While the vast majority of genome size variation in plants is due to differences in repetitive sequence, we know little about how selection acts on repeat content in natural populations. Here we investigate parallel changes in intraspecific genome size and repeat content of domesticated maize (Zea mays) landraces and their wild relative teosinte across altitudinal gradients in Mesoamerica and South America. We combine genotyping, low coverage whole-genome sequence data, and flow cytometry to test for evidence of selection on genome size and individual repeat abundance. We find that population structure alone cannot explain the observed variation, implying that clinal patterns of genome size are maintained by natural selection. Our modeling additionally provides evidence of selection on individual heterochromatic knob repeats, likely due to their large individual contribution to genome size. To better understand the phenotypes driving selection on genome size, we conducted a growth chamber experiment using a population of highland teosinte exhibiting extensive variation in genome size. We find weak support for a positive correlation between genome size and cell size, but stronger support for a negative correlation between genome size and the rate of cell production. Reanalyzing published data of cell counts in maize shoot apical meristems, we then identify a negative correlation between cell production rate and flowering time. Together, our data suggest a model in which variation in genome size is driven by natural selection on flowering time across altitudinal clines, connecting intraspecific variation in repetitive sequence to important differences in adaptive phenotypes.
Cultivation of KODO MILLET . made by Ghanshyam pptx
Parallel Altitudinal Clines Reveal Adaptive Evolution Of Genome Size In Zea mays
1. Jeffrey Ross-Ibarra
@jrossibarra • www.rilab.org
Plant Sciences • Center for Population Biology • Genome Center
University of California Davis
Adaptive evolution of genome size along
altitudinal clines in maize and teosinte
2. Abizar at English Wikipedia [CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0) or
GFDL (http://www.gnu.org/copyleft/fdl.html)], via Wikimedia Commons
Genome Size (bp)
3. By Nr387241 - Own work, CC BY-SA 3.0, https://
commons.wikimedia.org/w/index.php?
curid=14945255
Mycoplasma (0.0006Gb)
Abizar at English Wikipedia [CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0) or
GFDL (http://www.gnu.org/copyleft/fdl.html)], via Wikimedia Commons
Genome Size (bp)
4. By Gőtehal.jpg: Mathae derivative work: Bff (Gőtehal.jpg) [CC BY 2.5 (http://
creativecommons.org/licenses/by/2.5), CC-BY-SA-3.0 (http://
creativecommons.org/licenses/by-sa/3.0/) or GFDL (http://www.gnu.org/
copyleft/fdl.html)], via Wikimedia Commons
Protopterus (130Gb)
By Nr387241 - Own work, CC BY-SA 3.0, https://
commons.wikimedia.org/w/index.php?
curid=14945255
Mycoplasma (0.0006Gb)
Abizar at English Wikipedia [CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0) or
GFDL (http://www.gnu.org/copyleft/fdl.html)], via Wikimedia Commons
Genome Size (bp)
5. Genlisea (0.065Gb)
By Michal Rubeš [CC BY 3.0 cz
(http://creativecommons.org/
licenses/by/3.0/cz/deed.en)], via
Wikimedia Commons
By Gőtehal.jpg: Mathae derivative work: Bff (Gőtehal.jpg) [CC BY 2.5 (http://
creativecommons.org/licenses/by/2.5), CC-BY-SA-3.0 (http://
creativecommons.org/licenses/by-sa/3.0/) or GFDL (http://www.gnu.org/
copyleft/fdl.html)], via Wikimedia Commons
Protopterus (130Gb)
By Nr387241 - Own work, CC BY-SA 3.0, https://
commons.wikimedia.org/w/index.php?
curid=14945255
Mycoplasma (0.0006Gb)
Abizar at English Wikipedia [CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0) or
GFDL (http://www.gnu.org/copyleft/fdl.html)], via Wikimedia Commons
Genome Size (bp)
6. By alpsdake - Own work, CC0, https://commons.wikimedia.org/w/index.php?
curid=12228596
Paris (150Gb)
Genlisea (0.065Gb)
By Michal Rubeš [CC BY 3.0 cz
(http://creativecommons.org/
licenses/by/3.0/cz/deed.en)], via
Wikimedia Commons
By Gőtehal.jpg: Mathae derivative work: Bff (Gőtehal.jpg) [CC BY 2.5 (http://
creativecommons.org/licenses/by/2.5), CC-BY-SA-3.0 (http://
creativecommons.org/licenses/by-sa/3.0/) or GFDL (http://www.gnu.org/
copyleft/fdl.html)], via Wikimedia Commons
Protopterus (130Gb)
By Nr387241 - Own work, CC BY-SA 3.0, https://
commons.wikimedia.org/w/index.php?
curid=14945255
Mycoplasma (0.0006Gb)
Abizar at English Wikipedia [CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0) or
GFDL (http://www.gnu.org/copyleft/fdl.html)], via Wikimedia Commons
Genome Size (bp)
13. Domestication
10,000BP
Mexican Highlands
6,000BP
S. American lowlands
6,000BP
Andes
4,000BP
Takuno et al. (2015) Genetics
Lowland
K=3K=4
Highland Lowland Highland
Mesoamerica South America
Lowland
A B
K=2K=3K=4
Highland Lowland Highland
Mesoamerica South America
Altitude
17. altitude
GenomeSize(Mb) 77 landraces
S. America
Mexico
teosinte
95 mexicana
altitude
P = µ + alt ⇤ A + g + "
g ⇠ MV N (0, VAK)
" ⇠ N (0, V✏)
Genome Size Altitude
Additive
Component
Berg and Coop (2014) Plos Gen
18. altitude
GenomeSize(Mb) 77 landraces
S. America
Mexico
teosinte
95 mexicana
altitude
P = µ + alt ⇤ A + g + "
g ⇠ MV N (0, VAK)
" ⇠ N (0, V✏)
Genome Size Altitude
Additive
Component
Berg and Coop (2014) Plos Gen
landraces
landraces
Kinship
Additive
Genetic Var.
19. altitude
GenomeSize(Mb) 77 landraces
S. America
Mexico
teosinte
95 mexicana
altitude
P = µ + alt ⇤ A + g + "
g ⇠ MV N (0, VAK)
" ⇠ N (0, V✏)
Genome Size Altitude
Additive
Component
Berg and Coop (2014) Plos Gen
landraces
landraces
Kinship
Additive
Genetic Var.
-110Kb/m
-260Kb/m
20. Rosado et al. (2005) Maize
Genetics Newsletter (shh, secret)
Knob180
KnobTR1
Maize TEs
Sorghum TEs
Jiao et al. (2017) Nature
copy
number
21. Rosado et al. (2005) Maize
Genetics Newsletter (shh, secret)
Knob180
KnobTR1
Maize TEs
Sorghum TEs
Jiao et al. (2017) Nature
copy
number
22. Rosado et al. (2005) Maize
Genetics Newsletter (shh, secret)
Knob180
KnobTR1
Maize TEs
Sorghum TEs
Jiao et al. (2017) Nature
copy
number
34. Leiboff et al. (2015) Nat Comm
cell number (cell division rate)floweringtime
growth stage
35. 1. Genome size is a quantitative trait that can affect fitness,
and observed intraspecific variation may be adaptive
2. Selection for faster development leads to smaller
genomes across altitudinal clines in maize and teosinte
3. Selection on genome size likely impacts the evolution of
individual repeat classes
36. Acknowledgements
U Missouri
Patrice Albert
Jim Birchler
Cornell
Kelly Swarts
UC Davis
Jeremy Berg
Graham Coop
Mark Grote
Juvenal Quesada
Plant Genome
Research Program
HiLo
Lab Alumni
Paul Bilinski (West Shore College)
Anna O’Brien (U Toronto)
Jinliang Yang (U Nebraska-Lincoln)