Basic_QTL_Marker-assisted_Selection_Sourabh.ppt
- 1. Sourabh Kumar Department of Genetics and Plant Breeding Chaudhary Charan Singh University, Meerut Marker Assisted Selection
- 3. Molecular breeding uses molecular marker data to enhance breeding activities, improve selection efficiency, and optimize breeding program planning and execution. Molecular breeding
- 4. Continuous Traits Meristic Traits Categorical Traits Ordinal traits Binary Traits Quantitative Traits ?
- 6. QTL ? A gene/set of genes or genomic regions associated with the expression of a quantitative trait ; referred to as Quantitative Trait Locus(QTL). Different type of QTLs:- Main effect QTLs Small effect QTLs E-QTLs e-QTLs m-QTL p-QTLs etc.
- 8. 1. Mapping Population 2. Genotypic data 3. Phenotypic data 4. Marker Linkage Map 5. Appropriate software packages Pre-requisites for QTL Analysis
- 10. Genotypic data
- 13. • Quantitative trait locus (QTL) analysis: a statistical method links two types of information—phenotypic data (trait measurements) and genotypic data (usually molecular markers)—in an attempt to explain the genetic basis of variation in complex traits (Falconer & Mackay, 1996; Kearsey, 1998; Lynch & Walsh, 1998). Approaches for QTL Analysis: 1. Single Marker Analysis 2. Interval Mapping(IM):- Simple Interval Mapping (SIM) Composite Interval Mapping (CIM)-Including Inclusive IM Multiple Interval Mapping (MIM) etc. QTLs Analysis & Its Approaches
- 14. Single Marker Analysis (SMA) Detect associations between molecular markers and traits of interest Four Methods:- 1. ‘t’ Test 2. Regression Analysis 3. ANOVA 4. Maximum Likelihood Approach A a M m QTL Marker
- 16. ADVANTAGES AND LIMITATIONS OF SMA Advantages • Simplest method of QTL detection. • Use basic statistical software. • Not need linkage map. Disadvantages/Limitations Confounded QTL effects & position, no determine Statistical Power is low Epistasis interaction can not be determine So, many false positive
- 17. M1 A m1 a M2 m2 Simple Interval Mapping (SIM) Composite Interval Mapping (CIM) Use most significant markers as Cofactors CIM: Refinement of SIM CIM: Combining interval mapping with multiple regression approach Power of QTL detection is increased, reduction of bias in the estimation of QTL position and effects. Inclusive Composite Interval Mapping (ICIM)
- 19. Introduction to MAS Marker assisted selection or marker aided selection (MAS) is an indirect selection process where a trait of interest is selected based on a marker (morphological, biochemical or DNA based) linked to a trait of interest (e.g. productivity, biotic/abiotic stress or quality), rather than on the trait itself. This term first used by Beckmann and Soller (1983).
- 20. What is molecular marker ?
- 21. • Ideally markers should be <5 cM from a gene or QTL Note: Using a pair of flanking markers can greatly improve reliability but increases time and cost Marker A QTL 5 cM RELIABILITY FOR SELECTION Using marker A only: ~95% Marker A QTL Marker B 5 cM 5 cM Using markers A and B: ~99.5% Markers must be tightly-linked to target loci!
- 22. Markers must be polymorphic 1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8 RM84 RM296 P1 P2 P1 P2 Not polymorphic Polymorphic!
- 23. Bacterial blight Blast BPH Hopper Burn False Smut Sheath Blight Drought Heat Submergence Salinity Nutrients deficiency Major constraints: Biotic and abiotic Stresses
- 24. General Steps in MAS- 1.Selection of parents. 2.Development of Breeding Population. 3.Isolation of DNA. 4.Scoring of marker. 5.Correlation with Morphological traits.
- 25. (1) LEAF TISSUE SAMPLING (2) DNA EXTRACTION (3) PCR (4) GEL ELECTROPHORESIS (5) MARKER ANALYSIS Overview of ‘marker genotyping’
- 26. Marker Assisted Backcross Breeding (MABB) Foreground selection Recombinant selection Background selection Phenotypic selection X F1 RP X BC1F1 Target trait Yield Quality Stress resistance Donor Parent Recurrent Parent
- 27. F2 P2 F1 P1 x large populations consisting of thousands of plants Resistant Susceptible MARKER-ASSISTED SELECTION (MAS) MARKER-ASSISTED BREEDING Method whereby phenotypic selection is based on DNA markers
- 28. Marker-assisted backcrossing Selection for target gene or QTL 1 2 3 4 Target locus 1 2 3 4 1 2 3 4 BACKGROUND SELECTION TARGET LOCUS SELECTION FOREGROUND SELECTION BACKGROUND SELECTION Accelerates the recovery of the recurrent parent genome
- 35. Pusa Basmati 1
- 36. P1 x F1 P1 x P2 CONVENTIONAL BACKCROSSING BC1 VISUAL SELECTION OF BC1 PLANTS THAT MOST CLOSELY RESEMBLE RECURRENT PARENT BC2 MARKER-ASSISTED BACKCROSSING P1 x F1 P1 x P2 BC1 USE ‘BACKGROUND’ MARKERS TO SELECT PLANTS THAT HAVE MOST RP MARKERS AND SMALLEST % OF DONOR GENOME BC2
- 37. Discovered first high lysine mutant (1935) - o2 Reported second mutant for change in amino acid composition (1935) - fl2 Discovery of QPM Opaque2 – a gene for improving quality of protein in maize A natural spontaneous maize mutant with soft and opaque grain was found in a maize fields in USA during the 1920s which was later named as opaque2 (o2) maize by Singleton.
- 38. o2 utilization in breeding programmes Resulted Soft endosperm Damaged kernels Susceptibility to pests and fungal diseases Inferior food processing Reduced yields Early efforts and experiences in using o2 cultivars pleiotropic effects of this gene
- 39. Application of MAS 1.It is useful in gene pyramiding for disease and insect resistance. 2.Uses in backcrossing programme. 3.It is being used for transfer of male sterility into cultivated genotypes from different sources. 4.MAS is being used for improvement of quality characters in different crops such as for protein quality in maize, etc…
- 40. Advantage of MAS 1. Accuracy, 2. Rapid Method, 3. Non-transgenic Product, 4. Identification of Recessive Alleles, 5. Early Detection of Traits, 6. Screening of Difficult Traits, 7. Highly Reproducible, 8. Small Sample for Testing, etc…
- 41. Achievements of MAS 1.Rice-a. (PB1 x JRBB55) Improved Pusa Basmati 1, b. Improved Sambha Mahsuri(BPT5204), 2.Maize - Improved QPM-9, 3.Pearlmillet - HHB67-2, 4.Wheat - Patwin, etc
- 42. Revolutionary Basmati Rice Varieties Pusa Basmati 1 Improved Pusa Basmati 1
- 43. Current status of molecular breeding • A literature review indicates thousands of QTL mapping/GWAS studies but not many actual reports of the application of MAS in breeding • Why is this the case?
- 44. Some possible reasons to explain the low impact of MAS in crop improvement • Resources (equipment) not available • Markers may not be cost-effective • Accuracy of QTL mapping studies • QTL effects may depend on genetic background or be influenced by environmental conditions • Lack of marker polymorphism in breeding material • Poor integration of molecular genetics and conventional breeding