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Traits

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Develop the population. Genotype individuals. 3 point ... Washing film exp. Film development. Total time: 7-10 days. Rs=N/4b. rice (4.5x109 bp)~17x106 rs ... – PowerPoint PPT presentation

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Title: Traits


1
Traits
  • Qualitative traits
  • Quantitative traits
  • Different phenotypic classes
  • Continuous phenotypic distribution

2
Types of populations
  • F2
  • BCn
  • RILs
  • DHs

3
Making a linkage map
  • Develop the population
  • Genotype individuals
  • 3 point linkage analysis
  • Based on recombination freq..
  • Needs adjustment
  • I.e. 80 loci3160 pair wise combinations

Computers will do the job, if you know what you
are doing!
4
Types of Markers
  • Morphological markers
  • Molecular markers
  • Proteins
  • Isozymes
  • Anonymous proteins
  • Storage proteins

5
Types of Markers (cont.)
  • DNA markers
  • RADPs
  • RFLPs
  • AFLPs
  • SSRs
  • STSs, ESTs
  • SSCPs
  • SNPs

6
RFLPs
  • DNA Extraction
  • DNA restriction
  • Agarose gel electrophoresis
  • Southern blotting
  • Probe hybridization
  • Washing film exp.
  • Film development
  • Total time 7-10 days
  • RsN/4b
  • rice (4.5x109 bp)17x106 rs
  • Probe can be known DNA or anonymous
  • Uses 32P
  • Requires large amount of DNA (15 µg)

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9
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10
Parental Screening Blot
P1
P2
11
a
b
1
1 2 3
-
c
2
b
c
a
3

12
The PCR
13
SSRs
  • DNA extraction
  • DNA amplification (PCR)
  • Polyacrilamide gel electrophoresis
  • (Staining) (not in fluorescence systems)
  • Simple sequence repeats
  • 1-5 bp
  • I.e. (CA)n (CGT)n
  • Requires primers flanking the repeats

Total time 1-2 days
14
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15
SSRs
P1
P2
Segregating population
16
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17
AFLPs
  • DNA extraction
  • DNA restriction (2 enzymes)
  • Ligation of adapters
  • Amplification
  • Selective amplification (primers 3 select. Ns)
  • Polyacrilamide gel electrophoresis
  • Dominant
  • Low reproducibility

Total time 5-7 d.
18
AFLPs
19
Comparison
labor extraction cost not included
20
Sources of Markers
  • SSRs Publications
  • STS/ESTs Genomic databases (http//www.ncbi.nlm.n
    ih.gov)
  • RFLPs Publications clone repositories
    authors (http//wheat.pw.usda.gov)
  • AFLPs Publications, yourself

21
Association between markers and traits
  • Bulk segregant analysis techniques
  • Through linkage maps
  • QTL analysis
  • Good phenotypic characterization

22
Bulk segregant analysis
  • Develop population
  • Evaluate trait/s
  • Phenotypic classes
  • Genotyping individuals
  • Option Bulk DNA within classes
  • No need for linkage map
  • Very appropriate for qualitative traits
  • For quantitative traits use extreme individuals
  • ANOVA, t-test

From Kaeppler et al, TAG(1993)85
23
QTL analysis
  • Develop population
  • Evaluate trait
  • Several environments
  • Develop linkage map
  • Statistical analysis
  • Requires good map and good phenotype
  • Statistical analysis
  • Single makers
  • Interval mapping

24
QTL estimation
  • Size and type of population
  • Number and location of true loci
  • Trait heritability
  • Genome coverage
  • QTL analysis

25
Markers in Plant Breeding
  • Genetic knowledge
  • Number and effects of genes involved
  • Aid in selection
  • Morphological markers, storage proteins already
    being used

26
Using molecular markers in a plant breeding
program
  • Limitations
  • Cost
  • Integration in the program (Timing)
  • Markers are source depending
  • Potentials
  • Money/time savers
  • Increasing selection pressure
  • Earlier selection
  • Introgression of new alleles in the elite
    germplasm (backcross breeding)

27
Two forms of Marker Assisted Selection
  • Background selection
  • Using markers through the genome in order to
    recover as much of the recurrent parent as
    possible
  • Foreground selection
  • Using 1-2 markers per gene (or QTL) in order to
    select those individuals homozygous for the
    desired allele

A third form background and foreground selection
combined
28
Foreground selection for qualitative traits
  • Recessive alleles
  • Traits expressed after flowering
  • Costly phenotypic screening

In backcross
29
Foreground selection for qualitative traits
(cont.)
  • Two issues in marker assisted backcross breeding
  • Number of lines needed
  • Distance from the marker/s to the locus

We need to be certain to be able to find at least
one line with the desired genotype for the marker
locus
30
Foreground selection for quantitative traits
  • Most important traits are quantitative
  • Introgressing a QTL in elite germplasm (similar
    to foreground selection for qualititative traits)
  • Application to recurrent selection?

31
Relative efficiency (RE) of MAS for QTLS
  • RE increases with lower heritability
  • RE increases with higher proportion of additive
    variance associated with markers
  • RE increases with fewer QTLs
  • RE increases when marker and QTL are in coupling
    phase vs. repulsion phase

Simulation studies
32
How would you integrate MAS in your breeding
program?
33
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34
Some reading anyone?
  • Mol. Breeding (1999) 5143
  • TAG (1998) 96147
  • TAG (1992) 84803
  • Heredity (1998) 80489
  • Euphytica (1981) 30227
  • Statistical Genomics. B.H. Liu
  • http//nbpgr.delhi.nic.in/mmarker
  • Molecular dissection of complex traits. Paterson
    A.H. (ed)
  • Crop Sci. (1997) 371686
  • Genetics (1997) 1471469
  • Crop Sci. (1998) 381164

35
More reading!
  • Crop Sci. (1999)39967
  • New Phytologist (1997) 137 (1)165
  • TAG (1993) 85. Kaepler et al
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