Download 1 I. INTRODUCTION TO CROP EVOLUTION AND DOMESTICATION

I.
INTRODUCTION TO CROP EVOLUTION AND DOMESTICATION
Review Transmission Genetics
Effect of Selection (Differential Reproduction) on Allele Frequencies
Selection changes allele frequencies (and therefore genotype frequencies) and is vital for
E/D. Selection occurs when one individual leaves behind more progeny than another, thus it is
relatively more fit. The effect of selection on allele frequencies can be modeled for a simple
scenario involving one gene in a random mating population:
Increased fitness is dominant
Individual’s genotype
Individual’s relative fitness
Frequency
CC
1
p2
Cc
1
2pq
cc
1-s
q2
The variable “s” is the selection differential and for this model is equal to:
s = 1 -
Average number of progeny from "cc" genotypes
Average number of progeny from "CC" and "Cc" genotypes
We will assume that s is positive in all the discussions. Thus “cc” is less fit than “CC” or “Cc”.
The “c” allele is deleterious and the “C” allele is advantageous (confers increased fitness).
How fast will q change from one generation to the other?
∆q =
− sp q 2
= q1 − q 0
1− s q2
where q0 is the frequency of “c” in the population prior to selection and q1 is the frequency of “c”
after one generation of selection.
∆q will always be negative (e.g., frequency of “c” will always decrease) assuming that s is
positive. It is apparent that ∆q is a function of the selection differential (s) and the original allele
frequency (q). In the next generation following selection, q becomes:
− sp q 2
q1 = q0 + ∆q = q0 +
1 − sq 2
After many generations of selection, q and ∆q become very small. When s = 1, “c” is analogous
to a recessive lethal gene as “cc” individuals do not produce any progeny. s would equal 0.75
when every “cc” genotype produces 25% of the progeny that “CC’ or “Cc” genotypes do.
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“s” may be very small in natural selection. For example, s may equal 0.001 in a comparison of
two enzymes that have different efficiencies. In evolution, a new favorable allele (say “C”) may
arise by mutation in a large population so that p is very small (q therefore is very large) It can take
many generations for the new favorable allele that arises by mutation to become essentially fixed
(p ≈ 1) in a population. Lets assume that a new allele (“C”) is formed by mutation. In our initial
population lets assume p = 0.0001, q = 0.9999, and s = 0.01. It will take 10,001,972 generations
of natural selection for p to become 0.9999.
Frequency of "c" Allele After Selection With Different
Selection Differentials
0.50
Frequency of "c" Allele
0.45
0.40
0.35
s =1
0.30
s = 0.75
0.25
s = 0.50
0.20
s = 0.25
0.15
s = 0.01
0.10
0.05
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22
20
18
16
14
12
10
8
6
4
2
0
0.00
Generation of Selection
Figure. The effect of selection intensity and changes in allele frequency over time.
∆q becomes smaller as s decreases.
∆q can be modeled for any value of s for any genotype or for different s values for each genotype.
∆q varies by gene action as well. Above we modeled CC=Cc>cc for relative fitness (e.g. “c” is
recessive for decreased fitness). Other scenarios include CC>Cc>cc (e.g. additive gene action as
Cc has intermediate fitness relative to CC and cc), or CC<Cc>cc (e.g. heterozygote is most fit).
In practical situations where populations are finite, the “c” allele is likely to be eliminated due to
sampling with either the recessive or additive model of gene action. For example, if ten
individuals are selected to be intermated to form the next generation from a population where p =
0.95, then there is a 36% chance that all 10 will be “CC” and “c” will therefore be eliminated
from the population. Restricting effective population size is required to fix favorable alleles in
these selection scenarios.
∆q is a function of s, q, and mode of gene action.
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CROP EVOLUTION AND DOMESTICATION
Agriculture is a major innovation of humankind. The development of agriculture had a
dramatic impact on environment and society (history, power, political, creativity) and allowed
humans to develop other innovations and structures.
Hunters/gatherers (HG) for 4 M years, used a wide array of plants (Africa 23/85 edible
species). Needed to work perhaps 2.5 days per week to get enough food. Can collect 2 kg/hr of
einkorn in some good wild stands.
But the situation changed (population growth? Environment?) and people started farming
and became more sedentary. Agriculture started, a gradual transition. One ha can support 10100x more farmers/herders than HGs/
Human dispersal over the globe was fairly rapid. Agriculture seemed to arise in different
areas around the same time, perhaps 10,000 yrs ago. The fertile cresent, Mesopotamia was first.
Gave rise to first cities, etc.
Centers of domestication: Most crops were domesticated in one of six centers. These are
mainly in tropical and subtropical regions. Generally middle elevation, varied topography,
distinct wet/dry seasons. [each also had some large seeded cereal which became a staple, lead to
success of ag.]. A different set of species were domesticated in each region, but the species met a
similar set of needs (energy from carbohydrates, proteins from legumes, oils, fiber) Crops
domesticated in the six centers.
Cereals
Mesoamerica S.
America
Maize
Grain
legumes
Common
bean
Common
bean
Center
China
SE Asia
Near East
Africa
Rice,
millets
Rice
Sorghum,
rice, millet
Soybean,
adzuki
bean
Turnip,
yam
Pidgeon
pea
Rape
seed,
soybean
Coconut
Wheat,
barley,
rye, oat
Pea,
chickea,
lentil
Turnip,
carrot,
radish
Rapeseed,
safflower,
flax, olive
Roots/Tubers Sweet potato
Potato,
cassva
Oil crop
Cotton
Peanut,
cotton
Fiber
Cotton
Fruits
Cotton,
agave
Papaya
Pineapple
Peach,
apricot
Vegetable
Squash
Pepper
cabbage
Stimulants
Cacao
Coca
Tea
Yam, taro
Coconut
Orange,
lime,
banana
Cucumber,
eggplant
Cowpea
Yam
Oil
plam,
castor bean
Kenaf
Fig, grape,
apple,
pear, plum
Onion,
lettuce
Poppy
Watermelon,
melon
Okra
Coffee
(from Chrispeels and Sadava, page 335)
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Species: There are perhaps 230 crops in the world, with only 120-130 major crops. Vast amount
of our energy and protein is provided by very few crops (wheat, rice, maize, soy, beans, potato).
Diverse sampling of families, though many plant families are not represented.
Figure. Major food crops of the world (from Chrispeels and Sadava, page 53)
Some species were domesticated but the crop later became extinct. Some have become widely
distributed, some not.
Our knowledge of crop evolution and domestication (E/D) is inferential. Generally we can only
compare our present cultivars (past 100-200 years) to collections of current representative
accessions of putative ancestors. A probable picture is pieced together from many disciplines.
What is clear is that there were many avenues of crop domestication.
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Figure. Centers of crop evolution (from Chrispeels and Sadava, page 334)
Evolution and Domestication (E/D) PROCESSES
E/D process is a continual process starting with the wild species, then formation of the cultivated
species, then selection of improved strains of the species by growers (called landraces), then to
modern cultivars from scientific breeding. The process continues today.
Basic requirements and steps of E/D
1. A natural population with sufficient genetic variation (Vg) to allow phenotypic
variation (Vp) for traits desirable to humans. Many natural populations of plants have
considerable variation that arises from the geographic distribution and adaptive
requirements of the population.
Vg in a natural population arises from new combinations of existing genes within a
population. mutations, allele migration between populations, natural selection for local
adaptation, and random events. Vg is maintained in natural populations by multiple
genetic mechanisms and exposure to diverse environments. Vg is the fuel for the E/D
process. Vg can increase and decrease during the E/D process.
2. Change in allele frequency so that alleles conferring desirable traits become more
frequent (alleles conferring unfavorable traits become less frequent). Normally attributed
to selection (natural and human). Changing allele frequency is a constant feature of E/D
and crop improvement
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3. Reproductive isolation (limited migration) so that changes in allele frequencies are not
lost due to mixing with unselected populations. Necessary step in speciation.
Reproductive isolation can form instantaneously (some polyploidy, flowering mutations)
or gradually
Evolution continues throughout domestication and even today. Different variants of a crop
species could evolve into new species. New genes from same species, chromosome segments and
genes from related species, and novel genes from any species are being introduced to our current
crops during modern improvements
Gene Pools
A key concept in biodiversity preservation and utilization is the concept of gene pools. Breeders
use genetic resources to improve their crop. They classify place resources into one of four gene
pools based on ease of use
GP1: The crop itself and wild relatives that are easily intercrossed and produce fertile progeny.
GP2: Species that cross to GP1 but with difficulty and produce progeny with reduced viability
GP3: Species that cross to GP3 only using advanced techniques (embryo rescue, tissue culture)
and produce progeny with low viability
GP4: Other species that do not cross to GP1 at all. Must use molecular genetics and gene cloning
to use these genes.
Gene pools (from Chrispeels and Sadava, page 350)
Estimating Genetic Diversity
Biodiversity itself can be defined at many levels and in many ways. Thus collecting and
conserving diversity can be viewed from many ways. One can think of genetic diversity in terms
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of DNA sequences, alleles, genome-wide, within a population, within a species, within a
geographical region. In addition one can consider communities of species that may have coevolved, such a plants and their pests.
For plants, only a small fraction of the biodiversity may be useful but may be crucial to success of
the crop and for continued evolution (improvement) of the crop species. Thus collecting,
cataloging, and using this diversity is crucial to crop improvement. Collecting is the starting point
and really consists of sampling as it is impossible to collect everything. Effective collection
requires knowledge of genetic diversity.
There are several concepts of genetic diversity that must be considered and that can be used to
illustrate the diversity among plants.
Allele richness = A = The number of alleles in a population
Variation of allele frequencies = h = the eveness of allele frequencies
h = 1− ∑
p i2
Table. Example of A and h for two populations using frequency of flower color alleles
Flower color allele
White
Purple
Yellow
A
h
Population 1
0.05
0.05
0.90
3
0.185
Population 2
0.5
0.5
0
2
0.50
Based on number of alleles, population 1 is most diverse while population 2 is more diverse if we
look at variation of gene frequencies. The measures A and h describe a single population.
Using isozymes (protein markers), plants appear to be polymorphic (ie have more than 1 allele) at
about ½ of their loci, with an average of 2 alleles per locus (A=2) and with an average allele
variance of 0.15 (h=0.15). But within a single population, plants tend to be polymorphic at only
1/3 or their loci and A=1.5 and h=0.11. But there is HUGE difference in these values among
studies.
Table. Estimates of genetic diversity based on isozymes (from Frankel et al. page 14 who used
data from Hamrick and Godt (1989)).
Category
Mating system
Self pollinator
Outcrosser
Within species
A
h
1.69
2.4
0.12
0.16
Within population
A
h
Gst
1.31
1.80
0.07
0.15
0.51
0.10
Range
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Endemic
Wide
1.80
2.29
0.10
0.20
1.39
1.72
0.06
0.16
0.25
0.21
Life Form
Annual
Long-lived
2.07
2.19
0.16
0.18
1.48
1.79
0.11
0.15
0.36
0.08
Table. Estimates of genetic diversity based on isozymes (from Richards, 1997. page 453 who
used data from Hamrick, Linhart, and Mitton (1979)).
Class
Gymnosperms
Dicots
Monocots
A
2.1
1.5
2.1
h
0.27
0.11
0.16
Annual
Biennial
Long-lived
perrenial
1.7
1.3
2.0
0.13
0.06
0.27
Self fertilized
Mixed fertilized
Cross fertilized
1.3
1.8
1.8
0.06
0.18
0.18
Colonizer
Mid-succession
Climax
1.6
1.6
2.1
0.12
0.14
0.27
n= 5 to 10
n = 11 to 15
n = 16+
1.5
1.7
2.1
0.11
0.17
0.22
Trends in Plant Genetic Diversity
The data in the above tables shows that plants with a wide geographic range tend to be more
diverse than plants with narrow range, outcrossers are more diverse than selfers, perennials more
diverse than annuals, cross-fertilized more diverse than self fertilized, species with more
chromosomes are more diverse than species with fewer. While selfers are less diverse, they tend
to have more variation in their population structure (larger Gst value) than outcrossers. This
makes sense as their alleles do not disperse readily in pollen. The table shows trend and there are
many exceptions.
In addition, gymnosperms tend to be more diverse than monocots who are more diverse than
dicots. Species from boreal regions are more diverse than those from temperate regions who are
more diverse than those from tropical regions. Climax species are more diverse than species tha
first colonize a region. Again exceptions are plentiful.
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The population genetic concept of drift is very important in genetic resources. As populations
become smaller, alleles are lost (e.g the allele become extinct), inbreeding increases, genetic
uniformity increases, fitness decreases (generally fitness is greatest when inbreeding is the
lowest), ability to respond to new environments is reduced. While drift predicts allele extinction,
the concept is analogous to species extinction. Species with are more likely to become extinct
due to random events as population size decreases.
Ironically, while we strive to conserve biodiversity to improve agriculture, agriculture and its
accompanying habitat destruction and modification is the primary cause of the loss of
biodiversity.
Change in genetic diversity during domestication (from Chrispeels and Sadava, page 347)
Major Determinants of Genetic Diversity in Plant Populations
1. Physical environment (soil, water, light, temperature, atmosphere, etc): Genetic
differentiation often results when plant species are exposed to varying climates. The
divergence is clearly adaptive as plants display considerable local adaptation. Transplant
populations are often ½ as fit as native populations (Bradshaw, 1984: from Frankel et al.).
For example, biotypes from high altitudes in the tropics show considerable tolerance to high
UV radiation, while biotypes from low altitudes do not. One would predict that as UV
radiation increases (perhaps at 1.2% per year in alpine areas) with ozone depletion that the
tolerant species would be favored. Barley populations from high altitudes head later (grain
heads emerge from leaves later) and have more virus resistance than populations from low
altitudes
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The genetics of local adaptation are complex though some single genes are important. An
example would be single genes that modify flowering time and thus duration of life cycle.
Another is tolerance to high levels of copper in soils near mines. This topic will be dealt with
in more depth when we discuss adaptation and stress tolerance.
Populations exposed to more variable environments generally have more genetic variation
Examples from Tomato:
• ~75% of all resistance is from wild species (L. pennellii, L. peruvianum, L.
pimpinnellifolium, and others).
• Genes for high Beta-carotene from L. cheesmanii.
• Jointless pedicel for mechanical harvesting.
Examples from wheat:
• Powdery mildew resistance from Rye
• Increased biomass and yield? From Rye
• Leaf rust resistance from Aegilops elongatum
• Disease (Rust, scab, mildew), yield, and stress tolerance from Aegilops tauschii (D
genome donor)
Examples form Soybean:
• Resistance to Phytophthora root rot
• Resistance to cyst nematode
• Draught tolerance
Number of landraces used in rice, wheat and maize
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Human selection
Nature and people do not necessarily want the same phenotypes. Many features desired
by people are undesirable in nature. Nature strives to ensure reproduction over the array of
environments that will occur over long periods of time. Nature tends to produce a moderate
(middle) value for many traits, while people tend to want extremes. Yet natural populations
harbor the GV to produce many of the extreme phenotypes that people prefer. Plant populations
harbor this GV by having genetic and physiological homeostasis: genetic and metabolic systems
that resist disturbances.
Example of Crop Domestication: Tomato
The center of origin for tomato is Andean S. America, with ~10 species found on the
western coast from Columbia to Chile and extending to the Galapagos islands. When Europeans
arrived ~1523 the tomato had been domesticated in the region of modern Mexico. Note that this
is outside of the native distribution. It is believed the progenitor is the Peruvian Cherry tomato (L.
esculentum var. cerasiforme). The Spanish “explorers” introduced tomatoes to Europe.
Species
L. cheesmanii
Daylength Sowing
Preference Date
(Davis)*
short day
Mating
System
Nov - wk autogamous self
4
(SC)
July - wk
2
L. chmielewskii day neutral May - wk
2
L. chilense
Pollination # Plants / # Plants
Method
Gener.
per gal. pot
short day
allogamous mass sib
(SI)
facultative mass sib
(SC)
L. esculentum day neutral April - wk autogamous self
var. cerasiforme
2
(SC)
L. hirsutum
short day
2
50
5
50
5
6
(field)
3
facultative
(SC)
f. typicum
allogamous mass sib
(SI)
L. pennellii
10
July - wk
4
f. glabratum
L. parviflorum
Notes
self
or
facultative
day neutral May - wk autogamous self
2
(SC)
day neutral June - wk allogamous mass sib
1
(SI) or facult.
(SC)
Seed produced under
low light conditions is
of poor quality.
Forms edema on
leaves under high
humidity.
15
50
15
3
50
5
Use well-drained soil
and water sparingly.
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Species
Daylength Sowing
Preference Date
(Davis)*
Mating
System
Pollination # Plants / # Plants Notes
Method
Gener.
per gal. pot
L. peruvianum
mostly day June - wk allogamous mass sib
neutral
4
(SI) or
facultative
(SC)
50
5
day neutral April - wk autogamous self
2
(SC)
6
(field)
mostly short Feb - wk facultative
day
2
(SC)
50
5
f. glandulosum and
mountain races are
short day.
L.
pimpinellifolium
selfing pops:
outcrossing
pops:
mass sib
Regenerate in
greenhouse to limit
outcrossing.
Example of Crop Domestication: Wheat
Figure. Evolution of wheat. (from Chrispeels and Sadava, page 338)
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Figure. Geographical location of wheat domestication.
Figure. Spread of agriculture across Europe. It is estimated that agriculture spread at a rate of 1
to 5 km per year (0.62 to 3.1 miles per year) (Gepts, 2002)
Wheat in the US: Introduced from Europe by colonists
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Two species grown Triticum aestivum (common wheat, bread wheat) and Triticum turgidum
(durum wheat, pasta)
Early years: Varieties from other countries were brought to the US. Farmers grew them and
selected best. Often these varieties were quite heterogeneous such that farmers would
select superior plants from within a varietity, similar to early corn varieities.
1890s: crosses were made between wheat varieties, followed by inbreeding, line development,
and testing. These are called inbred varieties or pure lines.
1970s: Most varieties developed as described for 1890. Introductions also remain successful,
though most are products of breeding programs such a CIMMYT. There are also attempts
to produce hybrid wheat where the hybrid seed is sold to farmers, just like in corn.
Hybrids yield very well but seed is expensive. Most breeding performed by public
breeders. Establishment of Plant Variety Protection allows private companies to develop
varieties.
Present: Most US varieties are inbred, pure line, varieties. Very few hybrid varieties. Greater
than ½ of the acreage is planted to public varieties, private investment is substantial, but
still very low compared to corn or soybean.
Figure. Yield change in wheat
Changes associated with wheat yield improvement
• Reduced height, especially during green revolution
• Increased harvest index (greater proportion of dry matter in seeds vs vegetative parts)
• Some recent improvement in total biomass
• More uniform grain filling, more kernels
• Longer GFP
• Greater N utilization efficiency
• Adaptation to greater planting densities
Common traits selected for during domestication (Domestication Syndrome)
• Larger plant size
• Larger seeds
• Rapid and uniform germination (low dorminancy of seed/tubers, less growth inhibitors,
permeable seed coats)
• Non-shattering
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•
•
•
•
•
•
•
•
•
•
•
•
Unusual colors and forms
Loss of defensive structures (thorns, spines, hairs, etc)
No seeds (ornamentals)
Taste, digestibility, reduced toxins
Increased self pollination (fixes desirable genotypes in seed propagated crops)
Annual growth (less energy in roots, more to seeds)
Determinate, uniform flowering time
More seeds, better seed set
Seedling vigor
Reduced woodiness
Less branching, less vining
Increased ploidy in vegetatively propagated crops
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Examples of changes between domesticated and wild species resulting from selection (clockwise
from upper left: seed dormancy, seed size, branching, and seed dispersal) (from Chrispeels and
Sadava, pages 332, 343, 344) (seed size from UASD-ARS Agricultural Research, February, 2003 vol 51, page 13).
Interestingly, many of the traits that comprise the “domestication syndrome” are recessive
genes, indicating that they are mutations that produce a loss of function. In addition, many are
also deleterious in the wild. Indeed, many domesticate crop species would not survive in the wild
due to being non-competitive with their wild relatives or poor seed dispersal (Gepts, 2002. Thus,
the traits we selected for during domestication are mostly conferred by deleterious recessive
alleles in nature. As such, they would occur at very low frequency in natural population (see first
selection equation for ∆q). But as we have seen, they would remain in the population if it is
reasonably large.
It appears that the transition from wild species to domesticate type took perhaps 1000 years.
Some traits may have been nearly fixed in perhaps 200 years. There is even evidence to suggest
some of the breeding bottlenecks could have occurred in only 10 generations. Given the types of
traits selected for and our understanding of the genetics of these traits today, domestication would
have failed only if there was high outcrossing rates and high migration rates (bring wild type
alleles into the newly selected populations (Gepts, 2002).
Acknowledgements:
Thanks to Clay Sneller
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