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Development and Characterization of Maize-Teosinte Introgression Libraries

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.

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Development and Characterization of Maize-Teosinte Introgression Libraries

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

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

  3. 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 Evolutionary Genetics of Maize Selection

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

  5. BC1 BC2 BC3 BC4 B73 teosinte Development of Teo NIL Libraries 10 accessions F1 : B73 × teosinte B73 × teosinte(parviglumis) 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 • 887Near Isogenic Lines (NILs) IlluminaGoldenGate 768 SNP assay Z031E0035 Z035E0012

  7. Introgression Stats # Avg. # Avg. % Avg. % Avg. % Population Lines Regions Teosinte Het. Teozygous Coverage Ames 21785 96 2.5 4.5 2.9 1.6 4.3 Ames 21786 87 2.3 4.4 2.9 1.5 3.8 Ames 21789 93 2.5 3.9 2.9 1.1 3.6 Ames 21814 77 2.1 3.8 2.5 1.3 2.9 Ames 21889 91 2.7 4.7 3.3 1.3 4.2 Ames 21809 79 2.7 4.9 3.1 1.7 3.8 Ames 21812 82 2.1 4.6 3.1 1.5 3.8 PI 384065 53 2.5 4.2 2.4 1.7 2.2 PI 384066 64 2.2 4.0 2.5 1.5 2.6 PI 384071 82 2.3 4.1 2.6 1.5 3.3 PI 384071 - DH 83 1.4 1.9 0.1 1.8 1.6 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. Auxin response factor, ARF1 Inbreds Teosinte 0.02 Diversity (π) 0.01 0 1 1000 2000 3000 (bp) 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 Could be any trait!

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

  13. 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. Increase Flowering Time Decrease Flowering Time Significant QTL 12h 24h 36h Many QTL with small Effects Additive Allelic Effects 333 alleles significant at P = 0.05. Only 7 alleles had more than 24 hour effect. Buckler, et al. (2009) Science

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

  17. “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

  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 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 • Biological hypothesis: A loss of genetic variation results in a loss of phenotypic variation. • Breeding hypothesis: We can improve modern traits. Sucrose sh1: sucrose synthase UDP Glucose sh2, bt2: ADP-glucose pyrophosphorylase ADP Glucose su1 : debranchingenzyme ae1 : SBE-IIB wx1 : g.bstarch synthase Amylose Amylopectin SelectedGenesin Maize Starch Pathway; Whitt et al. 2002

  22. Teosinte (N = 11) Landraces (N = 17) Inbred Lines (N = 27) Kernel Traits α family 80 β 70 γ δ 60 50 Percent of Kernel Weight 40 30 20 Zein Profile 10 0 Carbohydrate Protein Fat • seed size Flint-Garcia et al. (2009) TAG

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

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

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

  26. Acknowledgements Syngenta AgReliant NSF Maize Diversity Project www.panzea.org

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