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markers in plant breeding. markers in plant breeding. Presentation Transcript

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