Multiple inbred founder lines are inter-mated for several generations prior to creating inbred lines, resulting in a diverse population whose genomes are fine scale mosaics of contributions from all founders.

1. Presented by:-
Asit Prasad Dash
Doctoral Seminar-II (PBG-692)
MAGIC Populations
and its Role in
Crop Improvement
Deptt. of Plant Breeding & Genetics
College of Agriculture, OUAT, BBSR

2. INTRODUCTION
 MAGIC- Multi-parent Advanced Generation Inter-cross
 A simple extension of the advanced intercross
 Multiple inbred founder lines are inter-mated for several
generations prior to creating inbred lines, resulting in a
diverse population whose genomes are fine scale mosaics
of contributions from all founders.
 First proposed and applied in mice taking 8 inbred
strains- Mott et al . (2000)
 Coined by Mackay and Powell (2008).
 In plants, this was first developed and described in
Arabidopsis (Kover et al., 2009 ) taking 19 founders.

3. 4 way MAGIC PopulationAdvanced Intercross Lines
Huang et al., 2012

4. WHY MAGIC?
• The identification of gene-trait associations for complex (multi-genic)
traits needs a mapping population.
1) Biparental crosses: Traditional experimental populations combine
the genomes of two parents with contrasting phenotypes to identify
regions of the genome affecting the trait.
Limitations:
• Only two alleles are analysed and
that genetic recombination in
these populations .
• The narrow genetic base Which
limits the resolution for QTL
detection and genetic mapping
• It is only possible to detect those
genomic regions which differ
between the two founders.

5. Limitations:
• It is predominantly influenced by unknown population structure,
leading to spurious association (Hirschhorn & Daly 2005).
• Requires very large samples to have sufficient power to detect
genomic regions of interest, and hence may have difficulty
detecting rare alleles of importance.
MAGIC Population
The weaknesses of existing designs have led to this new type of
complex experimental design i.e MAGIC population which is
intermediate to biparental and association mapping designs in
terms of power, diversity, and resolution.
2) Association mapping/ linkage disequilibrium mapping:
A method of mapping quantitative trait loci (QTLs) that takes
advantage of historic linkage disequilibrium to link phenotypes to
genotypes by sampling distantly related individuals. .

6. Comparison between Biparental Linkage Analysis,
Association Mapping and MAGIC
Properties Biparental Association MAGIC
Founder Parents 2 > 100 >8
Crossing requirement Yes No Yes
Time to establish Moderate Low Long
Populationsize ~200 ~100 ~1000
Suitability for coarse mapping Yes No Yes
Suitability for fine mapping No Yes Yes
Amount of genotyping required Low High High
Amount of phenotyping required Low High High
Statistically complexity Low High High
Use of germplasm variation Low High High
Practical Utility Low High High
Relevance over time Low High High

7. These populations are now attractive for
researches due to
 Marker system that allows genotyping of the populations
High–throughput SNP (Single nucleotide
polymorphism) genotyping platform
 Advances in statistical methods
 Requirements for a better Mapping population
 Genetic variability for target phenotypes
 Reproducible quantitative genotyping

8. Stages of MAGIC Population
development
1. Founder selection
2. Mixing
3. Advanced intercrossing
4. Inbreeding

9. 1. FOUNDER SELECTION
 Based on genetic and/or phenotypic diversity.
• Elite cultivars with geographical adaptation
• Material of more diverse origins i.e. worldwide
germplasm collections, distant relatives
 Genetic incompatibility in some species can cause a large
reduction in the number of progeny.
Founder lines
Worldwide
Collection

10. 2. MIXING
Multiple founder lines are
intercrossed to form a
broad genetic base.
The inbred founders are
paired off and inter-mated
in a prescribed order for
each line, known as funnel.
In this stage we get such set
of lines whose genome is
contributed by each of the
founders.
A C D E F G HB

11. Mixed lines from different funnels are randomly and
sequentially intercrossed as in the advanced intercross.
Main goal is to increase the number of recombinations.
At least six cycles of intercrosses are required for
constructing a good QTL map.
3. Advanced Intercrossing:

12. Development of
homozygous individuals
RILs produced through
single seed descent (SSD)
or double haploid
production
Doubled haploid production
is often faster
Multiple generations of
selfing introduces
additional recombinations
4. Inbreeding
SSD

13. Stages of MAGIC population development design for
eight founders (Huang et al., 2015)

14. Genetic analysis of MAGIC populations
 Linkage map construction
 QTLmapping approaches

15. The large number of polymorphic markers across all
founders and accumulation of recombination events through
many generations of the MAGIC pedigree can be used to
achieve dense and high-resolution mapping of the genome.
The first linkage map from a MAGIC population was
constructed in wheat (Huang et al., 2012)
The higher levels of recombination in the MAGIC
population can be seen most clearly in the region around
centromeres.
For four-parent MAGIC population sizes of 500 lines, most
markers spaced at least 2 cM apart can be confidently
ordered, while for larger populations of 1000 lines this
improves to 1 cM resolution.
1. Linkage map construction

16.  The use of heterogeneous stock improve the power to
detect and localize QTLs.
 The large number of parental accessions increases the
allelic and phenotypic diversity.
 The larger number of accumulated recombination events
increase the mapping accuracy of the detected QTL
compared to an biparental F2 cross.
2. QTL mapping approaches

17. Software tools designed for the simulation and analysis
of multi-parent populations (MPP)
Software
package
Applicability Functionality References
HAPPY General MPP
QTL analysis;
permutation
Mott et al. (2000)
R/qtl
4-way, 8-way, 16-way
MAGIC
Simulation; map
construction; QTL
analysis; imputation
Broman et al. (2003)
R/ricalc
MAGIC by selfing, sib-
mating
Simulation; probability
calculation
Broman (2005)
Genome_scan
General MPP; full
sequence
QTL analysis;
permutation
R/mpMap
4-way, 8-way MAGIC
by selfing
Simulation; map
construction; QTL
analysis; imputation
Huang and George
(2011)
R/spclust
NAM, 4-way, 8-way
MAGIC by selfing
Selective phenotyping Huang et al. (2013)
R/mpwgaim
4-way, 8-way MAGIC
by selfing
QTL analysis Verbyla et al. (2014a)
AlphaMPSim General MPP Simulation Hickey et al. (2014)

18.  Development of variety with several agronomically
beneficial traits.
 Variety which can adapt to several diverse regions of
the world and suitable for diverse climatic conditions.
 MAGIC populations may be used directly as a source
material for the extraction and development of
breeding lines and varieties.
 MAGIC can provide solution to a range of production
constraints ( Biotic and abotic)
Use of MAGIC in crop breeding

19.  It can help to create a novel diversity.
 It is a powerful method to increase the precision of
genetic markers linked to the quantitative trait loci
(QTL) for fine-mapping of multiple QTLs for
multiple traits in the same population.
Cont’d…

20. Status of MAGIC populations in crops
Crop Design Phenotyping Analyses References
Rice Eight indica cultivars crossed in half- diallel to produce
35 funnels: indica MAGIC (AI0RIL)
MAGIC PLUS (AI2RIL)
MAGIC PLUS DH (AI2DH)
Yield in multiple-environment trials, drought and
salinity tolerance, disease resistance,grain quality
QTL, GWAS Bandillo et al. (2013)
Rice Eight japonica cultivars crossed in half- diallel to produce
35 funnels: japonica MAGIC (AI0RIL, in progress)
Bandillo et al. (2013)
Rice Eight indica + eight japonica cultivars, each crossed in
half-diallel with 35 funnels, then intercrossed:
MAGIC GLOBAL (AI0RIL)
Bandillo et al. (2013)
Wheat Lour spring wheat cultivars, 1 funnel, AI0RIL Plant height, hectolitre weight, coleoptile length LMC, QTL Huang et al. (2012);
Cavanagh et al. (2013);
Rebetzke et al. (2014)
Wheat Eight spring wheat cultivars crossed in half-diallel with
315 funnels:AI0RIL, AI2RIL, ABRIL
LMC, QTL CSIRO
Wheat Eight winter wheat cultivars, crossed in half-diallel with
315 funnels, AI0RIL
Yield, flowering time, plant height, yellow rust,
fusarium, mildew, awn presence
QTL, GWAS Mackay et al. (2014);
Scutari et al. (2014)
Wheat 16 spring wheat (in progress), 125 funnels, AI0RIL - - CSIRO
Wheat 16 winter wheat, crossed in half-diallel with 15 funnels,
AI0RIL
- - NIAB (unpublished)
Wheat 60 parents randomly intercrossed, AI12RIL Heading date LDA,
GWAS
Thepot et al. (2015)
Chickpea Eight desi (complete) - - Gaur et al. (2012)
Chickpea Eight kabuli (in progress) - - ICRISAT
Pigeonpea Eight (in progress), 7 funnels - - ICRISAT
Peanut Eight (in progress), 14 funnels - - ICRISAT
Maize Eight parents crossed in half-diallel with 35 funnels,
AI0RIL
Plant height, ear height, yield, flowering time — Pea et al. (2013)

21. Advantages of MAGIC Populations
 More targeted traits
 Increased precision and resolution with which the QTLs
can be detected due to increased level of recombination.
 Shuffling of genes across different parents enabling novel
rearrangements of alleles.
 To interrogate multiple allele
 Greater genetic variability
 Chances to get best combination of desirable genes.
 Phenotypic selection in advance generation reduce the
frequency of deleterious/undesirable alleles from donors.
 MAGIC population will be a permanent mapping
population for precise QTL mapping

22.  Intensive labour for crossing
 Extensive segregation
 Large population size is required for recovery of
recombinants with all the desirable traits
 More time is required to develop the resource population
 Large scale phenotyping is required for a particular trait.
 Requires more inputs
Limitations:

25. Experimental details:
Eight indica founder lines
Eight japonica founder lines
Founder lines known to exhibit high yield potential,
good grain quality, and tolerance to a range of biotic and
abiotic stresses
 At the S4 stage of SSD a subset of MAGIC indica population
was genotyped using a SNP markers.
 The populations were phenotyped for multiple traits:
• Blast and bacterial blight resistance
• Salinity and submergence tolerance
• Grain quality

26. Germplasm/
variety
Varietal
type
Origin Agronomic relevance
Fedearroz 50 Indica Colombia
Popular variety in several countries, with stay
green/delayed senescence & quality traits, disease
tolerance, progenitor of many breeding lines
Shan-Huang Zhan-2
(SHZ-2)
Indica China
Blast resistant, high yielding; in the pedigrees of
many varieties in south China
IR64633-87-2-2-3-3
(PSBRc82)
Indica IRRI
High yielding and most popular variety of the
Philippines
IR77186-122-2-2-3
(PSBRc 158)
Indica /
tropical
japonica
background
IRRI
High yielding variety in New Plant Type II
background
IR77298-14-1-2-10 Indica IRRI
Drought tolerant in lowlands with IR64
background and tungro resistance
IR4630-22-2-5-1-3 Indica IRRI
Good plant type, salt tolerant at seedling and
reproductive stages
IR45427-2B-2-2B-1-1 Indica IRRI Fe toxicity tolerant
Sambha Mahsuri +
Sub1
Indica IRRI
Mega variety with wide compatibility, good grain
quality and submergence tolerance
Indica Founder Lines

27. Germplasm/
variety
Varietal type Origin Agronomic relevance
CSR 30 Basmati group India
Sodicity tolerance; Basmati type long aromatic
grain
Cypress Tropical japonica USA
High yielding, good grain quality and cold
tolerant
IAC 165 Tropical japonica
Latin
America
Aerobic rice adaptation
Jinbubyeo Temperate japonica Korea High yielding and cold tolerant
WAB 56-125
O. glaberrima in
indica background
WARDA
NERICA background (O. glaberrima); heat
tolerant
and early flowering
IR73571-3B-
11-3-K2
Cross between
tropical
japonica and indica
IRRI-
Korea
project
Tongil type, salinity tolerant
Inia Tacuari Tropical japonica Uruguay
With earliness, wide adaptation, & good grain
quality
Colombia XXI Tropical japonica Colombia High yielding and delayed senescence
Japonica Founder Lines

28. Bandilloet al. (2013)

29. Bandillo et al. (2013)

30.  Development of the indica MAGIC, japonica MAGIC,
MAGIC Plus and MAGIC Global populations .
 Developed thousands of lines and now checking for wider
adoptability
 Several major genes and QTLs were identified that includes:
 Blast: Chromosome 2(26Mb), 3(3.5Mb), 7(27Mb), 10(13Mb)
 Bacterial Blight: Chromosome 11(27.3-27.9Mb), 5(0.4Mb)
 Salt tolerance: Chromosome 1(11.8Mb)
 Submergence tolerance: Chromosome 9 (6.2-6.3 Mb)
 Grain length: Chromosome 3 (15-22.2 Mb)
 Grain width: Chromosome 7 (26.4Mb)
 Waxyness: Chromosome 6 (1.7 Mb)
OUTPUT:

32. Experimental details
• Heterogeneous stock of 19 intermated accessions of the plant
Arabidopsis thaliana
• MAGIC lines developed: a set of 527 RILs
• Genotyping with 1,260 SNP and phenotyping for development-
related traits
• Attempts to fine-map QTLs

33. OUTPUTS
• QTL affecting natural variation in flowering time, identified
on chromosome 5 (~3.5 Mb) .
• Detected two QTLs on chromosomes 3 and 4 for the number of
days to germination.
• QTL on chromosome 3(~15.9 Mb) for nitrilase gene cluster

34.  The MAGIC lines are a new panel of genetically diverse and
highly recombinant inbred lines.
 It is a powerful method to increase the precision of genetic
markers linked to the QTLs.
 They represent a significant improvement over standard RILs.
 Multiparental populations of all types are still in their infancy.
 Their value and potential is yet to be judged through their ability to
deliver solutions and understanding of the genetics.
 MAGIC populations are likely to bring model shift towards QTL
analysis, gene mapping, variety development etc. in plant species.
CONCLUSION

35.  Development of MAGIC population in other important crops.
 Detection of QTLs which responsible for stress resistance,
yield and other important traits.
 Development of varieties with novel combinations
 MAGReS: The individual inbreds identified (using MAS) to
have desirable gene combinations can be mated recurrently
using the concept of recurrent selection. The ultimate breeding
line will have all the target traits.
FUTURE LINE OF WORK

36. Thank You