Genetic resources – Classification, Diversity, Manipulation, and Preservation

Learning Objectives

Understand the scientific system used to classify and name plants.

Understand the necessity of maintaining genetic diversity in natural ecosystems, domesticated plant species, and crop systems.

Understand the concepts of natural selection, plant breeding, and genetic engineering.

Plant Scientific Classification

Plant Taxonomy

Classification and scientific naming of plants based on their relationships.

Originally based on similar physical characteristics, especially flowers.

Now, more and more based on evolutionary relationships based on DNA analysis.

Carl Linneaus: botanist credited with “fathering” the discipline of taxonomy. The “L” after many scientific names refers to Linneaus who was the first one to classify them.

Taxonomic groups or taxa used in H&CS 200:

Domain, Kingdom, Phylum/Division, Class, Order, Family, Genus, Species

Classification System

To avoid confusion and to allow for clear communication across all languages, a rigid naming system has been created called Binomial Nomenclature or scientific name.

Regardless of the native language of an area, the scientific name of a species is the same everywhere.

Okra’s classification is used as the example

Domain: eukarotesKingdom: Plantae

Phylum/Division: AnthophytaClass: Dicotyledones

Order: MalvalesFamily: Malvaceae

Genus: AbelmoschusSpecific Epithet: esculentus

(Species: Abelmoschus esculentus)

Protocol for Binomial Nomenclature

Genus specific epithet common name

Acer rubrum red maple or Acer rubrum

Zea mays corn or Zea mays

Always capitalize the genus, always underline or italicize the genus and specific epithet

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Kingdoms connection to plants

Archaebacteria Not applicable (found in hot, thermal springs and ocean vents)Eubacteria plant diseases, beneficialsProtista algae in/on soilFungi plant diseases, beneficialsPlantae crop plants and weedsAnimalia pests/herbivores/pollinators

The 12 Plant Phyla and economic importance

Seedless plants species type and economic importance

Hepatophyta 6000 liverworts: weeds in plant nurseryAnthocerophyta 100 hornwortsBryophyta 9500 mosses: lawn weeds and sphagnum (peat)Psilophyta 15 whisk ferns: greenhouse weedsLycophyta 1000 clubmosses: a few ornamentalsSphenophyta 16 horsetails: weedsPterophyta 11000 ferns: ornamentals and some weeds

Seed species type and economic importance

Coniferophyta 560 conifers: forest and ornamentalCycadophyta 140 cycads: tropical/indoor ornamentalGinkgophyta 1 maidenhair tree: ornamentalPsilophyta 15 whisk ferns: greenhouse weedsGnetophyta 70 Ephedra, etc.: medicinalAnthophyta 23500 flowering plants: crops, weeds, etc.

Often, the plants used by humans are categorized by their Class: monocotyledones or dicotyledones

The monocotyledones (monocots) have one cotyledon, dicotyledones (dicots) have two. There are other differences, but cotyledon number is easiest to see.

Cotyledons are the ‘leaves’ that are in the seed that provide the seedling with nourishment until it has time to develop it’s true leaves.

General anatomical differences between monocot and dicot species

Source: biologie.uni-hamburg.de

Many of the other differences are biochemical or physiological. We can use these differences to our advantage in crop growing, especially in weed control.

80% of world’s calorie intake comes from these 6 crops

Monocots: corn (Zea mays), rice (Oryza sativa), wheat (Triticum aestiva)2

Dicots: white potatoes (Solanum tuberosum),sweet potatoes (Ipomea batatas), cassava (Manihot esculentum).

Poaceae are the grasses Fabaceae are the beans

Families and species of forage crops.

Older literature usually refers to some families by their old name, but the new name is the correct version.

Families: Correct Name Old Name common family nameAsteraceae Compositae asterBrassicaceae Cruciferae cabbagePoaceae Graminae grassLamiaceae Labiatae mintFabaceae Leguminosae beanArecacaceae Palmae palmApiaceae Umbelliferae carrot

Only a very small number of species are grown as food crops or have other economic importance. Of the 235,000 flowering plant species, <6,000 are economically important. Ecologically, though, they are all important.

Although we would like to increase the diversity of crops, especially food crops, the difficulty with increasing diversity is that most crops suitable for food crops are tropical and cannot be grown in temperate climates.

Of the 10,000 species native to North America very few have been developed as food crops. However, there are several ornamental crops that are North American species. Switchgrass and asters are two of the many native North American species that were developed as ornamentals by

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the Europeans and reintroduced to the U.S. Switchgrass is now being considered as a possible biofuel source too. Many ornamental trees are native to North America.

Principles of diversity genetics, selection, and breeding as applied to the cultivvation of plants.

The stability of natural ecosystems depends on it having several different species.

Healthy and unhealthy ecosystems can be identified by the amount of diversity and the types of species present.

The stability of natural ecosystems depends on it having several different species and variability within species.

Over the years, the genetic variability in crop ecosystems and species has diminished as breeders selected or bred for specific, desirable traits.

Only those plants exhibited those traits were kept, others were destroyed along with all the genetic information they carried.

For the past few decades a concerted effort has been underway to preserve seemingly unimportant genes that are carried in wild relatives of crop species.

Review of the principles of cell division and heredity:

Cell division:

New cells carry same genetic information as parent cell

and have the same number of chromosomes (2n).

New cells carry only half as much genetic

information and chromosome number (1n) from parent cell.

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Crossing over can create changes in chromosome DNA,

even in homozygous pairs.

Terms and concepts that are commonly used in

genetics

Terms and concepts that are commonly used in genetics.

Homozygous – the genes for a trait are the same on paired chromosomes Heterozygous – the genes for a trait are different on each chromosome in a pair.

Alleles – the different genes that can be found in the same location on a chromosome.

Genotype – the genetic information in an individual

Phenotype – the characteristics of an individual as the result of gene expression and environment interactions.

Dominant – the gene that is expressed in a heterozygous situation.

Recessive – a gene that is only expressed when that gene is homozygous.

Genetics of crossing two parents that are homozygous but

for different traits. The F1 generation is all the same in appearance (phenotype) but the genotype

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is heterozygous resulting in differences in eggs and pollen. Y(y) refers to color, G(g) refers to smooth or hairy surface. The capital letter refers to the dominant trait.

Variability that comes from crossing two siblings from the

same F1 generation. The phenotype number refers to the times a phenotype will appear in all the 16 possible genotypes.

In a large, randomly mating population of F2 individuals, the

9:3:3:1 phenotypes will remain constant through the generations if no selection occurs and no genetic variation is introduced. (Hardy-Weinberg Law)

Although very few species feed, clothe or entertain us, within those species there exists a large amount of genetic variation.

Plant diversity and agricultural development.

• When farming started, the human population increased.

• Humans looked for ways to get better yields or quality from the crops to feed the growing population.

The shift from hunter/gather to farmer had a huge impact on the world.

Farming required the development of ___________.

Land needed per person is _______________ with farming compared to hunting/gathering.

Global population increased because of more ____________ source of food and less dangerous activities.

Farming may be a high risk occupation, but compared to hunting and gathering it is much safer.

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What lead to the concept and practice of plant breeding?

Most likely the flourishing trash (compost) heap caused an idea (hypothesis) that something in the trash heap was making the plants grow better.

Along with observing that the growing conditions might be causing better yields, probably came the idea of saving seed from the best plants to plant for the next season’s crop.

By selecting what they liked, humans gradually created new sub species of plants. In time science-based breeding techniques were developed.

Sometimes the new or different plants (variations) are the same species. Thevariations of the species called cultivars (cultivated varieties or cv’s.).

Sometimes you will see crops referred to as varieties (var.). Botanically speaking, varieties are naturally occurring morphological variants within a species. These variants if desirable can be selected and to produce plants with consistent and predictable traits.

Wild relatives and ancestors are an important part of breeding programs so we need to know where to find them.

Vavilov was the Russia botanist who first to tried to identify centers of origin for modern crops. His findings and those of others give information on where to find wild relatives.

Origins of some important crops:

The Fertile Crescent – wheat, barley, peas, lentils, onions, figs, pears

China – oranges, tea, soybeans

India and Indonesia – rice, banana, coconut, sugar cane

Ethiopia – coffee, millet, okra, sorghum

Central and South America – corn, beans, cotton, squash, sweet potato, potato, tomato, tobacco, strawberry, cassava, pineapple, rubber

Of the main crops grown in the US, Canada, and Australia, none are native.

European crops are 9% native.

African crops, 12% native.

China-Japan, 37% native.

Latin America, 44% native.

Indochina, 67% native.

Origins of some grasses:

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Kentucky Bluegrass is a cool season grass that has some strains that are native to the US, but most are from temperate regions of Eurasia.

Bermudagrass is a warm season grass native to Africa and commonly used in southern US lawns.

Big bluestem is a native North American grass used for grazing in western states. Buffalograss is a native N.A. grass used for turf and forage in the south.

Genetic Diversity in the Plants We Grow

Wheat ancestors and relatives. The numbers represent the number of chromosomes in each species. Notice they are all multiples of 14. This is an example of polyploidy.

Teosinte is a wild relative of corn. Modern breeding was done to try to create what was most likely a primitive type of domesticated corn by crossing teosinte with domesticated corn.

Ornamental crops, unlike most food and forage crops, have a broad genetic base both among and within species.

Many genera have been cultivated for 100’s and even 1,000’s of years.

They have been the target of plant explorers since those intrepid folks started tramping the fields and mountains of the world in search of exotic and beautiful plants.

We know the date of modern discovery and the discoverer of many ornamental plants.

The cultivation of the genus Rosa over several millennia has resulted in 1,000’s of named cultivars.

Lilies, irises, and tulips are native to Greece and Turkey and there are hundreds of cultivars of each.

Spiderwort and the Tulip Tree are native to the Eastern U.S.

Beardtongue, coreopsis, and gaillardia are summer flowering plants that are native to Mexico.

Azaleas, hostas, and maples are among the ornamentals that originated in China and Japan.

The common climate characteristics and proximity of N. America and Eastern Asia has resulted in several genera represented by species on both sides of the Pacific.

The scientific or common name often gives a clue to point of origin.

Non-native plants that came from the same region can be desirable or undesirable.

Plant Breeding with Wild Plant Material

usually, the native populations already knew they were there and were often already using them.

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Many things have to be done when developing a plant discovered in the wild with potential to be a crop plant:

We have to:

• Get it to perform well in what is most likely an environment different from its native habitat.

• Get it to produce the part we are interested in prolifically, uniformly, and with high quality.

• Insure that the plant is not likely to escape and become an invasive species.

Natural selection

Introduction from the wild starts with the natural variation in the wild population to preserve the breadth of the natural genetic resources.

During the selections process, the best individuals from each generation are chosen.

Through successive generations where selection has taken place, the gene pool becomes more homozygous (uniform) for the desired traits.

The genetic variation decreases.

This can result in the loss of hidden, but desirable traits such as pest resistance or tolerance of unusual weather conditions.

Reintroducing lost traits is a very expensive and time-consuming process.

The most dominant U.S. apple, ‘Red Delicious’, came from selection. It was a seedling naturally descended from the trees that John Chapman (Johnny Appleseed) planted throughout the midwest in the early 1800’s.

Someone observed that it grew well with little maintenance and produced desirable fruit. The seedling was selected and the rest is history.

It became the most produced cultivar in the United States. But the germplasm diversity of commercially grown apples became very small.

With time, ‘Red Delicious’ has fallen out of favor and other apples have become very popular, thus deepening the commercial apple gene pool again. But to develop the new cultivars, breeders had to look for native germplasm in Kazakhstan, the apple center of origin to help deepen the gene pool.

If you like the new apple cultivars, you might want to thank a Kazakhstani fruit farmer for hanging on to old germplasm!

Selective Breeding

Although selection can produce good plants for commercial use, most of the time now, human intervention hastens and focuses the process.

Generally all desirable traits are not found in one plant. Have to combine genes from several plants to get the desired combination.

Difficulty comes when there is little genetic variation so don’t have a whole lot to choose from.

If the variation isn’t in the existing species, may have to go to wild relatives or induce _______________ to increase variability.

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Review of DNA and what it does and how mutations occur. (If you do not already understand the relationship of DNA, RNA, and proteins, I strongly recommend you review the detailed process in a college level biology book)

DNA = long chains of nucleic acids in specific order in a double helix. The nucleic acids are: adenine (A), thymine (C), guanine (G) and cytosine (C). In the double helix, they pair up A/T and G/C.

When genes are activated, that portion of the helix opens up and the nucleic acids attract ribonucleotides (adenine, cytosine, guanine and uracil (U) – which matches up with adenine as A/U. This process is called transcription.

The string of ribonucleotides that forms is mRNA. mRNA leaves the nucleus.

mRNA matches up with transfer RNA (tRNA).

But it is not a 1;1 match, tRNA has 3 nucleotides that have to match up with a sequence of 3 mRNA nucleotides.

Each tRNA is attached to an amino acid.

The arrangement of the 3 tRNA nucleotides determines which amino acid it is carrying.

As the tRNA joins the mRNA a chain of amino acids is formed (called translation).

This chain is a protein that has its amino acid content determined by the original DNA gene.

Proteins direct all the biochemical activity in an organisms.

The alignment of 3 ribonucleotides with its specific amino acid is the same in all organisms.

Mutations occur when there is a change in the order in which the amino acids assemble.

Mutations are what give us the inestimable array of biodiversity among and within species.

Mutations are sometimes deliberately induced by X-raying plants. The results of inducing mutations are VERY unpredictable.

Colchicine is a natural chemical from a species of crocus that is often used to induce polyploidy (a type of mutation) in plants. If you ever use this stuff, be careful, it can cause polyploidy in yyoouu and your kkiiddss, too!

Remember that polyploidy occurs naturally too. See the wheat picture on page 8.

When done properly and scientifically, breeding can broaden the gene pool compared to selection.

Genotype vs phenotype variation

Genotype is the genetic makeup.

Phenotype is the interaction of genotype with environment.

Plants with the same genotype can have very different phenotypes when grown in different environments.

The same genotype can show different phenotypes in different environments, likewise, different genotypes can express the same phenotype if environments differ.

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A critical part of breeding is to test new var./cv.’s in several different environments to see how different regional environmental conditions affect desirable traits like productivity.

Heritability

Traits are measured by their heritability.

Heritability = genetic variation ÷ phenotypic variation

Can vary from 0 to 1. The lower the number, the less heritable a trait is and the more difficult it will be to improve the crop by breeding without inducing variation.

Soybeans are easy to breed for uniform ripening, but it’s been a real pain to improve yield using breeding techniques.

Lodging (or the tendency for the stem to fall over) is moderately difficult to overcome.

Breeding starts with finding parents that have the desired trait/s.

For example, a great commercial variety is susceptible to a new or new strain of a disease. We select the commercial variety for production characteristics as one parent and a disease resistant plant as the other parent. The resulting generation is called F1.

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The F1’s are self-pollinated to create the F2 generation.

Then a series of backcrosses and selections is performed to try to get the desired product. (Breeding parent to child is not considered to be incest in plants.)

The F2 generation from a cross like the one described above is highly variable and none may be commercially acceptable. But some may exhibit disease resistance.

Find offspring with good disease resistance and backcross them with the commercial parent. This may have to be done several times to get a disease resistant variety with good commercial characteristics.

In the past breeding programs like the one just described could take years to develop a cultivar with the desired traits because plants had to be grown to maturity, crossed with other plants, and allowed to set seed.

This could take several generations and many, many years.

In breeding, pollen is collected from the male plant and then used to fertilize the female plant. Care has to be taken to keep the female from receiving unwanted pollen. ( Husbands of philandering wives have the same issue.)

Using male-fertile plants to produce hybrid seed, means the male parts have to be emasculated before they mature. Using male-sterile plants that produce seeds but do not produce viable pollen eliminates this problem. An alternative is protecting the female from unwanted pollination.

Breeding requires meticulous attention to small details.

Single gene traits are the easiest to breed for.

The more genes involved, the more difficult it is to get everything into a single offspring, especially if those genes are on separate chromosomes.

In an organism with 3 chromosomes, the possible different gametes in the F1 generation is 8.

For corn, which has 20 chromosomes, the F1 generation has 1,024 possible gene combinations in its gametes,

The gamete possibilities for the F2 generation is over a million different combinations.

Imagine the combinations possible in humans who have 46 chromosomes.

When crossing over occurs on chromosomes, the number of different gametes that can be produced increases even more.

Once a breeding program has been started, after careful breeding and several generations, it is possible to develop a homozygous line from a single, self-pollinating plant.

However, when a population becomes completely or nearly homozygous, reduced vigor often occurs.

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Hybrid corn in the 70’s was very uniform but very susceptible to a new race of the organism causing corn blight. The devastating effect of corn blight on the U.S. corn crop in the 1970’s was the result of a very narrow genetic base in the crop.

Corn breeders had to scramble to introduce blight resistance into the crop. Fortunately, vigor can often be restored by crossing two different inbred lines.

In the case of corn, male-sterile mutants made those crosses much easier to do. The seed is formed on the male-sterile parent and is all genetically identical though heterozygous.

When hybrid seed was first introduced, farmers nearly rioted in anger. Any ideas why?

Our understanding of genes and DNA, and the ability to use molecular markers to see if a gene is present has sped up the selection process. In most cases, plants no longer have to be taken to maturity to see if they have a trait.

Each column represents a different plant. The marks in each

column indicate different genes. We can look for plants with the genes we want and keep those plants.

They do have to be taken to maturity though to produce seed. But you only have to do that with the plants you know carry the trait.

When the desired traits in a plant cannot be passed on by sexual reproduction, then vegetative or asexual propagation often can be used to create clones.

Cases where vegetative propagation is used:

• the parents are highly heterozygous and it is not likely a homozygous population can be created

• the parent is sterile and cannot produce seed.

A clone is a population with identical genetic makeup.

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With vegetative propagation, stock or “mother” (they do not have to be female) plants produce cuttings which are rooted and grow into complete plants. The cuttings all have the same genetic information as the parent and when each new plant produces cuttings, those also have the same genetic information. This uniformity continues unless there is a mutation.

Whether sexual or asexual, progress in plant breeding went hand in hand with the need for more fertilizers and pesticides.

Sustainable agriculture requires that we consider the need for inputs and the problems of unintended outputs.

By increasing the need for chemical inputs are we developing sustainable systems?

Sustainability is now a part of the evaluation process of selecting new crop species and cultivars.

Genetic Engineering and Crops

The discovery of the structure of the DNA molecule by Francis Crick, James Watson, and Rosalind Franklin led to the ability to identify, isolate, and transfer genes.

Plant breeding has been going on long before the discovery of DNA and how it functions.

However, with our very recent understanding of DNA came the discovery of a way to move genes from one species to another. Until then plant breeders could only work with traits found in closely related (sexually compatible) species.

Genetic engireering has ‘transformed’ plant breeding. We even call the process transformation.

Transformation is the incorporation of ‘foreign’ genes (DNA) into an organism. Foreign genes are those that come from organisms that are not naturally able to mate with the parent organism.

When that gene is expressed, the foreign trait will appear in the transformed organism.

Now genes from any organism can potentially be put in a plant. But it isn’t as simple as many people think it is.

It is not easy to transform organisms with foreign genes and it is even harder to get the organism to express the trait.

Gene expression of a trait is the result of the action of the protein (enzyme) produced by that gene.

Transformed organisms are often called:

Genetically engineered organisms, Biologically (bio) engineered organisms, Genetically modified organisms (GMO’s).

The two most widely used foreign genes in crops code for:

Bt toxin - a protein produced by the Bacillus thuringiensis bacterium that destroys the gut lining of caterpillars.

Glyphosate resistance - generated by an enzyme (protein) that enables a plant to survive when sprayed with the herbicide glyphosate (Round-UpÒ). Glyphosate inhibits the production of EPSP synthase which is needed for the synthesis of some amino acids.

The foreign gene can be introduced into an organism by a biological vector (carrier) or a Physical method.

Both are used in plant biotechnology.

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The biological vector works best for dicotyledonous plants.

The physical method works best for monocots.

The biological vector most often used in plants is an Agrobacterium that infects plants, often causing a gall.

The bacterium has a piece of circular DNA called a Ti plasmid.

It injects the plasmid into the cells of the plants it infects.

By inserting a new gene into the plasmid before injection, the new gene goes into the plant at the time of injection.

A promoter and a marker are also inserted into the plasmid DNA along with the desired gene. The promoter causes the new gene to be expressed when desired and the marker is used to make sure the gene has been inserted.

Physical (mechanical) methods also can be used to inject foreign DNA directly into plant cells. Although there are several ways to do the insertion, particle bombardment (gene gun) is the most frequently used.

Whether the process is biological or physical, only individual cells are transformed. The cells (protoplasts) have to be separated and grown into complete new plants. Usually it is not possible to tell by looking which cells have the new DNA and which do not.

By using an easily seen marker such as antibiotic _________________, we can select the cells that have been transformed. A plant that shows it has the marker (doesn’t die when exposed to the antibiotic) most likely has the desired gene too. The ‘marked’ plants are grown and tested for the desired trait.

Luciferase, the enzyme that makes fireflies glow, is another marker that is used. Where the plant “glows” the luciferase gene is being expressed along with any gene inserted with it .

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Once the we know we have the DNA for the desired trait in a plant, we can breed that plant conventionally or propagate it vegetatively to increase numbers and, in the case of breeding, get the gene into closely related species.

Bt resistant corn and cotton and glyphosate-resistant soybeans now account for much of the

acreage of those crops in the U.S.

Because of the cost of transformation, it is not likely that minor crops, including almost all ornamentals will be transformed in the foreseeable future.

Biotechnology works best by far with single gene traits. For traits that are determined by multiple genes, biotechnology is not expected to play a role for a long time, if ever.

Today. GMO’s are one of the most controversial issues in the world. A couple of websites that look at both sides of the issue.

http://www.purdue.edu/agbiotech/whobenefits.html

http://www.fao.org/english/newsroom/focus/2003/gmo8.htm

Glyphosate-resistant bentgrass has been very recently developed for lawns and golf courses and was ready for introduction fall 2004 but discovery that the gene may have escaped into a wild grass population from a test site put the release on hold, perhaps for a very long time. The controversy still continues in 2006.

Although food safety is sometimes the issue, most concern for GMO’s comes from fear that a foreign gene will ‘leak’ into a native population and create unforeseen problems.

The less closely related a GMO is to the native plant populations, the less likely the gene is to escape. In the case of the turfgrass, the gene was found 50 miles away in a native population.

Genetic contamination from modified corn has been reported in ancestral and wild types, e.g. Zea mays in Peru and Mexico.

On the other hand, the lack of __________________ of most domestic plants (their need for TLC, tender loving cultivation), to survive actually helps to control the escape of genes.

Domesticated plants cannot compete well in the wild for limited resources so they die out, taking any foreign genes to their grave with them.

In the U.S., because very few of our major crop plants are _____________ the risk of gene escape by GMO’s breeding with native species is lower than in areas where the crops are native.

Crop System Diversity

As important as genetic diversity is, so is crop system diversity.

Like a natural ecosystem, the more diversity in a crop system the healthier and stronger it is.

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Agriculture polycyltures are diverse but are less efficient to grow, maintain, and harvest than monocultures.

Monocultures however leave a lot of niches open that are filled by unwanted niche species, i.e.____________.

Monocultures abound in agriculture. Though easy to plant, grow, and harvest, these systems often are vulnerable to insects, diseases, and weed infestations.

Not only is a monoculture low on species diversity, it is also very low in genetic diversity.

You’ve already learned of the corn blight problem in the U.S. If you are of Irish heritage, chances are your ancestors came to the U.S. to avoid starving in the Irish potato famine of the 1800’s.

A monoculture of potato production opened the door to crop devastation of a type of late blight introduced from the European continent into Ireland.

Forages are often planted as a mix of legumes and a grass to give better production during a drought.

When choosing species to mix in a polyculture for a farm, choose species that are known to adapt well to environmental conditions of the site.

Cannot always do this in urban agriculture. Human preference often overrides ecological soundness.

Mixed groupings of ornamental plants will mostly likely stay attractive under a much wider range of weather and other environmental factors than large blocks of single species/cultivars. But some clients will still want mass plantings of the identical plants.

Permaculture is the term used to describe small scale, mixed annual (die after one reproductive cycle) and perennial (repeat reproductive cycle indefinitely) crop production.

This concept is being promoted for world-wide, including U.S., adoption.

Not new, many parts of the world have long included mixing several annuals and perennials in their cropping systems.

Agroforestry, a system that is being adopted in tropical areas, combines trees, annual, and perennial crop production to maintain soil fertility and crop health with low fertilizer and pesticide input.

There is a world-wide effort to preserve plant germplasm (genes). The USDA National Plant Germplasm Service has Centers located throughout the US (including the OSU campus) to maintain a collection of genes (germplasm) to preserve genetic variable.

Plant breeders from all over the world can receive this germplasm at no charge to include in their breeding programs.

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