This document summarizes the status of different MAGIC (Multi-parent Advanced Generation Inter-Cross) rice populations including Indica MAGIC, Japonica MAGIC, MAGIC Global, and MAGIC Plus. It discusses genome-wide association studies conducted on these populations that have identified loci associated with traits like submergence tolerance, amylose content, and disease resistance. Multi-environment trials of different MAGIC populations are ongoing in several countries. The document outlines future work including continued phenotyping, quantitative trait loci mapping, and distribution of MAGIC lines to breeding programs.

1. MAGIC Rice
Multi-parent Advanced Generation Inter-Cross
• Status of Different MAGIC Populations
• GWAS using Phenotypic and Genotypic data
• Multi-Environment Trials (MET)
• Seed Requests/Distribution
• Future Work

2. http://www.ricediversity.org/garrisfigure/
80% rice
produced
20% rice
produced
Major Types of Rice

3. Bandillo et al. 2013. RICE

5. Status of Different MAGIC Populations WS2013
Multi-Parent
Population
History
Breeding
Lines
Generation Breeding Method(s) Remarks
Indica MAGIC Intercrossing of
8 Indica
founder lines
1, 831 S8 Single Seed Descent Reserved seeds to maintain purity of Indica MAGIC AILs
1, 831 S6:8 Bulked Method Phenotypic evaluation and for sharing of Indica MAGIC AILs
MAGIC Plus Two extra
rounds of
intercrossing of
Indica MAGIC
2,214 S6 Single Seed Descent Generation advancement to develop AILs
144 S6 Pedigree Selection Phenotypic evaluation and purification of lines
48 S6 Bulked Method Observational yield trial
Japonica
MAGIC
Intercrossing of
8 Japonica
founder lines
400 S6 Single Seed Descent* SSD lines will be evaluated in Banaue, Philippines
400 S4:6 Bulked Method For evaluation in temperate environment; Bulked seeds were currently
planted in Korea and Taiwan
MAGIC Global Intercrossing of
Indica MAGIC
and Japonica
MAGIC
1, 402 S5 Single Seed Descent Generation advancement to develop MAGIC Global AILs
325 S5 Single Seed Descent Individual plant selection based on phenotypic acceptability
975 S5 Single Seed Descent Pedigree selection of promising lines for purification
MAGIC Multi-
Environment
Trials (MET)
MET-1 400 S2:4 Bulked Method Selected based on yield and agronomic evaluation of Indica MAGIC; With
3 sites in the Philippines and 1 site in Tanzania; A set of 200 lines were
sent to Senegal
MET-2 130 S2:4 Bulked Method Selected based on MET-1 yield and agornomc performance in 4 sites;
Evaluated in 3 sites in the Philippines and 1 site in Vietnam
MET-2 130 S6:8 Bulked Method Comparable phenotypic evaluation to MET-2 S2:4 population
MET-3 74 S2:4/S6:8 Combination of Pedigree
Selection and Bulked
Method
Best selected transgressive segregant of MAGIC based on yield and
phenotypic acceptability; Currently evaluated in 3 sites in the Philippines;
Top 10% will be submitted to IRRI MET pipeline as a candidate variety for
release
Doubled
Haploid Lines
Anther culture
of 80 F1s of
MAGIC Plus
800 Fixed Overall regenerants For future evaluation
76 Fixed Per callus counting For phenotypic and yield evaluation

6. Red Pericarp
Tall and late
flowering
Tall and early
maturity
Bird resistant
Very early
flowering Height and maturity differences
Wide leaves,
delayed senescence
Densed grain
Red awned pericarp
Purple culm
Large bold grain
Stained grain

7. http://www.maizegenetics.net/tassel
Genome-Wide Association (GWA) Mapping
Genotyping-by-Sequencing (GBS)
• Biotic – Blast and bacterial blight
•Abiotic – Salt tolerance,
Submergence tolerance
Salinity + Submergence
Phenotyping - 96 Indica MAGIC S1
lines at IRRI, Philippines

8. GWAS of MAGIC Plus S4
mapping bacterial blight resistance genes
Heins Zaw M.S. Thesis, 2013
Resistance to
bacterial blight
race PXO86
Resistance to
bacterial blight
race PXO61
Resistance to
bacterial blight
race PXO341
Salinity tolerance

9. indica MAGIC Indica MAGIC PLUS
17468172 – 19608153
P<10-9 2.14Mb
17902596 – 19608072
P<10-9 , 1.7Mb
MI
MP
• Mapping new resistance
gene against brown spot
disease
• Extra 2 rounds of crossing
appears to reduce mapping
interval
9

10. MAGIC PLUS
Fine mapping of
brown spot
resistance on chr 12
Defining SNP
haplotypes for
susceptible and
resistance lines
Associated markers within gene models

11. Trait Locus Chrom
No. of significant
makers
associated with
trait
p-value
cut-off
Physical distance
between the end
markers
Submergence
tolerance Sub1 9 16 5.43E-08 0.6 Mb
Amylose content waxy 6 14 7.48E-09 0.58 Mb
Grain length GS3 3 25 8.17E-05 6.7 Mb
Grain width GW8 8 4 4.20E-05 0.8 Mb
Gelatinization
temperature SSIIa 6 19 6.07E-15 1.8 Mb
Salt tolerance qSKC1 1 20 9.18E-04 3.0 Mb
Resistance to BLB
strain PXO86 xa5 5 3 7.21E-08 0.13 Mb
Resistance to BLB
strain PXO61 Xa4 11 8 9.62E-08 1.7 Mb
“Resolution” of applying GBS data to indica MAGIC
populations

12. TANZANIA
VIETNAMCHINA
CAMBODIA
SENEGAL
IRRI – Los Baños, Laguna
ILOILO
BUKIDNON
MAGIC Multi-Environment Trials (METs)
On-going Trials
Additional Target Sites
MYANMMAR
THAILAND

13. IR Number GY Mean GY Mean
Rank
ASV
Rank
YSI YSI Rank
IR 93342:35-B-15-11-B-B-B 3.81 7 9 16 1
IR 93334:57-B-25-23-B-B-B 3.58 21 6 27 2
IR 93330:50-B-21-10-B-B-B 3.84 6 23 29 3
IR 93342:13-B-20-13-B-B-B 3.69 12 17 29 4
IR 93346:1-B-13-7-B-B-B 3.99 2 37 39 5
IR 93335:55-B-9-12-B-B-B 3.50 31 13 44 6
IR 93330:6-B-21-8-B-B-B 3.48 36 8 44 7
IR 93337:37-B-15-15-B-B-B 3.62 16 30 46 8
IR 93336:57-B-24-17-B-B-B 3.53 27 19 46 9
IR 93353:4-B-21-17-B-B-B 3.57 22 26 48 10
IR 93339:41-B-10-14-B-B-B 3.56 23 25 48 11
IR 93334:55-B-16-20-B-B-B 3.53 26 22 48 12
IR 93343:1-B-6-3-B-B-B 3.44 43 5 48 13
IR 93337:43-B-9-5-B-B-B 3.93 4 47 51 14
IR 93336:46-B-6-18-B-B-B 3.45 41 11 52 15
IR 93329:17-B-16-5-B-B-B 3.38 51 4 55 16
IR 93342:28-B-24-10-B-B-B 3.91 5 51 56 17
IR 93342:27-B-23-2-B-B-B 3.50 32 24 56 18
IR 93329:11-B-18-22-B-B-B 3.45 42 15 57 19
IR 93354:6-B-6-22-B-B-B 3.61 18 40 58 20
Ranking of entries based on AMMI stability value (ASV) and
Yield Stability Index (YSI)

14. y = -74.262x + 469.76
R² = 0.433
Correlation=- 0.65
0
50
100
150
200
250
300
3.00 3.50 4.00 4.50 5.00 5.50 6.00
YieldStabilityIndex(YSI)
Grain Yield (GY) Mean
Relationship Between GY Mean and YSI

15. Outputs and Uses of MAGIC populations
as of 2013
Methodologies and new
knowledge
• Practical guide to produce
MAGIC —being used to create
additional MAGIC populations
(heat tolerance, biotic stress)
• Workflow for applying GWAS
mpMAP, Flapjack--using GBS
and phenotype data
• QTL for new traits (e.g.
resistance to brown spot)
Available Recombined
populations
• Indica MAGIC S6:8 population,
~1,800 lines
• Japonica MAGIC (S6), 400
lines
• Indica selections from Multi-
Environment Trials, 130 lines
• Global MAGIC (Indica x
japonica). >1500 S6 lines in
2014
• 20 lines with high Yield
Stability Index (YSI)

16. Summary and Future Work
Phenotyping , QTL mapping
Genetic basis of transgressive
segregation
Recombination questions:
LD decay, recombination
breakpoint,
Genome interactions and
epistasis,
Sequenced
(GBS) MAGIC
populations
Multi-Environment Trials to
evaluate GxE
Identify transgressive
segregations for new (or
enhanced) traits
Distribute to breeding programs
Breeding
Genetics

17. Activated, “rapid response genetic
resources”
• Sequenced breeding populations
with predictive power on gene-
phenotype relationships (e.g.,
MAGIC, NAM)
• Elite gene pools (in silico) that can
be readily evaluated for new traits

18. As an example: Bacterial leaf streak
disease
MAGIC lines
segregating for
resistance and
susceptibility
Susceptible Resistance

19. The MAGIC Team
Nonoy Bandillo Rea Muyco Ma. AnnaSevilla Irish Lobina Cesar Caspillo
Hein Zaw Rashid Ebna Syod
Vernie Carandang
Alex Olivo
Graduate Students:
Mae Rose Maoirat
Maricel Corpuz
Portaje Gianne
Ian Mari Reaño
Monaliza Jubay
Edilberto RedoñaGlenn Gregorio Chitra Raghavan Mike ThomsonRK Singh Emma Huang, CSIRO

20. MAGIC Nursery 2013 WS
MAGIC Global
Indica MAGIC
MAGIC MET- 3 at IRRI
MAGIC Plus
Thank you