markers in plant breeding.


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markers in plant breeding.

  1. 1. Term paper presentation on: Molecular markers: Applications in Plant Breeding For the Course Plant Breeding(PLPB.512) By Alemu Abate HARAMAYA UNIVERSITY May, 2011 HARAMAYA
  2. 2. Introduction <ul><li> </li></ul><ul><li> </li></ul><ul><li> </li></ul><ul><li> </li></ul><ul><li> </li></ul><ul><li> </li></ul>
  3. 3. Objectives of the term paper <ul><li>General objective </li></ul><ul><li>-> to review and summarize scientific information on molecular marker techniques and their applications in the current plant breeding programs. </li></ul><ul><li>Specific objectives : </li></ul><ul><li>  </li></ul><ul><li>-> To differentiate the different molecular marker techniques. </li></ul><ul><li>  </li></ul><ul><li>-> To identify and describe the different molecular marker types. </li></ul><ul><li>  </li></ul><ul><li>-> To describe the different application of molecular markers. </li></ul><ul><li>  </li></ul><ul><li>-> To compare importance of molecular markers. </li></ul><ul><li>  </li></ul><ul><li>-> To describe limitation of molecular markers. </li></ul>
  4. 4. Genetic markers <ul><li>The three types of genetic markers: </li></ul><ul><li>Morphological markers   </li></ul><ul><li>-> traditional markers, highly dependent on environmental factors, time consuming, labour intensive; need large populations of plants and large plots of land or greenhouse space. </li></ul><ul><li>Biochemical markers   </li></ul><ul><li>-> Proteins (Isozymes) or RNAs markers, less dependant on environmental factors, superior to morphological markers, less polymorphic differences (problem in commercial breeds of plants) </li></ul><ul><li>  -> Enzymes are separated on the basis of net charge and mass via electrophoresis gels. </li></ul><ul><li>Molecular markers </li></ul><ul><li>-> DNA marker, polymorphic, independent of environmental factors, easy, fast, co-dominant and reproducible but it is costly. </li></ul>
  5. 5. Molecular marker techniques <ul><li>Two types of molecular techniques </li></ul><ul><li>1. Hybridization-based methods </li></ul><ul><li>-> The first, includes restriction fragment length polymorphism (RFLP) and variable number tandem repeats. </li></ul><ul><li>-> Fragments are separated using agarose or polyacrylamide gel electrophoresis. </li></ul><ul><li>-> Polymorphisms are detected by hybridizing the restriction enzyme-digested DNA with labelled probes. </li></ul><ul><li>-> Procedure for hybridization: </li></ul><ul><li>1) DNA isolation 2) Restriction digest </li></ul><ul><li>3) Gel electrophoresis </li></ul><ul><li>4) Transfer to nitrocellulose membrane filter </li></ul><ul><li>5) Probe visualization- probes consist of radio labeled sequences </li></ul><ul><li>6) Analysis </li></ul>
  6. 6. Cont. <ul><li>2. Polymerase chain reaction (PCR)-based methods </li></ul><ul><li>-> Amplification of particular DNA sequences with arbitrary primers. </li></ul><ul><li>-> It includes random amplified polymorphic DNA (RAPD), and DNA amplification fingerprinting (DAF), Inter simple sequence repeats (ISSRs), amplified fragment length polymorphism (AFLP) </li></ul><ul><li>-> Amplified fragments are separated electrophoretically and banding patterns are detected by staining and autoradiography. </li></ul><ul><li>-> Procedure for PCR methods: </li></ul><ul><li>1) DNA fragmentaion with two restriction enzymes </li></ul><ul><li>2) Ligation of “adapters” to the ends of each fragment </li></ul><ul><li>3) Primers are designed from the known sequence of the adapter </li></ul><ul><li>4) PCR is performed </li></ul><ul><li>5) Visualization on agarose gels with ethidium bromide. </li></ul>
  7. 7. Table 1. Summary of advantages and disadvantages of some commonly used markers (Kumar et al. , 2009).
  8. 8. Table 2: Comparsion between different molecular methods for plant genome analysis (Sharma et al ., 2008).
  9. 9. Table 3. Comparison of the most common used markers (Kumar et al. , 2009).
  10. 10. Molecular marker applications in plant breeding <ul><li>Molecular markers are used in plant breeding, taxonomy, physiology, embryology, genetics, evolution, genetic engineering etc </li></ul><ul><li>Some of applications in plant breeding are: </li></ul><ul><li>1. Marker-assisted selection </li></ul><ul><li>-> It replaces evaluation of a trait (difficult or expensive). </li></ul><ul><li>-> It is not influenced by growth stage and environmental factors. </li></ul><ul><li>-> It can increase efficiency of selection for low-heritability. </li></ul><ul><li>2. Genetic diversity analysis </li></ul><ul><li>-> Plant breeding is dependant of genetic variation </li></ul><ul><li>-> Genetic diversity is measured by genetic distance (GD) or genetic similarity (GS = 1 - GD) </li></ul><ul><li>-> It is used to assess variation over time, protection of intellectual property rights, registration of germplasm, and evaluation of new sources of germplasm for their potential to increase genetic diversity </li></ul><ul><li>-> It is superior to morphological, pedigree, heterosis, and biochemical </li></ul>
  11. 11. Cont . <ul><li>3. Genetic mapping </li></ul><ul><li>-> Markers can be used for map construction. </li></ul><ul><li>-> It predicts the linear arrangement of markers on a chromosome and the recombination frequency. </li></ul><ul><li>4. Manipulating traits controlled by a few major loci </li></ul><ul><li>-> To map and transfer the gene of interest </li></ul><ul><li>5. Authentication or DNA fingerprinting </li></ul><ul><li>-> For diagnosis, protection property right and quality controlling </li></ul><ul><li>6.Phylogeny and evolution </li></ul><ul><li>Perform phylogenic analysis on a species by comparing the presence/absence of various markers in their genome. </li></ul><ul><li>For taxonomic classification to determine the primary, secondary or tertiary genepool of the system </li></ul>
  12. 12. Summary <ul><li>Plant breeding depends on genetic variation and selection. </li></ul><ul><li>Selection is difficult and assisted by morphological, biochemical and molecular markers. </li></ul><ul><li>Molecular markers are DNA marker, polymorphic, independent of environmental factors, easy, fast, co-dominant and reproducible but it is costly. </li></ul><ul><li>The two forms of molecular techniques( hybridization and PCR methods). </li></ul><ul><li>Many forms of molecular markers </li></ul><ul><li>-> RFLP, RAPD, VNTR, SSR, AFLP ……. </li></ul><ul><li>Molecular markers are used in diversity analysis, parent selection, germplasm characterization, identification, genetic fingerprinting, genetic diagnostics, genome organization and phylogenic analysis </li></ul>
  13. 13. Thank you