evolutionary genetics of hybrid maize
TRANSCRIPT
![Page 1: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/1.jpg)
Evolutionary Genetics of Hybrid Maize
Jeffrey Ross-Ibarra www.rilab.org @jrossibarra
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Gra
in Y
ield
Year
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Gra
in Y
ield
Year
How has breeding affected diversity across the maize genome?
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Gra
in Y
ield
Year
How has breeding affected diversity across the maize genome?
How has the genome responded to selection for increasing hybrid yield?
![Page 5: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/5.jpg)
Gra
in Y
ield
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?
![Page 6: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/6.jpg)
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
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!
IodentNon-Stiff Stalk (NSS)
Stiff Stalk
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!
1 2 30 1 2 3era
C0.
000.
100.
200.
30
BSS NSS IDT
man
hatta
n di
stan
ce
050
0015
000
2500
0
BSS NSS IDT
inv.
sim
pson
010
2030
40
Lanc
aste
r
Min
13
Rei
d
Mid
land
S. d
ent
pop
flint
0.0
0.1
0.2
0.3
0.4
0.5
a. c.b.
d. e.
era
1 2 3 1 2 3 1 2 3
1 2 3 1 2 3 1 2 3an
cest
ry p
ropo
rtio
n
12
30
12
3er
a
C0.000.100.200.30
BS
SN
SS
IDT
manhattan distance
050001500025000
BS
SN
SS
IDT
inv.simpson
010203040
Lancaster
Min13
Reid
Midland
S. dent
pop
flint
0.0
0.1
0.2
0.3
0.4
0.5
a.c.
b.
d.e.
era
12
31
23
12
3
12
31
23
12
3
IodentNSSSS
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AC
TGTG
AC
TCCA
TC
G
A
Inbred 1
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AC
TGTG
AC
TCCA
TC
G
A
GTG
AC
TC
TC
G
TC
G
AC
G
AC
TGTG
AC
TCCA
TG
T
G
Inbred 1 2 3
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AC
TGTG
AC
TCCA
TC
G
A
GTG
AC
TC
TC
G
TC
G
AC
G
AC
TGTG
AC
TCCA
TG
T
G
Inbred 1 2 3
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AC
TGTG
AC
TCCA
TC
G
A
GTG
AC
TC
TC
G
TC
G
AC
G
AC
TGTG
AC
TCCA
TG
T
G
Inbred 1 2 3
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AC
TGTG
AC
TCCA
TC
G
A
AC
TGTG
AC
TCCA
TG
T
G
Inbred 1 3
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AC
TGTG
AC
TCCA
TC
G
A
AC
TGTG
AC
TCCA
TG
T
G
Inbred 1 33
2
1
0
time
cate
gory
SSNSS
Iodent
![Page 15: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/15.jpg)
SS
0.0
0.1
0.2
0.3
0.4
unde
fined
O
H43
C
I31A
H
Y
B8
B10
B1
4
B96
B3
7
I205
O
H07
C
I3A
C
I187
-2
CI5
40
I224
W
D45
6
Oh3
167B
Tr
9-1-
1-6
FE
2
LE77
3
ND
203
B7
3
A634
A6
35
N28
H
100
B6
4
B14A
B6
8
CM
105
B8
4
A632
N
196
LH
195
LH
205
LH
196
LH
194
99
1
LH74
PH
G39
LH
132
G
80
7800
4
7801
0
4676
A
7800
2A
794
LP
5
PHT5
5
H84
31
1 2 3
NSS
0.0
0.1
0.2
0.3
0.4
unde
fined
C
103
O
H43
W
F9
A73
K5
5
A375
A5
56
I159
P8
38
-11
B2
33
-16
H
5
HY
K1
55
OH
40B
K4
W
22 A
B10
B3
7
T8
CO
109
O
H07
W
182B
C
I187
-2
CI5
40
Ill.1
2E
AH83
W
D
CM
37
M14
B7
0
H99
A6
54
VA26
W
117
B5
5
MO
17
R16
8
LH38
LH
39
LH51
PH
G35
M
BNA
LH
57
PHR
36
LH59
M
BST
PH
J31
PH
M57
PH
N37
PH
N73
1 2 3
IDT1 2 3
0.0
0.1
0.2
0.3
0.4
unde
fined
O
H43
W
F9
A375
A5
09
A556
I1
98
B2
H5
H
Y
B164
G
N
D20
3
B10
B1
4
L317
I2
05
CI1
87-2
C
49A
I2
24
AH83
Tr
9-1-
1-6
C
11
IDT
A6
38
M14
20
7
PHN
34
PHP7
6
PHW
86
PHG
50
PHG
35
PHG
71
IB01
4
PHG
83
LH15
0
PHG
29
PHG
72
PHG
84
PHZ5
1
PHV7
8
PHK4
2
PHN
11
PHH
93
PHJ3
3
PHN
73
PHR
62
12
30
12
3er
a
C0.000.100.200.30
BS
SN
SS
IDT
manhattan distance
050001500025000
BS
SN
SS
IDT
inv.simpson
010203040
Lancaster
Min13
Reid
Midland
S. dent
pop
flint
0.0
0.1
0.2
0.3
0.4
0.5
a.c.
b.
d.e.
era
12
31
23
12
3
12
31
23
12
3
exPVP1960’s1940’s
1960’s1940’s exPVP
IodentNSSSS
time
line origin
![Page 16: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/16.jpg)
SS
0.0
0.1
0.2
0.3
0.4
unde
fined
O
H43
C
I31A
H
Y
B8
B10
B1
4
B96
B3
7
I205
O
H07
C
I3A
C
I187
-2
CI5
40
I224
W
D45
6
Oh3
167B
Tr
9-1-
1-6
FE
2
LE77
3
ND
203
B7
3
A634
A6
35
N28
H
100
B6
4
B14A
B6
8
CM
105
B8
4
A632
N
196
LH
195
LH
205
LH
196
LH
194
99
1
LH74
PH
G39
LH
132
G
80
7800
4
7801
0
4676
A
7800
2A
794
LP
5
PHT5
5
H84
31
1 2 3
NSS
0.0
0.1
0.2
0.3
0.4
unde
fined
C
103
O
H43
W
F9
A73
K5
5
A375
A5
56
I159
P8
38
-11
B2
33
-16
H
5
HY
K1
55
OH
40B
K4
W
22 A
B10
B3
7
T8
CO
109
O
H07
W
182B
C
I187
-2
CI5
40
Ill.1
2E
AH83
W
D
CM
37
M14
B7
0
H99
A6
54
VA26
W
117
B5
5
MO
17
R16
8
LH38
LH
39
LH51
PH
G35
M
BNA
LH
57
PHR
36
LH59
M
BST
PH
J31
PH
M57
PH
N37
PH
N73
1 2 3
IDT1 2 3
0.0
0.1
0.2
0.3
0.4
unde
fined
O
H43
W
F9
A375
A5
09
A556
I1
98
B2
H5
H
Y
B164
G
N
D20
3
B10
B1
4
L317
I2
05
CI1
87-2
C
49A
I2
24
AH83
Tr
9-1-
1-6
C
11
IDT
A6
38
M14
20
7
PHN
34
PHP7
6
PHW
86
PHG
50
PHG
35
PHG
71
IB01
4
PHG
83
LH15
0
PHG
29
PHG
72
PHG
84
PHZ5
1
PHV7
8
PHK4
2
PHN
11
PHH
93
PHJ3
3
PHN
73
PHR
62
12
30
12
3er
a
C0.000.100.200.30
BS
SN
SS
IDT
manhattan distance
050001500025000
BS
SN
SS
IDT
inv.simpson
010203040
Lancaster
Min13
Reid
Midland
S. dent
pop
flint
0.0
0.1
0.2
0.3
0.4
0.5
a.c.
b.
d.e.
era
12
31
23
12
3
12
31
23
12
3
exPVP1960’s1940’s
1960’s1940’s exPVP
IodentNSSSS
time
line origin
![Page 17: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/17.jpg)
12
30
12
3er
a
C0.000.100.200.30
BS
SN
SS
IDT
manhattan distance
050001500025000
BS
SN
SS
IDT
inv.simpson
010203040
Lancaster
Min13
Reid
Midland
S. dent
pop
flint
0.0
0.1
0.2
0.3
0.4
0.5
a.c.
b.
d.e.
era
12
31
23
12
3
12
31
23
12
3
exPVP1960’s1940’s
SS
0.0
0.1
0.2
0.3
0.4
unde
fined
O
H43
C
I31A
H
Y
B8
B10
B1
4
B96
B3
7
I205
O
H07
C
I3A
C
I187
-2
CI5
40
I224
W
D45
6
Oh3
167B
Tr
9-1-
1-6
FE
2
LE77
3
ND
203
B7
3
A634
A6
35
N28
H
100
B6
4
B14A
B6
8
CM
105
B8
4
A632
N
196
LH
195
LH
205
LH
196
LH
194
99
1
LH74
PH
G39
LH
132
G
80
7800
4
7801
0
4676
A
7800
2A
794
LP
5
PHT5
5
H84
31
1 2 3
NSS
0.0
0.1
0.2
0.3
0.4
unde
fined
C
103
O
H43
W
F9
A73
K5
5
A375
A5
56
I159
P8
38
-11
B2
33
-16
H
5
HY
K1
55
OH
40B
K4
W
22 A
B10
B3
7
T8
CO
109
O
H07
W
182B
C
I187
-2
CI5
40
Ill.1
2E
AH83
W
D
CM
37
M14
B7
0
H99
A6
54
VA26
W
117
B5
5
MO
17
R16
8
LH38
LH
39
LH51
PH
G35
M
BNA
LH
57
PHR
36
LH59
M
BST
PH
J31
PH
M57
PH
N37
PH
N73
1 2 3
IDT1 2 3
0.0
0.1
0.2
0.3
0.4
unde
fined
O
H43
W
F9
A375
A5
09
A556
I1
98
B2
H5
H
Y
B164
G
N
D20
3
B10
B1
4
L317
I2
05
CI1
87-2
C
49A
I2
24
AH83
Tr
9-1-
1-6
C
11
IDT
A6
38
M14
20
7
PHN
34
PHP7
6
PHW
86
PHG
50
PHG
35
PHG
71
IB01
4
PHG
83
LH15
0
PHG
29
PHG
72
PHG
84
PHZ5
1
PHV7
8
PHK4
2
PHN
11
PHH
93
PHJ3
3
PHN
73
PHR
62
1960’s1940’s exPVP
IodentNSSSS
time
line origin
![Page 18: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/18.jpg)
1 2 30 1 2 3era
C0.
000.
100.
200.
30
BSS NSS IDT
man
hatta
n di
stan
ce
050
0015
000
2500
0
BSS NSS IDT
inv.
sim
pson
010
2030
40
Lanc
aste
r
Min
13
Rei
d
Mid
land
S. d
ent
pop
flint
0.0
0.1
0.2
0.3
0.4
0.5
a. c.b.
d. e.
era
1 2 3 1 2 3 1 2 3
1 2 3 1 2 3 1 2 3
effe
ctiv
e #
anc
esto
rs
exPVP1960’s1940’s
12
30
12
3er
a
C0.000.100.200.30
BS
SN
SS
IDT
manhattan distance
050001500025000
BS
SN
SS
IDT
inv.simpson
010203040
Lancaster
Min13
Reid
Midland
S. dent
pop
flint
0.0
0.1
0.2
0.3
0.4
0.5
a.c.
b.
d.e.
era
12
31
23
12
3
12
31
23
12
3
![Page 19: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/19.jpg)
1 2 30 1 2 3era
C0.
000.
100.
200.
30
BSS NSS IDT
man
hatta
n di
stan
ce
050
0015
000
2500
0
BSS NSS IDT
inv.
sim
pson
010
2030
40
Lanc
aste
r
Min
13
Rei
d
Mid
land
S. d
ent
pop
flint
0.0
0.1
0.2
0.3
0.4
0.5
a. c.b.
d. e.
era
1 2 3 1 2 3 1 2 3
1 2 3 1 2 3 1 2 3
effe
ctiv
e #
anc
esto
rs
1 2 30 1 2 3era
C0.
000.
100.
200.
30
BSS NSS IDT
man
hatta
n di
stan
ce
050
0015
000
2500
0
BSS NSS IDT
inv.
sim
pson
010
2030
40
Lanc
aste
r
Min
13
Rei
d
Mid
land
S. d
ent
pop
flint
0.0
0.1
0.2
0.3
0.4
0.5
a. c.b.
d. e.
era
1 2 3 1 2 3 1 2 3
1 2 3 1 2 3 1 2 3
dive
rsity
of a
nces
tors
exPVP1960’s1940’s
12
30
12
3er
a
C0.000.100.200.30
BS
SN
SS
IDT
manhattan distance
050001500025000
BS
SN
SS
IDT
inv.simpson
010203040
Lancaster
Min13
Reid
Midland
S. dent
pop
flint
0.0
0.1
0.2
0.3
0.4
0.5
a.c.
b.
d.e.
era
12
31
23
12
3
12
31
23
12
3
![Page 20: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/20.jpg)
1 2 30 1 2 3era
C0.
000.
100.
200.
30
BSS NSS IDT
man
hatta
n di
stan
ce
050
0015
000
2500
0
BSS NSS IDT
inv.
sim
pson
010
2030
40
Lanc
aste
r
Min
13
Rei
d
Mid
land
S. d
ent
pop
flint
0.0
0.1
0.2
0.3
0.4
0.5
a. c.b.
d. e.
era
1 2 3 1 2 3 1 2 3
1 2 3 1 2 3 1 2 3
effe
ctiv
e #
anc
esto
rs
1 2 30 1 2 3era
C0.
000.
100.
200.
30
BSS NSS IDT
man
hatta
n di
stan
ce
050
0015
000
2500
0
BSS NSS IDT
inv.
sim
pson
010
2030
40
Lanc
aste
r
Min
13
Rei
d
Mid
land
S. d
ent
pop
flint
0.0
0.1
0.2
0.3
0.4
0.5
a. c.b.
d. e.
era
1 2 3 1 2 3 1 2 3
1 2 3 1 2 3 1 2 3
dive
rsity
of a
nces
tors
exPVP1960’s1940’s
0 1 2 3
01
23
4
6 snp 5 snp 8 snp 7 snp 10 snp 9 snp 15 snp 15 snp
erara
tio o
bser
ved/
rand
omiz
ed0 10000 20000 30000 40000 50000 60000
0.0
0.1
0.2
0.3
0.4
0.5
0.6
bp
Mora
n’s
I
12
30
12
3er
a
C0.000.100.200.30
BS
SN
SS
IDT
manhattan distance
050001500025000
BS
SN
SS
IDT
inv.simpson
010203040
Lancaster
Min13
Reid
Midland
S. dent
pop
flint
0.0
0.1
0.2
0.3
0.4
0.5
a.c.
b.
d.e.
era
12
31
23
12
3
12
31
23
12
3
![Page 21: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/21.jpg)
!
sele
ctio
nan
cest
ry
devia
tion
num
ber
ance
stor
s
0 1 2 3
0.0
0.2
0.4
0.6
0.8
1.0
era
p
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!
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0 1 2 3
0.0
0.2
0.4
0.6
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1.0
era
p
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ersi
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Genome Sequence
Selective Sweep
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10,000 ft view: drift and diversity loss
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10,000 ft view: drift and diversity loss
• increasingly small, homogeneous germplasm making up ancestry of modern lines
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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
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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
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Genetic change within a single program: BSSS/BSCB1
Gerke et al. 2015 Genetics
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Genetic change within a single program: BSSS/BSCB1
Gerke et al. 2015 Genetics
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BSSS1
BSCB11
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BSSS1
BSCB11
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BSSS1
BSCB11
S1
S1
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BSSS1
BSCB11
yield trials
S1
S1
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BSSS1
BSCB11
yield trials
S1
S1
Ne~20
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BSSS1
BSCB11
yield trials
S1
S1
BSSS2
BSCB2
Ne~20
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Morell, Buckler, and Ross-Ibarra. Nat. Rev. Genetics. 2012
Box 1 | Genetic load
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 of protein function. These types of mutations are frequently associated with Mendelian disorders in humans, providing direct evidence that loss-of-function changes tend to be deleterious, particularly when homozygous122. Although most nonsynonymous mutations in plants are strongly deleterious, a sizable proportion are only slightly so, and these mutations may segregate at appreciable frequencies123.
Unambiguously deleterious mutations are fairly common in crop genomes17,54,124. Statistical analysis of homologous sequence from multiple genomes can identify amino acid changes that are likely to be disadvantageous (for example, REF. 125), but these comparative analyses benefit from transcriptomic data, as transcript variation among individuals may render some putatively deleterious mutations inconsequential120. Part a of the figure shows a hypothetical alignment of coding sequence from multiple grass species. The conserved nature of the histidine amino acid across species suggests that the nonsynonymous change (indicated by the red ‘G’) observed in maize is likely to be deleterious. Synonymous changes are shown in black.
Selection against deleterious mutations is hindered by Hill–Robertson effects — because of linkage, selection can only act on the net effect of both beneficial and deleterious mutations. Deleterious mutations should thus be enriched in regions of the genome in which recombination is suppressed and around the targets of strong positive selection126,127. Although neither prediction has yet been explicitly demonstrated in crops, patterns of residual heterozygosity in the maize genome support the first prediction14, and evidence from humans128 bears out the second. Whereas inbreeding can act to purge deleterious mutations129,130, drift can increase the frequency of deleterious mutations in small populations131,132. Drift is a stochastic process, and unique sets of deleterious alleles would be expected to increase in frequency in different breeding populations (for example, REF. 124). This is illustrated in part b of the figure, in which two nonsynonymous mutations (indicated by the red ‘A’s) in the ancestral population increase in frequency in two derived populations. Because drift operates independently in isolated populations, different breeding programs are likely to have a number of distinct, high-frequency deleterious mutations. Given that most deleterious mutations are at least partially recessive, crosses between lines from different breeding populations should exhibit complementation at these loci, explaining, at least in part, the widespread observation of heterosis.
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
a
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 C C A C C T C . . .
. . . A A C C A C C T T . . .
. . . A A T G C G T T C . . .
. . . A A C G C G T T C . . .
Ancestral populationb
Rice
Brachypodium
Sorghum
Maize
Gene 1
REVIEWS
NATURE REVIEWS | GENETICS ADVANCE ONLINE PUBLICATION | 5
© 2012 Macmillan Publishers Limited. All rights reserved
![Page 47: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/47.jpg)
Morell, Buckler, and Ross-Ibarra. Nat. Rev. Genetics. 2012
Box 1 | Genetic load
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 of protein function. These types of mutations are frequently associated with Mendelian disorders in humans, providing direct evidence that loss-of-function changes tend to be deleterious, particularly when homozygous122. Although most nonsynonymous mutations in plants are strongly deleterious, a sizable proportion are only slightly so, and these mutations may segregate at appreciable frequencies123.
Unambiguously deleterious mutations are fairly common in crop genomes17,54,124. Statistical analysis of homologous sequence from multiple genomes can identify amino acid changes that are likely to be disadvantageous (for example, REF. 125), but these comparative analyses benefit from transcriptomic data, as transcript variation among individuals may render some putatively deleterious mutations inconsequential120. Part a of the figure shows a hypothetical alignment of coding sequence from multiple grass species. The conserved nature of the histidine amino acid across species suggests that the nonsynonymous change (indicated by the red ‘G’) observed in maize is likely to be deleterious. Synonymous changes are shown in black.
Selection against deleterious mutations is hindered by Hill–Robertson effects — because of linkage, selection can only act on the net effect of both beneficial and deleterious mutations. Deleterious mutations should thus be enriched in regions of the genome in which recombination is suppressed and around the targets of strong positive selection126,127. Although neither prediction has yet been explicitly demonstrated in crops, patterns of residual heterozygosity in the maize genome support the first prediction14, and evidence from humans128 bears out the second. Whereas inbreeding can act to purge deleterious mutations129,130, drift can increase the frequency of deleterious mutations in small populations131,132. Drift is a stochastic process, and unique sets of deleterious alleles would be expected to increase in frequency in different breeding populations (for example, REF. 124). This is illustrated in part b of the figure, in which two nonsynonymous mutations (indicated by the red ‘A’s) in the ancestral population increase in frequency in two derived populations. Because drift operates independently in isolated populations, different breeding programs are likely to have a number of distinct, high-frequency deleterious mutations. Given that most deleterious mutations are at least partially recessive, crosses between lines from different breeding populations should exhibit complementation at these loci, explaining, at least in part, the widespread observation of heterosis.
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
a
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 C C A C C T C . . .
. . . A A C C A C C T T . . .
. . . A A T G C G T T C . . .
. . . A A C G C G T T C . . .
Ancestral populationb
Rice
Brachypodium
Sorghum
Maize
Gene 1
REVIEWS
NATURE REVIEWS | GENETICS ADVANCE ONLINE PUBLICATION | 5
© 2012 Macmillan Publishers Limited. All rights reserved
Box 1 | Genetic load
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 of protein function. These types of mutations are frequently associated with Mendelian disorders in humans, providing direct evidence that loss-of-function changes tend to be deleterious, particularly when homozygous122. Although most nonsynonymous mutations in plants are strongly deleterious, a sizable proportion are only slightly so, and these mutations may segregate at appreciable frequencies123.
Unambiguously deleterious mutations are fairly common in crop genomes17,54,124. Statistical analysis of homologous sequence from multiple genomes can identify amino acid changes that are likely to be disadvantageous (for example, REF. 125), but these comparative analyses benefit from transcriptomic data, as transcript variation among individuals may render some putatively deleterious mutations inconsequential120. Part a of the figure shows a hypothetical alignment of coding sequence from multiple grass species. The conserved nature of the histidine amino acid across species suggests that the nonsynonymous change (indicated by the red ‘G’) observed in maize is likely to be deleterious. Synonymous changes are shown in black.
Selection against deleterious mutations is hindered by Hill–Robertson effects — because of linkage, selection can only act on the net effect of both beneficial and deleterious mutations. Deleterious mutations should thus be enriched in regions of the genome in which recombination is suppressed and around the targets of strong positive selection126,127. Although neither prediction has yet been explicitly demonstrated in crops, patterns of residual heterozygosity in the maize genome support the first prediction14, and evidence from humans128 bears out the second. Whereas inbreeding can act to purge deleterious mutations129,130, drift can increase the frequency of deleterious mutations in small populations131,132. Drift is a stochastic process, and unique sets of deleterious alleles would be expected to increase in frequency in different breeding populations (for example, REF. 124). This is illustrated in part b of the figure, in which two nonsynonymous mutations (indicated by the red ‘A’s) in the ancestral population increase in frequency in two derived populations. Because drift operates independently in isolated populations, different breeding programs are likely to have a number of distinct, high-frequency deleterious mutations. Given that most deleterious mutations are at least partially recessive, crosses between lines from different breeding populations should exhibit complementation at these loci, explaining, at least in part, the widespread observation of heterosis.
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
a
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 C C A C C T C . . .
. . . A A C C A C C T T . . .
. . . A A T G C G T T C . . .
. . . A A C G C G T T C . . .
Ancestral populationb
Rice
Brachypodium
Sorghum
Maize
Gene 1
REVIEWS
NATURE REVIEWS | GENETICS ADVANCE ONLINE PUBLICATION | 5
© 2012 Macmillan Publishers Limited. All rights reserved
![Page 48: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/48.jpg)
Morell, Buckler, and Ross-Ibarra. Nat. Rev. Genetics. 2012
Box 1 | Genetic load
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 of protein function. These types of mutations are frequently associated with Mendelian disorders in humans, providing direct evidence that loss-of-function changes tend to be deleterious, particularly when homozygous122. Although most nonsynonymous mutations in plants are strongly deleterious, a sizable proportion are only slightly so, and these mutations may segregate at appreciable frequencies123.
Unambiguously deleterious mutations are fairly common in crop genomes17,54,124. Statistical analysis of homologous sequence from multiple genomes can identify amino acid changes that are likely to be disadvantageous (for example, REF. 125), but these comparative analyses benefit from transcriptomic data, as transcript variation among individuals may render some putatively deleterious mutations inconsequential120. Part a of the figure shows a hypothetical alignment of coding sequence from multiple grass species. The conserved nature of the histidine amino acid across species suggests that the nonsynonymous change (indicated by the red ‘G’) observed in maize is likely to be deleterious. Synonymous changes are shown in black.
Selection against deleterious mutations is hindered by Hill–Robertson effects — because of linkage, selection can only act on the net effect of both beneficial and deleterious mutations. Deleterious mutations should thus be enriched in regions of the genome in which recombination is suppressed and around the targets of strong positive selection126,127. Although neither prediction has yet been explicitly demonstrated in crops, patterns of residual heterozygosity in the maize genome support the first prediction14, and evidence from humans128 bears out the second. Whereas inbreeding can act to purge deleterious mutations129,130, drift can increase the frequency of deleterious mutations in small populations131,132. Drift is a stochastic process, and unique sets of deleterious alleles would be expected to increase in frequency in different breeding populations (for example, REF. 124). This is illustrated in part b of the figure, in which two nonsynonymous mutations (indicated by the red ‘A’s) in the ancestral population increase in frequency in two derived populations. Because drift operates independently in isolated populations, different breeding programs are likely to have a number of distinct, high-frequency deleterious mutations. Given that most deleterious mutations are at least partially recessive, crosses between lines from different breeding populations should exhibit complementation at these loci, explaining, at least in part, the widespread observation of heterosis.
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
a
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 C C A C C T C . . .
. . . A A C C A C C T T . . .
. . . A A T G C G T T C . . .
. . . A A C G C G T T C . . .
Ancestral populationb
Rice
Brachypodium
Sorghum
Maize
Gene 1
REVIEWS
NATURE REVIEWS | GENETICS ADVANCE ONLINE PUBLICATION | 5
© 2012 Macmillan Publishers Limited. All rights reserved
Box 1 | Genetic load
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 of protein function. These types of mutations are frequently associated with Mendelian disorders in humans, providing direct evidence that loss-of-function changes tend to be deleterious, particularly when homozygous122. Although most nonsynonymous mutations in plants are strongly deleterious, a sizable proportion are only slightly so, and these mutations may segregate at appreciable frequencies123.
Unambiguously deleterious mutations are fairly common in crop genomes17,54,124. Statistical analysis of homologous sequence from multiple genomes can identify amino acid changes that are likely to be disadvantageous (for example, REF. 125), but these comparative analyses benefit from transcriptomic data, as transcript variation among individuals may render some putatively deleterious mutations inconsequential120. Part a of the figure shows a hypothetical alignment of coding sequence from multiple grass species. The conserved nature of the histidine amino acid across species suggests that the nonsynonymous change (indicated by the red ‘G’) observed in maize is likely to be deleterious. Synonymous changes are shown in black.
Selection against deleterious mutations is hindered by Hill–Robertson effects — because of linkage, selection can only act on the net effect of both beneficial and deleterious mutations. Deleterious mutations should thus be enriched in regions of the genome in which recombination is suppressed and around the targets of strong positive selection126,127. Although neither prediction has yet been explicitly demonstrated in crops, patterns of residual heterozygosity in the maize genome support the first prediction14, and evidence from humans128 bears out the second. Whereas inbreeding can act to purge deleterious mutations129,130, drift can increase the frequency of deleterious mutations in small populations131,132. Drift is a stochastic process, and unique sets of deleterious alleles would be expected to increase in frequency in different breeding populations (for example, REF. 124). This is illustrated in part b of the figure, in which two nonsynonymous mutations (indicated by the red ‘A’s) in the ancestral population increase in frequency in two derived populations. Because drift operates independently in isolated populations, different breeding programs are likely to have a number of distinct, high-frequency deleterious mutations. Given that most deleterious mutations are at least partially recessive, crosses between lines from different breeding populations should exhibit complementation at these loci, explaining, at least in part, the widespread observation of heterosis.
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
a
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 C C A C C T C . . .
. . . A A C C A C C T T . . .
. . . A A T G C G T T C . . .
. . . A A C G C G T T C . . .
Ancestral populationb
Rice
Brachypodium
Sorghum
Maize
Gene 1
REVIEWS
NATURE REVIEWS | GENETICS ADVANCE ONLINE PUBLICATION | 5
© 2012 Macmillan Publishers Limited. All rights reserved
Box 1 | Genetic load
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 of protein function. These types of mutations are frequently associated with Mendelian disorders in humans, providing direct evidence that loss-of-function changes tend to be deleterious, particularly when homozygous122. Although most nonsynonymous mutations in plants are strongly deleterious, a sizable proportion are only slightly so, and these mutations may segregate at appreciable frequencies123.
Unambiguously deleterious mutations are fairly common in crop genomes17,54,124. Statistical analysis of homologous sequence from multiple genomes can identify amino acid changes that are likely to be disadvantageous (for example, REF. 125), but these comparative analyses benefit from transcriptomic data, as transcript variation among individuals may render some putatively deleterious mutations inconsequential120. Part a of the figure shows a hypothetical alignment of coding sequence from multiple grass species. The conserved nature of the histidine amino acid across species suggests that the nonsynonymous change (indicated by the red ‘G’) observed in maize is likely to be deleterious. Synonymous changes are shown in black.
Selection against deleterious mutations is hindered by Hill–Robertson effects — because of linkage, selection can only act on the net effect of both beneficial and deleterious mutations. Deleterious mutations should thus be enriched in regions of the genome in which recombination is suppressed and around the targets of strong positive selection126,127. Although neither prediction has yet been explicitly demonstrated in crops, patterns of residual heterozygosity in the maize genome support the first prediction14, and evidence from humans128 bears out the second. Whereas inbreeding can act to purge deleterious mutations129,130, drift can increase the frequency of deleterious mutations in small populations131,132. Drift is a stochastic process, and unique sets of deleterious alleles would be expected to increase in frequency in different breeding populations (for example, REF. 124). This is illustrated in part b of the figure, in which two nonsynonymous mutations (indicated by the red ‘A’s) in the ancestral population increase in frequency in two derived populations. Because drift operates independently in isolated populations, different breeding programs are likely to have a number of distinct, high-frequency deleterious mutations. Given that most deleterious mutations are at least partially recessive, crosses between lines from different breeding populations should exhibit complementation at these loci, explaining, at least in part, the widespread observation of heterosis.
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
a
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 C C A C C T C . . .
. . . A A C C A C C T T . . .
. . . A A T G C G T T C . . .
. . . A A C G C G T T C . . .
Ancestral populationb
Rice
Brachypodium
Sorghum
Maize
Gene 1
REVIEWS
NATURE REVIEWS | GENETICS ADVANCE ONLINE PUBLICATION | 5
© 2012 Macmillan Publishers Limited. All rights reserved
Complementation & Hybrid Vigor
![Page 49: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/49.jpg)
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Genetic change within a single program: BSSS/BSCB1
![Page 53: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/53.jpg)
Genetic change within a single program: BSSS/BSCB1
• genetic drift explains most change in diversity
![Page 54: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/54.jpg)
Genetic change within a single program: BSSS/BSCB1
• genetic drift explains most change in diversity
• little overlap in selected regions
![Page 55: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/55.jpg)
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
![Page 56: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/56.jpg)
How important are deleterious variants?
Mezmouk & Ross-Ibarra G3 2014
![Page 57: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/57.jpg)
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similar AAlikely neutral
![Page 59: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/59.jpg)
similar AAlikely neutral
different AAlikely deleterious
![Page 60: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/60.jpg)
similar AAlikely neutral
different AAlikely deleterious
![Page 61: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/61.jpg)
![Page 62: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/62.jpg)
nss
ts
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
00.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
NSS
TRO
PICA
LDeleterious allele frequency
![Page 63: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/63.jpg)
nss
ts
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
00.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
NSS
TRO
PICA
L
nss
ts0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
00.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
ss
nss
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1SS
NSS
Deleterious allele frequency
![Page 64: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/64.jpg)
nss
ts
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
00.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
NSS
TRO
PICA
L
nss
ts0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
00.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
ss
nss
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1SS
NSS
Deleterious allele frequency
![Page 65: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/65.jpg)
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23
45
67
89
chr10
−log10(p)
20 40 60 80 100 120 140
●
●●● ●
●
●
●●
●
●
●
![Page 67: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/67.jpg)
Chromosome 1
Prop
ortio
n no
nsyn
omyo
us
0.0
0.4
0.8
7 42 77 119 168 217 266
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Chromosome 1
Prop
ortio
n no
nsyn
omyo
us
0.0
0.4
0.8
7 42 77 119 168 217 266
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Chromosome 1
Prop
ortio
n no
nsyn
omyo
us
0.0
0.4
0.8
7 42 77 119 168 217 266
![Page 70: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/70.jpg)
Gore et al. 2009 ScienceLarièpe et al. 2012 Genetics
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Gore et al. 2009 ScienceLarièpe et al. 2012 Genetics
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How important are deleterious variants?
![Page 73: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/73.jpg)
How important are deleterious variants?
• deleterious alleles common, usually at low frequency in at least one group
![Page 74: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/74.jpg)
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
![Page 75: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/75.jpg)
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
![Page 76: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/76.jpg)
Experimental test of deleterious complementation
Yang et al. bioRxiv 2017
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B73 Mo17 PHZ51
B73
Mo17
PHZ51
![Page 78: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/78.jpg)
B73 Mo17 PHZ51
B73
Mo17
PHZ51
![Page 79: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/79.jpg)
B73 Mo17 PHZ51
B73
Mo17
PHZ51
Flowering Time
Height
Yield
![Page 80: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/80.jpg)
GERP = Neutral rate - Estimated rate
High GERP (high function)
Low GERP (low function)
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●
●●●
●●●
●
TW DTP
DTS AS
I
PHT
EHT
GY
0
50
100
150
200
BPH
(100
%)
●
●
●
●
●
●
●
●
●
●
●
●●
●●●●●
●
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●
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−10 −5 0 5
0.0
0.2
0.4
0.6
GERP Score
Del
eter
ious
Alle
le F
requ
ency
●
●
LR MZ LR MZ LR MZ
0.08
0.12
0.16
0.20
Del
eter
ious
Loa
d pe
r bp
0.6
0.8
1.0
1.2
Quantiles of cM/Mb
GER
P Sc
ore
25 50 75 100
a b
c d
All Sites
Fixed Segregating
![Page 82: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/82.jpg)
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.
![Page 83: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/83.jpg)
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.
![Page 84: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/84.jpg)
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
![Page 85: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/85.jpg)
0.00
0.01
0.02
0.03
0.0 0.5 1.0 1.5 2.0GERP Score
Add
itive
Effe
ct
0.00
0.01
0.02
0.03
0.0 0.5 1.0 1.5 2.0GERP Score
Dom
inan
t Effe
ct
0.0
0.1
0.2
0.3
0.4
0.0 0.5 1.0 1.5 2.0GERP Score
Deg
ree
of D
omia
nce
(k)
TW DTP DTS ASI PHT EHT GY
−1
0
1
2
Deg
ree
of D
omin
ance
(k)
TraitsTWDTPDTSASIPHTEHTGY3.
5e−0
64.
0e−0
64.
5e−0
65.
0e−0
6
0.1 0.2 0.3 0.4 0.5
Allele Frequency
Varia
nce
Expl
aine
d
ba
c d e
0.00
0.01
0.02
0.03
0.0 0.5 1.0 1.5 2.0GERP Score
Add
itive
Effe
ct
0.00
0.01
0.02
0.03
0.0 0.5 1.0 1.5 2.0GERP Score
Dom
inan
t Effe
ct
0.0
0.1
0.2
0.3
0.4
0.0 0.5 1.0 1.5 2.0GERP Score
Deg
ree
of D
omia
nce
(k)
TW DTP DTS ASI PHT EHT GY
−1
0
1
2
Deg
ree
of D
omin
ance
(k)
TraitsTWDTPDTSASIPHTEHTGY3.
5e−0
64.
0e−0
64.
5e−0
65.
0e−0
6
0.1 0.2 0.3 0.4 0.5
Allele Frequency
Varia
nce
Expl
aine
d
ba
c d e
![Page 86: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/86.jpg)
0.00
0.01
0.02
0.03
0.0 0.5 1.0 1.5 2.0GERP Score
Add
itive
Effe
ct
0.00
0.01
0.02
0.03
0.0 0.5 1.0 1.5 2.0GERP Score
Dom
inan
t Effe
ct
0.0
0.1
0.2
0.3
0.4
0.0 0.5 1.0 1.5 2.0GERP Score
Deg
ree
of D
omia
nce
(k)
TW DTP DTS ASI PHT EHT GY
−1
0
1
2
Deg
ree
of D
omin
ance
(k)
TraitsTWDTPDTSASIPHTEHTGY3.
5e−0
64.
0e−0
64.
5e−0
65.
0e−0
6
0.1 0.2 0.3 0.4 0.5
Allele Frequency
Varia
nce
Expl
aine
d
ba
c d e
0.00
0.01
0.02
0.03
0.0 0.5 1.0 1.5 2.0GERP Score
Add
itive
Effe
ct
0.00
0.01
0.02
0.03
0.0 0.5 1.0 1.5 2.0GERP Score
Dom
inan
t Effe
ct
0.0
0.1
0.2
0.3
0.4
0.0 0.5 1.0 1.5 2.0GERP Score
Deg
ree
of D
omia
nce
(k)
TW DTP DTS ASI PHT EHT GY
−1
0
1
2
Deg
ree
of D
omin
ance
(k)
TraitsTWDTPDTSASIPHTEHTGY3.
5e−0
64.
0e−0
64.
5e−0
65.
0e−0
6
0.1 0.2 0.3 0.4 0.5
Allele Frequency
Varia
nce
Expl
aine
d
ba
c d e
![Page 87: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/87.jpg)
0.00
0.01
0.02
0.03
0.0 0.5 1.0 1.5 2.0GERP Score
Add
itive
Effe
ct
0.00
0.01
0.02
0.03
0.0 0.5 1.0 1.5 2.0GERP Score
Dom
inan
t Effe
ct
0.0
0.1
0.2
0.3
0.4
0.0 0.5 1.0 1.5 2.0GERP Score
Deg
ree
of D
omia
nce
(k)
TW DTP DTS ASI PHT EHT GY
−1
0
1
2
Deg
ree
of D
omin
ance
(k)
TraitsTWDTPDTSASIPHTEHTGY3.
5e−0
64.
0e−0
64.
5e−0
65.
0e−0
6
0.1 0.2 0.3 0.4 0.5
Allele Frequency
Varia
nce
Expl
aine
d
ba
c d e
0.00
0.01
0.02
0.03
0.0 0.5 1.0 1.5 2.0GERP Score
Add
itive
Effe
ct
0.00
0.01
0.02
0.03
0.0 0.5 1.0 1.5 2.0GERP Score
Dom
inan
t Effe
ct
0.0
0.1
0.2
0.3
0.4
0.0 0.5 1.0 1.5 2.0GERP Score
Deg
ree
of D
omia
nce
(k)
TW DTP DTS ASI PHT EHT GY
−1
0
1
2
Deg
ree
of D
omin
ance
(k)
TraitsTWDTPDTSASIPHTEHTGY3.
5e−0
64.
0e−0
64.
5e−0
65.
0e−0
6
0.1 0.2 0.3 0.4 0.5
Allele Frequency
Varia
nce
Expl
aine
d
ba
c d e
![Page 88: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/88.jpg)
GenotypeGERP Scores
*
* * *
YieldFlowering Height
GERP
YieldFlowering Height
random
![Page 89: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/89.jpg)
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%
![Page 90: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/90.jpg)
Heterosis yield
Duvick 2005 Maydica
Hybrid yield
Inbred yield
![Page 91: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/91.jpg)
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
![Page 92: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/92.jpg)
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
![Page 93: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/93.jpg)
Joost van Heerwaarden
Justin Gerke
Sofiane Mezmouk
Jinliang Yang
Wageningen University
Dupont Pioneer KWS U. Nebraska Lincoln
![Page 94: Evolutionary genetics of hybrid maize](https://reader031.vdocuments.net/reader031/viewer/2022022415/58ed54391a28abe9278b466b/html5/thumbnails/94.jpg)