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Marker assisted selection lecture


Marker Assisted Selection in Crop Breeding

Marker Assisted Selection is a value addition to conventional methods of Crop Breeding. It has been gaining importance in plant breeding with new generation of plant breeders and to get accurate and fast desired result from plant breeding.

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Marker Assisted Selection in Crop Breeding

  1. 1. MARKER ASSISTED SELECTION IN CROP BREEDING Presented By:– Pawan Kumar ROLL. NO. – 143G03 Deptt:- Plant Breeding & Genetics Submitted To:- Dr. A. K. Saxena
  2. 2. MAS  Marker assisted selection The use of DNA markers that are tightly-linked to target loci as a substitute for or to assist phenotypic screening DNA markers can reliably predict phenotype Assumption
  3. 3. Breeding for specific traits in plants is expensive and time consuming The progeny often need to reach maturity before a determination of the success of the cross can be made The greater the complexity of the trait, the more time and effort needed to achieve a desirable result The goal to MAS is to reduce the time needed to determine if the progeny have trait The second goal is to reduce costs associated with screening for traits If we can detect the distinguishing trait at the DNA level we can identify positive selection very early.
  4. 4. Gene vs. Markers  The gene of interest directly causes production of protein(s) or RNA that produce a desired trait or phenotype.  Markers (a DNA sequence or the morphological or biochemical markers produced due to that DNA) are genetically linked to the gene of interest.  The gene of interest and the marker tend to move together during segregation of gametes due to their proximity on the same chromosome and concomitant reduction in recombination (chromosome crossover events) between the marker and gene of interest.  If the gene of interest is not known, markers linked to the gene of interest can still be used to select for individuals with desirable alleles of the gene of interest.  The term 'perfect marker' is sometimes used when tests are performed to detect a SNP or other DNA polymorphism in the gene of interest,
  5. 5. Marker types Morphological markers: markers are often detectable by eye, by simple visual inspection. leaf sheath coloration, height, grain color, aroma of rice etc. Biochemical Markers: A protein that can be extracted and observed; for example, isozymes and storage proteins. Cytological Markers: The chromosomal banding produced by different strains; for example, G banding. DNA based or Molecular Markers: A unique gene (DNA sequence), occurring in proximity to the gene or locus of interest, can be identified by a range of molecular techniques such as RFLP, RAPD, AFLP, DAF, SCAR, microsatellite, or single- nucleotide polymorphism (SNP) detection.
  6. 6. Important properties of ideal markers for MAS  Easy recognition of all possible phenotypes (homo- and heterozygotes) from all different alleles  Demonstrates measurable differences in expression between trait types or gene of interest alleles, early in the development of the organism  Testing for the marker does not have variable success depending on the allele at the marker locus or the allele at the target locus (the gene of interest that determines the trait of interest).  Low or null interaction among the markers allowing the use of many at the same time in a segregating population  Abundant in number  Polymorphic.
  7. 7. Prerequisites for an efficient marker-assisted breeding program  Appropriate marker system and reliable markers: For a plant species or crop, a suitable marker system and reliable markers available are critically important to initiate a marker-assisted breeding program. suitable markers should have following attributes:  Ease and low-cost of use and analysis;  Small amount of DNA required;  Co-dominance;  Repeatability/reproducibility of results;  High levels of polymorphism; and  Occurrence and even distribution genome wide
  8. 8. F2 P2 F1 P1 x large populations consisting of thousands of plants PHENOTYPIC SELECTION Field trials Glasshouse trials DonorRecipient CONVENTIONAL PLANT BREEDING Salinity screening in phytotron Bacterial blight screening Phosphorus deficiency plot
  9. 9. F2 P2 F1 P1 x large populations consisting of thousands of plants ResistantSusceptible MARKER-ASSISTED SELECTION (MAS) MARKER-ASSISTED BREEDING Method whereby phenotypic selection is based on DNA markers
  10. 10. Activities of marker-assisted breedingMarker-assisted breeding involves the following activities provided the prerequisites are well equipped or available:  Planting the breeding populations with potential segregation for traits of interest or polymorphism for the markers used.  Sampling plant tissues, usually at early stages of growth, e.g. emergence to young seedling stage.  Extracting DNA from tissue sample of each individual or family in the populations, and preparing DNA samples for PCR and marker screening.  Running PCR or other amplifying operation for the molecular markers associated with or linked to the trait of interest.  Separating and scoring PCR/amplified products, by means of appropriate separation and detection techniques, e.g. PAGE, AGE, etc.  Identifying individuals/families carrying the desired marker alleles.  Selecting the best individuals/families with both desired marker alleles for target traits and desirable performance/phenotypes of other traits, by jointly using marker results and other selection criteria.
  11. 11. The situations favorable for MAS include  The selected character is expressed late in plant development, like fruit and flower features or adult characters with a juvenile period  The target gene is recessive  Special conditions are required in order to invoke expression of the target gene(s), as in the case of breeding for disease and pest resistance or the expression of target genes is highly variable with the environments.  The phenotype of a trait is conditioned by two or more unlinked genes.
  12. 12. Advantages of MAS  Simpler method compared to phenotypic screening ◦ Especially for traits with laborious screening ◦ May save time and resources  Selection at seedling stage ◦ Important for traits such as grain quality ◦ Can select before transplanting in rice  Increased reliability ◦ No environmental effects ◦ Can discriminate between homozygotes and heterozygotes and select single plants
  13. 13. Potential benefits from MAS  More accurate and efficient selection of specific genotypes ◦ May lead to accelerated variety development  More efficient use of resources ◦ Especially field trials Crossing house Backcross nursery
  14. 14. (1) LEAF TISSUE SAMPLING (2) DNA EXTRACTION (3) PCR (4) GEL ELECTROPHORESIS (5) MARKER ANALYSIS Overview of ‘marker genotyping’
  15. 15. Marker assisted breeding schemes 1. Marker-assisted backcrossing 2. Marker-assisted recurrent selection (MARS) 3. Gene Pyramiding 4. Early generation selection 5. ‘Combined’ approaches
  16. 16. Marker-assisted backcrossing The general procedure of MABC is as follow  Select parents and make the cross, one parent is recurrent parent (RP), and the other one used as donor parent (DP)  Plant F1 population and detect the presence of the marker allele(s) at early stages of growth to eliminate false hybrids, and cross the true F1 plants back to the RP.  Plant BCF1 population, screen individuals for the marker(s) at early growth stages, and cross the individuals carrying the desired marker allele(s) (in heterozygous status) back to the RP.  Plant the final backcrossing population (e.g. BC4F1), and screen individual plants with the marker(s) for the target trait. Have the individuals with required marker allele(s) selfed and harvest them.  Plant the progenies of backcrossing-selfing (e.g. BC4F2), detect the markers and harvest individuals carrying homozygous DP marker allele(s) of target trait for further evaluation and release.
  18. 18. Marker-assisted recurrent selection (MARS)  The long selection cycles impose restrictions on the practicability of recurrent selection method of breeding.  In continuous nursery programs pre flowering genotypic information is used for marker assisted selection and controlled pollination.  It is possible today to define an ideal genotype as a pattern of QTLs, all QTLs carrying favorable alleles from various parents.  It is likely that through such a MARS breeding scheme higher genetic gain will be achieved than through MABC.
  19. 19. Gene Pyramiding  Widely used for combining multiple disease resistance genes for specific races of a pathogen  Pyramiding is extremely difficult to achieve using conventional methods Consider: phenotyping a single plant for multiple forms of seedling resistance – almost impossible  Important to develop ‘durable’ disease resistance against different races
  20. 20. F2 F1 Gene A + B P1 Gene A x P1 Gene B MAS Select F2 plants that have Gene A and Gene B Genotypes P1: AAbb P2: aaBB F1: AaBb F2 AB Ab aB ab AB AABB AABb AaBB AaBb Ab AABb AAbb AaBb Aabb aB AaBB AaBb aaBB aaBb ab AaBb Aabb aaBb aabb Process of combining several genes, usually from 2 different parents, together into a single genotype x Breeding plan
  21. 21. Early generation MAS  MAS conducted at F2 or F3 stage  Plants with desirable genes/QTLs are selected and alleles can be ‘fixed’ in the homozygous state ◦ plants with undesirable gene combinations can be discarded  Advantage for later stages of breeding program because resources can be used to focus on fewer lines
  22. 22. F2 P2 F1 P1 x large populations (e.g. 2000 plants) ResistantSusceptible MAS for 1 QTL – 75% elimination of (3/4) unwanted genotypes MAS for 2 QTLs – 94% elimination of (15/16) unwanted genotypes
  23. 23. P1 x P2 F1 PEDIGREE METHOD F2 F3 F4 F5 F6 F7 F8 – F12 Phenotypic screening Plants space- planted in rows for individual plant selection Families grown in progeny rows for selection. Preliminary yield trials. Select single plants. Further yield trials Multi-location testing, licensing, seed increase and cultivar release P1 x P2 F1 F2 F3 MAS SINGLE-LARGE SCALE MARKER- ASSISTED SELECTION (SLS-MAS) F4 Families grown in progeny rows for selection. Pedigree selection based on local needs F6 F7 F5 F8 – F12 Multi-location testing, licensing, seed increase and cultivar release Only desirable F3 lines planted in field Benefits: breeding program can be efficiently scaled down to focus on fewer lines
  24. 24. Combined approaches In some cases, a combination of phenotypic screening and MAS approach may be useful 1. To maximize genetic gain (when some QTLs have been unidentified from QTL mapping) 2. Level of recombination between marker and QTL (in other words marker is not 100% accurate) 3. To reduce population sizes for traits where marker genotyping is cheaper or easier than phenotypic screening
  25. 25. ‘Marker-directed’ phenotyping BC1F1 phenotypes: R and S P1 (S) x P2 (R) F1 (R) x P1 (S) Recurrent Parent Donor Parent 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 … SAVE TIME & REDUCE COSTS *Especially for quality traits* MARKER-ASSISTED SELECTION (MAS) PHENOTYPIC SELECTION (Also called ‘tandem selection’) Use when markers are not 100% accurate or when phenotypic screening is more expensive compared to marker genotyping
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Marker Assisted Selection is a value addition to conventional methods of Crop Breeding. It has been gaining importance in plant breeding with new generation of plant breeders and to get accurate and fast desired result from plant breeding.


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