Vision and reflection on Mining Software Repositories research in 2024
Rootstocks: the other half of the shoot phenotype and heterosis equation
1. Rootstocks: the Other Half of the
Shoot Phenotype and Heterosis Equation
Dan Chitwood
Donald Danforth Plant Science Center
IPG Heterosis Symposium
May 27, 2016
2. Evolutionary distance of genomes
Physicaldistanceofgenomes
Adjacent
genomes
Adjacent
cells
Adjacent
organs/su
b-organ
systems
Adjacent
organ
systems
Adjacent
organisms
Intra species Interspecies Inter-genus Inter-family Inter-kingdom…
“kissing trees”??
e.g. Root –
Mycorrhizae
Microbiome/
symbioses
Organ transplant
Bud-sporting
Puppy-monkey-baby
Brainbow
Variegated plants
Microchimerism
Graft-chimeras
Asexual graft-hybrid
Allopolyploid plant hybrids
Animal hybrids
Natural root grafting??
Rootstock-Scion grafting
Protoplast fusion
Injection
Margaret Frank, Chitwood Lab
Michael McKain, Kellogg Lab
3. Evolutionary distance of genomes
Physicaldistanceofgenomes
Adjacent
genomes
Adjacent
cells
Adjacent
organs/su
b-organ
systems
Adjacent
organ
systems
Adjacent
organisms
Intra species Interspecies Inter-genus Inter-family Inter-kingdom…
“kissing trees”??
e.g. Root –
Mycorrhizae
Microbiome/
symbioses
Organ transplant
Bud-sporting
Puppy-monkey-baby
Brainbow
Variegated plants
Microchimerism
Graft-chimeras
Asexual graft-hybrid
Allopolyploid plant hybrids
Animal hybrids
Natural root grafting??
Rootstock-Scion grafting
Protoplast fusion
Injection
Margaret Frank, Chitwood Lab
Michael McKain, Kellogg Lab
4. Evolutionary distance of genomes
Physicaldistanceofgenomes
Adjacent
genomes
Adjacent
cells
Adjacent
organs/su
b-organ
systems
Adjacent
organ
systems
Adjacent
organisms
Intra species Interspecies Inter-genus Inter-family Inter-kingdom…
“kissing trees”??
e.g. Root –
Mycorrhizae
Microbiome/
symbioses
Organ transplant
Bud-sporting
Puppy-monkey-baby
Brainbow
Variegated plants
Microchimerism
Graft-chimeras
Asexual graft-hybrid
Allopolyploid plant hybrids
Animal hybrids
Natural root grafting??
Rootstock-Scion grafting
Protoplast fusion
Injection
Margaret Frank, Chitwood Lab
Michael McKain, Kellogg Lab
5. Evolutionary distance of genomes
Physicaldistanceofgenomes
Adjacent
genomes
Adjacent
cells
Adjacent
organs/su
b-organ
systems
Adjacent
organ
systems
Adjacent
organisms
Intra species Interspecies Inter-genus Inter-family Inter-kingdom…
“kissing trees”??
e.g. Root –
Mycorrhizae
Microbiome/
symbioses
Organ transplant
Bud-sporting
Puppy-monkey-baby
Brainbow
Variegated plants
Microchimerism
Graft-chimeras
Asexual graft-hybrid
Allopolyploid plant hybrids
Animal hybrids
Natural root grafting??
Protoplast fusion
Injection
Rootstock-Scion grafting
Margaret Frank, Chitwood Lab
Michael McKain, Kellogg Lab
6. Evolutionary distance of genomes
Physicaldistanceofgenomes
Adjacent
genomes
Adjacent
cells
Adjacent
organs/su
b-organ
systems
Adjacent
organ
systems
Adjacent
organisms
Intra species Interspecies Inter-genus Inter-family Inter-kingdom…
“kissing trees”??
e.g. Root –
Mycorrhizae
Microbiome/
symbioses
Organ transplant
Bud-sporting
Puppy-monkey-baby
Brainbow
Variegated plants
Microchimerism
Graft-chimeras
Asexual graft-hybrid
Allopolyploid plant hybrids
Animal hybrids
Natural root grafting??
Rootstock-Scion grafting
Protoplast fusion
Injection
Margaret Frank, Chitwood Lab
Michael McKain, Kellogg Lab
7. Rootstocks modify shoot phenotypes:
Physiology, ionomics, morphology
Experiments with long-lived woody perennials:
Transplant experiments across transects and time
The importance of rootstocks:
Diversity and domestication
Overview
8. Rootstocks modify shoot phenotypes:
Physiology, ionomics, morphology
Experiments with long-lived woody perennials:
Transplant experiments across transects and time
The importance of rootstocks:
Diversity and domestication
Overview
9. Warchefsky et al. 2016
Trends in Plant Sci
FAOSTAT, 2013
The importance of rootstocks:
Diversity
10. The importance of rootstocks:
Domestication
Warchefsky et al. 2016
Trends in Plant Sci
11. The importance of rootstocks:
Domestication
Warchefsky et al. 2016
Trends in Plant Sci
12. The importance of rootstocks:
Root phenotypes
Warchefsky et al. 2016
Trends in Plant Sci
13. The importance of rootstocks:
Shoot phenotypes
Warchefsky et al. 2016
Trends in Plant Sci
14. The importance of rootstocks:
Shoot phenotypes
Warchefsky et al. 2016
Trends in Plant Sci
15. Rootstocks modify shoot phenotypes:
Physiology, ionomics, morphology
Experiments with long-lived woody perennials:
Transplant experiments across transects and time
The importance of rootstocks:
Diversity and domestication
Overview
16. Rootstocks modify shoot phenotypes:
Physiology, ionomics, morphology
Experiments with long-lived woody perennials:
Transplant experiments across transects and time
The importance of rootstocks:
Diversity and domestication
Overview
17. Rootstocks modify shoot phenotypes:
North American Vitis spp. as rootstocks
https://en.wikipedia.org/wiki/Phylloxera
https://en.wikipedia.org/wiki/Charles_Valentine_Riley
North American Vitis
Vitis vinifera Charles Valentine Riley
18. Rootstocks modify shoot phenotypes:
North American Vitis spp. as rootstocks
PLANTS database, USDA
V. riparia
V. rupestris
V. berlandieri High-density,
Wet
conditions
Drought
tolerant,
lime soils
V. ber.
X
V. rup.
V. ber.
X
V. rip.
Lime soils,
nematode
resistance
V. rip.
X
V. rup.
http://iv.ucdavis.edu/Viticultural_Information/
19. Rootstocks modify shoot phenotypes:
Mt. Vernon ‘Chambourcin’ vineyard
University of Missouri
20. Rootstocks modify shoot phenotypes:
Mt. Vernon ‘Chambourcin’ vineyard
University of Missouri
21. Rootstocks modify shoot phenotypes:
Physiology
Misha Kwasniewski
Arianna Bozzolo
Grape & Wine Institute
University of Missouri
22. Rootstocks modify shoot phenotypes:
Ionomics
Ivan Baxter
Donald Danforth
Plant Science Center
23. Rootstocks modify shoot phenotypes:
Leaf morphology
Viktoriya Coneva
Margaret Frank
Donald Danforth
Plant Science Center
Laura Klein
Allison Miller
Saint Louis University
24. Rootstocks modify shoot phenotypes:
Physiology, ionomics, morphology
Experiments with long-lived woody perennials:
Transplant experiments across transects and time
The importance of rootstocks:
Diversity and domestication
Overview
25. Rootstocks modify shoot phenotypes:
Physiology, ionomics, morphology
Experiments with long-lived woody perennials:
Transplant experiments across transects and time
The importance of rootstocks:
Diversity and domestication
Overview
26. Experiments with long-lived woody perennials:
Transplant experiments across transects and time
Alcohol and Tobacco Tax and Trade Bureau
28. Experiments with long-lived woody perennials:
Transplant experiments across transects and time
Dal Santo et al.: The plasticity of the grapevine
berry transcriptome. Genome Biology (2013)
29. Experiments with long-lived woody perennials:
Transplant experiments across transects and time
Chitwood et al., Plant Physiol. (2016)
Morphometric information: genotype, development, and environment
30. Experiments with long-lived woody perennials:
Transplant experiments across transects and time
Chitwood et al., Plant Physiol. (2016)
More pronounced lobing in the colder, drier year
31. Experiments with long-lived woody perennials:
Transplant experiments across transects and time
Chitwood and Sinha , Curr Biol. (2016)
More pronounced dissection correlates with the paleoclimate.
Plasticity and evolution in same direction?
33. Thanks!
Chitwood Lab
Viktoriya Coneva
Margaret Frank
Danforth REU undergrads
Darren Li (WashU)
Susan Rundell (Yale)
Quaneisha Woodford (Fort Valley
State)
Tommy Yu (WashU)
Danny Greenblatt (high school
student)
Miller Lab
Saint Louis University
Allison Miller
Laura Klein
Regan O’Hanlon
Steven Chacko
Matthew Greg
Cassandra Kitchen
University of Northern Iowa
Julie Kang
Jose Lopez
University of South Dakota
Anne Fennel
USDA Geneva, NY
Jason Londo
Missouri State
Laszlo Kovacs
Mizzou
Arianna Bozzolo
Misha Kwasniewski
E&J Gallo Winery
Peter Cousins