Role of MAGIC population in vegetable crops

1. Role of MAGIC population in
Vegetable improvement
Presented by:
Anusha K.R
L-2021-H-88-D

2. However, the identification of QTLs remains a challenge for plant breeders
Identification of QTLs that
contribute to improving yield
and quality traits
Key factor in promoting
a new Green Revolution.
Marker-assisted selection
(MAS)
Introgression breeding
Pyramiding of QTLs
Improved
cultivars

3. Production of
mapping
population
Identification
of
polymorphism
Appropriate experimental
design to evaluate the
environmental effects and
statistical methods to
detect and locate QTLs
Genetic Mapping
Mortal Immortal
Double Haploids (DH)
Recombinant inbred lines
(RIL’s)
Near Isogenic Lines (NIL’s)
F2Population
F2derived F3 Population
Backcross population
MAGIC population

4. Limitations of Biparental populations
• Shortage of diversity
• Limited opportunities for genetic recombination events
• Only two alleles are analyzed, with a maximum resolution of 10–30
cM

5. • Population sub-structure
• Unbalanced allele frequencies
• Requires very large samples and many markers
• Efficiency is limited by unknown pedigrees
Limitations of GWAS

6. M •Multi-parent
A •Advanced
G •Generation
I •Inter
C •Crosses

7. Idea of MAGIC
• coined by Mackay and Powell (2007)
• are panels of RILs that are fine-scale mosaics with equal proportions of the founder
genomes
• a powerful next-generation MP to precisely map the agronomically important QTLs
• represent a bridge between linkage mapping and association mapping
• Increases the mapping resolution by incorporating multiple founders with increased
genetic and phenotypic diversity

8. (Stadlmeier et al 2018)

9. MAGIC Development Strategies
• Founder Selection
• Population Size
• Cross-Designs
• Analysis Software for QTL Mapping

10. Founder Selection
• should cover a broad phenotypic,
genetic, and geographic diversity to
exploit the potential of the population
• well characterized at the molecular
and physiological levels
• Wild species, landraces, commercial
cultivars, or elite breeding lines with
desirable traits
(Arrones et al 2020)

11. Population Size
• Large population sizes are essential in each generation
• MP of at least 100-250 individuals is required for coarse QTL mapping
• As the population size increases, the power and resolution of QTL mapping also increases
• could be affected by the plants with poor development, fruit setting, or by the appearance of
parthenocarpic fruits

12. • Organisms with large genomes require an offspring of at least 500 individuals to provide a resolution
power of the subcentimorgan range enough to detect a single QTL.
• Organisms with smaller genomes can reduce their population size while maintaining the same
resolution power.
(Arrones et al 2020)

13. Cross-Designs
• MAGIC populations can be developed by different breeding designs that give rise to
different population structures.
• Basically, the two main approaches to develop MAGIC populations are the following :
1. The Funnel Approach
2. The Diallel Approach

14. The Funnel Approach
• The development of MAGIC population starts with a funnel
breeding scheme.
• Several generations of inter-crossing among a number (n) of elite
parental lines to obtain n/2 F1 hybrids
• Subsequently intercrossed in a set mating design to combine the
genomes of all founders in the progeny lines.
(Scott et al 2020)

15. The Diallel Approach
• Inter-crossing the founders in multiple funnels by a
half-diallel mating system
• Inter-crossing of the resulting F1s until all the
founders are represented in a single generation
• Similar to the funnel approach, but covers all possible
2-way, 4-way, and 8-way cross combinations
• Eight founders = 28 two-way, 14 four-way, and 7
eight-way crosses
(Scott et al 2020)

16. Advanced intercrossing
• Mixed lines from different funnels are
sequentially intercrossed
• Main goal is to increase the number of
recombinations in the population
(Huang et al 2015)

17. Inbreeding
• progressed to create homozygous
individuals
• RILs in plants can be created via SSD or
DH production
• DH production is faster but, the multiple
generations of selfing will introduce
additional recombination
(Huang et al 2015)

18. Analysis Software for QTL Mapping
• R/mpMap
• R package for 4-way and 8-way MAGIC populations
• Developed for analyzing MP designs with greater flexibility in pedigree definition and
• Accommodate linear mixed models to simultaneously assess genetic and environmental
variation

19. Advantages

20. MAGIC population - primarily used for
two purposes:
Permanent immortal MP for precise
QTL location
Development of new elite material to be
directly released as pre-breeding
material

21. QTL detection
Large number of accumulated recombinant events achieved
over multiple rounds of inter-crossing and selfing
Improves QTL mapping accuracy
Greater resolution
Increases the
number of
QTLs that
segregate in
the cross
Higher
genetic and
phenotypic
diversity
within a
single MP
Combination
of multiple
founders
Promote
novel
rearrangement
of alleles

22. Immortal RILs that constitute
the final MAGIC population
Exploited in breeding programs for the
development of improved lines and hybrids
Analyzed across a wide range of
environments to increase the
understanding of G×E interaction and
phenotypic plasticity

23. • More investment in time
• Greater efforts to be developed due to their complex crossing scheme
• Requires a larger population size compared to a bi-parent population.
• Logistically challenging and labor-intensive.
• Many molecular markers are required
• When wild species are in the panel of founder parents, genetic incompatibility may appear.
Limitations

24. Comparison of advantages and limitations of
biparental, association and MAGIC MPs
Characteristic Population Type
Bi-Parental Association MAGIC
Investment in time to be established - + - -
Required population size + - -
Genetic and phenotypic diversity - + + +
Suitability for coarse mapping + - +
Suitability for fine mapping - + +
QTL resolution - + + +
Required marker density + - -
Recombination rate - + +
Low population sub-structure + - +
Low LD + - +
(Arrones et al 2020)
+ Advantages ; - Limitations

25. Species Founders Details Genotype data References
Tomato
(Solanum lycopersicum)
8 4 S. lycopersicum and 4 S.
lycopersicum var.
cerasiforme diverse lines,
crossed in 1 funnel, 397
RILs
4 million SNPs from
WGS of founders
(6.7–16.6x);1536
KASP SNPs
genotyped in 397
RILs
(Causse et al 2013,
Pascual et al 2015)
8 4 cherry and 4 large-fruited
tomato accessions crossed
in 1 funnel, 124 RILs
7400 SNP markers
and a total of 25
QTLs were mapped
(Burgos et al 2021)
Brinjal
(Solanum melongena)
8 7 S. melongena and 1 S.
incanum
7724 SNP markers
genotyped in 420
RILs
(Mangino et al 2022)
Common bean
(Phaseolus vulgaris L)
8 8 Mesoamerican breeding
lines
20,615 polymorphic
markers in 996 RILs
(Diaz et al 2020)
Cowpea
(Vigna unguiculata)
8 1 US cultivar and 7
cultivars from sub-Saharan
Africa chosen for
agronomic traits, crossed in
6 funnels, 305 RILs
32130 genotyping
array SNPs in 305
RILs
(Huynh et al. 2018)
MAGIC population studies in Vegetables

26. Case studies

27. • Material used: seven cultivated eggplants, i.e., MM1597 (A), DH ECAVI (B), AN-S-26 (D), H15 (E), A0416
(F), IVIA- 371 (G) and ASI-S-1 (H), and the S. incanum accession MM577- Funnel breeding scheme
• Genotyping : eggplant 5k probes SPET platform and
• Phenotyping: anthocyanin presence in vegetative plant tissues (PA) and fruit epidermis (FA) and
Pigmentation Under the Calyx(PUC)

28. Genome-wide founder haplotype blocks assignment
across the entire S3MEGGIC population

29. • PA - revealed two major peaks on chromosome 9 and 10 with seven significant SNPs
• FA - 11 SNPs above the Bonferroni threshold were plotted on three major peaks located on
chromosomes 1, 9, and 10
• Pigmentation Under the Calyx- 7 main peaks on chromosomes 1 , 3 and 10 with 23 SNPs above the
Bonferroni threshold.

30. • BLAST analysis of the SMEL_001 onto the tomato genome indicated that this gene corresponded to the
orthologue SlANT1-like with 70.99% identity.
• The eggplant SMEL_010 corresponded to the tomato orthologue SlAN2-like with a 73.73% identity,
which is the best candidate gene for the anthocyanin fruit biosynthesis in tomato.
• A single duplication event and a translocation of a fragment of at least 357 kb from chromosome 10 to 1
occurred during eggplant evolution
Tomato-eggplant microsynteny representation of a tomato region from
chromosome 10 (Solyc10), eggplant region of chromosome 10 (SMEL_010),
where candidate genes for anthocyanins synthesis are located.

31. Results
o The 7,724 filtered high-confidence single-nucleotide polymorphisms (SNPs) confirmed
• low residual heterozygosity (6.87%) and
• a lack of genetic structure in the S3MEGGIC population
o Duplication of an ancestral gene with a translocation from chromosome 10 to chromosome 1 was
compared with the tomato genome.
• A candidate gene, related to light-dependent anthocyanin biosynthesis in fruits, was detected at the
beginning of chromosome10

32. • Aim: To develop a common bean MAGIC to identify genomic regions associated with yield,
micromineral accumulation, and physiological traits under drought conditions.
• Material used: inter-crossing of eight Mesoamerican elite breeding lines
• Genetic mapping was carried out with two methods, using association mapping with GWAS,
and linkage mapping with haplotype-based interval screening

33. Assessment of population structure for 629 MAGIC lines and
8 founders using GBS data

34. Distribution of the founder’s haplotypes in the MAGIC population

37. Results
• Founder haplotypes in the population were identified using GBS. No major population structure
was observed.
• Thirteen high confidence QTL were identified using both methods and several QTL hotspots were
found controlling multiple traits.
• Major QTL hotspot located on chromosome Pv01 for phenology traits and yield was identified.
• Major QTL for seed Fe content was contributed by MIB778, the founder line with highest
micromineral accumulation.

38. Conclusion
• MAGIC populations represent powerful tools for the detection of QTLs present in the set of
parents, with considerable advantages over bi-parental and germplasm sets.
• Recombinant elite lines can be directly selected by breeders for being introduced in breeding
programs.
• Increases the precision of QTL mapping.
• MAGIC populations will play an important role in addressing the formidable challenges faced by
breeders in a scenario of climate change by significantly contributing to the development of new
generations of resilient, highly productive, and resource-efficient cultivars.

39. Thank you
Acknowledgment
Dr. Mamta Pathak Dr. Hira Singh Dr. S.K.Jindal