Genetic Variation

1
Genetic Variation
1

• Occurrence of heritable or non-heritable
  differences
• Among populations, among individuals, among cells
• Variation divided into three primary categories
• Phenotypic total biological variation
• Continuous that variation from quantitative
  characters
• Discontinuous that variation from qualitative
  characters
• In a segregating population, variation can be
  expressed as
• Vp Vg Ve
• Where g genetic factors and eenvironmental
  factors
• Proportion due to genetics is heritability
• Vg can be due to additivity, dominance, and/or
  epistasis

2
2
Sources of Genetic Variation

• Mutation
• Chromosome aberrations
• Recombination
• Crossing Over
• Independent Assortment

3
3
Mutation

• Highly variable across loci in maize (Stadler,
  1942)
• Gene Gametes Tested Mutations
  Rate
• R 554,786 273 492 per million
• Su 1,678,736 4 2.4 per
  million
• Wx 1,503,744 0 0 per
  million

4
4
Variation Under Domestication
Darwin, Variation Under Domestication, 1868

• Domesticated forms vary more than wild
  progenitors
• Slight variations are preserved by humans
• The most variation is found in the characters
  with the most importance, such as the seed of the
  bean
• Species have been selected into varieties, which
  vary greatly for particular characters
• It may be that..a gooseberry larger than the
  London variety (will not be produced), but he
  would be a bold man who would assert that the
  extreme limit in these respects has been finally
  attained.

5
5
The part of the plant of greatest interest to man
is the part that is modified the most. - J.R.
Harlan
6
Who Domesticated Whom?

• Through trial and error these plant species
  have found that the best way to do that is to
  induce animals- bees or people, it hardly mattes-
  to spread their genes. How? By playing on the
  animals desires, conscious and otherwise. The
  flowers and spuds that manage to do this most
  effectively are the ones that get to be fruitful
  and multiply.
• So the question arose in my mind that day Did I
  choose to plant these potatoes, or did the potato
  make me do it?
• Michael Pollan, The Botany of Desire

7
6
Centers of Origin

• De Candolle proposed crop origins in late 19th
  century
• Vavilov made collections from 1916-1938, proposed
  eight major centers of origin for cultivated
  plants

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
8
7
Centers of Origin

• Darlington and Hanaki Ammal described 12 centers,
  1945 increasing contribution from the Americas
• Zhukovskij proposed megagene centers in 1968,
  increasing size of centers
• Harlan suggested centers and non-centers in 1971,
  where non-center refers to a large geographic
  area in which domestication may have occurred in
  multiple events

Vavilovs centers and crop examples
Chinese Lettuce, rhubarb, soybean,
turnip Indian Cucumber, mango, cotton,
rice Indo-Malayan Banana, coconut, yam Central
Asia Almond, cantaloupe, flax, lentil Near
Eastern Alfalfa, apple, cabbage,
rye Mediterranean Celery, chick pea, durum
wheat Ethiopian Coffee, sorghum, millet Central
American Lima bean, maize, papaya, cotton South
American Cotton, potato, pumpkin, tomato
9
8
Natural and Agricultural Variation

• Wild
• Naturally-occurring populations
• Weedy
• Plant populations not desired for cultivation but
  modified by the practice of agriculture, either
  directly or indirectly, and growing in wild or
  cultivated environments. Plant out of place
  definition works here.
• Landrace
• Selected for use in agriculture, often highly
  heterogenous populations, broad-based, possessing
  large amounts of genetic variability

10
9
Law of Homologous Series

• Vavilov Law of Homologous Series in variation
• The more similar species are, the more similar
  are their variations
• Common occurrence of characters in similar
  species or in particular geographic regions
• Natural selection favored certain phenotypes in
  particular environments
• Disease resistance an example
• Similar to modern ideas used in comparative
  mapping and genomics

11
10
Politics and Germplasm

• Vavilov was a brilliant geneticist
• All-Union Institute of Plant Breeding
• Suggested crop improvement strategies through
  collection of wild relatives from crop centers
  and carrying out breeding programs
• These programs typically take a long time
• His ideas challenged by Trofim Lysenko, a
  favorite of Stalin
• Lysenko (peasant background) was a Lamarckian,
  suggested cold treatments could hasten maturity
  in heritable way

12
11
Politics and Germplasm

• Lysenko promised quick gains in crop improvement
• Mendelian heredity was held in low regard by
  Stalins regime, as was germplasm collecting and
  fascistic foreign science in general
• Vavilov was removed from his post in 1935,
  despite being elected president to the Seventh
  International Congress of Genetics
• He was replaced by Lysenko and eventually
  arrested in 1940 while on a collecting trip in
  the Ukraine
• Vavilov died in prison in 1943
• His ideas form the foundation of the way plant
  breeders view germplasm resources today
• He was Martyr to Genetic Truth (Crow, 1993,
  Genetics134)

13
12
Public Exploration

• Commerce and Trade
• Centers of production were far removed from
  centers of origin
• Commodities trade caused plant introduction
• European diet changed introduction of the potato
• The Potato (Larry Zuckerman) outlines cultural
  and political trends affecting adoption of potato
  by Europeans
• Royal Botanic Gardens at Kew, England, 1760
• U.S. Government
• U.S. Navy and introduction of the Lima bean
• Japanese expedition
• Morrill Act in 1862
• David Fairchild, U.S. plant explorer
• The World Was My Garden
• Mark Carleton, Kharkov Red Winter Wheat

14
13
The work of Charles Rick has made UC-Davis a home
for the use of variation in tomato breeding for
50 years
UW-Madison, and particularly the potato breeding
programs, have focused on use of variation in
breeding efforts
15
14
Genetic Variation Theoretical Implications
Rasmusson and Phillips, 1997, Crop Sci. 37303-310

• Given that progress in plant breeding continues
  at a high rate
• Favorable alleles are increasing in frequency in
  populations
• Theoretically, favorable alleles will become
  fixed
• And genetic variation should become reduced
• So it would make sense to continuously bring in
  new variation
• However, programs designed to do this have not
  been as successful as those programs using only
  elite germplasm
• For many crops, standard breeding procedures
  systematically reduce genetic diversity
• For many crops, few germplasm sources make up
  much of the modern germplasm base (corn, barley,
  onion, etc.)

16
15
Why have selection limits not been reached in the
Illinois long Term Selection experiment
despite 100 generations of continued selection?
17
16
Barley Improvement

• Rasmusson and Phillips, 1997, Crop Science37
• Manchuria barley introduced early in 20th century
• Many of the breeding programs in the Midwest and
  Canada shared germplasm
• Industry Quality Guidelines required a profile
  of 22 traits- which dictated new cultivars like
  the old ones
• The main cultivars, developed in the Minnesota
  breeding program, have increased in performance
  over the past 50 years, however all are closely
  related
• Modest levels of genetic diversity based on
  pedigree information permit sizeable genetic
  gains
• Performance gains cant necessarily be explained
  because genetic diversity is so low

18
17
Barley Improvement

• Rasmusson and Phillips, 1997, Crop Science37
• Breeders have stayed away from exotic germplasm
  because only rarely do elite x exotic crosses
  lead to gains
• Gene frequency changes have been huge between
  elite and exotic populations, making it hard to
  recover desirable types
• Questions to be asked include
• How much useful diversity is in elite breeding
  germplasm?
• How successful are efforts to introduce exotic
  diversity?
• Is useful variation being created within working
  elite germplasm?

19
18
Questioning Diversity

• Rasmusson and Phillips, 1997, Crop Science37
• Did all useful diversity exist in parental
  populations, or is novel variation arising during
  the breeding process?
• Two new sources are mutations and epistatic
  interactions
• Fixation does not appear to have been reached in
  the ILTSE, despite highly inbred strains and 100
  generations of selection
• Models tell us we should arrive at allele
  fixation after much selection and inbreeding
• Does this suggest a dis-connect between
  traditional theory and actual practice?

20
19
De Novo Variation?

• Rasmusson and Phillips, 1997, Crop Science37
• Intragenic recombination clearly demonstrated
• Unequal crossing over common- many genes in
  tandem array, and displaced pairing followed by
  crossing over can generate novel variants
• Transposable elements and retrotransposons
• DNA methylation associated with gene expression
• Paramutation, which involves interaction of
  alleles in a heterozygote
• Gene amplification
• All of these mechanisms can cause new variation
  during the breeding process