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Adaptation in plant genomes:
a role for genome size?
Jeffrey Ross-Ibarra
@jrossibarra • www.rilab.org
Dept. Plant Sciences • Center for Population Biology • Genome Center
University of California Davis
photo by lady_lbrty
Kew C-Value Database
Gaut and Ross-Ibarra 2008
Paris Japonica
150GB Genome
Genlisia aurea
63MB Genome Michal Rubeš
wide variation in genome size in plants
Kew C-Value Database
what explains genome size variation?
Lynch & Connery 2003 ScienceWhitney et al. 2010 Evolution
Kew C-Value Database
what explains genome size variation?
Lynch & Connery 2003 ScienceWhitney et al. 2010 Evolution
seed weight
Knight et al 2005 AoB
genome size
genomesize
leafarea
correlates of genome size:
phenotypes across species
elevation
genomesize
Bilinski et al. In Prep
correlates of genome size:
altitude within Zea mays
0
10
20
30
100 105 110
DNA
plants
cycle
0
6
genome size
late flowering
early flowering
Rayburn et al. 1994 Plant Breeding
#plants
hard
sweep
how do genomes adapt?
hard
sweep
how do genomes adapt?
hard
sweep
how do genomes adapt?
hard
sweep
multiple
mutations
standing
variation
“soft” sweeps
how do genomes adapt?
hard
sweep
multiple
mutations
polygenic
adaptation
standing
variation
“soft” sweeps
how do genomes adapt?
M T G P H R L
GGTCGAC ATG ACT GGT CCA CAT CGA CTG TAG
M T G P H R L
GGTCGAC ATG ACT GGT CCA CAT CGA CTG TAG
M T N P H R L
GGTCGAC ATG ACT GAT CCA CAT CGA CTG TAG
structural
change to protein
M T G P H R L
GGTAAAC ATG ACT GGT CCA CAT CGA CTG TAG
GG—-AC ATG ACT GGT CCA CAT CGA CTG TAG
regulatory change to
expression
1.5
2.5
3.5
4.5
Angiosperm
average
6400 Mb
Non-TE DNA
TE DNA
Log(genomesizeinMb)
0
1,500
3,000
4,500
6,000
0 1500 3000 4500 6000
Genomesize(Mb)
TE content (Mb)
r = 0.99
Arabidopsisthaliana
Arabidopsislyrata
Brachypodiumdistachyon
Papaya
Rice
Lotusjaponicus
Blackcottonwood
Grapevine
Cabbage
Medicagotrunculata
Sorghum
Soybean
Levantcotton
Maize
Aegilopsspeltoides
Barley
Thursday, May 6, 2010
Tenaillon et al. 2010 TIP
Springer et al. 2016 Plant Cell
Tenaillon et al. 2010 TIP
Springer et al. 2016 Plant Cell
Ne individuals, µ beneficial mutation rate per trait
bigger genome, larger mutation target, higher µ
selection from standing variation when 2Neµ > 1
predict that larger genomes adapt via
noncoding changes, standing variation
Hancock et al 2011 Science
enrichment?
no<———>yes
Arabidopsis adaptation predominantly coding
intergenic
synonymous
nonsynonymous
maize (2.5Gb)Arabidopsis
log 1C genome size
Suketoshi
how does adaptation work in maize?
maizeteosinte
standing variation
RE GENETICS ADVANCE ONLINE PUBLICATION 3
on rate21, strongly suggesting that the Hopscotch insertion (and
he older Tourist as well) existed as standing genetic variation in
osinte ancestor of maize. Thus, we conclude that the Hopscotch
on likely predated domestication by more than 10,000 years and
urist insertion by an even greater amount of time.
identified four fixed differences in the portion of the proximal
stal components of the control region that show evidence of
on. We used transient assays in maize leaf protoplasts to test
r differences for effects on gene expression. Maize and teosinte
osomal segments for the portions of the proximal and distal
onents with these four differences were cloned into reporter
ucts upstream of the minimal promoter of the cauliflower
c virus (mpCaMV), the firefly luciferase ORF and the nopaline
se (NOS) terminator (Fig. 4). Each construct was assayed for
escence after transformation by electroporation into maize pro-
t. The constructs for the distal component contrast the effects
Tourist insertion plus the single fixed nucleotide substitution
istinguish maize and teosinte. Both the maize and teosinte
ucts for the distal component repressed luciferase expression
that acts as a repressor. The functional importance of this segment is
supported by its low level of nucleotide diversity (Fig. 3a), suggesting
a history of purifying selection.
The constructs for the proximal component of the control region
contrast the effects of the Hopscotch insertion plus a single fixed nucleo-
tide substitution that distinguish maize and teosinte. The construct
with the maize sequence including Hopscotch increased expression of
the luciferase reporter twofold relative to the teosinte construct for
the proximal control region and the minimal promoter alone (Fig. 4).
Luciferase expression was returned to the level of the teosinte con-
struct and the minimal promoter construct by deleting the Hopscotch
element from the full maize construct. These results indicate
that the Hopscotch element enhances luciferase expression and, by
Teosinte cluster
haplotype
Maize cluster
haplotype
Transient assay constructs
mpCaMV luc
luc
luc
luc
luc
luc
luc
luc
Hopscotch
Tourist
mpCaMV
T-dist
M-dist
T-prox
M-prox
0 0.5 1.0 1.5 2.0
∆M-dist
∆M-prox
ProximalcontrolregionDistalcontrolregion
Relative expression
4 Constructs and corresponding normalized luciferase expression
Transient assays were performed in maize leaf protoplast. Each
uct is drawn to scale. The construct backbone consists of the
al promoter from the cauliflower mosaic virus (mpCaMV, gray box),
ase ORF (luc, white box) and the nopaline synthase terminator
box). Portions of the proximal and distal components of the
region (hatched boxes) from maize and teosinte were cloned
striction sites upstream of the minimal promoter. “ ” denotes
ision of either the Tourist or Hopscotch element from the maize
uct. Horizontal green bars show the normalized mean with s.e.m.
h construct.
relative expressionconstruct
Studer et al. 2011 Nat. Gen.; Vann et al. 2015 PeerJ
enhances expression
teosinte branched - tb1
hard sweep
Figure 1.
Phenotypes. a. Maize ear showing the cob (cb) exposed at top. b. Teosinte ear with the rach
internode (in) and glume (gl) labeled. c. Teosinte ear from a plant with a maize allele of tga
Wang et al. Page 1
NIH-PAAuthorManuscriptNIH-PAAuthorManuscript
Wang et al. 2015 Genetics
protein change
teosinte glume architecture - tga1
multiple mutations
Wills et al. 2013 PLoS Genetics
teosinte maize
Clint Whipple, BYU
grassy tillers - gt1
5’ control region 3’ UTRmodifies expression
hard sweep
M T N P H R L
GGTCGA ATG ACT GAT CCA CAT CGA CTG TAG
tga1
gt1
tb1
Multiple
Mutations
Standing
Variation
M T G P H R L
GGTAAA ATG ACT GGT CCA CAT CGA CTG TAG
Hufford et al. 2012 Nat. Gen.
Chia et al. 2012 Nat. Gen
13 teosinte
23 maize
genomes:
genome-wide evidence of adaptation
Hufford et al. 2012 Nat. Gen.
Chia et al. 2012 Nat. Gen
13 teosinte
23 maize
genomes:
genome-wide evidence of adaptation
Hufford et al. 2012 Nat. Gen.
Chia et al. 2012 Nat. Gen
13 teosinte
23 maize
genomes:
5-10% selected regions do
not include genes
genome-wide evidence of adaptation
E
D
Mb
nd targets of selection during improvement and/or domestication. (A) Venn diagram
that occur in genomic regions that have evidence for selective sweeps during maize
oexpression networks for three genes (GRMZM2G068436, GRMZM2G137947, and
pression networks are shown. Although the differentially expressed gene (red node) is
ize. However, some parts of the teosinte network are still conserved in maize. (C) Cross-
vidence for a selective sweep that occurs on chromosome 9. The tick marks along the x
ZM2G448355) that was chosen as the candidate target of selection and is differentially
ExpressionGenealogy
teosinte
maize
• ~500 selected regions
• 11M shared vs 3000 fixed SNPs
• show differential expression,
decreased expression variation
selection on regulatory sequence,
standing variation
Hufford et al. 2012 Nat. Gen.
Swanson-Wagner et al. 2012 PNAS
Beissinger et al. BioRxiv
nucleotidediversity
distance to nearest substitution (cM)
hard sweeps in genes play minor role in maize
Beissinger et al. BioRxiv
nucleotidediversity
distance to nearest substitution (cM)
hard sweeps in genes play minor role in maize
Wallace et al. 2014 PLoS Genetics
QTL alleles enriched for noncoding
Rodgers-Melnick et al. 2016 PNAS
Variance PartitioningGWAS candidate SNPs
Makarevitch et al. 2015 PLoS Genetics
Makarevitch et al. 2015 PLoS Genetics
single TE family
many genes
Makarevitch et al. 2015 PLoS Genetics
single TE family
many genes
w insertions activate expression
GRMZM2G071206
stress/control)
2
4
6
8
10
12
-2
0
2
4
6
8
10
12
14
Lines with the
TE insertion
Lines without the
TE insertion
GRMZM2G108149
A
B
Log2(stress/control)
httpDownloaded from
Oh43
B73
Mo17
alaw
dagaf
etug
flip
gyma
ipiki
jeli
joemon
naiba
nihep
odoj
pebi
raider
riiryl
ubel
uwum
Zm00346
Zm02117
Zm03238
Zm05382
Salt
UV
Heat
Cold
on September 9, 2014http://biorxiv.org/Downloaded from
*
**
**
*
*
single gene,
many individuals
how to adapt: Zea mays
M T G P H R L
GGTAAA ATG ACT GGT CCA CAT CGA CTG TAG
regulatory variation (including TEs)
multiple
mutations
“soft” sweeps
standing
variation
Sattah et al. 2011 PLoS Gen.
Williamson et al. 2014 PLoS Gen
Hernandez et al. 2011 ScienceRoss-Ibarra et al. 2009 Genetics
Sattah et al. 2011 PLoS Gen.
Williamson et al. 2014 PLoS Gen
Hernandez et al. 2011 ScienceRoss-Ibarra et al. 2009 Genetics
Sattah et al. 2011 PLoS Gen.
Williamson et al. 2014 PLoS Gen
Hernandez et al. 2011 Science
diversity
distance from substitution
Ross-Ibarra et al. 2009 Genetics
Sattah et al. 2011 PLoS Gen.
Williamson et al. 2014 PLoS Gen
Hernandez et al. 2011 Science
diversity
distance from substitution
20% nonsyn. adaptive 10% nonsyn. adaptive
50% nonsyn. adaptive 40% nonsyn. adaptive
Ross-Ibarra et al. 2009 Genetics
Ne effective number of diploid individuals
s selection coefficient
selection is effective if 2Nes > 1
differences in adaptation due to drift and
small population size?
0.05Na
Na
Na
3NaNe ~ 450,000
Beissinger et al. BioRxiv
0.05Na
Na
Na
3NaNe ~ 450,000
Beissinger et al. BioRxiv
Ne ~ 1,000,000
0.05Na
Na
Na
3NaNe ~ 450,000
Beissinger et al. BioRxiv
Ne ~ 1,000,000
1e+05
1e+07
1e+09
1e+03 1e+042e+04 1e+05
years(u=3e−8, generation=1)
effectivepopulationsize
pop
BKN_4Hap
BKN_6Hap
TIL_4Hap_Jalisco
TIL_6Hap
Ne ~ 1,000,000,000
0.05Na
Na
Na
3NaNe ~ 450,000
Beissinger et al. BioRxiv
Ne ~ 1,000,000
1e+05
1e+07
1e+09
1e+03 1e+042e+04 1e+05
years(u=3e−8, generation=1)
effectivepopulationsize
pop
BKN_4Hap
BKN_6Hap
TIL_4Hap_Jalisco
TIL_6Hap
Ne ~ 1,000,000,000
Ne ~ 5,000,000,000
Sattah et al. 2011 PLoS Gen.
Williamson et al. 2014 PLoS Gen
Hernandez et al. 2011 Science
diversity
Ne >> 1,000,000 Ne ~ 10,000*
Ne ~ 2,000,000 Ne ~ 600,000
Sattah et al. 2011 PLoS Gen.
Williamson et al. 2014 PLoS Gen
Hernandez et al. 2011 Science
diversity
µ ∝ 2,500 Mbp µ ∝ 3,100 Mbp
µ ∝ 130 Mbp µ ∝ 220 Mbp
Pyhäjärvi et al. GBE 2013
enrichment
no<———>yes
large genomes enriched in noncoding
adaptive variants
intergenic
synonymous
nonsynonymous
enrichment
intergenic<———>coding
Hancock et al 2011 Science
Fraser et al. 2013 Gen. Research
Pyhäjärvi et al. GBE 2013
large genomes enriched in noncoding
adaptive variantsenrichment
intergenic<———>coding
excessadaptiveSNPs
Hancock et al 2011 Science
Fraser et al. 2013 Gen. Research
• Adaptation in maize occurs from standing variation
and targets regulatory variants
• Large genomes may have more targets, more standing
variation, and more regulatory adaptation
• Efforts to identify functional variation should consider
genome size in designing experiments and genotyping
Genome Size and Adaptation
Kew C-Value Database
Acknowledgments
Maize Diversity Group
Peter Bradbury
Ed Buckler
John Doebley
Theresa Fulton
Sherry Flint-Garcia
Jim Holland
Sharon Mitchell
Qi Sun
Doreen Ware
Collaborators
CSI Davis
Nathan Springer
Lab Alumni
Tim Beissinger (USDA-ARS, Mizzou)
Kate Crosby (Monsanto)
Matt Hufford (Iowa State)
Tanja Pyhäjärvi (Oulu)
Shohei Takuno (Sokendai)
Joost van Heerwaarden (Wageningen)
JGI: Genome size impacts on plant adaptation

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JGI: Genome size impacts on plant adaptation

  • 1. Adaptation in plant genomes: a role for genome size? Jeffrey Ross-Ibarra @jrossibarra • www.rilab.org Dept. Plant Sciences • Center for Population Biology • Genome Center University of California Davis photo by lady_lbrty
  • 2. Kew C-Value Database Gaut and Ross-Ibarra 2008 Paris Japonica 150GB Genome Genlisia aurea 63MB Genome Michal Rubeš wide variation in genome size in plants
  • 3. Kew C-Value Database what explains genome size variation? Lynch & Connery 2003 ScienceWhitney et al. 2010 Evolution
  • 4. Kew C-Value Database what explains genome size variation? Lynch & Connery 2003 ScienceWhitney et al. 2010 Evolution
  • 5. seed weight Knight et al 2005 AoB genome size genomesize leafarea correlates of genome size: phenotypes across species
  • 6. elevation genomesize Bilinski et al. In Prep correlates of genome size: altitude within Zea mays 0 10 20 30 100 105 110 DNA plants cycle 0 6 genome size late flowering early flowering Rayburn et al. 1994 Plant Breeding #plants
  • 12. M T G P H R L GGTCGAC ATG ACT GGT CCA CAT CGA CTG TAG
  • 13. M T G P H R L GGTCGAC ATG ACT GGT CCA CAT CGA CTG TAG M T N P H R L GGTCGAC ATG ACT GAT CCA CAT CGA CTG TAG structural change to protein
  • 14. M T G P H R L GGTAAAC ATG ACT GGT CCA CAT CGA CTG TAG GG—-AC ATG ACT GGT CCA CAT CGA CTG TAG regulatory change to expression
  • 15. 1.5 2.5 3.5 4.5 Angiosperm average 6400 Mb Non-TE DNA TE DNA Log(genomesizeinMb) 0 1,500 3,000 4,500 6,000 0 1500 3000 4500 6000 Genomesize(Mb) TE content (Mb) r = 0.99 Arabidopsisthaliana Arabidopsislyrata Brachypodiumdistachyon Papaya Rice Lotusjaponicus Blackcottonwood Grapevine Cabbage Medicagotrunculata Sorghum Soybean Levantcotton Maize Aegilopsspeltoides Barley Thursday, May 6, 2010 Tenaillon et al. 2010 TIP Springer et al. 2016 Plant Cell
  • 16. Tenaillon et al. 2010 TIP Springer et al. 2016 Plant Cell
  • 17. Ne individuals, µ beneficial mutation rate per trait bigger genome, larger mutation target, higher µ selection from standing variation when 2Neµ > 1 predict that larger genomes adapt via noncoding changes, standing variation
  • 18. Hancock et al 2011 Science enrichment? no<———>yes Arabidopsis adaptation predominantly coding intergenic synonymous nonsynonymous
  • 19. maize (2.5Gb)Arabidopsis log 1C genome size Suketoshi how does adaptation work in maize?
  • 21. standing variation RE GENETICS ADVANCE ONLINE PUBLICATION 3 on rate21, strongly suggesting that the Hopscotch insertion (and he older Tourist as well) existed as standing genetic variation in osinte ancestor of maize. Thus, we conclude that the Hopscotch on likely predated domestication by more than 10,000 years and urist insertion by an even greater amount of time. identified four fixed differences in the portion of the proximal stal components of the control region that show evidence of on. We used transient assays in maize leaf protoplasts to test r differences for effects on gene expression. Maize and teosinte osomal segments for the portions of the proximal and distal onents with these four differences were cloned into reporter ucts upstream of the minimal promoter of the cauliflower c virus (mpCaMV), the firefly luciferase ORF and the nopaline se (NOS) terminator (Fig. 4). Each construct was assayed for escence after transformation by electroporation into maize pro- t. The constructs for the distal component contrast the effects Tourist insertion plus the single fixed nucleotide substitution istinguish maize and teosinte. Both the maize and teosinte ucts for the distal component repressed luciferase expression that acts as a repressor. The functional importance of this segment is supported by its low level of nucleotide diversity (Fig. 3a), suggesting a history of purifying selection. The constructs for the proximal component of the control region contrast the effects of the Hopscotch insertion plus a single fixed nucleo- tide substitution that distinguish maize and teosinte. The construct with the maize sequence including Hopscotch increased expression of the luciferase reporter twofold relative to the teosinte construct for the proximal control region and the minimal promoter alone (Fig. 4). Luciferase expression was returned to the level of the teosinte con- struct and the minimal promoter construct by deleting the Hopscotch element from the full maize construct. These results indicate that the Hopscotch element enhances luciferase expression and, by Teosinte cluster haplotype Maize cluster haplotype Transient assay constructs mpCaMV luc luc luc luc luc luc luc luc Hopscotch Tourist mpCaMV T-dist M-dist T-prox M-prox 0 0.5 1.0 1.5 2.0 ∆M-dist ∆M-prox ProximalcontrolregionDistalcontrolregion Relative expression 4 Constructs and corresponding normalized luciferase expression Transient assays were performed in maize leaf protoplast. Each uct is drawn to scale. The construct backbone consists of the al promoter from the cauliflower mosaic virus (mpCaMV, gray box), ase ORF (luc, white box) and the nopaline synthase terminator box). Portions of the proximal and distal components of the region (hatched boxes) from maize and teosinte were cloned striction sites upstream of the minimal promoter. “ ” denotes ision of either the Tourist or Hopscotch element from the maize uct. Horizontal green bars show the normalized mean with s.e.m. h construct. relative expressionconstruct Studer et al. 2011 Nat. Gen.; Vann et al. 2015 PeerJ enhances expression teosinte branched - tb1
  • 22. hard sweep Figure 1. Phenotypes. a. Maize ear showing the cob (cb) exposed at top. b. Teosinte ear with the rach internode (in) and glume (gl) labeled. c. Teosinte ear from a plant with a maize allele of tga Wang et al. Page 1 NIH-PAAuthorManuscriptNIH-PAAuthorManuscript Wang et al. 2015 Genetics protein change teosinte glume architecture - tga1
  • 23. multiple mutations Wills et al. 2013 PLoS Genetics teosinte maize Clint Whipple, BYU grassy tillers - gt1 5’ control region 3’ UTRmodifies expression
  • 24. hard sweep M T N P H R L GGTCGA ATG ACT GAT CCA CAT CGA CTG TAG tga1 gt1 tb1 Multiple Mutations Standing Variation M T G P H R L GGTAAA ATG ACT GGT CCA CAT CGA CTG TAG
  • 25. Hufford et al. 2012 Nat. Gen. Chia et al. 2012 Nat. Gen 13 teosinte 23 maize genomes: genome-wide evidence of adaptation
  • 26. Hufford et al. 2012 Nat. Gen. Chia et al. 2012 Nat. Gen 13 teosinte 23 maize genomes: genome-wide evidence of adaptation
  • 27. Hufford et al. 2012 Nat. Gen. Chia et al. 2012 Nat. Gen 13 teosinte 23 maize genomes: 5-10% selected regions do not include genes genome-wide evidence of adaptation
  • 28. E D Mb nd targets of selection during improvement and/or domestication. (A) Venn diagram that occur in genomic regions that have evidence for selective sweeps during maize oexpression networks for three genes (GRMZM2G068436, GRMZM2G137947, and pression networks are shown. Although the differentially expressed gene (red node) is ize. However, some parts of the teosinte network are still conserved in maize. (C) Cross- vidence for a selective sweep that occurs on chromosome 9. The tick marks along the x ZM2G448355) that was chosen as the candidate target of selection and is differentially ExpressionGenealogy teosinte maize • ~500 selected regions • 11M shared vs 3000 fixed SNPs • show differential expression, decreased expression variation selection on regulatory sequence, standing variation Hufford et al. 2012 Nat. Gen. Swanson-Wagner et al. 2012 PNAS
  • 29. Beissinger et al. BioRxiv nucleotidediversity distance to nearest substitution (cM) hard sweeps in genes play minor role in maize
  • 30. Beissinger et al. BioRxiv nucleotidediversity distance to nearest substitution (cM) hard sweeps in genes play minor role in maize
  • 31. Wallace et al. 2014 PLoS Genetics QTL alleles enriched for noncoding Rodgers-Melnick et al. 2016 PNAS Variance PartitioningGWAS candidate SNPs
  • 32. Makarevitch et al. 2015 PLoS Genetics
  • 33. Makarevitch et al. 2015 PLoS Genetics single TE family many genes
  • 34. Makarevitch et al. 2015 PLoS Genetics single TE family many genes w insertions activate expression GRMZM2G071206 stress/control) 2 4 6 8 10 12 -2 0 2 4 6 8 10 12 14 Lines with the TE insertion Lines without the TE insertion GRMZM2G108149 A B Log2(stress/control) httpDownloaded from Oh43 B73 Mo17 alaw dagaf etug flip gyma ipiki jeli joemon naiba nihep odoj pebi raider riiryl ubel uwum Zm00346 Zm02117 Zm03238 Zm05382 Salt UV Heat Cold on September 9, 2014http://biorxiv.org/Downloaded from * ** ** * * single gene, many individuals
  • 35. how to adapt: Zea mays M T G P H R L GGTAAA ATG ACT GGT CCA CAT CGA CTG TAG regulatory variation (including TEs) multiple mutations “soft” sweeps standing variation
  • 36. Sattah et al. 2011 PLoS Gen. Williamson et al. 2014 PLoS Gen Hernandez et al. 2011 ScienceRoss-Ibarra et al. 2009 Genetics
  • 37. Sattah et al. 2011 PLoS Gen. Williamson et al. 2014 PLoS Gen Hernandez et al. 2011 ScienceRoss-Ibarra et al. 2009 Genetics
  • 38. Sattah et al. 2011 PLoS Gen. Williamson et al. 2014 PLoS Gen Hernandez et al. 2011 Science diversity distance from substitution Ross-Ibarra et al. 2009 Genetics
  • 39. Sattah et al. 2011 PLoS Gen. Williamson et al. 2014 PLoS Gen Hernandez et al. 2011 Science diversity distance from substitution 20% nonsyn. adaptive 10% nonsyn. adaptive 50% nonsyn. adaptive 40% nonsyn. adaptive Ross-Ibarra et al. 2009 Genetics
  • 40. Ne effective number of diploid individuals s selection coefficient selection is effective if 2Nes > 1 differences in adaptation due to drift and small population size?
  • 42. 0.05Na Na Na 3NaNe ~ 450,000 Beissinger et al. BioRxiv Ne ~ 1,000,000
  • 43. 0.05Na Na Na 3NaNe ~ 450,000 Beissinger et al. BioRxiv Ne ~ 1,000,000 1e+05 1e+07 1e+09 1e+03 1e+042e+04 1e+05 years(u=3e−8, generation=1) effectivepopulationsize pop BKN_4Hap BKN_6Hap TIL_4Hap_Jalisco TIL_6Hap Ne ~ 1,000,000,000
  • 44. 0.05Na Na Na 3NaNe ~ 450,000 Beissinger et al. BioRxiv Ne ~ 1,000,000 1e+05 1e+07 1e+09 1e+03 1e+042e+04 1e+05 years(u=3e−8, generation=1) effectivepopulationsize pop BKN_4Hap BKN_6Hap TIL_4Hap_Jalisco TIL_6Hap Ne ~ 1,000,000,000 Ne ~ 5,000,000,000
  • 45. Sattah et al. 2011 PLoS Gen. Williamson et al. 2014 PLoS Gen Hernandez et al. 2011 Science diversity Ne >> 1,000,000 Ne ~ 10,000* Ne ~ 2,000,000 Ne ~ 600,000
  • 46. Sattah et al. 2011 PLoS Gen. Williamson et al. 2014 PLoS Gen Hernandez et al. 2011 Science diversity µ ∝ 2,500 Mbp µ ∝ 3,100 Mbp µ ∝ 130 Mbp µ ∝ 220 Mbp
  • 47. Pyhäjärvi et al. GBE 2013 enrichment no<———>yes large genomes enriched in noncoding adaptive variants intergenic synonymous nonsynonymous enrichment intergenic<———>coding Hancock et al 2011 Science Fraser et al. 2013 Gen. Research
  • 48. Pyhäjärvi et al. GBE 2013 large genomes enriched in noncoding adaptive variantsenrichment intergenic<———>coding excessadaptiveSNPs Hancock et al 2011 Science Fraser et al. 2013 Gen. Research
  • 49. • Adaptation in maize occurs from standing variation and targets regulatory variants • Large genomes may have more targets, more standing variation, and more regulatory adaptation • Efforts to identify functional variation should consider genome size in designing experiments and genotyping Genome Size and Adaptation Kew C-Value Database
  • 50. Acknowledgments Maize Diversity Group Peter Bradbury Ed Buckler John Doebley Theresa Fulton Sherry Flint-Garcia Jim Holland Sharon Mitchell Qi Sun Doreen Ware Collaborators CSI Davis Nathan Springer Lab Alumni Tim Beissinger (USDA-ARS, Mizzou) Kate Crosby (Monsanto) Matt Hufford (Iowa State) Tanja Pyhäjärvi (Oulu) Shohei Takuno (Sokendai) Joost van Heerwaarden (Wageningen)