632.
  2. Evans D. And Gruba, P. 2003. How to Write a Better Thesis. 2nd ed. Melbourne University Publishing.
  3. Kothari C.K. 2004. Research Methodology: Methods and Techniques. New Age International, New Delhi
  4. Krishnaswamy, K.N., Sivakumar, Appa Iyer and Mathiranjan M. 2006. Management Research Methodology; Integration of Principles, Methods and Techniques. Pearson Education, New Delhi.

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Bangladesh Agricultural University, Mymensingh

Department of Genetics and Plant Breeding

Syllabus for MS in Genetics and Plant Breeding

Course: GPB 525 Crop Evolution and Plant Genetic Resources (Elective)

Credit hours: 2

 

  1. Genetic factors operating in the evolution of new crop species –variation, mutation, recombination and selection.
  2. Reproductive isolation and formation of new species – regulatory changes in speciation disruptive selection and isolation (ecological, temporal, geographical)
  3. Role of introgressive hybridization and polyploidy in the evolution of new crop species.      
  4. Centre of diversity and domestication (primary, secondary, tertiary centers) of major   cultivated crop plants.
  5. Needs of Plant Genetic Resources (PGR), present status of PGR collection, documentation and future strategies in Bangladesh and PGR for food security in Bangladesh.
  6. Types and sources of PGR, their importance as base for plant breeding and the use of wild relatives in crop improvement.
  7. Diversity of PGR, characteristics and utilization pattern along with their role in plant breeding. Classical methods of using genetic resources in plant breeding.
  8. Management activities of plant genetic resources.  Methods of genetic conservation. Molecular tools in plant genetic resources conservation. Causes of genetic erosion in ecosystem and vulnerability of PGR.
  9. National Plant Genetic Resources Institute-its justification, objectives and mandate of PGRI in Bangladesh.
  10. Intellectual property rights and plant protection act.

       

References

  1. Chopra, V.L. (ed). 1989. Plant breeding: theory and practices. Oxford and IBH publishing Co., New Delhi.
  2. Frankel, O.H. and Bennett, E. (eds). 1975. Crop genetic resources for today and tomorrow. Cambridge Univ. Press. Cambridge.
  3. Hajjar, R. and Hodgkin, T. 2007. The use of wild relatives in crop improvement: A survey of developments over the last 20 years. Euphytica 156:1–13.
  4. Haussmann, B. I. G., Parzies, H. K., Presterl T., Susic, Z., and Miedaner, T. 2003. Plant genetic resources in crop improvement. Plant Genetic Resources 2(1); 3–21.
  5. Karp, A., Kresovich, S., Bhat, K.V., Ayad W.G. and Hodgkin T. 1997. Molecular tools in plant genetic resources conservation:  a guide to the technologies. IPGRI TECHNICAL BULL. NO. 2
  6. Lodzinky, G. and Aldev. 1976. The origin of chickpea, Cieer arietinum L. Euphytica 25: 211-257.
  7. Pandey, A., Tomer, A.K., Bhandari, D. C. and Pareek S. K. 2008. Towards collection of wild relatives of crop plants in India. Genet Resour Crop Evol 55:187–202.
  8. Rahman, L. 2012. Sustainable agriculture for nutritional food security: policies for plant breeding and seed system in Bangladesh. RDF resource development foundation, Dhaka, Bangladesh.
  9. Sharma, J.R. 1994. Principles and practices of plant breeding. Tata McGraw–Hill publishing Co. Ltd., New Delhi.
  10. Simonds, N.W. 1962. Variability in crop plants, its use and conservation, Biol. Rev. 37: 422-465.
  11. Simonds, N.W. 1976. Evolution of crop plants. Longman, London.

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Bangladesh Agricultural University, Mymensingh

Department of Genetics and Plant Breeding

Syllabus for MS in Genetics and Plant Breeding

Course: GPB 527 Hybrid Breeding (Elective)

Credit hours: 2

 

  1. Hybrid Breeding and Related Concept: Heterosis and hybrid vigour phenomenon in crop plants; cytoplasmic and molecular basis for expression of heterosis; Genetic diversity and their potentials in use.
  2. Exploitation of Heterosis: Types of hybrids, techniques for detecting potential parents and hybrids, methods of enhancing the levels of heterosis.
  3. Hybrid Breeding Program:
  1. Development, evaluation and maintenance of parental lines. Purification and improvement of parental lines.
  2. Use of various breeding techniques: CMS, GMS, Self-incompatibility, apomixes and chemicals.
  • Hybrid seed production in self and cross-pollinated crops at both experimental and commercial levels.
  1. Evaluation of hybrids.
  2. Quality assurance procedure in hybrid breeding.
  1. Development of Hybrid Varieties in Crop Plants: Production technologies of hybrids varieties in important field crops; hybrid seed production of rice, maize, and vegetables.
  2. Heterosis in population development: Development and exploitation of F2 hybrids, synthetics and composites
  3. Biotechnological approaches in hybrid breeding.         

 

References:

  1. Fehr, W.R. and Hadley, H.H. (Eds.) 1980. Hybridization of Crop Plants. American Society of Agronomy and Crop Science Society of America, Pubs. U.S.A.   
  2. Flestritzer W.P. and A.F. Kelly (Eds.) 1987. Hybrid seed production of selected cereals and vegetable crops, FAO Pub. Rome.
  3. Frankel, R. (Eds.) 1983. Heterosis –Reappraisal of Theory and Practice. Springer—Verlag, Berlin.
  4. Gallais, A. 1988. Heterosis: Its genetic basis and its utilization in plant breeding, Euphytica, 39(3): 95-104.
  5. Hayward, M.D. 1983. Exploitation of incompatibility mechanism for the production of F1 hybrid forage grasses. Euphytica. 39: 33-37.
  6. Jain, H. K., Kharkwal, M. C. (eds.) 2004. Plant Breeding- Mendelian to Molecular Approaches. Narosa Publishing House, New Delhi, India.
  7. Phillip, R.R. 1963. The application of incompatibility in Plant Breeding. Genetics Today. 3: 649-656.
  8. Rai, D. 1979.  Heterosis Breeding, Agro. Bio. Pub., Delhi. 
  9. Samuel, R.A. Walter, O.S. and Leng, E.R. 1982. Modern Corn Production. The Asia Foundation, San Francisco, California, USA.
  10. Simonds, N.W. 1979. Principles of Crop Improvement, Longman, London and New York.
  11. van der Have, D.J. 1979. Plant Breeding Perspectives. Centre for Agricultural Publishing Documentation Wageningen.   
  12. Virmani, S.S. (Ed.) 1994. Hybrid Rice Technology. New Developments and Future Prospects. IRRI. 
  13. Virmani, S.S. 1994. Heterosis and Hybrid and Hybrid Rice Breeding. Springer –Verlag, Berlin.
  14. Virmani, S.S. 1996. Hybrid Rice. Advances in Agron. Academy Press, Inc. 57: 378-462.
  15.  Walden, D.B. 1978. Maize Breeding and Genetics. Wilson, P. and Driscoll, C.J. 1983. Hybrid Wheat (In Monographs on Theoretical and Applied Genetics, Vol. 6 Heterosis, ed. by R. Frankel) Springer-Verlag Berlin Heidelberg.
  16. Wilson, P. and Driscoll, C.J. 1983. Hybrid Wheat (In Monographs on Theoretical and Applied Genetics, Vol. 6 Heterosis, ed. by R. Frankel) Springer-Verlag Berlin Heidelberg.

 

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Bangladesh Agricultural University, Mymensingh

Department of Genetics and Plant Breeding

Syllabus for MS in Genetics and Plant Breeding

Course: GPB 529: Experimentation and Data Analysis (Elective)

Credit hours: 2

 

  1. Field plot techniques for genetic and plant breeding experiments: Sources of variation, control of error variation, accuracy and precision, sampling and data collection.
  2. Variety testing experiments: Choice of design, layout randomization, data analysis.
  3. Randomized complete block design, b) Latin square design, c) Lattice design d) Augmented design and e) Combined analysis of data of on-station trails.
  4. Factorial experiments: Choice of design, layout, randomization and data analysis –plot experiment, and b) Strip-plot experiment.
  5. Comparison between test entries and treatment means: a) Least significant difference, b) Duncun multiple range test, c) Tukey’s W test
  6. Chi-square test: Test for a fixed ratio, test for independence in a contingency table, test for homogeneity of variance, heterogeneity of Chi-square.
  7. Simple and multiple correlation and regression analysis.
  8. Analysis of problem data a) Estimation of missing data and b) Transformation of data.
  9. Computational data analysis using Minitab, SAS or R software.

 

References:

  1. Dewey, D.R. and K.H. Lu 1959. Correlation and path coefficient analysis of components of created wheatgrass seed production. Agronomy. 51: 515-518.
  2. Gomez, K.A. 1972. Techniques for field Experiments with Rice. International Rice Research Institute. Los Bemos, Philippines.
  3. Gomez, K.A. and A.A. Gomez. 1984. Statistical Procedures for Agricultural Research. 2nd edition. John Wiley and Sons, New York.
  4. Good, P.I. 2012. A practitioner’s guide to resampling for data analysis, data mining, and remodeling. Boca Raton FL, CRC press.
  5. Li, C.C. 1966. The concept of path coefficient and its impact on population genetics. Biometrics. 12: 190-210.
  6. Little, T.M. and F.J. Hills. 1978. Agricultural Experimentations. John Wiley and Sons, New York.
  7. Panse V.G. and P.V. Sukhatme 1967. Statistical Methods for Agricultural Workers. Indian Council of Agricultural Research, New Delhi.
  8. Peterson, R.G. 1985. Augmented design for preliminary yield trials. Rachis. 4: 27-32.
  9. Peterson, R.G. 1986. Combined analysis of on station yield trials. Rachis. 4: 27-32.
  10. Steel, R.G.D. and J.H. Torrie 1960.  Principles and Procedures of Statistics. McGraw Hill Book Company, Inc., New York.
  11. Zaman, S.M.H., K. Rahim and M. Howlader 1982. Simple Lessons from Biometry. Bangladesh Rice Research Institute, Joydebpur. Dhaka.