Week 1 (Unit 2)

Genetics, Evolution, & Selection

Basic genetic concepts
Origin of genetic diversity
Darwin, natural selection, evolution
Morphological and genetic changes during domestication
Assignments
References

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Basic Genetic Concepts

Crops are plants that are grown and utilized for economic gain. In order to understand the diversity among crop species, and how they were domesticated and improved through breeding, we need to know how important characteristics are transmitted from one generation to the next. In the first part of this lecture we will review some basic concepts in Genetics, which is the study of inheritance and variation among organisms.

This course was developed by plant breeders, who tend to throw genetic terms around without even realizing it. Since this is a Baccalaureate-Core course, we expect to have students with diverse backgrounds. If it's been a while since you took biology, we hope this review will help. If this is all old hat, then you can skip ahead to the next section on the Origin of Genetic Diversity.

Review of genetic terms

(also see the glossary on the 'Resources' menu)

Gene - The fundamental physical and functional unit of heredity, which carries information from one generation to the next.

Locus - a specific place on a chromosome where a gene is located.

Allele - one of the different forms of a gene that can exist at a single locus. The form of the gene is determined by its DNA sequence. When an individual has different forms of an allele at a locus, it is a heterozygote. When its alleles are the same, it is a homozygote.

Central dogma of biology - DNA from alleles at a genetic locus is transcribed into RNA, which in turn is translated into proteins. Structural proteins are used to construct the cells, and enzymatic proteins provide the basis for cellular machinery.

There are many excellent resources available that provide basic information about DNA structure and function. Here are a few:

DNA, RNA and Heredity: Genetic Code [http://members.aol.com/Bio50/LecNotes/lecnot07.html]
DNA and Heredity: Transcription and Translation [http://members.aol.com/Bio50/LecNotes/lecnot08.html]

You could also use Kimball's Biology Pages [http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html] to find the following key words:

Genotype - The sum total of all the alleles at all the loci in an organism. Considered as a measure of ‘breeding value’ for evolution and crop improvement efforts. The term is also used to refer to the specific alleles that an individual possesses at a particular locus. One allele comes from the male parent, and one from the female parent.

Phenotype - The external and observable expression of the genes, and the result of genes interacting with the environment. The appearance of individuals.

Phenotype (P) = Genotype (G) + Environment (E) + (GXE)

An individual's phenotype can be viewed as the sum of the effects due to genes, the effects of the environment, and interactions between the genes and the environment (GXE).

Heritability - The proportion of total phenotypic variance at the population level that is contributed by genetic variance. If a trait is largely determined by environmental factors, then the heritability will be low. Traits that are largely controlled by genes have a high heritability and consequently are more likely to change in response to selection.

In higher plants, chromosomes occur in cells in homologous pairs. Members of a pair contain the same loci, but may have different alleles at any given locus. One chromosome from each pair came from the male parent, and one from the female parent. Each plant species has a characteristic number of chromosomes in its cells.

Genome - The entire complement of genetic material in a chromosome set. The number of chromosomes in one nuclear genome is designated 'n', which is equivalent to the haploid number.

Diploid species have one set of homologous chromosome pairs, so their total number of chromosomes is 2n. Some species are polyploid which means that they have multiple sets of n chromosomes (triploids are 3n, tetraploids are 4n, etc.).

Mitosis and Meiosis

When cells undergo mitosis, the chromosomes in the cell nucleus are replicated. The cell divides, and each daughter cell contains a complete copy of the genes from the parent cell. All of the daughter cells are identical to each other and to the parent cell.

During meiosis, chromosome replication is followed by two successive nuclear divisions. A single diploid (2n) cell produces four haploid (n) cells (gametes). Homologous chromosomes pair and segregate so that each daughter cell receives a single copy of each chromosome. The daughter cells all have the same loci, but may receive different combinations of alleles. Meiosis occurs only in specialized sex cells. When a male and female gamete unite, the diploid number is restored. New individuals are formed through the sexual process.

Mendel's Laws

Gregor Johann Mendel was an Austrian monk who experimented with crosses of garden peas in the 1850's. He studied seven characteristics and observed the ratios of phenotypes among progeny in the F1 (the hybrid from the cross) and F2 generations. Peas are normally self-pollinating, so the F2 generation was obtained by harvesting the seeds produced by the hybrid plants. For each characteristic, he observed that the F1 hybrids were all identical to each other and that they resembled the parent with the dominant phenotype. In the F2 generation, the progeny segregated in a ratio of 3:1. Three-quarters of the progeny had the dominant phenotype and one-quarter had the recessive phenotype.

Mendel was the first person to realize that the units of heredity are discrete rather than a blend of characteristics from the parents. For the cross between peas with yellow and green seed color, he designated the dominant allele for yellow seeds with a 'Y' and the recessive allele for green seeds with a 'y'. He represented the crosses he made as follows:

Because these gametes combine at random, the expected ratios in the F2 generation are:

¼ YY (pure-breeding yellow) ½ Yy (hybrid yellow) ¼ yy (pure-breeding green)

The genotypic ratio is 1:2:1 and the phenotypic ratio is 3 yellow: 1 green.

For some characteristics, the F1 hybrid will have a phenotype that is intermediate between the two parents. If this trait is controlled by a single gene, then it is said to show incomplete dominance. An example is the four-o'clock plant. The two homozygotes have red and white flowers, but the heterozygote is pink.

Law of Segregation - segregation refers to the separation of alleles at the same locus during meiosis. Mendel showed that each gamete has a 50% chance of receiving a particular allele from its parent cell.

Mendel also observed the frequencies of phenotypes in progeny from dihybrid crosses, where parents differ for two characteristics.

If these four gamete types are intermated at random, then the expected ratios in the F2 are:

 
                1 RRYY (round, yellow)
                2 RRYy (round, yellow)
                1 RRyy (round, green)
                2 RrYY (round, yellow)
                4 RrYy (round, yellow)
                2 Rryy (round, green)
                1 rrYY (wrinkled, yellow)
                2 rrYy (wrinkled, yellow)
                1 rryy (wrinkled, green)
				  
               The phenotypic ratio is 9:3:3:1.

Law of Independent Assortment - segregation of alleles at one locus occurs independently from segregation at another locus. In the example above, the RY and ry gametes are parental types and Ry and rY are nonparental types. If there is independent assortment, then the F1 will produce parental and nonparental gametes in equal frequency.

Exceptions to Mendel's Laws

If two loci occur close together on a chromosome then they are linked, and parental gametes will be more prevalent than nonparental gametes. In order to obtain nonparental gametes from the F1, a crossover between the loci must occur when homologous chromosomes are paired during meiosis. The frequency of recombination (crossing over) is used to estimate the distance between loci on a chromosome. Loci that are at least 50 centimorgans apart assort independently, even though they are on the same chromosome.

When genes are very tightly linked, the frequency of recombination is extremely rare. One might have to grow thousands of offspring to obtain a single recombinant genotype. In this case it might be difficult to determine experimentally if the two traits are controlled by the same gene (pleiotropy) or if they are controlled by tightly linked genes.

Qualitative vs Quantitative characters

So far, we have been talking about qualitative traits, for which the phenotypes can be classified into discrete categories (smooth vs wrinkled; yellow vs green, etc.). For most traits of interest to plant breeders and crop producers, variation occurs on a continuous scale. Examples of quantitative traits include plant height and yield. In general, qualitative traits are controlled by one or a few genes with major effects, whereas quantitative traits are controlled by many genes with small effects (polygenes). Quantitative traits tend to be more influenced by environmental conditions.

Expression of quantitative characters can be understood as an extension of Mendel's Laws for simply inherited traits. Let's consider a situation where a trait is controlled by one gene with incomplete dominance. Assume that an 'aa' individual has a value of 10, and having the favorable allele 'A' increases the trait by 10 units. In a sample of 100 F2 progeny, we would expect a 1:2:1 ratio of phenotypes, as shown in Figure 3. If we assume that there are two genes controlling the trait, and that having a favorable 'A' or 'B' allele adds a value of +5 to the phenotype, we would have 6 different classes of F2 progeny. It is not hard to imagine, that with a few more genes and some environmental influence, the histogram would be begin to resemble a bell-shaped curve. Quantitative traits typically have a normal distribution of phenotypes.

Populations

A population is a community of individuals that share a common gene pool. It is 'a breeding group' of individuals that may intermate. The genetic constitution of a population is described by the array of gene frequencies and alleles that are present at each locus.

In studying the genetics of a population, we are concerned with transmission of genes from one generation to the next. During transmission, genotypes of the parents are broken down, genes transmitted in the form of gametes, and new sets of genotypes are created in the progeny. Genes have continuity from generation to generation, but the genotypes in which they appear do not.

Origin of Genetic Diversity

We have already described how sexual reproduction allows genes to be reshuffled into new combinations in each generation. However, if meiosis, crossing over, and intermating were the only sources of genetic diversity, there would be no directional change in populations over time. Gene frequencies would remain constant and evolution could not occur.

In the next sections, we will consider the fundamental bases for genetic diversity:

Mutation
Migration
Genetic drift
Selection

Mutation

Mutation is an important source of genetic variability that is critical for evolution. Mutations can be classified as beneficial, harmful, or neutral. Harmful mutations are eliminated through selection if they reduce the fitness of an individual. Neutral alleles are neither beneficial nor detrimental to an individual. If the environment changes, a neutral allele or a new mutant allele may be favored and eventually become the dominant allele in that population. If a mutation is beneficial to the species as a whole, migration must occur for it to spread to other populations of the species.

Mutations can occur by

Point mutation - changes in a single nucleotide
Small insertions or deletions of the nucleotide sequence
Whole genes or blocks of genes could be duplicated

A mutation may be transparent (resemble an allele already in the population). Alternatively, it could generate an entirely new allele. Most of these mutations will be detrimental and lost.

Gene duplication favors and facilitates mutational events. The duplicated gene can undergo mutations to generate a new gene that has a similar, but a slightly modified function for the organism. The original gene maintains the function that was adaptive in the initial environment. This type of evolution generates multigene families (Examples: gluten proteins and other seed storage genes, photosynthetic genes in plants).

Types of mutations

Chromosomal Mutations - Large sections of chromosomes can be altered or shifted, leading to changes in the way the genes on them are expressed.

Translocations - involve the interchange of large segments of DNA between two different chromosomes.
- Expression of a gene at the translocation breakpoint may change - it might lose function or it might be reattached to a new promoter region, which would change the way that it is regulated.
- Translocations may create linkage blocks of genes and reduce recombination within the block.

Inversions - Occur when a region of DNA flips its orientation with respect to the rest of the chromosome. This can lead to the same problems as translocations.

Deletions - Large regions of a chromosome are deleted. This can lead to a loss of important genes.

Nondisjunction - Sometimes chromosomes do not segregate properly during cell division, especially if large segments are rearranged. One of the daughter cells will end up with more or less than its share of DNA.

Point mutations - single base pair changes.

Nonsense mutation - creates a stop codon (i.e. UAA, UGA, or UGG) where none previously existed. This shortens the resulting protein, possibly removing essential regions.

Missense mutation - changes the code of the mRNA. If an AGU is changed to an AGA, the protein will have the amino acid arginine where a serine was meant to go. This might alter the shape or properties of the protein.

Silent mutation - has no effect on protein sequence. If an AGU were changed to an AGC, the protein would still have the appropriate serine at that position.

Frame shift mutation- a deletion or insertion of a single nucleotide, a nucleotide pair, or any other group of nucleotides not divisible by three. Causes a shift in the reading frame used for translation.

How and why do mutations occur?

Mutations may result from errors in cellular replication. They can be induced by radiation, chemicals, or even stress.

The frequency of naturally occurring mutations due to errors in DNA replication and repair is estimated to be approximately 1 in 10⁷ to 10⁸ (1 in 100 million based on bacterial studies). Mutation events that have a positive influence on fitness or survival are extremely rare.

Transposons

Transposons are mobile genetic elements that can move in and out of chromosomes, which can alter gene expression. These mutations are inherently unstable. Changes in somatic cells may occur over the lifespan of an organism, creating a variagated pattern due to activation and deactivation of particular genes. Transposons have been found in all organisms studied to date, and thus are an important force for generating diversity as a basis for evolution.

For more information, see the lecture notes on Transposable Genetic Elements by Phillip E. McClean at North Dakota State University.

Migration

Migration involves the movement of individuals, or their seeds or propagules (any plant part that can be used for reproduction) to a new area. Migration will change gene frequencies by bringing in more copies of alleles already in the population or by bringing in new alleles that have arisen by mutation. In order for this to occur, an exotic plant must mate successfully with members of the indigenous population. The term that is used to described this introduction of new alleles is
gene flow.

The effects of migration are to:

increase variability within a population
prevent a population of that species from diverging to the extent that it becomes a new species.

Genetic Drift

When a population becomes very small, some alleles may be lost due to chance. Genes that are neutral (impart no selective advantage) are particularly subject to genetic drift. These changes will accumulate over time. Genetic drift can lead to evolutionary changes in a population, but it does not necessarily improve fitness. Genetic drift is aimless, not adaptive.

Darwin, Natural Selection & Evolution

Charles Darwin published his book "The Origin of Species" in 1859. He presented two major arguments:

The theory of evolution - all species alive today are descendants from earlier species. Life is continually changing.
The mechanism of evolution is natural selection or survival of the fittest. Changes occur gradually over time.

His findings generated a storm of criticism, some of which continues to the present. The concept of evolution was disturbing to people because it seemed to contradict the literal interpretation of the story of creation in the Bible, and because it implied that humans had evolved from some apelike ancestor. From a scientific standpoint, Darwin's ideas ran counter to the prevailing paradigm of fixed species that had been proposed by Carolus Linnaeus in the 1700's. Today, the question we ask is not so much whether evolution occurs, but how does it occur?

Natural Selection

Living things produce more offspring than the finite resources available to them can support, so they face a constant struggle for existence. The individuals in a population vary in their phenotypes, and some of that variation is due to genetic differences. Fitness is the relative ability of an individual to survive and transmit its genes to the next generation. A population undergoes selection when certain alleles are found at greater frequency in a new generation because they imparted greater fitness to the parent. The forces of natural selection act on phenotypes but evolution occurs only if there is a change in the genotypes in a population.

There are several ways that fitness can be achieved:

Survival or mortality selection - ability to survive to a reproductive age
Mating success or sexual selection - in plants, for example, this could refer to the likelihood that a female flower will receive male pollen
Family size or fecundity selection - number of offspring produced.

Evolution involves two related phenomena:

Adaptation - refers to genetically determined characteristics that enhance an individual's ability to cope with its environment.
Speciation - a single species can give rise to two or more descendant species when isolated by geography or ecologically divergent space.

Evolution may be caused by a 'lack of fit' between a population and its environment. A species evolves when gene frequencies change and the species moves to a higher level of adaptation for a specific ecological niche.

If environmental conditions are constant for a long period of time, a population may reach equilibrium, where optimum fitness is attained and there is little change in gene frequencies from one generation to the next.

Changes in environment may result in ‘lack of fit’ of a static population. Many factors, biotic and abiotic, can act to change fitness. The maintenance of adaptation requires that natural selection operate constantly in every generation to maintain the fit of a population to its environment.

The classic example of natural selection is 'industrial melanism' of the peppered moth in England. Prior to the industrialization of central England, the light-colored moths would hide on the white-barked trees and avoid bird predation. Pollution generated by the new industries stained the light-colored trees dark. A black mutant was first observed in Manchester in 1849. Moths that carried that allele could camouflage themselves on the stained trees and avoid being eaten by their bird predators. Within a century, this black form had increased to 90% of the population in this region. Clearly the population had evolved to a higher adaptive condition, in response to a change in the environment. With pollution controls put in place since WWII, the frequency of white colored moths has increased once again.

The effects of selection on populations

Directional selection

When one extreme of a population is favored over another, selection will tend to move the mean of the population in that direction. Changes may be small between one generation and the next, but will accumulate over time. Examples include traits such as yield, fertility, stress tolerance, and disease tolerance.

Stabilizing selection

Natural selection often works to weed out individuals with extreme phenotypes. Stabilizing selection reduces variation in a population and favors individuals with an average phenotype over the extremes. This mode of selection is often referred to as optimizing selection. Examples in plants include maturity, seed size, and plant height.

Disruptive Selection

Disruptive selection acts against the individuals in the middle of the range of phenotypes and tends to favor individuals in the extremes. In the long term, disruptive selection can create two distinct gene pools from a single gene pool. Such a force is required for the origin of new species.

Response to selection

Heritability (h²) measures how well offspring resemble their parents, or the amount of additive genetic variance (σ_A²) as a proportion of the total variance among phenotypes (σ_P²):

The selection differential is an indicator of selection intensity:

s = mean after selection – mean before selection

If expression of a trait is due to a large number of polygenic loci, then Response to selection is a function of both the heritability of a trait (i.e., additive genetic variance) and the strength of selection on the trait (selection differential).

Response = h² x s

With either low heritability or weak selection, response to selection is slow. Conversely, with a high heritability and high selection pressure, response to selection will be rapid.

Artificial selection

Modern food crops would not have evolved under ‘natural conditions or processes’ without man’s selection and interference. The process of domestication has led to striking changes in morphological traits of plants. This is continuing through modern plant breeding.

Plant breeding is a means by which artificial selection is imposed on plant populations to change morphological traits, increase tolerance to biotic and abiotic stress, and improve agronomic performance.

Speciation

A species is a group of organisms that are capable of interbreeding freely with each other. They do not interbreed with other species even when they have the opportunity (or if they do mate the offspring are sterile).

How do new species originate? What is the mechanism? There are two theories proposed:

Phyletic gradualism - change due to natural selection is gradual and progressive (Darwin's view)
Punctuated equilibrium - sudden changes punctuate long periods of little change. (Gould and Eldridge). Small, isolated populations may evolve more rapidly.

The formation of two or more species often requires geographical isolation of subpopulations of the species. Only then can natural selection or perhaps genetic drift produce distinctive gene pools.

In general, a stimulus like an environmental change causes the evolution into a new species. The organism must either:

Adapt to changing conditions if possible
Survive by changing habits or migrating into another area
Go extinct.

Morphological and Genetic Changes During Domestication

In the "Origin of Species", Darwin used domesticated plants and animals as evidence to support his theory of evolution:

"Domesticated races show adaptation, not indeed to the animal's or plant's own good, but to man's use or fancy."

"Very many of the most strongly-marked domestic varieties could not possibly live in a wild state."

Gigantism of harvested organs: e.g., seeds of domesticated plants.

Artificial selection has created tremendous diversity within crop species for the parts of the plant that have economic value (flowers, leaves, pods, or tubers). In comparison, there is little variation within species for parts of the plant that are not of interest to man.

The process of plant domestication occurs as early wild-type crops are sown from seed gathered from wild stands. The key to domestication is the selective advantage of rare mutant alleles, which are necessary for survival in cultivation, but unnecessary for survival in the wild. The process of selection continues until the mutant phenotype dominates the population.

Cultivation also creates selection pressure, resulting in allele frequency changes, gradations within and between species, fixation of major genes, and improvement of quantitative traits.

Early domestication and important plant traits

	Seeds from domestic crops (inner circle) are usually larger, lighter in color, and more uniform than their wild relatives. Clockwise from top: Peanuts, corn, rice, coffee, soybean, hops, pistachio, and sorghum.
Photo by Stephen Ausmus, USDA

Selection associated with cultivation, harvesting, and food uses

Loss of seed dispersal mechanisms and seed dormancy traits are most important in the domestication process.

Non-shattering - crop seeds remain attached to the plant until harvest
Non-brittle rachis - the rachis (central axis of the inflorescence) remains intact in crop species
Non-dehiscence - fruits do not split open to release contents at maturity
Free threshing

Changes in growth habit

Compact growth habit
Reduction in branching
Synchronous tillering
Synchronous flowering

Example: climbing to bush habit in beans

In the wild, a climbing habit allows plants to access limited light. More compact plants are often favored by domestication.

Reduction in internode length
Reduction in number of nodes, branches
Suppression of twining reponse
Determinacy (simultaneous flowering)

Harvesting: Increases in seed yield

Reduction in daylength sensitivity - provides broader adaptation (plants will flower at wider latitudes); there is an adaptive value for daylength sensitivity in wild plants (ensures that they germinate at the right time of the year)
Increased number of seeds
Reduced sterility
Larger inflorescence size
Increased number of inflorescences
Increased harvest index (weight of harvested portion of the plant to the weight of the whole plant)

Planting: increased seedling vigor

Larger seeds
- More carbohydrates; increased reserves
- Fewer number, larger seeds
Non-dormant seeds
- Dormancy has an adaptive value for the wild type, ensuring that it germinates when environmental conditions are most favorable (e.g. there is enough water or temperatures are stable.) However, it is not a desirable character for a crop. A farmer wants the seeds that he plants to germinate quickly and uniformly throughout the field.
- Conflict – lack of dormancy may cause premature germination (e.g. sprouting of a cereal head before harvest)
- Correlated response: reduced chaff

Reproductive system

Shift from outcrossing to predominantly self-pollination for many crops
Reduced or absence of sexual reproduction in some crops - banana, plantain, navel orange
Vegetatively propagated crops - instant domestication, because the selected plants can be reproduced without further changes occuring through meiosis

Adaptation for taste and food utilization

Color, flavor, texture, storage quality, cooking quality, uniformity, etc.

Reduced toxic compounds
- Cyanogenic glucoside: cassava and lima bean
- Bitterness; phenols, etc., in wild seeds and plants
Processing and cooking quality
- Selection for starch, protein and oils

Genetic control of domestication is relatively simple:

There are few genes and genomic regions involved
Several genes have major phenotypic effects
Genes for domestication represent a small subset of genes/traits for that species
Domestication could occur quite rapidly
In some cases only a limited amount of the available genetic diversity is carried through the domestication process - wild relatives represent an important reservoir of genetic diversity for the crop

Collectively, the changes that frequently occur with domestication are known as "the domestication syndrome".

Attributes of Domesticated Plants vs Wild Relatives

Attribute	Wild/Weedy Relative	Domesticate
Ecogeographical distribution and microenvironmental niche	Sometimes restricted, may be intolerant of periodically disturbed soils. Many exceptions known (Avena, Sorghum).	For major crops, often rather more widespread than wild relative, adapted to survival under cultivation
Dispersal mechanism	Usually present (shattering)	Often absent
"Domesticated" organ	Often smaller, fewer, and more uniform	Often larger, more numerous and more highly variable; attractive patterns and colors; better processing quality
Defense mechanism	Better-developed (spines, thorns, anti-nutritional factors)	Reduced or absent
Growth pattern	In herbs, often indeterminate and resource-limited	In herbs, often determinate; less branching
Maturity	Irregular	Uniform; shorter life cycle
Seed and seedling	Often smaller, dormancy mechanism well developed	Often larger, dormancy mechanism absent (e.g. photoperiod and vernalization requirements)
Sexual reproduction	Present	Mechanisms may be lost
Breeding systems	Often more allogamous (outcrossing)	More autogamous (self-pollinating)

Assignment

Quiz

Take the quiz on this Unit on the Blackboard.

Optional assignment

On the discussion board, suggest a book related to the material in this course that you think would be of interest to you and other students. Let us know how you learned about the book and why you think it would be relevant.

References

Falconer, D.S. and T.F.C. Mackay. 1996 Introduction to quantitative genetics, 4th edition. Longman, Essex, England.

Gepts, P. 2002. Who's Who in the History of Crop Evolution Studies.
http://www.agronomy.ucdavis.edu/gepts/pb143/lec02/pb143l02.htm

Gepts, P. 2002. What is a crop? The domestication syndrome. http://www.agronomy.ucdavis.edu/gepts/pb143/lec08/pb143l08.htm

Kimball, J.W. 2003. Kimball's Biology Pages. Evolution and Adaptation.
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/E/Evolution.html

Kimball, J.W. 2003. Kimball's Biology Pages. Speciation. http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/S/Speciation.html

Levetin, E. and K. McMahon. 2005. Genetics. Chapter 7 in Plants and Society, 4th edition. McGraw-Hill, New York, NY. Additional on-line notes and references:
http://highered.mcgraw-hill.com/sites/0072528427/student_view0/chapter7/chapter_outline.html

McClean, P.E. 2004. On-line lecture note for Intermediate Genetics course.
http://www.ndsu.nodak.edu/instruct/mcclean/plsc431/431g.htm

Online Library of Literature. 2002.
http://www.literature.org/authors/darwin-charles/the-origin-of-species/