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Sherry Flint-Garcia USDA-ARS Columbia, MO

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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 size
10 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

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