1. Sherry Flint-Garcia USDA-ARS Columbia, MO
Development and Characterization of Maize-Teosinte Introgression Libraries
Sherry Flint-Garcia USDA-ARS Columbia, MO

2. Outline
Introduction Development of Teo NIL Libraries Applications of Teo NIL Libraries Lofty Ideas

3. Evolutionary Genetics of Maize
Selection
Domesticated from Zea mays ssp. parviglumis, existed/exists in an intermediate form of landraces
Single domestication event in Mexican highlands
6,000~9,000 years ago

4. Impact of Artificial Selection
GENOMICS
Nested Association Mapping (NAM)
BREEDING
Germplasm Enhancement
of Maize (GEM)
Teosinte Introgression Libraries
GENETICS
Teosintes
Maize
Landraces
Inbred Lines
Unselected
(Neutral) Gene
Domestication Gene
Improvement Gene
Artificial
Selection
Plant Breeding
Domestication
98% (~49,000)
maize genes
2% (~1,000) maize genes

5. Development of Teo NIL Libraries
B73 × teosinte (parviglumis) 10
accessions
F1 :
B73 × teosinte
teosinte
BC1
BC2
BC3
BC4
B73 F1

6. Library Development
161 BC4S2 NILs: 2 libraries (done in 2009) 643 BC4S2 NILs: 8 libraries (done in 2008) 83 BC4DH NILs: duplicated library 887 Near Isogenic Lines (NILs)
Z031E0035
Z035E0012
Illumina GoldenGate
768 SNP assay

7. Expected Genotype Ratios for BC4S2 (sibbed):
Introgression Stats
# Avg. # Avg. % Avg. % Avg. %
Population Lines Regions Teosinte Het. Teozygous Coverage
Ames
Ames
Ames
Ames
Ames
Ames
Ames PI PI PI
PI DH
Expected Genotype Ratios for BC4S2 (sibbed):
95% BB, 3% BT het., 1.5% TT

8. Library Coverage c1 c2 c3 c4 c5 c6 c7 c8 c9 c10
10 maize-teosinte libraries
804 BC4S2 NILs and 83 BC4DH NILs
Each line:
2.3 chromosomal segments
4.1% of the teosinte genome
3.3X genome coverage

9. BC4S2 vs BC4DH Coverage c1 c2 c3 c4 c5 c6 c7 c8 c9
c10

10. Applications of Teosinte NILs

11. 1. Empirical Genetics Questions
1000 Selected Genes
What do these selected genes do?
What traits were targeted by artificial selection during domestication/breeding?
Are selected genes important?
Tillering/branching? ?
Auxin-mediated
Protein
Degradation
Auxin response factor, ARF1
0.01
0.02
1000
2000
3000 1
(bp)
Diversity (π)
Inbreds
Teosinte
Could be any trait!

12. 2. Evaluate Allele Series
Trait Value
B73
Maize
Alleles
Teosinte
Examine the range of allele effects of maize versus teosinte. Validate QTL identified by NAM.

13. Nested Association Mapping (NAM) Flowering Time
A Brief Digression
Nested Association Mapping (NAM)
Flowering Time
Ed Buckler, Jim Holland, Mike McMullen, et al
Buckler, et al. (2009) Science

14. Flowering Genetic Architecture
At least 39 QTL explain flowering architecture
Genetic architecture of maize is very complex and very different than Arabidopsis.
Buckler, et al. (2009) Science

15. Many QTL with small Effects
Significant QTL
24h
36h
Increase Flowering Time
Decrease Flowering Time
Additive Allelic Effects
333 alleles significant at P = Only 7 alleles had more than 24 hour effect.
Buckler, et al. (2009) Science

16. ……………….………………. QTL……………………….……….
Allele Series 1
……………….………………. QTL……………………….………. 39
Additive Allelic Effects (days)
69% of QTLs had both alleles with both positive and negative effects.
Buckler, et al. (2009) Science

17. “Gene Stacking”
Earliest
Latest
Large differences in parental lines (32 day span) are the product of stacking large numbers of modest effect QTL.
Buckler, et al. (2009) Science

18. Back To Teosinte

19. Flowering Evaluation ~850 NILs from 10 libraries
Days to Anthesis (DTA) from:
Ithaca, NY (2 reps), Rebecca Nelson & Oliver Ott
Ithaca, NY (2 reps), Buckler lab
Raleigh, NC (8 reps), Peter Balint-Kurti
Madison, WI (1 rep), Loren Trimble
St. Paul, MN (1 rep), Nathan Springer
Columbia, MO (4 reps)
TOTAL 18 reps

20. Teosinte Introgressions vs. NAM
Photo- period
Gene?
Teosinte NILs
Additive Effect
(days)
-1.0
-1.1
-2.6
-4.1
0.7
-0.9
0.7
-2.9
-0.7
-2.3
-1.0
-1.2
1.0
0.7
1.6
3.2
4.2
2.2
1.1
2.3
1.9
1.3
2.2
2.4
2.8
0.8
3.8
4.5

21. 3. Reintroduce Genetic Variation
Sucrose
UDP Glucose
ADP Glucose
Amylose
Amylopectin
sh1 : sucrose synthase
sh2, bt2 : ADP-glucose
pyrophosphorylase
su1 : debranching enzyme
ae1 : SBE-IIB
wx1 : g.b starch synthase
Selected Genes in Maize Starch Pathway; Whitt et al. 2002
Biological hypothesis: A loss of genetic variation results in a loss of phenotypic variation. Breeding hypothesis: We can improve modern traits.

22. Kernel Traits Zein Profile α family β γ δ seed size10 20 30 40 50 60 70 80
Carbohydrate
Protein
Fat
Percent of Kernel Weight
Teosinte (N = 11)
Landraces (N = 17)
Inbred Lines (N = 27) β γ
α family δ
Zein Profile
Flint-Garcia et al. (2009) TAG

23. Teosinte NIL Evaluations
Hoekenga – Iron Bioavailability
Tracy – Germination
AgReliant – Agronomic Traits
Buckler – Flowering
Harmon – Circadian
Clock
Nelson – NCLB
Brutnell – Shade Avoidance Response
Dallo – Mal de Rio Cuarto Disease
Balint-Kurti – SCLB and GLS
Smith – Smut
Hibbard – Corn Rootworm Resistance
Flint-Garcia –
Starch, Protein, Oil
Zein Profile
Amino Acid Profile

24. Lofty Ideas ? Agronomics Fertilizer Density Mechanization 7000 BC 2010
Select only on yield
ideotype

25. Teosinte Synthetic
75% B73 (SS), 25% teosinte

26. NSF Maize Diversity Project
Acknowledgements
Syngenta
AgReliant
NSF Maize Diversity Project