Racial and Allelic Diversity

1
Racial and Allelic Diversity
Germplasm Enhancement of Maize

• S. Flint-Garcia, USDA-ARS, Columbia, MO
• - August 17, 2006 -

2
Evolutionary Genetics of Maize
Selection

• Domesticated from Zea mays ssp. parviglumis
• Single domestication event in Mexican highlands
• 6,0009,000 years ago

• Plant architecture
• e.g. tb1
• Seed coat
• e.g. tga1

Doebley et al. (1997) Nature 386
485-488 Matsuoka et al. (2002) PNAS 99
6080-6084 Wang et al. (2005) Nature 436 714-719
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The Bottom Line for Diversity
Selection Screens
Unselected Gene
Domestication
Plant Breeding
In which category do the genes responsible for
YOUR trait belong?
2 - 4 (1200) of maize genes have undergone
selection
Genes that contribute to agronomic traits have
been targets of selection.
4
Population Statistical Analysis

• Diversity Statistics
• p average number of pair-wise differences per
  nucleotide site

Average pinbreds 0.0065
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Relative Loss of Diversity (p)

• Average pteosinte 0.0098
• Average pinbred 0.0065

66 diversity retained
Yamasaki et al. (2005) Plant Cell 17
2859-2872 Wright et al. (2005) Science 308
1310-1314
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kernel wt
T vs LR


















LR vs Inb











T vs Inb


















Valine
Lysine
Serine
Proline
Alanine
Glycine
Leucine
Arginine
Cysteine
Histidine
Tyrosine
Total Amino Acid
Isoleucine
Threonine
Methionine
Tryptophan
Aspartic Acid
Phenylalanine
Glutamic Acid
7
Adapted from Buchanan et al 2000
8
Percent
Ash
Carbohydrate
Crude Fat
Crude Fiber
Moisture
Crude Protein


ns

ns

LR vs Inb






T vs LR






T vs Inb
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Testing for Phenotypic Effects
B73
B73
Teosinte-B73 NILs
B73
B73
Mu transposon insertion knockout
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7-24-06
12 tall
9 tall
6 tall
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Teosinte BC2
12
Landraces
13
B73 x Landraces
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• Linkage Mapping

Association Mapping
Structured population High power Low
resolution Analysis of 2 alleles Moderate marker
density Genome scan
Unstructured population Low power High
resolution Analysis of many alleles High marker
density Candidate gene testing
Nested Association Mapping (NAM)
Structured sub-populations nested within an
unstructured population High Power High
resolution Analysis of many alleles Moderate
marker density
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NAM Population Development
The 26 founder inbreds capture 80-85 of the
diversity present in public maize inbreds (i.e.
302 assoc. pop.)
Tropical CML103 CML228 CML247 CML277 CML322 CML33
3 CML52 CML69 Ki11 Ki3 NC350 NC358 Tzi8
Non-Stiff Stalk B97 Ky21 M162W MS71 Oh43 Oh7B Mo
17 (IBM)
Mixed M37W Mo18W Tx303
Other HP301 IL14H P39
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Nested Association Analysis
25 DL
B97 CML103 CML228 CML247 CML277 CML322 CML333 CML5
2 CML69 Hp301 Il14H Ki11 Ki3 Ky21 M162W M37W Mo18W
MS71 NC350 NC358 Oh43 Oh7B P39 Tx303 Tzi8
B73
F1s
Yu, Holland, McMullen, and Buckler (in progress)
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(No Transcript)
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Linkage Mapping
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Quantitative Trait Locus (QTL) Mapping of Stalk
Traits

• Identify genomic regions that contribute to
  variation and estimate QTL effects

Genotype Phenotype Composite Interval Mapping
Flint-Garcia et al. (2003) Crop Sci. 43 13-22
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Association Mapping
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Association Analysis
1.3m
1.4m
1.5m
1.8m
2.0m
2.0m

• Utilize natural populations
• Exploit extensive ancestral recombination
• Evaluate several alleles simultaneously

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Linkage Disequilibrium (LD)

• MaizeLandraces lt 1 kb
• Diverse Inbreds 1.5 kb
• Elite Inbreds gt 100 kb
• Arabidopsis 250 kb

• Correlation between polymorphisms
• Extent of LD in the population determines the
  resolution of association analysis

Flint-Garcia et al. (2003) Ann. Rev. Plant Biol.
54 357-374.
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Association Analysis Methodology
Choose Candidate Gene
Choose Germplasm
PCR Amplify Sequence
Choose Target Trait
Obtain Independent Genome-wide Marker Data
Contig and Align Sequences
Identify Polymorphisms (C)
Estimate Population Structure (Q)
Evaluate Trait in Replicated Trials (T)
Association Analysis T Q C e
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Population Structure and Associations
G
T
G
G
G
G
T
T
T
G
T
T
Kernel Hue
P ltlt 0.001
T
G
True association