I. INTRODUCTION TO CROP EVOLUTION AND … › hcs625 › 625CropEvo.pdfVg in a natural population...

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1 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 CC Cc cc Individual’s relative fitness 1 1 1-s Frequency p 2 2pq q 2 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 0 q 1 q 2 s 1 q 2 sp = = q where q 0 is the frequency of “c” in the population prior to selection and q 1 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: q 1 = q 0 + q = q 0 + sp q 1 sq 2 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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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 CC Cc cc Individual’s relative fitness 1 1 1-s Frequency p2 2pq q2 The variable “s” is the selection differential and for this model is equal to:

s = 1 - Average number of progeny from "cc" genotypesAverage 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?

q0q1q2s1

q2sp−=

−=∆q

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:

q1 = q0 + ∆q = q0 + −−sp q

1 sq

2

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

0.00

0.05

0.10

0.15

0.20

0.25

0.30

0.35

0.40

0.45

0.50

0 2 4 6 8 10 12 14 16 18 20 22 24

Generation of Selection

Freq

uenc

y of

"c"

Alle

le

s = 1

s = 0.75

s = 0.50

s = 0.25

s = 0.01

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 10-100x 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. Center Mesoamerica S.

America China SE Asia Near East Africa

Cereals Maize Rice, millets

Rice Wheat, barley, rye, oat

Sorghum, rice, millet

Grain legumes

Common bean

Common bean

Soybean, adzuki bean

Pidgeon pea

Pea, chickea, lentil

Cowpea

Roots/Tubers Sweet potato Potato, cassva

Turnip, yam

Yam, taro Turnip, carrot, radish

Yam

Oil crop Cotton Peanut, cotton

Rape seed, soybean

Coconut Rapeseed, safflower, flax, olive

Oil plam, castor bean

Fiber Cotton, agave

Cotton Coconut Kenaf

Fruits Papaya Pineapple Peach, apricot

Orange, lime, banana

Fig, grape, apple, pear, plum

Watermelon, melon

Vegetable Squash Pepper cabbage Cucumber, eggplant

Onion, lettuce

Okra

Stimulants Cacao Coca Tea Poppy 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 co-evolved, 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

∑−= pih 21

Table. Example of A and h for two populations using frequency of flower color alleles

Flower color allele Population 1 Population 2

White 0.05 0.5 Purple 0.05 0.5 Yellow 0.90 0

A 3 2 h 0.185 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)).

Within species Within population Category A h A h Gst Mating system Self pollinator 1.69 0.12 1.31 0.07 0.51 Outcrosser 2.4 0.16 1.80 0.15 0.10 Range

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Endemic 1.80 0.10 1.39 0.06 0.25 Wide 2.29 0.20 1.72 0.16 0.21 Life Form Annual 2.07 0.16 1.48 0.11 0.36 Long-lived 2.19 0.18 1.79 0.15 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 A h Gymnosperms 2.1 0.27 Dicots 1.5 0.11 Monocots 2.1 0.16 Annual 1.7 0.13 Biennial 1.3 0.06 Long-lived perrenial

2.0 0.27

Self fertilized 1.3 0.06 Mixed fertilized 1.8 0.18 Cross fertilized 1.8 0.18 Colonizer 1.6 0.12 Mid-succession 1.6 0.14 Climax 2.1 0.27 n= 5 to 10 1.5 0.11 n = 11 to 15 1.7 0.17 n = 16+ 2.1 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 Daylength Preference

Sowing Date (Davis)* Mating

System

Pollination Method

# Plants / Gener.

# Plants per gal. pot

Notes

L. cheesmanii short day Nov - wk 4

autogamous (SC)

self 10 2 Seed produced under low light conditions is of poor quality.

L. chilense short day July - wk 2

allogamous (SI)

mass sib 50 5

L. chmielewskii day neutral May - wk 2

facultative (SC)

mass sib 50 5

L. esculentum var. cerasiforme

day neutral April - wk 2

autogamous (SC)

self 6 (field)

L. hirsutum

f. glabratum facultative

(SC) self 15

f. typicum allogamous

(SI) mass sib 50

short day July - wk 4

or facultative

3 Forms edema on leaves under high humidity.

L. parviflorum day neutral May - wk 2

autogamous (SC)

self 15 3

L. pennellii day neutral June - wk 1

allogamous (SI) or facult. (SC)

mass sib 50 5 Use well-drained soil and water sparingly.

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Species Daylength Preference

Sowing Date (Davis)*

Mating System

Pollination Method

# Plants / Gener.

# Plants per gal. pot

Notes

L. peruvianum mostly day neutral

June - wk 4

allogamous (SI) or facultative (SC)

mass sib 50 5 f. glandulosum and mountain races are short day.

L. pimpinellifolium

selfing pops: day neutral April - wk

2 autogamous (SC)

self 6 (field)

outcrossing pops:

mostly short day

Feb - wk 2

facultative (SC)

mass sib 50 5 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