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Racial and Allelic Diversity

Racial and Allelic Diversity. G ermplasm E nhancement of M aize. S. Flint-Garcia, USDA-ARS, Columbia, MO - August 17, 2006 -. Domesticated from Zea mays ssp. parviglumis Single domestication event in Mexican highlands 6,000~9,000 years ago. Plant architecture e.g. tb1 Seed coat

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Racial and Allelic Diversity

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  1. Racial and Allelic Diversity Germplasm Enhancement of Maize S. Flint-Garcia, USDA-ARS, Columbia, MO - August 17, 2006 -

  2. Domesticated from Zea mays ssp. parviglumis Single domestication event in Mexican highlands 6,000~9,000 years ago Plant architecture e.g. tb1 Seed coat e.g. tga1 Teosinte Landraces Modern Inbreds Evolutionary Genetics of Maize Selection Doebley et al. (1997) Nature 386: 485-488 Matsuoka et al. (2002) PNAS 99: 6080-6084 Wang et al. (2005) Nature 436: 714-719

  3. Domestication Gene Improvement Gene Teosintes Maize Landraces Maize Inbred Lines Very low genetic diversity 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. 0 differences in 66 (12*11/2) comparisons Inbreds (N=12) Teosinte (N=13) 42 differences in 78 (13*12/2) comparisons Population Statistical Analysis • Diversity Statistics • π = average number of pair-wise differences per nucleotide site Average πinbreds = 0.0065

  5. Proline Dehydrogenase Neutral Gene -adh1 Auxin response factor, ARF1 0.08 Inbreds 0.04 Inbreds Inbreds Teosinte 0.06 Teosinte Teosinte 0.02 0.03 π 0.04 π π 0.02 0.01 0.02 0.01 0 (bp) 0 0 200 400 600 0 (bp) 1 1000 2000 1 1000 2000 3000 (bp) Relative Loss of Diversity (π) • Average πteosinte = 0.0098 • Average πinbred = 0.0065 ~ 66% diversity retained Yamasaki et al. (2005) Plant Cell 17: 2859-2872 Wright et al. (2005) Science 308: 1310-1314

  6. 0.25 35 30 0.2 25 0.15 20 % total AA Teosintes 15 Landraces 0.1 Inbred Lines 10 0.05 5 0 0 % kernel wt ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** T vs LR LR vs Inb ** ** ** ** ** ** ** ** ** ** ** T vs Inb ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** Valine Lysine Serine Proline Glycine Alanine Leucine Arginine Tyrosine Histidine Cysteine Total Amino Acid Isoleucine Threonine Methionine Tryptophan Aspartic Acid Phenylalanine Glutamic Acid

  7. Trans-cinnamic acid Lignin PAL Glucose Phenylalanine Tyrosine Glycine Serine O-Acetylserine 3-Phospho- glycerate Prephenate Cysteine synthase Erythrose 4-P Chorismate mutase Cysteine 2-isopropyl- malate synthase Phosphoenol pyruvate DAHP Shikimate Chorismate Leucine Anthranilate Synthase β Pyruvate Alanine Pyruvate Anthranilate Valine Acetyl-CoA Acetohydroxy acid synthase Indole-3-glycerol phosphate Asparagine Isoleucine Tryptophan Synthase β1 Aspartate Amino- transferase Asparagine synthetase Tryptophan 2-Ketobutyrate Aspartate Oxalo- acetate Threonine deaminase TCA Cycle Aspartate kinase Glutamate Threonine Aspartate 4-seminaldehyde NH4 Arginine α-Keto- glutarate DHDP synthase Proline Homoserine 4-phosphate Proline dehydrogenase Glutamate dehydrogenase Cysteine 2,3-Dihydro- dipicolinate Cystathionine γ-synthase Glutamate Cystathionine Homocysteine Lysine Glutamine NH4 NO3– NO2– Methionine Nitrate Reductase Histidine SAM synthetase I SAM synthetase II Hexokinase (N:C sensing) S-Adenosyl- methionine Adapted from Buchanan et al 2000

  8. 80 70 60 50 Teosintes Landraces Inbred Lines 40 30 20 10 0 Percent Ash Carbohydrate Crude Fat Crude Fiber Moisture Crude Protein ** ** * ** ns ns LR vs Inb ** ** ** ** ** ** T vs LR ** ** ** ** ** ** T vs Inb

  9. Unselected (Neutral) Gene Domestication/ Improvement Gene Teosintes Selection Inbred Lines Effect of teo background & teo allele B73 B73 Effect of B73 allele if additive gene action Testing for Phenotypic Effects B73 B73 Teosinte-B73 NILs B73 B73 Mu transposon insertion knockout

  10. B73 x teosinte BC1 3’ tall Teosinte (ssp. parviglumis) B73 x teosinte BC1 7-24-06 8-7-06 8-7-06 7-24-06 12’ tall 9’ tall 6’ tall

  11. Ames21814 Ames21785 PI384066 7-24-06 7-24-06 7-24-06 8-7-06 7-24-06 PI384063 PI384071 Ames21786 7-24-06 8-7-06 8-7-06 PI384065 Ames21889 Ames21789 7-24-06 8-7-06 8-7-06 7-24-06 Teosinte BC2

  12. Landraces Cateto Sulino Chapalote Costeno Bolita Cristalino Norteno Chalqueno Conico Serrano Dzit Bacal Sabanero Guirua Gordo Tuson Nal-tel Pissccotunto

  13. B73 x Landraces 7-24-06 8-7-06

  14. CM37 R4 K148 Mo46 Ky228 Hi27 Mo47 NC344 K4 DE-3 Yu796-NS OH7B NC360 Mo45 CMV3 CO106 A682 Mt42 W401 B97 MO17 CI91B NC362 NC262 NC222 A556 DE811 NC258 B103 Tzi25 B105 NC342 NC364 CI187-2 CI3A B77 W117HT Tzi16 MS153 DE1 STIFF STALK SD40 A641 NC290A A214N NC250 B164 NON STIFF STALK NC236 CM7 N7A N28HT H100 DE-2 B57 H84 I205 B64 C123 H105W A635 CO109 ND246 A632 C103 B68 CO125 B79 H91 A634 B84 B14A Hy B76 Ky21 CM174 B104 A661 WD CM105 A554 B75 CI21E 38-11 B37 MS71 Os420 NC260 NC328 R229 Mo44 A679 Mo1W A680 R168 B73Htrhm NC294 NC326 B73 B109 NC368 N192 NC324 NC292 NC314 NC322 NC330 W64A Pa875 NC308 NC372 NC306 NC312 CH9 H49 NC268 NC310 A619 B10 WF9 B46 SD44 A239 Pa880 T8 A188 OH43 Pa762 C49A C49 VA26 Va102 Ky226 A654 W153R Va35 Va14 Va59 A659 CI-7 Oh43E Oh40B Va17 R177 Va22 W22 H95 W182B Va99 PA91 H99 M14 CI90C 33-16 Va85 CH701-30 NC33 VaW6 4226 NC232 L317 B115 R109B MoG I137TN K55 CI66 CI44 NC230 81-1 CI31A MEF 156-55-2 CI64 IL677A K64 M162W SWEET CORN Ia5125 E2558W N6 IA2132 IL14H P39 T234 SC357 L578 CML52 IL101 CML69 CML14 CML38 B52 CML287 EP1 Tzi11 F2 NC366 CML108 CML103 F7 SC213R CO255 CML9 GT112 CML61 NC238 CML254 CML5 T232 GA209 CML314 CML264 Mp339 CI28A CML258 Q6199 CML10 B2 U267Y CML341 CML332 CML11 CML45 MS1334 CML261 CML331 Mo24W D940Y Sg1533 SG18 IDS28 F2834T HP301 IDS69 SA24 IDS91 CML277 M37W CML238 CML322 CML321 A6 F44 Ki14 CML247 Ki11 4722 Ki2021 F6 I-29 CML157Q Ki44 Oh603 Ki43 CML328 NC340 Ki21 CML323 Ki2007 CML228 NC300 CML92 A272 Tx303 CML218 NC320 NC356 NC302 CML77 NC318 Ki3 NC332 SC55 A441-5 NC338 NC358 NC334 POPCORN CML154Q TROPICAL-SUBTROPICAL NC354 TZI18 NC370 TZI10 NC264 Ab28A CML220 Mo18W Tzi9 TX601 CML349 NC350 CML158Q CML333 NC304 TZI8 CML91 CML311 MIXED CML281 NC346 NC296A parvi-03 NC336 NC352 NC296 NC348 NC298 parvi-14 parvi-30 parvi-49 parvi-36 OUTGROUP

  15. 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

  16. NAM Population Development The 26 founder inbreds capture 80-85% of the diversity present in public maize inbreds (i.e. 302 assoc. pop.) Non-Stiff Stalk B97 Ky21 M162W MS71 Oh43 Oh7B Mo17 (IBM) Tropical CML103 CML228 CML247 CML277 CML322 CML333 CML52 CML69 Ki11 Ki3 NC350 NC358 Tzi8 Mixed M37W Mo18W Tx303 Other HP301 IL14H P39

  17.            SSD    1 2 NAM    200 Nested Association Analysis 25 DL B97 CML103 CML228 CML247 CML277 CML322 CML333 CML52 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)

  18. CM37 R4 K148 Mo46 Ky228 Hi27 Mo47 NC344 K4 DE-3 Yu796-NS OH7B NC360 Mo45 CMV3 CO106 A682 Mt42 W401 B97 MO17 CI91B NC362 NC262 NC222 A556 DE811 NC258 B103 Tzi25 B105 NC342 NC364 CI187-2 CI3A B77 W117HT Tzi16 MS153 DE1 STIFF STALK SD40 A641 NC290A A214N NC250 B164 NON STIFF STALK NC236 CM7 N7A N28HT H100 DE-2 B57 H84 I205 B64 C123 H105W A635 CO109 ND246 A632 C103 B68 CO125 B79 H91 A634 B84 B14A Hy B76 Ky21 CM174 B104 A661 WD CM105 A554 B75 CI21E 38-11 B37 MS71 Os420 NC260 NC328 R229 Mo44 A679 Mo1W A680 R168 B73Htrhm NC294 NC326 B73 B109 NC368 N192 NC324 NC292 NC314 NC322 NC330 W64A Pa875 NC308 NC372 NC306 NC312 CH9 H49 NC268 NC310 A619 B10 WF9 B46 SD44 A239 Pa880 T8 A188 OH43 Pa762 C49A C49 VA26 Va102 Ky226 A654 W153R Va35 Va14 Va59 A659 CI-7 Oh43E Oh40B Va17 R177 Va22 W22 H95 W182B Va99 PA91 H99 M14 CI90C 33-16 Va85 CH701-30 NC33 VaW6 4226 NC232 L317 B115 R109B MoG I137TN K55 CI66 CI44 NC230 81-1 CI31A MEF 156-55-2 CI64 IL677A K64 M162W SWEET CORN Ia5125 E2558W N6 IA2132 IL14H P39 T234 SC357 L578 CML52 IL101 CML69 CML14 CML38 B52 CML287 EP1 Tzi11 F2 NC366 CML108 CML103 F7 SC213R CO255 CML9 GT112 CML61 NC238 CML254 CML5 T232 GA209 CML314 CML264 Mp339 CI28A CML258 Q6199 CML10 B2 U267Y CML341 CML332 CML11 CML45 MS1334 CML261 CML331 Mo24W D940Y Sg1533 SG18 IDS28 F2834T HP301 IDS69 SA24 IDS91 CML277 M37W CML238 CML322 CML321 A6 F44 Ki14 CML247 Ki11 4722 Ki2021 F6 I-29 CML157Q Ki44 Oh603 Ki43 CML328 NC340 Ki21 CML323 Ki2007 CML228 NC300 CML92 A272 Tx303 CML218 NC320 NC356 NC302 CML77 NC318 Ki3 NC332 SC55 A441-5 NC338 NC358 NC334 POPCORN CML154Q TROPICAL-SUBTROPICAL NC354 TZI18 NC370 TZI10 NC264 Ab28A CML220 Mo18W Tzi9 TX601 CML349 NC350 CML158Q CML333 NC304 TZI8 CML91 CML311 MIXED CML281 NC346 NC296A parvi-03 NC336 NC352 NC296 NC348 NC298 parvi-14 parvi-30 parvi-49 parvi-36 OUTGROUP

  19. Linkage Mapping

  20. Position (cM) 100 110 120 130 140 Parent 1 Parent 2 80 90 30 40 50 60 70 10 20 0 9 8 7 6 5 LOD Score F1 4 3 F2 population 2 1 0 b1520 b2077 u1622 u1552 b2277 m231 b1225 b2248 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

  21. Association Mapping

  22. Utilize natural populations Exploit extensive ancestral recombination Evaluate several alleles simultaneously C G A A G C G A A T T A A A G T A G C T T G G A T C G G A G Association Analysis 1.3m 1.4m 1.5m 1.8m 2.0m 2.0m

  23. Correlation between polymorphisms Extent of LD in the population determines the resolution of association analysis MaizeLandraces < 1 kb Diverse Inbreds 1.5 kb Elite Inbreds > 100 kb Arabidopsis 250 kb dwarf3 0 10 kb 20 kb 30 kb 40 kb 50 kb Linkage Disequilibrium (LD) Flint-Garcia et al. (2003) Ann. Rev. Plant Biol. 54: 357-374.

  24. 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) Evaluate Trait in Replicated Trials (T) Estimate Population Structure (Q) Association Analysis T = Q + C + ε

  25. Andes U.S. 10 200 180 8 160 6 Plant Height 140 4 120 P = 0.04 2 100 80 T G 0 Non-functional association Population Structure and Associations G G G G G T T T G T T T Kernel Hue P << 0.001 T G True association

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