This is the post graduate level course of Plant Breeding and Genetics. It focuses on quantitative genetics, molecular dissection of complex traits, QTL and linkage analysis. At the end of the course students will be able to learn mapping, DNA extraction, primer designing, and in silico mapping and their applications in crop improvement.



  1. Introduction to molecular breeding.
  2. Quantitative genetics and plant improvement.
  3. Genotype x environment interaction (GEI), Molecular dissection of GEI.
  4. Applications of molecular markers.
  5. Development of mapping populations.
  6. Molecular dissection of complex traits.
  7. Molecular maps and types of mapping.
  8. Introduction to quantitative trait loci.
  9. QTL mapping, Multiple QTLs.
  10. Understanding the genetic architecture of quantitative traits.
  11. Bayesian and linkage disequilibrium mapping.
  12. Linkage analysis, map construction, experimental design and testing marker segregating patterns.
  13. Assumptions of different map functions.
  14. Problems and possible solutions in QTL analysis.
  15. Construction of molecular linkage map – a case study from cereals.
  16. Fine mapping of QTL and map based cloning.
  17. Markers assisted selection.
  18. Validation of marker-trait associations.
  19. Marker assisted gene introgression, selection for QTLs.
  20. Future prospects in molecular plant breeding.
  21. Genotyping by sequencing.


  1. DNA extraction, Primer designing.
  2. PCR, gel scoring, phenotypic and genotypic data collection.
  3. Software based data analysis to develop QTLs.
  4. In silico mapping – physical position of a marker- a case study in completely sequenced plant genome.
  5. Analysis of upstream and downstream genes of a marker.
  6. Genome browsing of sequenced plant genomes.
  7. Promoter analysis.


Recommended Books:

  1. Camp N.J., and A. Cox  2002. Quantitative Trait Loci: Methods and Protocols: Humana Printing Inc.
  2. Kang, M.S. 2002. Quantitative Genetics, Genomics, and Plant Breeding: CABIPublishing.

Suggested Books:

  1. Kole, C. 2007. Genome Mapping and Molecular Breeding in Plants: Springer.
  2. Wu, R, C. Ma and G. Casella. 2010. Statistical Genetics of Quantitative Traits: Linkage, Maps and QTL: Springer Publishing Company, Incorporated.
  3. Xu, Y. 2010. Molecular Plant Breeding: CABI Publishing