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Evolutionary genetics of hybrid maize
The document discusses how breeding has impacted genetic diversity in maize genomes over time. It examines changes in ancestry across the maize genome and how the genome has responded to selection for increasing hybrid yield. Specifically, it finds that changing ancestry, not selection sweeps, has driven diversity loss across heterotic groups. The diversity of ancestral lines making up modern inbreds has decreased as germplasm pools have become smaller and more homogeneous. Within a single breeding program, genetic drift in small breeding populations also reduced diversity despite selection for yield.
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Evolutionary genetics of hybrid maize
- 1. Evolutionary Genetics of HybridMaize Jeffrey Ross-Ibarra www.rilab.org @jrossibarra
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- 3. GrainYield Year How has breedingaffected diversity across the maize genome?
- 4. GrainYield Year How has breedingaffected diversity across the maize genome? How has the genome responded to selection for increasing hybrid yield?
- 5. GrainYield Year How has breedingaffected diversity across the maize genome? How has the genome responded to selection for increasing hybrid yield? What is the genetic basis of hybrid vigor?
- 6. van Heerwaarden etal. 2012 PNAS 99 94 70 137 land races <1950 inbreds 1960-1970 inbreds ex-PVP 0 1 2 3 (Oh43,W22, B14) (B73, 207, Mo17) 10,000 ft view of US Corn Belt
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- 8. ! 1 2 301 2 3 era C 0.000.100.20 BSS NSS IDT manhattan 050001500 BSS NSS IDT inv.simpson 010203040 Lancaster Min13 Reid Midland S.dent pop flint 0.0 0.1 0.2 0.3 0.4 0.5 d. e. era 1 2 3 1 2 3 1 2 3 1 2 3 1 2 3 1 2 3 ancestryproportion 23 BSSNSS manhattandistance 050001500025 0.1 0.2 0.3 0.4 0.5 e. era 1231231 Iodent NSS SS
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- 15. SS 0.0 0.1 0.2 0.3 0.4 undefined OH43 CI31A HY B8 B10 B14 B96 B37 I205 OH07 CI3A CI187-2 CI540 I224 WD456 Oh3167B Tr9-1-1-6 FE2 LE773 ND203 B73 A634 A635 N28 H100 B64 B14A B68 CM105 B84 A632 N196 LH195 LH205 LH196 LH194 991 LH74 PHG39 LH132 G80 78004 78010 4676A 78002A 794 LP5 PHT55 H8431 1 2 3 NSS 0.4 12 3 manhattandistance 50001500025000 c.b. exPVP 1960’s 1940’s 1960’s1940’s exPVP Iodent NSS SS time line origin
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- 18. 1 2 301 2 3 era BSS NSS IDT BSS NSS IDT inv.simpson 010203040 Lancaster Min13 Reid Midland S.dent pop 0.0 0.1 0.2 0.3 0.4 0.5 d. e. era 1 2 3 1 2 3 1 2 3 effective#ancestors exPVP 1960’s 1940’s BSSNSSIDT manhattandistance 050001500025000 123123123
- 19. 1 2 301 2 3 era BSS NSS IDT BSS NSS IDT inv.simpson 010203040 Lancaster Min13 Reid Midland S.dent pop 0.0 0.1 0.2 0.3 0.4 0.5 d. e. era 1 2 3 1 2 3 1 2 3 effective#ancestors 1 2 30 1 2 3 era BSS NSS IDT manhattandistance 050001500025000 040 0.3 0.4 0.5 c.b. e. era 1 2 3 1 2 3 1 2 3 diversityofancestorsexPVP 1960’s 1940’s BSSNSSIDT manhattandistance 050001500025000 123123123
- 20. 1 2 301 2 3 era BSS NSS IDT BSS NSS IDT inv.simpson 010203040 Lancaster Min13 Reid Midland S.dent pop 0.0 0.1 0.2 0.3 0.4 0.5 d. e. era 1 2 3 1 2 3 1 2 3 effective#ancestors 1 2 30 1 2 3 era BSS NSS IDT manhattandistance 050001500025000 040 0.3 0.4 0.5 c.b. e. era 1 2 3 1 2 3 1 2 3 diversityofancestorsexPVP 1960’s 1940’s 0 1 2 3 01234 6 snp 5 snp 8 snp 7 snp 10 snp 9 snp 15 snp 15 snp era ratioobserved/randomized 0 0.00.10.20.30.40.50.6 Moran’sI BSSNSSIDT manhattandistance 050001500025000 123123123
- 21. ! selection ancestry deviation number ancestors 0 1 23 0.00.20.40.60.81.0 era p
- 22. ! selection ancestry deviation number ancestors 0 1 23 0.00.20.40.60.81.0 era p
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- 27. 10,000 ft view:drift and diversity loss
- 28. 10,000 ft view:drift and diversity loss • increasingly small, homogeneous germplasm making up ancestry of modern lines
- 29. 10,000 ft view:drift and diversity loss • increasingly small, homogeneous germplasm making up ancestry of modern lines • changing ancestry not selection (sweeps) drives diversity across all heterotic groups
- 30. 10,000 ft view:drift and diversity loss • increasingly small, homogeneous germplasm making up ancestry of modern lines • changing ancestry not selection (sweeps) drives diversity across all heterotic groups • no evidence that popular lines have more good alleles
- 31. Genetic change withina single program: BSSS/BSCB1 Gerke et al. 2015 Genetics
- 32. Genetic change withina single program: BSSS/BSCB1 Gerke et al. 2015 Genetics
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- 46. Morell, Buckler, andRoss-Ibarra. Nat. Rev. Genetics. 2012 Genetic load refers to the reduction in fitness caused by suboptimal genotypes in a population121 . Genetic load can arise in a number of ways, including directional selection, recombination or mutation. Mutational load — the presence of deleterious mutations segregating in a population — is of particular interest for crop genomics. Deleterious mutations are most readily detected in protein-coding genes and can take several forms, including premature stop codons, splice site variants or insertions and deletions (indels) that result in the loss or impairment Nature Reviews | Genetics . . . A A C G C C T T C . . . . . . A A C G A C T T C . . . . . . A A C G C C T T C . . . . . . A A C G A C T T C . . . . . . A A C G A C T T C . . . . . . A A C G A C T T C . . . . . . A G A G G A C T C . . . . . . C G A G G A C T C . . . . . . A G G G G A C T C . . . . . . A G G G G A C T C . . . . . . A G G G G A C T C . . . . . . A G A G G A C T C . . . . . . A A C G A C T T C . . . . . . A A C G C C T T C . . . . . . A G A G G A C T C . . . . . . C G A G G C C T C . . . . . . A G G G G A C T C . . . . . . A G A G G A C T C . . . . . . A A C G C C T T C . . . . . . A A C G C C T T C . . . . . . A A C G C C T T T . . . . . . A A C G C C T T T . . . . . . A A C G C C T T T . . . . . . A G A A G A C T C . . . . . . A G A A G A C T C . . . . . . A G A A G A C T A . . . . . . A G A A G A C T C . . . . . . A G A G G A C T C . . . . . . A G A A G A C T C . . . Derived population 1 Derived population 2 . . . A A T G C C T T C . . . . . . A A C G C C T T T . . . . . . A A C G C C T T T . . . . . . A G G G G A C T C . . . . . . A G A A G A C T C . . . Gene 1 Gene 2 Gene 2 Gene 1 Gene 2 . . . A A C G A T C T C . . . HisAsn Leu AspAsn Leu . . . A A T C A T C T C . . . . . . A A T G C G T T C . . . . . . A A C G C G T T C . . . Ancestral populationb Sorghum Maize Gene 1
- 47. Morell, Buckler, andRoss-Ibarra. Nat. Rev. Genetics. 2012 Genetic load refers to the reduction in fitness caused by suboptimal genotypes in a population121 . Genetic load can arise in a number of ways, including directional selection, recombination or mutation. Mutational load — the presence of deleterious mutations segregating in a population — is of particular interest for crop genomics. Deleterious mutations are most readily detected in protein-coding genes and can take several forms, including premature stop codons, splice site variants or insertions and deletions (indels) that result in the loss or impairment Nature Reviews | Genetics . . . A A C G C C T T C . . . . . . A A C G A C T T C . . . . . . A A C G C C T T C . . . . . . A A C G A C T T C . . . . . . A A C G A C T T C . . . . . . A A C G A C T T C . . . . . . A G A G G A C T C . . . . . . C G A G G A C T C . . . . . . A G G G G A C T C . . . . . . A G G G G A C T C . . . . . . A G G G G A C T C . . . . . . A G A G G A C T C . . . . . . A A C G A C T T C . . . . . . A A C G C C T T C . . . . . . A G A G G A C T C . . . . . . C G A G G C C T C . . . . . . A G G G G A C T C . . . . . . A G A G G A C T C . . . . . . A A C G C C T T C . . . . . . A A C G C C T T C . . . . . . A A C G C C T T T . . . . . . A A C G C C T T T . . . . . . A A C G C C T T T . . . . . . A G A A G A C T C . . . . . . A G A A G A C T C . . . . . . A G A A G A C T A . . . . . . A G A A G A C T C . . . . . . A G A G G A C T C . . . . . . A G A A G A C T C . . . Derived population 1 Derived population 2 . . . A A T G C C T T C . . . . . . A A C G C C T T T . . . . . . A A C G C C T T T . . . . . . A G G G G A C T C . . . . . . A G A A G A C T C . . . Gene 1 Gene 2 Gene 2 Gene 1 Gene 2 . . . A A C G A T C T C . . . HisAsn Leu AspAsn Leu . . . A A T C A T C T C . . . . . . A A T G C G T T C . . . . . . A A C G C G T T C . . . Ancestral populationb Sorghum Maize Gene 1 Genetic load refers to the reduction in fitness caused by suboptimal genotypes in a population121 . Genetic load can arise in a number of ways, including directional selection, recombination or mutation. Mutational load — the presence of deleterious mutations segregating in a population — is of particular interest for crop genomics. Deleterious mutations are most readily detected in protein-coding genes and can take several forms, including premature stop codons, splice site variants or insertions and deletions (indels) that result in the loss or impairment Nature Reviews | Genetics . . . A A C G C C T T C . . . . . . A A C G A C T T C . . . . . . A A C G C C T T C . . . . . . A A C G A C T T C . . . . . . A A C G A C T T C . . . . . . A A C G A C T T C . . . . . . A G A G G A C T C . . . . . . C G A G G A C T C . . . . . . A G G G G A C T C . . . . . . A G G G G A C T C . . . . . . A G G G G A C T C . . . . . . A G A G G A C T C . . . . . . A A C G A C T T C . . . . . . A A C G C C T T C . . . . . . A G A G G A C T C . . . . . . C G A G G C C T C . . . . . . A G G G G A C T C . . . . . . A G A G G A C T C . . . . . . A A C G C C T T C . . . . . . A A C G C C T T C . . . . . . A A C G C C T T T . . . . . . A A C G C C T T T . . . . . . A A C G C C T T T . . . . . . A G A A G A C T C . . . . . . A G A A G A C T C . . . . . . A G A A G A C T A . . . . . . A G A A G A C T C . . . . . . A G A G G A C T C . . . . . . A G A A G A C T C . . . Derived population 1 Derived population 2 . . . A A T G C C T T C . . . . . . A A C G C C T T T . . . . . . A A C G C C T T T . . . . . . A G G G G A C T C . . . . . . A G A A G A C T C . . . Gene 1 Gene 2 Gene 2 Gene 1 Gene 2 . . . A A C G A T C T C . . . HisAsn Leu AspAsn Leu . . . A A T C A T C T C . . . . . . A A T G C G T T C . . . . . . A A C G C G T T C . . . Ancestral populationb Sorghum Maize Gene 1
- 48. Morell, Buckler, andRoss-Ibarra. Nat. Rev. Genetics. 2012 Genetic load refers to the reduction in fitness caused by suboptim arise in a number of ways, including directional selection, recomb presence of deleterious mutations segregating in a population — Deleterious mutations are most readily detected in protein-codin premature stop codons, splice site variants or insertions and dele of protein function. These types of mutations are frequently assoc providing direct evidence that loss-of-function changes tend to b . . . A A C G C C T T C . . . . . . A A C G A C T T C . . . . . . A A C G C C T T C . . . . . . A A C G A C T T C . . . . . . A A C G A C T T C . . . . . . A A C G A C T T C . . . . . . A G A G G A C T C . . . . . . C G A G G A C T C . . . . . . A G G G G A C T C . . . . . . A G G G G A C T C . . . . . . A G G G G A C T C . . . . . . A G A G G A C T C . . . . . . A . . . A . . . A . . . A . . . A Derived population 1 . . . A ed by suboptimal genotypes in a population121 . Genetic load can ection, recombination or mutation. Mutational load — the population — is of particular interest for crop genomics. protein-coding genes and can take several forms, including tions and deletions (indels) that result in the loss or impairment Nature Reviews | Genetics C . . . C . . . C . . . C . . . C . . . C . . . . . . A A C G C C T T C . . . . . . A A C G C C T T C . . . . . . A A C G C C T T T . . . . . . A A C G C C T T T . . . . . . A A C G C C T T T . . . . . . A G A A G A C T C . . . . . . A G A A G A C T C . . . . . . A G A A G A C T A . . . . . . A G A A G A C T C . . . . . . A G A G G A C T C . . . . . . A G A A G A C T C . . . Derived population 2 Gene 1 Gene 2 . . . A A T G C G T T C . . . Genetic load refers to the reduction in fitness caused by suboptimal genotypes in a population121 . Genetic load can arise in a number of ways, including directional selection, recombination or mutation. Mutational load — the presence of deleterious mutations segregating in a population — is of particular interest for crop genomics. Deleterious mutations are most readily detected in protein-coding genes and can take several forms, including premature stop codons, splice site variants or insertions and deletions (indels) that result in the loss or impairment Nature Reviews | Genetics . . . A A C G C C T T C . . . . . . A A C G A C T T C . . . . . . A A C G C C T T C . . . . . . A A C G A C T T C . . . . . . A A C G A C T T C . . . . . . A A C G A C T T C . . . . . . A G A G G A C T C . . . . . . C G A G G A C T C . . . . . . A G G G G A C T C . . . . . . A G G G G A C T C . . . . . . A G G G G A C T C . . . . . . A G A G G A C T C . . . . . . A A C G A C T T C . . . . . . A A C G C C T T C . . . . . . A G A G G A C T C . . . . . . C G A G G C C T C . . . . . . A G G G G A C T C . . . . . . A G A G G A C T C . . . . . . A A C G C C T T C . . . . . . A A C G C C T T C . . . . . . A A C G C C T T T . . . . . . A A C G C C T T T . . . . . . A A C G C C T T T . . . . . . A G A A G A C T C . . . . . . A G A A G A C T C . . . . . . A G A A G A C T A . . . . . . A G A A G A C T C . . . . . . A G A G G A C T C . . . . . . A G A A G A C T C . . . Derived population 1 Derived population 2 . . . A A T G C C T T C . . . . . . A A C G C C T T T . . . . . . A A C G C C T T T . . . . . . A G G G G A C T C . . . . . . A G A A G A C T C . . . Gene 1 Gene 2 Gene 2 Gene 1 Gene 2 . . . A A C G A T C T C . . . HisAsn Leu AspAsn Leu . . . A A T C A T C T C . . . . . . A A T G C G T T C . . . . . . A A C G C G T T C . . . Ancestral populationb Sorghum Maize Gene 1 Complementation & Hybrid Vigor
- 52. Genetic change withina single program: BSSS/BSCB1
- 53. Genetic change withina single program: BSSS/BSCB1 • genetic drift explains most change in diversity
- 54. Genetic change withina single program: BSSS/BSCB1 • genetic drift explains most change in diversity • little overlap in selected regions
- 55. Genetic change withina single program: BSSS/BSCB1 • genetic drift explains most change in diversity • little overlap in selected regions • complementation of deleterious alleles rather than overdominance likely basis of heterosis
- 56. How important aredeleterious variants? Mezmouk & Ross-Ibarra G3 2014
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- 59. similar AA likely neutral differentAA likely deleterious
- 60. similar AA likely neutral differentAA likely deleterious
- 62. nss ts 0 0.1 0.20.3 0.4 0.5 0.6 0.7 0.8 0.9 1 00.10.20.30.40.50.60.70.80.91 NSS TROPICAL Deleterious allele frequency
- 63. nss ts 0 0.1 0.20.3 0.4 0.5 0.6 0.7 0.8 0.9 1 00.10.20.30.40.50.60.70.80.91 NSS TROPICAL nss ts 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 00.10.20.30.40.50.60.70.80.91 ss nss 00.10.20.30.40.50.60.70.80.91 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 SS NSS Deleterious allele frequency
- 64. nss ts 0 0.1 0.20.3 0.4 0.5 0.6 0.7 0.8 0.9 1 00.10.20.30.40.50.60.70.80.91 NSS TROPICAL nss ts 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 00.10.20.30.40.50.60.70.80.91 ss nss 00.10.20.30.40.50.60.70.80.91 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 SS NSS Deleterious allele frequency
- 66. 23456789 chr10 −log10(p) 20 40 6080 100 120 140 ● ●●● ● ● ● ● ● ● ● ●
- 67. Chromosome 1 Proportionnonsynomyous 0.00.40.8 7 4277 119 168 217 266
- 68. Chromosome 1 Proportionnonsynomyous 0.00.40.8 7 4277 119 168 217 266
- 69. Chromosome 1 Proportionnonsynomyous 0.00.40.8 7 4277 119 168 217 266
- 70. Gore et al.2009 ScienceLarièpe et al. 2012 Genetics
- 71. Gore et al.2009 ScienceLarièpe et al. 2012 Genetics
- 72. How important aredeleterious variants?
- 73. How important aredeleterious variants? • deleterious alleles common, usually at low frequency in at least one group
- 74. How important aredeleterious variants? • deleterious alleles common, usually at low frequency in at least one group • all traits show enrichment of genes with deleterious alleles
- 75. How important aredeleterious variants? • deleterious alleles common, usually at low frequency in at least one group • all traits show enrichment of genes with deleterious alleles • complementation of deleterious alleles in low recombination regions likely important for heterosis
- 76. Experimental test ofdeleterious complementation Yang et al. bioRxiv 2017
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- 79. B73 Mo17 PHZ51 B73 Mo17 PHZ51 FloweringTime Height Yield
- 80. GERP = Neutralrate - Estimated rate High GERP (high function) Low GERP (low function)
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- 82. aj, additive effectof the jth GERP-SNP; Xij, 0-1-2 coding of jth GERP-SNP on ith hybrid; dj, dominance effect of the jth GERP-SNP; Wij, 0-1-0 coding of jth GERP-SNP on ith hybrid.
- 83. Heterosis increasing Height YieldFloweringTime aj, additive effect of the jth GERP-SNP; Xij, 0-1-2 coding of jth GERP-SNP on ith hybrid; dj, dominance effect of the jth GERP-SNP; Wij, 0-1-0 coding of jth GERP-SNP on ith hybrid.
- 84. Heterosis increasing Height YieldFloweringTime aj, additive effect of the jth GERP-SNP; Xij, 0-1-2 coding of jth GERP-SNP on ith hybrid; dj, dominance effect of the jth GERP-SNP; Wij, 0-1-0 coding of jth GERP-SNP on ith hybrid. k > 1 Overdominance k = 1 Dominance k = -1 Recessive k < -1 Underdominance k = 0 Additive
- 85. 0.000.010.020.03 0.0 0.5 1.01.5 2.0 GERP Score AdditiveEffect 0.000.010.020.03 0.0 0.5 1.0 1.5 2.0 GERP Score DominantEffect 0.00.10.20.30.4 0.0 DegreeofDomiance(k) c d e 0.5 1.0 1.5 2.0 GERP Score 0.00.10.20.30.4 0.0 0.5 1.0 1.5 2.0 GERP Score DegreeofDomiance(k) TW DTP DTS ASI PHT EHT GY −1 0 1 2 Traits TW DTP DTS ASI PHT EHT GY e
- 86. 0.000.010.020.03 0.0 0.5 1.01.5 2.0 GERP Score AdditiveEffect 0.000.010.020.03 0.0 0.5 1.0 1.5 2.0 GERP Score DominantEffect 0.00.10.20.30.4 0.0 DegreeofDomiance(k) c d e 0.5 1.0 1.5 2.0 GERP Score 0.00.10.20.30.4 0.0 0.5 1.0 1.5 2.0 GERP Score DegreeofDomiance(k) TW DTP DTS ASI PHT EHT GY −1 0 1 2 Traits TW DTP DTS ASI PHT EHT GY e
- 87. 0.000.010.020.03 0.0 0.5 1.01.5 2.0 GERP Score AdditiveEffect 0.000.010.020.03 0.0 0.5 1.0 1.5 2.0 GERP Score DominantEffect 0.00.10.20.30.4 0.0 DegreeofDomiance(k) c d e 0.5 1.0 1.5 2.0 GERP Score 0.00.10.20.30.4 0.0 0.5 1.0 1.5 2.0 GERP Score DegreeofDomiance(k) TW DTP DTS ASI PHT EHT GY −1 0 1 2 Traits TW DTP DTS ASI PHT EHT GY e
- 88. GenotypeGERP Scores * * ** YieldFlowering Height GERP YieldFlowering Height random
- 89. Experimental test ofdeleterious complementation • yield shows more dominance than other traits • how deleterious an allele is matters for yield • deleterious alleles are recessive (for yield) • modeling complementation improves prediction of hybrid yield and heterosis 5-10%
- 90. Heterosis yield Duvick 2005Maydica Hybrid yield Inbred yield
- 91. Unasked for opinionson heterotic groups from a guy who knows nothing about breeding • The Good: • intellectual & genetic control of germplasm • hybrid vigor (it’s not all dominance) • The Bad: • diversity loss • inefficient selection
- 92. Unasked for opinionson heterotic groups from a guy who knows nothing about breeding • Option 1: • heterotic groups, but large Ne and genotype to enrich for recombination • Option 2: • mass (genomic) selection on randomly mated populations
- 93.