Development and Characterization
of Maize-Teosinte
Introgression Libraries
Sherry Flint-Garcia
USDA-ARS Columbia, MO
Outline
Introduction
Development of Teo NIL Libraries
Applications of Teo NIL Libraries
Lofty Ideas
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
Impact of Artificial Selection
Teosinte Introgression Libraries
GENETICS
Unselected
(Neutral) Gene
Domestication Gene
Improvement Gene
Teosintes
Domestication
Artificial
Selection
Maize
Landraces
Plant Breeding
Maize
Inbred Lines
98% (~49,000)
maize genes
GENOMICS
Nested Association Mapping (NAM)
2% (~1,000) maize genes
BREEDING
Germplasm Enhancement
of Maize (GEM)
Development of Teo NIL Libraries
10
F1 :
B73 × teosinte
accessions
B73 × teosinte
(parviglumis)
B73
teosinte
F1
BC1
BC2
BC3
BC4
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
Illumina
GoldenGate
Z035E0012
768 SNP
assay
Introgression Stats
#
Lines
Population
Ames 21785
Ames 21786
Ames 21789
Ames 21814
Ames 21889
Ames 21809
Ames 21812
PI 384065
PI 384066
PI 384071
PI 384071 - DH
96
87
93
77
91
79
82
53
64
82
83
Avg. #
Regions
2.5
2.3
2.5
2.1
2.7
2.7
2.1
2.5
2.2
2.3
1.4
Avg. %
Teosinte
4.5
4.4
3.9
3.8
4.7
4.9
4.6
4.2
4.0
4.1
1.9
Avg. % Avg. %
Het. Teozygous Coverage
2.9
2.9
2.9
2.5
3.3
3.1
3.1
2.4
2.5
2.6
0.1
1.6
1.5
1.1
1.3
1.3
1.7
1.5
1.7
1.5
1.5
1.8
Expected Genotype Ratios for BC4S2 (sibbed):
95% BB, 3% BT het., 1.5% TT
4.3
3.8
3.6
2.9
4.2
3.8
3.8
2.2
2.6
3.3
1.6
Library Coverage
c1
c2
c3
c4
c5
c6
c7
c8
c9
c10
KEY
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
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BC4S2 vs BC4DH Coverage
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Applications of
Teosinte NILs
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 response factor, ARF1
Diversity (π)
Teosinte
0.02
0.01
0
1
1000
?
Auxin-mediated
Protein
Degradation
Inbreds
2000
3000 (bp)
Could be any trait!
2. Evaluate Allele Series
Trait Value
B73
Maize
Alleles
Teosinte
Alleles
Examine the range of allele effects of maize versus
teosinte.
Validate QTL identified by NAM.
A Brief Digression
Nested Association Mapping (NAM)
Flowering Time
Ed Buckler, Jim Holland, Mike McMullen, et al
Buckler, et al. (2009) Science
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
Many QTL with small Effects
333 alleles
significant at
P = 0.05.
150
100
Frequency of QTL
Increase Flowering Time
50
0
-50
Decrease Flowering Time
Only 7 alleles had
more than 24 hour
effect.
-100
Significant QTL
-150
12h
24h
36h
Additive Allelic Effects
Buckler, et al. (2009) Science
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
“Gene Stacking”
Large differences
in parental lines
(32 day span) are
the product of
stacking large
numbers of
modest effect
QTL.
Earliest
Latest
Buckler, et al. (2009) Science
Back To Teosinte
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
Teosinte Introgressions vs. NAM
90
80
70
60
50
40
30
20
10
0
NAM
0
100
200
300
400
500
600
700
800
900
1000
1100
1200
1300
1400
800
900
1000
1100
1200
1300
1400
Teosinte NILs
50
40
30
Photoperiod
Gene?
20
10
0
0
100
Additive
Effect -1.0 -1.1
(days) 1.6 3.2
200
300
-2.6 -4.1 0.7
4.2 2.2 1.1
400
-0.9
2.3
500
600
700
0.7
1.9
-2.9
1.3
-0.7
2.2
-2.3
2.4
-1.0
2.8
-1.2
0.8
1.0
3.8
0.7
4.5
3. Reintroduce Genetic Variation
Sucrose
sh1 : sucrose synthase
UDP Glucose
sh2, bt2 : ADP-glucose
pyrophosphorylase
ADP Glucose
wx1 : g.b starch synthase
Amylose
su1 : debranching enzyme
ae1 : SBE-IIB
Amylopectin
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.
Kernel Traits
80
seed size
Percent of Kernel Weight
70
60
Teosinte (N = 11)
Landraces (N = 17)
Inbred Lines (N = 27)
α family
50
β
40
γ
δ
30
20
Zein Profile
10
0
Carbohydrate
Protein
Fat
Flint-Garcia et al. (2009) TAG
Teosinte NIL Evaluations
Tracy –
Germination
Harmon –
Circadian
Clock
AgReliant –
Agronomic
Traits
Hoekenga –
Iron Bioavailability
Buckler – Flowering
Nelson – NCLB
Brutnell – Shade
Avoidance Response
Balint-Kurti –
SCLB and GLS
Hibbard –
Corn Rootworm
Resistance
Dallo –
Mal de Rio Cuarto Disease
Smith – Smut
Flint-Garcia –
Starch, Protein, Oil
Zein Profile
Amino Acid Profile
Lofty Ideas
7000 BC
2010
Agronomics
Fertilizer
Density
Mechanization
?
ideotype
Select only on yield
Teosinte Synthetic
75% B73 (SS), 25% teosinte
Acknowledgements
Syngenta
NSF Maize
AgReliant
Diversity Project
www.panzea.org