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

http://www.ricediversity.org/garrisfigure/

80% rice produced

20% rice produced

Major Types of Rice

Bandillo et al. 2013. RICE

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

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

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

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

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

MAGIC PLUS Fine mapping of brown spot resistance on chr 12 Defining SNP haplotypes for susceptible and resistance lines

Associated markers within gene models

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

TANZANIA

VIETNAM

CHINA

CAMBODIA

SENEGAL

IRRI – Los Baños, Laguna

ILOILO

BUKIDNON

MAGIC Multi-Environment Trials (METs)

On-going Trials

Additional Target Sites

MYANMMAR

THAILAND

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)

y = -74.262x + 469.76R² = 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

Yiel

d St

abili

ty In

dex

(YSI

)

Grain Yield (GY) Mean

Relationship Between GY Mean and YSI

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)

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

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

As an example: Bacterial leaf streak disease

MAGIC lines segregating for resistance and susceptibility

Susceptible Resistance

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 Redoña Glenn Gregorio Chitra Raghavan Mike Thomson RK Singh Emma Huang, CSIRO

MAGIC Nursery 2013 WS

MAGIC Global

Indica MAGIC

MAGIC MET- 3 at IRRI

MAGIC Plus Thank you