Backcross Segregation Data

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Molecular Data and Crop EvolutionGraduate Seminar
Wrap-up and summary
Wheat by Thomas Hart Benton (1967), from The
Emergence of Agriculture, B. Smith
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Plant Breeding is Just the Current Phase of
Crop Evolution -N.W. Simmonds
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Crop Domestication and Evolution
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• 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 gt6,000 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 3 2 2a
7 8 8a 8b
5 4 6
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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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Domesticated and wild Chenopods
Wild and domesticated March elder (top) Sunflower
(middle) Squash (bottom)
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 large-seeded grasses with
  non-shattering habit
• Paterson et al. (1995) studied shattering, seed
  mass, daylength-insensitive 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

• 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

Teosinte Maize
Teosinte Maize
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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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England
New World
Boston
510
410
London
L
D
Dorchester
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Daylength and Onion Adaptation
Source Magruder, 1937, J. Agr. Res. 54719
Variety Native Latitude Tops Down Dry
Foliage 12hr 14 16 18 Wolska 52o
0 0 25 60 Yellow Rijnsburg 52o
0 0 53 55 Yellow Zittau 51o 0
12 33 42
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Origin of Yellow Storage Germplasm
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White Portugal / Silverskin, common yellow
Yellow Globe Danvers
Extra Early Yellow Mountain Danvers Downing YG
Southport YG
Roch. Bronze MSU Inbreds Brigham YG W
Series Inbreds B Series
IYG Early
Hybrids IA/ MSU
Early YG B Series Inbreds Early Hybrids
MSU4535
B2215C
W202
B2108
Bonanza
IA736
Pioneer
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Concepts in Crop Evolution

• Population Bottlenecks
• Hilton and Gaut (1998, Genetics 150863-872)
  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 954441-4446)
  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, 384223-224 and
  Genetics 150899-909) 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 Annes 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 X Unknown
2n2x14
2n2x14 AA BB
AB Doubled AABB 2n4x48
X Triticum tauschii 2n2x14 DD
Triticum turgidum
ABD Doubled AABBDD Triticum aestivum
2n6x42
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Case Studies in Crop Evolution

• Lowman and Purugganan, 1999. J. Hered. 90514-520
• 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
Selection for seed
nigra (BB)
Biennial habit, bulbing
Annual oil seed
Turnip
juncea (AABB)
Raph. Sativus (RR)
chinensis pekinensis
Selection for leafiness
napus (AACC)
Brassicoraphanus (AARR)
napocampestris (AAAACC)
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Case Studies in Crop Evolution

• Potato (Solanum tuberosum)

Wild diploids 2n24
Selection for low alkaloids in tubers
Cultivated Autotetraploids 2n48
Cultivated diploids
Used in breeding
Wild allopolyploids
Cultivated triploids
Tuberosum group
Moved to Europe
Tetraploids
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(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