4. GrainYield
Year
How has breeding affected diversity across the
maize genome?
How has the genome responded to selection for
increasing hybrid yield?
5. GrainYield
Year
How has breeding affected 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 et al. 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
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
46. Morell, Buckler, and Ross-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, and Ross-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, and Ross-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
53. Genetic change within a single
program: BSSS/BSCB1
• genetic drift explains most change in
diversity
54. Genetic change within a single
program: BSSS/BSCB1
• genetic drift explains most change in
diversity
• little overlap in selected regions
55. Genetic change within a 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 are deleterious
variants?
Mezmouk & Ross-Ibarra G3 2014
73. How important are deleterious variants?
• deleterious alleles common, usually at low
frequency in at least one group
74. How important are deleterious 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 are deleterious 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
82. 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.
83. Heterosis increasing
Height YieldFlowering Time
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 YieldFlowering Time
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 1.0 1.5 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 1.0 1.5 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 1.0 1.5 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
89. Experimental test of deleterious
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%
91. Unasked for opinions on 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 opinions on 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