Molecular Data and Crop
Evolution
Graduate Seminar
Wrap-up and summary
Wheat by Thomas Hart Benton (1967), from The Emergence of Agriculture, B. Smith
Crop evolution is a special and
difficult case in systematics
• synthetic field: systematics, archaeology,
genetics (breeders), anthropology
• from wild progenitors to fully domesticated
races (and everything in between)
• domestication is a whole plant concerted
selection process (habit, flowering, breeding
system, physiology, seed dormancy, life
cycle, secondary compounds)
Whole plant concerted selection process
•Non-shattering habit
•Reduced seed dormancy
•Reduced plant size, determinate growth habit
•Shorter life cycles
•Less branching, fewer flowers
•Altered photoperiodic or vernalization
requirements
•Reductions in defense mechanisms and defense
compounds
•Changes in flower, seed, and fruit color . . .
Whole plant concerted selection process
•Autopolyploidy where fertility is relatively
unimportant
•Allopolyploidy where fertility is important
•Clonal propagation
•Inbreeding tolerance or derivation from
outcrossing
•Sex expression, apomixis
but, much of this change is due to few
major genes and often convergent
Convergent domestication in Poaceae
• Domesticated between 7,000 and 12,000 years ago
• Despite independent domestication of the four major
complexes: Rice (Asia), Wheat/Oats (Near East), Corn
(America), Sorghum (Africa)
• All were converted from small-seeded shattering grasses to
large-seeded grasses with non-shattering habit
• Paterson et al. (1995) studied shattering, seed mass, daylengthinsensitive flowering time in sorghum, rice, and corn
• Conservation across 65 my in grasses of genes affecting these
traits was unexpected
Crop evolution is a special and
difficult case in systematics
• synthetic field: systematics, archaeology,
genetics (breeders), anthropology
• from wild progenitors to fully domesticated
races (and everything in between)
• domestication is a whole plant concerted
selection process
• domestication can have intense divergent
selection
Then . . . throw in divergent selection
Turnip (Brassica campestris)
AA Genome, wild
Turnip
Biennial habit,
bulbing
chinensis
pekinensis
napus (AACC)
napocampestris
(AAAACC)
Selection for seed
nigra (BB)
Annual oil seed
juncea (AABB)
Selection for leafiness
Raph. sativus (RR)
Brassicoraphanus
(AARR)
Phylogenetic issues
or, why molecular phylogenetics of crop plants is not easy
1. Recent origin from close relatives (<12Ky)
back in time
Are you studying taxonomic units in which gene
trees provide an “emerging” species tree?
As you go back in time to
earlier generations, the
genetic connections appear as
a network within the
population of interbreeding
individuals
1 Population
back in time
Are you studying taxonomic units in which gene
trees provide an “emerging” species tree?
But further back, they appear
as dichotomous branching
ropes
Designation of species, subspecies,
etc., although important, impedes
research!
Are you studying taxonomic units in which gene
trees provide an “emerging” species tree?
Situation in crop plants is probably
much like that proposed by O’Hara
as common in natural speciation
Genetic discontinuity to present
Genetic discontinuity ephemeral
Designation of species, subspecies,
etc., although important, impedes
research!
(Modified after O’Hara, 1993, Syst Biol 42)
Phylogenetic issues
or, why molecular phylogenetics of crop plants is not easy
1. Recent origin from close relatives (<12Ky)
2. Morphological, but not molecular, variation great
• therefore the search for “markers” [RFLPs,
RAPDs, SSRs, ISSRs, AFLPs, etc.]
• issues with how to analyze & interpret these
“trees”, “phylograms”, “networks”, “PCA diagrams”
Is this the appropriate “diagram” for this kind of marker data?
cluster analysis in Solanum
From Dr. Marc Ghislain’s presentation at the 2nd Solanaceae Genome workshop 2005, Ischia - Italy
Gene
pool structure analyses I
Or this?
factorial analysis in Solanum
From Dr. Marc Ghislain’s presentation at the 2nd Solanaceae Genome workshop 2005, Ischia - Italy
One of the better
analyses using genetic
data as it uses a model
based approach to ID
placement of wild and
domesticated Helianthus
strains
from Harter et al 2004
Phylogenetic issues
or, why molecular phylogenetics of crop plants is not easy
1. Recent origin from close relatives (<12Ky)
2. Morphological, but not molecular, variation great
3. Sampling critical (wild progenitors, landraces,
outgroups)
• how many times this semester were you
frustrated by the lack of sampling of critical taxa,
or different samplings from study to study?
=
Nuclear ribosomal ITS
• No M. sylvestris!
Robinson et al 2001
Phylogenetic issues
or, why molecular phylogenetics of crop plants is not easy
1. Recent origin from close relatives (<12Ky)
2. Morphological, but not molecular, variation great
3. Sampling critical
4. Hybridization, introgression, polyploidy common
• gene trees will not equal “species” tree (whatever
the latter means)
Hybridization and introgression jumped at almost immediately,
even when wrong
Eubanks, 1997
Is this the prevailing “icon” for crop plants, rather than a
branching “species” tree?
Prevalence of polyploidy (both alloand auto-) presents homology
issues in use of nuclear genes or
anonymous markers
All these genome transfers
requires multiple data sets
from different genomes in
most phylogenetic studies of
crop plants
Phylogenetic issues
or, why molecular phylogenetics of crop plants is not easy
1. Recent origin from close relatives (<12Ky)
2. Morphological, but not molecular, variation great
3. Sampling critical
4. Hybridization, introgression, polyploidy common
5. Biogeography is complex (both natural and human
induced movements)
How should we biogeographically interpret (or analyze!)
the distribution of these MDH alleles or phenotypes ?
Artocarpus
(breadfruit)
Should there be more phylogeographical analysis of
molecular data ?
Phylogeography of G3pdh
haplotypes in Manihot (cassava)
Should there be more clock
calibrations for determining timing
of species formation or even
domestication?
Sechium edule chayote
(Cucurbitaceae)
Where do we go from here?
• 200 plant species have been domesticated out of
approximately 275,000 angiosperms
• < 20 crops in 8 families provide most of the
world’s food (wheat, rice, corn, beans, sugarcane,
sugar beet, cassava, potato, sweet potato, banana,
coconut, soybean, peanut, barley, and sorghum Harlan, 1992)
• only 8 plant families stand between most humans
and starvation
Where do we go from here?
• major crops (and some minor - sunflower) are well
known from systematic and genomic perspectives
• their study often revolutionizes systematics in
terms of techniques
• providing new methods do address questions of
evolution and speciation in plants
• sequenced genomes, libraries, EST approaches,
FISH and GISH chromosomal analyses
Can we go beyond these markers?
From Darwin’s Harvest
Tragopogon - goat’s beard
Fluorescent in situ
hybridization (FISH) mainly
used on crop plants but
some wild species
(Modified after Pires & al, 2004,
AJB 91)
Future of crop evolution?
Questions
What do we want to learn?
Why is it important?
Molecular Data and Crop
Evolution
Graduate Seminar
Wrap-up and summary
Wheat by Thomas Hart Benton (1967), from The Emergence of Agriculture, B. Smith
http://www.infojardin.com/fichas/hortalizas-verduras/col-china-coleschinas-repollo-chino.htm
http://gettle.org/gallery/d/242-1/Chayote.jpg
http://www.uc.cl/sw_educ/hortalizas/imagenes/chayote/diversidad_ch
ayote2_f.jpg