The document discusses MAGIC (Multi-parent Advanced Generation Inter-Cross) populations, which are a new resource for plant genetics that allow for more precise mapping of quantitative trait loci (QTLs). MAGIC populations are developed by intercrossing multiple diverse founder lines over multiple generations, increasing recombination and genetic diversity. This allows for both coarse and fine mapping of QTLs contributing to complex traits. The document provides details on the development of MAGIC populations, including founder selection, mixing, advanced intercrossing, and inbreeding. It also discusses applications in breeding programs and case studies mapping traits like disease resistance in rice MAGIC populations.

1. TOPIC- “MAGIC population its
development and application”
SUBMITTED TO :
Dr. Amar Sakure
Associate professor
Course Teacher (MBB501)
Department of plant biotechnology
Anand agricultural university
SUBMITTED BY :
Boddu Sangavi
Reg : 2010120093
M.sc agriculture 1st semester
Genetics and plant breeding

2. CONTENTS:
 MAGIC –meaning and purpose
 Advanced inter cross lines
 Why magic?
 Steps in development of magic lines
 Genetic analysis of magic population
 Applications Of Magic Lines In Breeding Programs
 Future line of work
 Advantages and limitations
 Institutes Involved In Development Of Magic Populations
 Case study

3. MAGIC POPULATION- A NEW RESOURCE FOR PLANT GENETICS
M-multi parent
A -advanced
G -generation
I-inter
C-cross
• It is a second generation mapping resource for discovery , characterization and
deployment of genes responsible for complex traits.
PURPOSE :
• Genetic dissection of complex traits
• It identifies genes that contribute to quantitative variation
• Most traits of biological and economic interest are quantitative in nature
• They display continuous variation (polygenic control)
• Identification of gene-trait associations for complex traits is difficult

4. MAGIC POPULATION
• Magic population is an extension of AILs
• It is a second generation mapping resource for discovery , characterization and
deployment of genes responsible for complex traits.
• Magic population is heterogenous stock
• Magic population is 1st introduced by Mott et.al 2000 in mice using 8 inbred
strains as an improvement over the AIC
• Term magic population is coined by Mackay and Powell 2008
• In plants magic population was 1st developed and described in Arabidopsis by
taking 19 founders Kover et al in 2009
• Intercrossed mapping population is created from multiple founder lines
• The intercrossed recombination and diversity of MAGIC gives greater precision
in QTL location and greater oppurtunity to detect more QTL
• Each generation reduces the extend of linkage disequilibrium thus allowing QTL
to be mapped more accurately
• Lines derived from early generations can be used for QTL detection and coarse
mapping
Cavanagh et al.,2008

5. Cavanagh et al.,2008

6. ADVANCED INTERCROSS LINES (AIL)
• It is an extension of RILs
• Proposed by Darvasi and Soller in 1995
• Consists of repetitively intermated f2 population followed by selfing to derive AILs
• The additional rounds of intermating reduce the level of LD and increase the
precision of QTL location
• Higher accuracy than RILs

7. What is the difference between RIL and AIL ?
Cavanagh et al.,2008

8. Why MAGIC ?
• For both coarse and fine mapping
• Incorporation of multiple parents ensures the segregation of population for multiple
QTL for multiple traits
• Negligible impact from population structure
• Increased mapping resolution by taking the advantages of both historical and
synthetic recombination
• To overcome the demerits of linkage analysis and association mapping like
 Lower power to detect QTL ,Sensitive to population structure
 QTLs are located with very large confidence interval (10-30cM)
 The narrow genetic base
DEVELOPMENT OF MAGIC LINES
1. Founder Selection
2. Mixing
3. Advanced Intercrossing
4. Inbreeding

9. FOUNDER SELECTION
• Based on genetic and phenotypic diversity
• Founder should be elite cultivars
• Founder material should be of more diverse origins like world wide germplasms
collections , distant relatives
• Founder parents generally will be 8 in number and each of them should be carefully
selected as a donor for at least one major trait in an improve background
Founder lines
World wide germplasm
collections
Huang et al.,2015

10. MIXING
• Multiple parents are intercrossed to form a broad genetic base
• Mixing of parents together in predefined patterns and intermated
• The inbred founders are paired off and inter mated , known as funnel
• The results of this stage is a set of lines whose genomes comprised contributions
from each of the founders
Funnel-1
Huang et al.,2015

11. ADVANCED INTERCROSSING
• Mixed lines from different funnels are randomly and sequentially intercrossed as in the
advanced intercross
• The main goal is to increase the number of recombination in the populations
• Selection is based on phenotype for further reducing frequency of the deleterious allele from
the donor
AIL-1 AIL-2
• Yamamoto et al 2014 concluded that at least 6 cycles of intercrossing is required for large
improvements in QTL mapping power
Funnels
Huang et al.,2015

12. INBREEDING
• Development of homozygous individuals
• RILs in plant can be created by single seed descent method
• The multiple generation of selfing will introduce additional
recombination but less than during the mixing and advanced
intercrossing stages
MAGIC effective population size :
 1000 magic individuals are adequate to map a single additive locus that accounts for
5% of the phenotypic variation to within 0.96cM distance
- Valder etal.,2006
 500 lines ,sufficient resolution may be obtained even in presence of high epistasis

13. GENETIC ANALYSIS OF MAGIC POPULATION
1.LINKAGE MAP CONSTRUCTION:
• 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 1st linkage map from a magic population was constructed in wheat
( Huang et al.2012)
2.QTL MAPPING APPROACH
• The use of heterogenous stock improves the power to detect and localize QTL
• The large number of parental accession increases the allelic and phenotypic
diversity
• The large number of accumulated recombination events increase the mapping
accuracy of the detected QTL compared to an f2 cross

14. APPLICATIONS OF MAGIC LINES IN BREEDING PROGRAMS
• Magic population can be used directly as source materials for the extraction
and development of breeding lines and varieties
• Development of variety with several agronomically beneficial traits
• Can provide solutions to a range of production constraints particularly stress
tolerance
• An assessment and understanding of the potential of enhanced
recombination in generating novel diversity
FUTURE LINE OF WORK :
• Development of magic population in more important crops
• Detection of QTLs which is responsible for stress resistance , yield and other
important traits
• Development of varieties with novel combinations

15. ADVANTAGES OF MAGIC POPULATION:
• 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
• Greater genetic variability
• Chances to get best combination of desirable genes
• Phenotypic selection in advance generation reduce the frequency of deleterious or
undesirable alleles from donors
• Magic population will be a permanent mapping population for precise QTL mapping
LIMITATIONS :
• Intensive labour of crossing
• 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

16. INSTITUTES INVOLVED IN DEVELOPMENT OF MAGIC POPULATIONS
CROP INSTITUTE
BREAD WHEAT NIAB
DURUM WHEAT University of Bologna ,ITALY
RICE IRRI
OATS IBERS
BARLEY SAC
SORGHUM ICRISAT
COWPEA IITA

17. Case study
Bandillo et al., (2013) have developed

18. The global population includes eight indica and
eight japonica founder lines, which carry QTLs conferring
tolerance of biotic and abiotic stresses. A, B, C, D, E, F, G
and H – represent the 8 indica parents; I, J, K, L, M, N, O
and P – represent the 8 japonica parents
Development of the indica
MAGIC population

19. Result of the study
Each population is comprised of 8 founder lines and were phenotyped for multiple traits :
Blast disease:
• Detected 3 contributing QTLs on chromosome 2,6 and 9
• Out of 8 founders ,6 were resistant to blast disease under natural conditions in the blast
nursery at IRRI
Bacterial blight :
• The subset of indica magic lines and the 8 founders were screened at maximum
tillering stage in the screen house at IRRI ,results indicate that majority of 200 lines
carried the Xa4 gene which is resistant for bacterial blight
Salt tolerance:
• Presence of good level of tolerance lines , presumably from the salt tolerant parents
IR4630-22-2-5-1-3 or IR45427-2B-2-2B-1-1
Submergence tolerance:
• Detected 54 associated markers out of which 49 were detected on chromosome 9 in the
region of sub1 locus
Grain quality:
• GWAS detected known major effect QTLs along with several potentially novel QTLs
for grain quality and grain shape