Transcript Backcross Segregation Data

Molecular Data and Crop
Evolution
Graduate Seminar
Wrap-up and summary
Wheat by Thomas Hart Benton (1967), from The Emergence of Agriculture, B. Smith
Plant Breeding is
Just the Current
Phase of Crop Evolution
-N.W. Simmonds
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Crop Domestication and Evolution
• Domestication
• Alteration from wild state to cultivated state
• Process renders inability to survive in the wild
• Results in large changes from wild populations
• Three centuries enough to domesticate certain grasses
• Continuously occurring
• Earliest cases are approximately 10,000 years ago
• Wheat, lentil, Cucurbits, Phaseolus older crops
• Rice, sorghum, sugarcane, soybean ca. 5,000 years ago
• Sugarbeet, oil palm, rubber, forage grasses very recent
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Early Agriculture in the Americas
• When did farming begin?
• Prevailing view has been the transition from hunter-gatherer to
agriculturist happened ca. 3500 years ago
• Several millennia behind Near East and Asia
• Time from domestication until ag economy is ca. 1000 years
• However, data from Smith (1997) suggest much older
agriculture in the Americas- perhaps 10,000 years ago
• New AMS technique revealed date of squash fragments
• Transition to farming may have been >6,000 years
• No clear distinction between the two phases, suggesting
overlap and cultivation of crops while hunting/gathering
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Ecogeographical Considerations
• Centers of Origin
• De Candolle (1886) recognized crop origins
• N. Vavilov developed center of origin concept, proposed 12 centers
• Harlan modified and broadened these views in the 1970s, suggested
multiple centers due to dynamic nature of crop evolution
1 China
2 India
2a Indo-Ma
3 C. Asia
4 Near East
5 Medit.
6 Ethiopia
7 Mexico
8 S. Amer.
8a Chile
8b Brazil
1
7
3
8
8a
8b
2a
5
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2
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Ecogeographical Considerations
• Centers of Origin and Centers of Diversity
• In practice, most crops have multiple centers or ‘non-centers’
• Centers remain critically important for crop collections
• Centers and non-centers as depicted by Harlan (1975)
• Domestication occurs in centers and non-centers
• Non-centers: multiple domestications possible
Centers
Non-centers
Near East (oat, cabbage)
Africa (sorghum, oil palm)
China (rice, cucumber)
Southeast Asia (sugarcane, banana)
Mesoamerica (maize, squash) South America (peanut, tobacco)
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Features of Crop Evolution
• Morphology and Physiology
• 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
• Multiple uses
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Wild and domesticated
March elder (top)
Sunflower (middle)
Squash (bottom)
Domesticated and wild
Chenopods
Two row and six row
barley
Source: B. Smith
The Emergence of Agriculture
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Features of Crop Evolution
• Genetic Changes
• Autopolyploidy where fertility is relatively unimportant
• Allopolyploidy where fertility is important
• Clonal propagation
• Inbreeding tolerance
• Hybridization with weedy or wild relatives
• Speciation within cultivated germplasm
• Sex expression, apomixis
• Mating System
• Derivation of inbreeders from outbreeders
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Concepts in Crop Evolution
• Convergent Domestication
• Poaceae family contains the cereals
• 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 largeseeded grasses with non-shattering habit
• Paterson et al. (1995) studied shattering, seed mass, daylengthinsensitive flowering time in sorghum, rice, and corn
• Conservation of gene order is well known, however
• Conservation of genes affecting these traits was unexpected
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Concepts in Crop Evolution
• Implications of Convergent Domestication
• Unity of cereal crop genomes now recognized
• Paterson et al. (1995) study shows correspondence (map position) of
genes associated with independent domestication events
• “Correspondence of these (genes) transcends 65 million years of
reproductive isolation”
• Few genes with large effects involved in major steps in domestication
• Genes may be identical in the various species
• Suggests rapidity of cereal domestication- major gene changes were
very important
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Case Studies in Crop Evolution
• The Maize-Teosinte Story (J. Doebley and colleagues)
• Modern corn (maize) was derived from the wild Mexican grass known
as teosinte (Zea mays ssp. Parviglumis)
• Mangelsdorf of Harvard debated Beadle of Chicago regarding maize
origins; Beadle supported teosinte as maize ancestor, Mangelsdorf
suggested small ears from Tehuacan Valley were primitive maize
• In recent years, research by Doebley has shown maize evolved from
teosinte by few major modifications, each involving a major gene
• Maize is also a model for genome-size evolution in crop plants
• Recent work by Bennetzen and Wessler reveals causes of genome
increase
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Case Studies in Crop Evolution
• Genome size evolution in maize
• The maize genome is highly duplicated (up to 72% of genome)
• Single genes exist in a ‘sea’ of repetitive DNA
• Much of this repetitive DNA is from transposable elements
• Copy number of elements ranges from 600 to 54,000 per haploid
• Many are the LTR retrotransposon, in copies up to 30,000
• Other classes of repetitive DNA are the elements Tourist, Stowaway
• Increase in size also due to segmental allopolyploidization
• Two diploid ancestors diverged ca. 20.5 M years ago
• Maize evolution driven by polyploidy, transposable elements, and
major regulatory genes controlling key morphological traits
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Case Studies in Crop Evolution
Teosinte
Teosinte
Maize
Maize
Two genes from maize (White and Doebley, TIG, 1998
• Teosinte has hard fruitcase, Teosinte Glume
Architecture (Tga1) contributes to silica deposition in
epidermal cells, causing shiny hard surface
• tga1reduces lignification, slower glume/rachis
growth rates- suggests regulatory gene
• Unlike maize, teosinte has lateral branches with
terminal tassels (male)
• Maize has very short lateral branches with terminal
ears (female)
• Teosinte-branched (tba1) represses growth of lateral
branches and selection for increased apical
dominance
• 2x RNA levels in ear primordia of maize compared to
teosinte- suggests regulatory gene
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Case Studies in Crop Evolution
• The Maize-Teosinte Story (J. Doebley and colleagues)
• Doebley and Stec (1991 and others) have demonstrated five major
genomic regions (QTLs) explain the genetic difference between maize
and teosinte
• These major regions control inflorescence development and structure
and plant branching patters
• Two of these regions contain tb1 and tga1
• Single mutations selected over time in incremental steps or major
mutations followed by selection of modifying genes?
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Case Studies in Crop Evolution
• The Gossypium Story (J. Wendel and colleagues)
• Polyploidy key in cotton, wheat, coffee, oat, soybean evolution
• Tetraploid cotton formed 1-2 M years ago in the New World when the
Old World ‘A’ genome hybridized with the New World ‘D’ genome
• Wild ‘A’ diploids and cultivated ‘AD’ tetraploid cottons produce
spinnable fibers, a fact likely involved in their domestication
• Both G. hirsutum and G. barbadense are AD cultivated tetraploids
• The former has been selected for yield, the latter for fiber length,
strength, and fineness (extra long-staple cottons)
• QTLs generally do not correspond in the A and D genomes, in
contrast to reported cereal domestication-QTL correspondence
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Case Studies in Crop Evolution
• The Gossypium Story (J. Wendel and colleagues)
• Most QTLs influencing fiber quality and yield are from the D genome
• Recall that the D genome does not produce spinnable fibers
• AD cultivars are superior to A cultivars, likely because of D genome
• “Merger of two genomes with different evolutionary histories in a
common nucleus offers unique avenues for response to selection”
• May compensate for corresponding reduction in quantitative variation
associated with polyploid formation (due to founder effect)
• Contribution of non-cultivated genome (D) to improvements in
agricultural productivity via polyploid formation
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New World
England
Boston
410
London
D
Dorchester
L
510
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Daylength and Onion Adaptation
Source: Magruder, 1937, J. Agr. Res. 54:719
Variety
Native Latitude Tops Down & Dry Foliage
12hr 14
Wolska
16
18
52o
0
0
25
60
Yellow Rijnsburg 52o
0
0
53
55
Yellow Zittau
0
12
33
42
51o
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Origin of Yellow Storage Germplasm
White Portugal / Silverskin, common yellow
Yellow Globe Danvers
Extra Early Yellow Mountain Danvers Downing YG Southport YG
Early YG
B Series Inbreds
B2108
Early Hybrids
Pioneer
Roch. Bronze
MSU Inbreds Brigham YG
MSU4535
W Series Inbreds
B Series
IYG
B2215C
W202
Early Hybrids
Bonanza
IA/ MSU
IA736
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Concepts in Crop Evolution
• Population Bottlenecks
• Hilton and Gaut (1998, Genetics 150:863-872) showed modern maize
contains 60% of the level of genetic diversity of its progenitor based
on data from the globulin-1 gene
• Eyre-Walker et al. (1998, PNAS 95:4441-4446) showed modern maize
had 75% of sequence diversity at Adh1 compared to its wild
progenitor
• Modeling studies revealed very few Z. mays parviglumis individuals
(ca. 20 for 10 gens) could be responsible for founding modern maize
• Based on duration of wheat domestication (300 years), 586 individuals
could explain sequence diversity found at maize Adh1
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Concepts in Crop Evolution
• Population Bottlenecks and Wild Species
• Only a small portion of the genetic variation present in native plant
populations is captured during domestication
• This ‘bottleneck’ can substantially reduce genetic variation
• Similar to founder effect in nature
• Paradigm: wild species thought useful only for few well-chosen traits
• Xiao et al. (1996, Nature, 384:223-224 and Genetics 150:899-909)
showed genes from wild rice could increase yield of cultivated rice
• This wild rice species had never been tapped for useful genes
• O. rufipogon was used in a backcross strategy to introduce
chromosome segments influencing yield of a high-yielding variety
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Case Studies in Crop Evolution
• Carrot (Daucus carota)
• Wild carrot (Queen Anne’s lace) ubiquitous weed
• Origin of Eastern or Anthocyanin carrot is Afghanistan
• Mostly purple with some yellow coloration in root
• Moved to Turkey, North Africa, and Europe by 13th century
• Carotenoids can confer orange, red, yellow
• Gave rise to carotene (Western) carrot, likely via mutations selected in
17th century in Netherlands
• Orange carrot selected in Netherlands: several populations developed
• All orange carrot traces to Late Half Long, Early Half Long, Early
Scarlet Horn (Banga)
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Case Studies in Crop Evolution
• Wheat (Triticum aestivum)
Triticum monococcum
2n=2x=14
AA
X
Unknown
2n=2x=14
BB
AB
Doubled
Triticum turgidum
AABB
2n=4x=48
X Triticum tauschii
2n=2x=14
DD
ABD
Doubled
AABBDD Triticum aestivum
2n=6x=42
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Case Studies in Crop Evolution
•Lowman and Purugganan, 1999. J. Hered. 90:514-520
•Cauliflower phenotype (Brassica oleracea)
•Protein that causes phenotype is truncated by an insertion
•The wild-type allele lacks the insertion
•These alleles are likely impaired in their ability to handle
floral meristem activity
•Cauliflower curd has a dense mass of arrested infloresence meristems
•It is likely that the these alleles are responsible, at least in part, for
domesticated cauliflower
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Case Studies in Crop Evolution
• Turnip (Brassica campestris)
AA Genome, wild
Turnip
Biennial habit,
bulbing
chinensis
pekinensis
Selection for seed
Annual oil seed
nigra (BB)
juncea (AABB)
Raph. Sativus (RR)
Selection for leafiness
napus (AACC)
napocampestris
(AAAACC)
Brassicoraphanus
(AARR)
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Case Studies in Crop Evolution
• Potato (Solanum tuberosum)
Wild diploids 2n=24
Selection for low alkaloids in tubers
Cultivated
Autotetraploids
2n=48
Cultivated diploids
Cultivated triploids
Moved to Europe
Tuberosum group
Tetraploids
Used in breeding
Wild allopolyploids
(from Ford-Lloyd)
Beta section
Southern Europe
Turkey, Near East
B. cicla
B. maritima
B. vulgaris
Medicinal plant
and herb use during
Greek and Roman periods
Selection for foliage
in Europe
Selection for swollen roots
Leaf beet, chard
Red-rooted ‘garden’ beet
Mangolds
Early Fodder
Beet
Flat, globe shapes selected
Fodder Beet
Swiss Chard
Sugarbeet
Red beet
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