magic :multiparent advanced generation intercross and qtl discovery
DESCRIPTION
MAGIC or multiparent advanced generation inter-crosses is an experimental method that increases the precision with which genetic markers are linked to quantitative trait loci (QTL). This method was first introduced by (Mott et al., 2000) in animals as an extension of the advanced intercrossing (AIC) approach suggested by (Darvasi and Soller , 1995)for fine mapping multiple QTLs for multiple traits. Advanced Intercrossed Lines (AILs) are generated by randomly and sequentially intercrossing a population initially originating from a cross between two inbred lines. MAGIC involves multiple parents, called founder lines, rather than bi-parental control. AILs increase the recombination events in small chromosomal regions for the purpose of fine mapping. These lines are then cycled through multiple generations of outcrossing. Each generation of random mating reduces the extent of linkage disequilibrium (LD), allowing the QTL to be mapped more accurately.TRANSCRIPT
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G.Kalidasan
MAGIC, Multiparent advanced generation intercross a new genetic resource for multiple trait improvement and QTL discovery in crops
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Quantitative traits
Phenotype expression
Natural variation
Experimental System
Selection or Natural Population
Experimental Population
Multiparent Advanced Generation Intercross Population
Case Studies
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Selection experiments
Marker allele frequency –
Unrelated individuals
Many generations
Difference in phenotype
LD between QTL and marker
LD around a QTL
Selection and Natural populations
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Comparison of allele frequency
Without phenotypic information
Loci subject to selection
Domestication
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Exploits LD in diverse population
Human
Crops
Maize
Advantage
Cheaper and high density markers
Disadvantage
Spurious associations
Greater precision but low power
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Mutant population
Spontaneous mutation
Induced mutation
Mutagenesis
Large resources
Poly ploidy
TILLING
Phenotyping screen
Knowledge on genes controlling trait
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F2 and backcross (BC) populations
Additive effects
Few meioses
Recombinant inbred lines
RILs are advanced homozygous
lines
Increased recombination events
and improved map resolution
Epistatic interactions
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Near isogenic lines(NIL)
Target trait is required for the generation of NILs.
High-resolution mapping
Double haploids
100% purity and genetic uniformity.
Genetic studies
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Randomly and sequentially
intercrossed population.
Phenotypic selection to further
reduce the frequency of deleterious
alleles from the donor.
Detect QTLs with epistatic effects
Useful meiotic recombination
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Linkage mapDNA Markers Position and relative genetic distance For identifying chromosomal regions that contain genes
controlling simple or complex traits using QTL analysis
QTL mapping
Advantage
High detection powerFew markers are required
Disadvantage
Large confidence interval of upto 5 to 30cMLimited resolutionOnly two alleles tested
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Animals. (Mott et al., 2000) and (Yalchin et al., 2005)
Fine-mapping of multiple QTLs for multiple traits in the same population.
Advanced intercrossed lines (AILs)
Each generation reduces the extent of linkage disequilibrium (LD), thus allowing QTL to be mapped more accurately.
Lines derived from early generations can be used for QTL detection and coarse mapping
While those derived from later generations will only detect marker-trait associations if markers are located very close to the QTL.
Multiparent advanced generation intercross
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Extended to plants
(Cavanagh et al., 2008)
Diverse founder lines
n/2 generations
RILs
Increased intercrossing cycles
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Short generation period- Arabidopsis
Eight founder lines
G1
G2
G3
G4
G10-12
SNP genotyping platforms
SSR Markers
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Statistics tools
Linear mixed effect model and Hierarchical Bayes QTL mapping - study the interrelationship between individuals MLs and founder lines and increases the precision to detect QTL
HAPPY- a software package for Multipoint QTL Mapping in Genetically Heterogeneous Animals
R/mp Map- A computational platform for the genetic analysis of
multi-parent recombinant inbred lines
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Advantages
Shuffling the genes across different parents enable accurately ordering the genes
Increased recombination - novel rearrangements of alleles and greater genetic diversity.
Best combinations of genes for important traits development
1000 Magic individuals
Seeds retained - fine mapping
Epistatic and G X E interactions
Facilitate the discovery, identification and manipulation of new forms of allelic variability
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Disadvantages
Extensive segregation
More time
Large scale phenotyping
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(Rakshit et al., 2012)
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In Arabidopsis fine mapping of QTL for germination and bolting time (Kover et al. 2009)
Studies in flowering time candidate genes
(Ehrenreich et al. 2009)
Developed computational platform R/mp Map for Genetic analysis (Huang and George, 2011)
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19 ‘‘founder’’ accessions
Wide geographical distribution
Staggered planting scheme
Replanted families – randomly
assigned crosses
342 F4 outcrossed families
Each F4 family derived up to 3
MLs followed by selfing 6
generations
527 lines taken out of 1026
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Developmental quantitative traits
Measured the heritability (h2)
h2 L is the proportion of variation that is due to genetic differences between lines, using the phenotypic average of the replicates within each line
h2 P is an estimate of the genetic variance if only one replicate per line were phenotyped
h2L ≥ h2P
h2L increases with the number of replicates
Mean of each line is used for QTL mapping
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Phenotypic variance
Diallelic population - 0.5
Magic – 0.052
Average minor allele frequency in
founder lines is 0.22
70% of SNP shared between any pair
of founders
Increasing replication within line
reduces non- genetic variance
Improves power of QTL
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A hidden Markov model (HMM) is used to make a multipoint probabilistic reconstruction of the genome of each ML as a mosaic of the founder haplotypes.
Diallelic SNPs cannot distinguish between all founders so information from neighboring SNPs is used to compute the posterior probability Pis
(L) is that at a given locus L, the ML i is descended from founder s.
Locus is defined to be the interval between two adjacent genotyped SNPs, labeled by the name of the left-hand SNP.
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Used fixed-effects QTL models but to accommodate population structure, in different ways used multiple-QTL modeling or random effects to explain the correlations introduced in population structure
Checked with hierarchical Bayesian random effects model
All approaches model the mosaic structure of the MAGIC genomes as described in and implemented in the R package HAPPY
Detected two QTLs on chromosomes 3 and 4 for the number of days to germination and bolting time.
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Constructed a linkage map from a four parent MAGIC population and validate it against a comprehensive DArT consensus map drawing together maps from over 100 biparental populations
Incorporated the alien introgressions in to the linkage map
Level of LD across the genome and compare it with previous estimates for LD from previous studies
The power and precision of MAGIC for QTL mapping for plant height , an important trait for yield potential
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Selected four elite wheat cultivar , A- Yitpi , B- Baxter, C- Chara, D- Westonia
Genetic diversity based on genetic survey of international wheat samples
Diverse geographical distribution
Phenotypic diversity for a range of traits
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Genotyping
Used 1285 DArT markers, 57 SSR markers and 1536 SNPs
384 SNPs observed to be polymorphic among the parental lines
were selected for genome wide coverage
Phenotyping
1100 RILs – Plant height was recorded
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R package mpMap
Filtered with monomorphic markers
Estimated the recombination fraction all pairs of loci with function ‘mpestrf’
Grouped the markers based on estimated recombination fractions and LOD scores with the function ‘mpgroup’
For map resolution computed recombination events for all lines using the function ‘mpprob’
Which calculates the multipoint probablity at each locus that the observed genotype is inherited from each of the four founder
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Both internal and external comparisons was done
Examined a series of diagnostic plots to propose changes to ordering which were then tested through ‘ compare orders’ function in R/mpMap
Used heatmaps based on both recombination fractions and LD using R/Ldheatmap
The tool provided visualization of the relationships between all pairs of markers
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External comparison
Diagnostic checks are compared it to an external DArT consensus wheat map
Each individual consensus map was based on genotyping involving the analyis of between 206 and 1525markers, with an average density of 582 markers
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Test the introgression in magic population
Sr36 is an introgression from Triticum timopheevii for stem rust resistance – carried in variety Baxter on chromosome 2B cause segregation distortion
Aimed to identify markers associated with it and identify lines containing it
Computed the degree of segregation distortion for which i) the Baxter allele differed from all other founder alleles
ii) mutual recombination of < 0.05 was observed were tagged as potential markers in the introgression
Estimated the probablity of a line having inherited an allele from the founder Baxter for the identified markers(‘mpprob’)
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Linkage disequilbrium
Multipoint probablities were computed using the function ‘mpprob’ in R/mpMap and LD was computed using the function ‘mpcalcld’
QTL Mapping
For all analyses used the ‘mplMmm’ function in the R package mpMap, which performs the interval mapping in the context of a linear mixed model
Three QTL for plant height were detected near known genes on chromosomes 2D, 4B, 4D.
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(MAGIC) populations combine the advantages of linkage analysis and association studies.
The increased recombination in MAGIC populations leads to novel
rearrangements of alleles and greater genetic diversity
Can facilitate the discovery, identification and manipulation of new forms of allelic variability
They require longer time and more resource to be generated and they are likely to show extensive segregation for developmental traits.
MAGIC populations are likely to bring paradigm shift towards QTL analysis in plant species
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The experimental method was underway since it has to be studied in many crops
The tools used for QTL mapping are very complex, so simplified models has to be developed in near future for understanding.
In near future the method will bring success in finding our economic interest of traits in plants.