How did plants evolve under domestication? Fate of genetic diversity

Or: Why are the British tea drinkers? Why is the basketball team in Boston called the Celtics?

© Paul Gepts 2006

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PLB143: Readings - Lecture 15

• Required:
  • National Research Council (1972) Genetic vulnerability of crops. National Academy of Sciences, Washington, DC: pp. 5-22, 286-304   UCD access only (Kerberos password)
• Additional readings:
  • Buckler E, Thornsberry J and Kresovich S (2001) Molecular diversity, structure, and domestication of grasses. Genetical Research 77:213-218
  • Crow JF, Kimura M (1970) An introduction to population genetics theory. Harper & Row, NY
  • Duvick DN (1984) Genetic diversity in major farm crops on the farm and in reserve. Econ. Bot. 38: 161-178
  • Hargrove TR, Coffman WR, Cabanilla VL (1979) Genetic interrelationships of improved rice varieties in Asia. IRRI Reseach Paper Series No. 23
  • Hobhouse H (1986) Seeds of change. Harper & Row, NY
  • Hoyt E (1988) Conserving the wild relatives of crops. International Board Plant Genet. Res., Rome
  • Saghai Maroof MA, Soliman, KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer-length polymorphisms in barley, Mendelian inheritance, chromosomal location, and population dynamics. Proc. Nat. Acad. Sci. 81: 8014-8018
• Presentation slides
  • Pdf format (2008 version)

Lecture 15 Plan

• Major directions in crop evolution research
• What is genetic diversity and how do we measure it?
• Uncoupling of trends in genetic diversity at the molecular and phenotypic levels. How do we explain that?
• Why is genetic diversity important? The case of disease resistance
• How diverse or uniform are our crops?

Two major directions in crop evolution research

• Search for the ancestor
  • First part of the course
  • Traditional goal of crop evolution studies
• Evolution under domestication
  • Compare wild progenitor and cultivated descendant
  • This lecture and the 2 following ones will deal with differences that have appeared under domestication: genetic diversity, phenotype differences and their genetic control, and physiological and ecological differences.

The domestication process

• Definition:
  • Selection process for adaptation to the human (cultivated) environment (farmers and consumers)
• Stages:
  • initial domestication
  • dispersal within the region of domestication
  • long-range dispersal
• Effects on genetic diversity?

What is genetic diversity?

• Types of traits
  • growth habit
  • disease and pest resistances
  • tolerance to abiotic stresses
  • quality
  • harvest index and yield
• Types of plant materials
  • Gene pools: I, II, III, IV (see Lecture 5 )
  • Primary gene pool
  • wild progenitor, landraces, obsolete cultivars, advanced breeding lines, modern cultivars

How do we measure genetic diversity?

• Morphological (phenotypic) traits
  • usually of agronomic importance:
    • growth habit, seed size and shape
    • phenology
  • problem: gene expression
• Molecular markers
  • see Lecture 5: RFLP, RAPD
  • problem: more cumbersome
• Contrasting results

Experiments to measure evolution of genetic diversity at the molecular level

1. Chloroplast DNA in various species (Doebley 1992)
2. Cereal diversity (Buckler et al. 2001)
3. M13-homologous sequences in common-bean (Sonnante et al. 1994)

• Chloroplast DNA
  
  
• Cereal nuclear sequence diversity
  Pdf file
  
• RFLPs for M13-related sequences
  
  

Relative genetic uniformity of major U.S. crops

(National Research Council 1972)

Interpretation of the uncoupling in genetic diversity trends

• What do we expect?
  • Evolutionary factors
  • Domestication in a limited area
• What is an important difference between mutations with a phenotypic advantage/disadvantage and neutral mutations?
  • Probability of survival of mutant genes in large populations
  • Different evolutionary factors involved
    

• 
  Crow and Kimura 1970

Evolutionary factors

• •Selection: effect on genetic diversity: ↓–

  • Initial domestication

  –

  • Later dispersal
  • Modern plant breeding, but…
• Genetic drift: effect on genetic diversity: ↓–

• Sampling during domestication

–

• Later dispersal•

Mutation: effect on genetic diversity: ↑ or ↓–

• Selection of novelties •

Migration/hybridization: effect on genetic diversity: ↑ or ↓

Other causes of genetic erosion

• Genetic erosion: loss in genetic diversity, usually of crop plants or domestic animals
• Causes:
  • Release of modern cultivars: 
  • example: modern rice cultivars in the Philippines
  • Overgrazing
  • Loss of natural vegetation
    
    <==> overpopulation

• Area planted to improved rice varieties, Philippines
  
  Hargrove et al. 1979
  

Potential effect of lack of diversity on crop disease status

Three examples

• In 1970, country-wide epidemic leading to a loss of 15% of corn production
  • Started in Florida and moved northwards
  • Leaf disease caused by a fungus, Helmintosporium maydis
    • Known to exist before the epidemic
  • Only maize with T cytoplasm

• Southern corn leaf blight epidemic (1970)
  
  

• What is the T cytoplasm?
  • Maize varieties = hybrid varieties to use heterosis:
    A (female) x B (male)--> F1 with yield >>  A or B
  • To get high levels of hybrid seeds:
    • traditional way: "detasselling"
    • novel way: cytoplasmic sterility: gene in mtDNA leads to male sterility --> no need to detassel; requires male fertility restorer gene in B to restore fertility in F1!
  • New strain of H. maydis in 1969-1970:
    • More virulent on maize lines with T cytoplasm
    • Because utilization of T cytoplasm had become widespread --> epidemic affecting most of U.S. corn belt

• Coffea arabica originated in Ethiopia (mountainous area!) but coffee growing and brewing may have started in Ethiopia or Arabia. When?
  • First historical records: Yemen (14th century) --> export via port of Mocha (limited to Yemen until 1700)
  • First European coffee house: Venice (1615)
• Introduction of coffee elsewhere: live plants (non-dormant seeds); Dutch: to India, Ceylon, and Java; French: to island of Bourbon (Reunion) --> S. America (Colombia) 
• Java --> Amsterdam --> Hawaii: Kona or Surinam --> Brazil or Paris --> Martinique, Jamaica (Blue Mountain), etc.
• In 1868, Ceylon was the leading coffee producer (export of 100 million lbs); by 1885, no coffee could be exported
  • leaf disease caused by a fungus, Hemileia vastatrix
  • Java 1876; East Africa 1894; Brazil 1970
  • made worse by limited diversity; highly variable pathogen
  • controlled by fungicides --> uneconomical in many regions except where optimal climate
  • genetic resistance: C.canephora (Robusta); lower quality: cheap blends and instant coffee
  • replace by other crops: e.g., tea

• Coffee leaves, flowers, berries
  
  
• Coffee bushes
  
  
• Coffee-growing region in Colombia
  
  
  

• Introduced into Europe (Isle of Wight) in 1845 from Americas
• Quick dispersal in the British islands and the continent; in Ireland, major epidemics in 1845-46: island-wide potato failure
• Control measures known at that time: plant only every 6th year, use clean seed tubers not connected to diseased field; do not feed diseased tubers to stock w/o boiling
• Ireland = agricultural colony of Great Britain
  • absentee (foreign) landlords - Irish serfs
  • potato = major staple; wheat = export crop
  • no major industries: elimination of competition with GB; high unemployment
  • 9 million people before epidemic; 1 million deaths: starvation, diseases (cholera, typhus, etc.)
  • 1.5 million emigrants after epidemic; 5.5 million emigrants until WWI, many to U.S. East Coast (Boston!)

• Late blight symptoms on potato leaves
  
  
• Ireland scene around 1848
  
  Courtesy of S. Taylor, http://vassun.vassar.edu/~sttaylor/FAMINE/ . Accessed 09/26/2001.
  

How is uniformity of our crops evolving (Duvick 1984)?

• Proportion (%) of area grown to 6 most popular cultivars
  
  

• Genetic diversity over time
  

Lecture 13 Main Findings

• Major directions in crop evolution research:
  • Identification of wild ancestor
  • Comparison of wild ancestor and cultivated descendant
• What is genetic diversity and how do we measure it?
  • Useful (phenotypic) traits: farmer, consumer
  • Molecular markers: RAPDs, RFLPs, etc.
• Uncoupling of trends in genetic diversity at the molecular and phenotypic levels. How do we explain that?
  • Phenotypic traits: increase in diversity; molecular markers: decrease in diversity
  • Inevitable reduction in genetic diversity:
    • domestication: selection, dispersal
    • economic and cultural pressures
  • Major difference between the two types of traits: probability of survival in cultivated environment: favors survival of phenotypic traits with major, "favorable" effect
• Why is genetic diversity important?
  • The case of disease resistance: lack of diversity leads to genetic vulnerability, i.e. development of large-scale disease epidemics
  • Limited progress from selection in breeding programs to improve crops
• How diverse or uniform are our crops?
  • Our crops are generally very uniform; however, there is a reversal in longtime trend towards increased diversification, both in space and time