WheatWheat by Thomas Hart Benton (1967), from by Thomas Hart Benton (1967), from The Emergence of Agriculture, B. The Emergence of Agriculture, B. SmithSmith

Molecular Data and Molecular Data and Crop EvolutionCrop Evolution

Graduate SeminarGraduate Seminar

Wrap-up and summaryWrap-up and summary

Crop evolution is a special Crop evolution is a special and difficult case in and difficult case in systematicssystematics• synthetic fieldsynthetic field: systematics, : systematics,

archaeology, genetics (breeders), archaeology, genetics (breeders), anthropologyanthropology

• from from wildwild progenitors to fully progenitors to fully domesticateddomesticated races (and everything in races (and everything in between)between)

• domestication is a domestication is a whole plant whole plant concerted selection processconcerted selection process (habit, (habit, flowering, breeding system, physiology, flowering, breeding system, physiology, seed dormancy, life cycle, secondary seed dormancy, life cycle, secondary compounds)compounds)

•Non-shattering habitNon-shattering habit

•Reduced seed dormancyReduced seed dormancy

•Reduced plant size, determinate growth habitReduced plant size, determinate growth habit

•Shorter life cyclesShorter life cycles

•Less branching, fewer flowersLess branching, fewer flowers

•Altered photoperiodic or vernalization Altered photoperiodic or vernalization

requirementsrequirements

•Reductions in defense mechanisms and Reductions in defense mechanisms and

defense compoundsdefense compounds

•Changes in flower, seed, and fruit color . . .Changes in flower, seed, and fruit color . . .

Whole plant concerted selection Whole plant concerted selection processprocess

•Autopolyploidy where fertility is relatively Autopolyploidy where fertility is relatively

unimportantunimportant

•Allopolyploidy where fertility is importantAllopolyploidy where fertility is important

•Clonal propagationClonal propagation

•Inbreeding tolerance or derivation from Inbreeding tolerance or derivation from

outcrossingoutcrossing

•Sex expression, apomixis Sex expression, apomixis

Whole plant concerted selection Whole plant concerted selection processprocess

but, much of this change is due to but, much of this change is due to few major genes and often few major genes and often convergentconvergent

• Domesticated between 7,000 and 12,000 years agoDomesticated between 7,000 and 12,000 years ago

• Despite Despite independentindependent domestication of the four major domestication of the four major

complexes: Rice (Asia), Wheat/Oats (Near East), Corn complexes: Rice (Asia), Wheat/Oats (Near East), Corn

(America), Sorghum (Africa)(America), Sorghum (Africa)

• All were converted from small-seeded shattering grasses to All were converted from small-seeded shattering grasses to

large-seeded grasses with non-shattering habitlarge-seeded grasses with non-shattering habit

• Paterson et al. (1995) studied shattering, seed mass, Paterson et al. (1995) studied shattering, seed mass,

daylength-insensitive flowering time in sorghum, rice, and daylength-insensitive flowering time in sorghum, rice, and

corncorn

• Conservation across 65 my in grasses of genes affecting Conservation across 65 my in grasses of genes affecting

these traits was unexpectedthese traits was unexpected

Convergent domestication in Convergent domestication in PoaceaePoaceae

Crop evolution is a special Crop evolution is a special and difficult case in and difficult case in systematicssystematics• synthetic fieldsynthetic field: systematics, : systematics,

archaeology, genetics (breeders), archaeology, genetics (breeders), anthropologyanthropology

• from from wildwild progenitors to fully progenitors to fully domesticateddomesticated races (and everything in races (and everything in between)between)

• domestication is a domestication is a whole plant whole plant concerted selection processconcerted selection process

• domestication can have intensedomestication can have intense divergent selectiondivergent selection

Then . . . throw in divergent Then . . . throw in divergent selectionselection

Turnip (Turnip (Brassica campestrisBrassica campestris))

AA Genome, wildAA Genome, wild Selection for seedSelection for seed

Annual oil seedAnnual oil seed

Selection for Selection for leafinessleafiness

chinensischinensispekinensispekinensis

Biennial Biennial habit, habit, bulbingbulbing

TurnipTurnip

napusnapus (AACC) (AACC)

napocampestrisnapocampestris (AAAACC)(AAAACC)

nigranigra (BB) (BB)

junceajuncea (AABB) (AABB)

Raph. sativusRaph. sativus (RR)(RR)

Brassicoraphanus Brassicoraphanus (AARR)(AARR)

Phylogenetic Phylogenetic issuesissues

1. Recent origin from close relatives 1. Recent origin from close relatives (<12Ky)(<12Ky)

or, why molecular phylogenetics of crop plants is not or, why molecular phylogenetics of crop plants is not easyeasy

back

in t

ime

back

in t

ime As you go back in time to As you go back in time to

earlier generations, the earlier generations, the genetic connections appear genetic connections appear as a network within the as a network within the population of interbreeding population of interbreeding individualsindividuals

1 Population1 Population

Are you studying taxonomic units in which Are you studying taxonomic units in which gene trees provide an “emerging” species gene trees provide an “emerging” species tree? tree?

back

in t

ime

back

in t

ime But further back, they But further back, they

appear as dichotomous appear as dichotomous branching ropesbranching ropes

Are you studying taxonomic units in which Are you studying taxonomic units in which gene trees provide an “emerging” species gene trees provide an “emerging” species tree? tree?

Designation of species, Designation of species, subspecies, etc., although subspecies, etc., although important, impedes research!important, impedes research!

(Modified after O’Hara, 1993, Syst Biol 42)

Designation of species, Designation of species, subspecies, etc., although subspecies, etc., although important, impedes research!important, impedes research!

Are you studying taxonomic units in which Are you studying taxonomic units in which gene trees provide an “emerging” species gene trees provide an “emerging” species tree? tree?

Situation in crop plants is Situation in crop plants is probably much like that probably much like that proposed by O’Hara as common proposed by O’Hara as common in natural speciationin natural speciation

Genetic discontinuity to presentGenetic discontinuity to present

Genetic discontinuity ephemeralGenetic discontinuity ephemeral

Phylogenetic Phylogenetic issuesissues

1.1. Recent origin from close relatives (<12Ky)Recent origin from close relatives (<12Ky)

2.2. Morphological, but not molecular, variation Morphological, but not molecular, variation greatgreat

or, why molecular phylogenetics of crop plants is not or, why molecular phylogenetics of crop plants is not easyeasy

• therefore the search for “markers” [RFLPs, therefore the search for “markers” [RFLPs, RAPDs, SSRs, ISSRs, AFLPs, etc.]RAPDs, SSRs, ISSRs, AFLPs, etc.]

• issues with how to analyze & interpret these issues with how to analyze & interpret these “trees”, “phylograms”, “networks”, “PCA “trees”, “phylograms”, “networks”, “PCA diagrams” diagrams”

From Dr. Marc Ghislain’s presentation at the 2nd Solanaceae Genome workshop 2005, Ischia - Italy

Is this the appropriate “diagram” for this kind of marker data?Is this the appropriate “diagram” for this kind of marker data?

cluster analysis in cluster analysis in SolanumSolanum

Gene pool structure analyses I

From Dr. Marc Ghislain’s presentation at the 2nd Solanaceae Genome workshop 2005, Ischia - Italy

Or this?Or this?

factorial analysis in factorial analysis in SolanumSolanum

from Harter et al 2004

One of the better One of the better analyses using genetic analyses using genetic data as it uses a data as it uses a model based approach model based approach to ID placement of wild to ID placement of wild and domesticated and domesticated HelianthusHelianthus strains strains

Phylogenetic Phylogenetic issuesissues

1.1. Recent origin from close relatives (<12Ky)Recent origin from close relatives (<12Ky)

2.2. Morphological, but not molecular, variation Morphological, but not molecular, variation greatgreat

3.3. Sampling critical (wild progenitors, landraces, Sampling critical (wild progenitors, landraces, outgroups)outgroups)

or, why molecular phylogenetics of crop plants is not or, why molecular phylogenetics of crop plants is not easyeasy

• how many times this semester were you how many times this semester were you frustrated by the frustrated by the lack of sampling of critical lack of sampling of critical taxataxa, or , or different samplingsdifferent samplings from study to from study to study?study?

Nuclear ribosomal ITS

Robinson et al 2001Robinson et al 2001

• No No M. sylvestris!M. sylvestris!

=

Phylogenetic Phylogenetic issuesissues

1.1. Recent origin from close relatives (<12Ky)Recent origin from close relatives (<12Ky)

2.2. Morphological, but not molecular, variation Morphological, but not molecular, variation greatgreat

3.3. Sampling criticalSampling critical

4.4. Hybridization, introgression, polyploidy Hybridization, introgression, polyploidy commoncommon

or, why molecular phylogenetics of crop plants is not or, why molecular phylogenetics of crop plants is not easyeasy

• gene trees will not equal “species” tree gene trees will not equal “species” tree (whatever the latter means)(whatever the latter means)

Eubanks, 1997Eubanks, 1997

Hybridization and introgression jumped at almost Hybridization and introgression jumped at almost immediately, even when wrongimmediately, even when wrong

Is this the prevailing “icon” for crop plants, rather than a Is this the prevailing “icon” for crop plants, rather than a branching “species” tree?branching “species” tree?

Prevalence of polyploidy (both Prevalence of polyploidy (both allo- and auto-) presents allo- and auto-) presents homology issueshomology issues in use of in use of nuclear genes or anonymous nuclear genes or anonymous markersmarkers

All these genome transfers All these genome transfers requires requires multiple data setsmultiple data sets from from different genomes different genomes in in most phylogenetic studies most phylogenetic studies of crop plantsof crop plants

Phylogenetic Phylogenetic issuesissues

1.1. Recent origin from close relatives (<12Ky)Recent origin from close relatives (<12Ky)

2.2. Morphological, but not molecular, variation Morphological, but not molecular, variation greatgreat

3.3. Sampling criticalSampling critical

4.4. Hybridization, introgression, polyploidy Hybridization, introgression, polyploidy commoncommon

5.5. Biogeography is complex (both natural and Biogeography is complex (both natural and human induced movements)human induced movements)

or, why molecular phylogenetics of crop plants is not or, why molecular phylogenetics of crop plants is not easyeasy

How should we biogeographically interpret (or How should we biogeographically interpret (or analyze!) the distribution of these MDH alleles or analyze!) the distribution of these MDH alleles or phenotypes ?phenotypes ?

ArtocarpusArtocarpus (breadfruit)(breadfruit)

Phylogeography of G3pdh Phylogeography of G3pdh haplotypes in haplotypes in ManihotManihot (cassava)(cassava)

Should there be more Should there be more phylogeographicalphylogeographical analysis of analysis of molecular data ?molecular data ?

Should there be more Should there be more clock clock calibrations for determining calibrations for determining timing of species formation or timing of species formation or even domesticationeven domestication??

Sechium eduleSechium edule - - chayote chayote (Cucurbitaceae)(Cucurbitaceae)

Where do we go from here?Where do we go from here?

• 200 plant species have been domesticated 200 plant species have been domesticated out of approximately 275,000 angiospermsout of approximately 275,000 angiosperms

• < 20 crops in 8 families provide most of the < 20 crops in 8 families provide most of the world’s food (wheat, rice, corn, beans, world’s food (wheat, rice, corn, beans, sugarcane, sugar beet, cassava, potato, sweet sugarcane, sugar beet, cassava, potato, sweet potato, banana, coconut, soybean, peanut, potato, banana, coconut, soybean, peanut, barley, and sorghum - Harlan, 1992)barley, and sorghum - Harlan, 1992)

• only 8 plant families stand between most only 8 plant families stand between most humans and starvationhumans and starvation

Where do we go from here?Where do we go from here?

• major crops (and some minor - sunflower) are major crops (and some minor - sunflower) are well known from systematic and genomic well known from systematic and genomic perspectivesperspectives• their study often revolutionizes systematics in their study often revolutionizes systematics in terms of techniquesterms of techniques

• providing new methods do address questions providing new methods do address questions of evolution and speciation in plantsof evolution and speciation in plants

• sequenced genomes, libraries, EST sequenced genomes, libraries, EST approaches, FISH and GISH chromosomal approaches, FISH and GISH chromosomal analysesanalyses

Can we go beyond these markers?Can we go beyond these markers?

From From Darwin’s HarvestDarwin’s Harvest

Tragopogon - goat’s beard

(Modified after Pires & al, 2004, AJB 91)

Fluorescent in situ Fluorescent in situ hybridization (FISH) hybridization (FISH) mainly used on crop mainly used on crop plants but some wild plants but some wild speciesspecies

Future of crop evolution?Future of crop evolution?

What do we want to learn?What do we want to learn?

Why is it important?Why is it important?

QuestionsQuestions

WheatWheat by Thomas Hart Benton (1967), from by Thomas Hart Benton (1967), from The Emergence of Agriculture, B. The Emergence of Agriculture, B. SmithSmith

Molecular Data and Molecular Data and Crop EvolutionCrop Evolution

Graduate SeminarGraduate Seminar

Wrap-up and summaryWrap-up and summary

http://www.infojardin.com/fichas/hortalizas-verduras/col-china-coles-chinas-repollo-chino.htm

http://gettle.org/gallery/d/242-1/Chayote.jpg

http://www.uc.cl/sw_educ/hortalizas/imagenes/chayote/diversidad_chayote2_f.jpg