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GRM 2013: MAGIC Rice Multi-parent Advanced Generation Inter-Cross -- H Leung

CGIAR Generation Challenge Programme
CGIAR Generation Challenge Programme
CGIAR Generation Challenge ProgrammeCGIAR Generation Challenge Programme

GRM 2013: MAGIC Rice Multi-parent Advanced Generation Inter-Cross -- H Leung

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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
GRM 2013: MAGIC Rice Multi-parent Advanced Generation Inter-Cross -- H Leung
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
Ad

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GRM 2013: MAGIC Rice Multi-parent Advanced Generation Inter-Cross -- H Leung

  • 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
  • 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

Editor's Notes

  1. Pilot