Evolutionary Genetics of Complex Genome
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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)
- 7. Lynch and Connnery (2003) Science
- 8. Whitney et al. (2010) Evolution Contrast in Ne ContrastinGenomeSize
- 9. Knight (2005) Ann Bot Seed Weight (+) Seed Weight GenomeSize(2Cpg) Leaf Size (-) Genome Size (2C pg) specificleafarea Whitney et al. (2010) Evolution Contrast in Ne ContrastinGenomeSize
- 10. maize landrace diploidgenomesize Díez et al. (2013) New Phyt
- 11. Z. mays ssp. parviglumis Z. mays ssp. mexicana Pyhäjärvi et al. (2013) GBE
- 12. 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
- 13. altitude GenomeSize(Mb) 77 landraces S. America Mexico parviglumis mexicana teosinte altitude3250 3125 3000 2875 2750
- 14. altitude GenomeSize(Mb) 77 landraces S. America Mexico teosinte 95 mexicana altitude
- 15. altitude GenomeSize(Mb) 77 landraces S. America Mexico teosinte 95 mexicana altitude genome size (bp) #individuals h2~0.9
- 16. 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
- 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 landraces landraces Kinship Additive Genetic Var.
- 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. -110Kb/m -260Kb/m
- 19. Rosado et al. (2005) Maize Genetics Newsletter (shh, secret) Knob180 KnobTR1 Maize TEs Sorghum TEs Jiao et al. (2017) Nature copy number
- 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. r2=0.77 r2=0.74
- 23. P = µ + alt ⇤ A + GS ⇤ GS + g + " g ⇠ MV N (0, VAK) " ⇠ N (0, V✏) AltitudeRepeat Genome Size as Covariate Additive Component
- 24. altitude B-repeatreads
- 25. altitude MbTE maize mexicana S. America Mexico Region
- 26. altitude MbTE maize mexicana S. America Mexico Region altitude knob180 knobTR1 Knobabundance(Mb) maize mexicana maize mexicana
- 27. High SAm Mex SAm Mex Low Flint-Garcia et al. (unpublished) floweringtime(days)
- 28. Nature Education 2013 https://www.nature.com/scitable/content/ne0000/ne0000/ne0000/ne0000/113371527/14707478.jpg DNA Replication Francis et al. (2008) Ann Bot FIG. 2. DNA C-value (pg) and cell cycle time (h) in the root apic istem of a range of (A) eudicots and monocots (n ¼ 110), and (B) e (n ¼ 60). See Table 2 for regression analyses.
- 29. Bennett (1972) Proc Roy Soc B #species cellcycletime(h) annual perennial annual perennial genome size (pg of 3C)
- 30. mother(n=202plants) genome size
- 31. Leaf Elongation (LER) Cell Size (CS) Cell Production (CP) Genome Size (GS) + - log(CP) = 0 + GS ⇤ log(GS) log(LER) = ⌧0 + ⌧GS ⇤ log(GS) log(CS) = 0 + GS ⇤ log(GS) GS = ⌧GS GS Posterior Density of βGS Posterior Density of γGS Šímová and Herben (2012) Proc Roy Soc B Walker and Smith (2002) Development
- 32. Leaf Elongation (LER) Cell Size (CS) Cell Production (CP) Genome Size (GS) + - log(CP) = 0 + GS ⇤ log(GS) log(LER) = ⌧0 + ⌧GS ⇤ log(GS) log(CS) = 0 + GS ⇤ log(GS) GS = ⌧GS GS Posterior Density of βGS Posterior Density of γGS Šímová and Herben (2012) Proc Roy Soc B Walker and Smith (2002) Development
- 33. Leiboff et al. (2015) Nat Comm cell number (cell division rate)floweringtime growth stage
- 34. 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
- 35. 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)
- 36. large small GENOME SIZE
- 37. large small GENOME SIZE slow fast CELL DIVISION Density of βGS
- 38. large small GENOME SIZE late early FLOWERING TIME slow fast CELL DIVISION Density of βGS
