1. Crop ImprovementCrop Improvement

2. Sexual and Asexual Reproduction
• Long term survival requires reproduction. Even the longest-lived
organisms are less than 10,000 years old.
– Cellular machinery wears out, or gets clogged with waste products.
– Environmental conditions change
• Plants often reproduce asexually, through cuttings or runners or buds
(e.g. potatoes). The resulting plants are clones: they are genetically
identical to the parent.
– Used to preserve good combinations of traits.
• Sexual reproduction is also found in plants, and in all animals. Sexual
reproduction means combining genes from two different parents,
resulting in new combinations of genes. Each parent contributes a
randomly-chosen half of their genes to the offspring.
– This can be a good thing, because some new combinations will survive
better than the old ones.
– It can also be bad: lack of uniformity in the offspring.

3. Vegetative Propagation
• Plant meristems are usually capable of
generating all the tissue types found in a plant.
• Some plants naturally propagate vegetatively,
usually through modified stems: flower bulbs,
corms, and rhizomes; suckers; stolons (runners).
• Artificial vegetative propagation can be down by
taking a cutting from the stem (containing at
least one meristem) and encouraging it to grow
roots.
• Citrus trees use “nucellar embryony”. Some of
the cells surrounding the ovule (nucellus cells)
spontaneously turn into embryos when the
ovule is fertilized by pollen. The seeds contain
both the regular embryo derived from male x
female, and also the nucellar embryos (maternal
genes only)
• More advanced methods include grafting and

4. Grafting
• Grafting is common among fruit trees: the stem
tissue of one plant is fused to a stem from
another plant.
• Commonly done: a hardy rootstock is grafted to
the stem of a better fruit variety.
• Another method: attaching a bud form one plant
to the stem of another. You can produce an
apple tree bearing several different types of apple
this way.
• The cambium layers of the two plants being
grafted need to be brought into contact. This
allows the xylem and phloem to connect to each
other
• It is possible to graft a potato rootstock to a
tomato top, so both underground potato tubers
and aboveground tomato fruits are formed on
the same plant.

5. Tissue Culture
• A more modern way of propagating plants
vegetatively is through tissue culture. This is often
called “micropropagation”.
– Useful for genetically engineered plants, for plants
that don’t set viable seeds, and for rare and valuable
plants.
• Unlike animals, many plant cells, especially in the
meristems, are totipotent: they can generate an
entire plant under the proper conditions.
• Pieces of the plant are cut out and placed on an
agar medium under sterile conditions.
• Manipulating plant hormones is the key: an excess
of auxin produces roots, and excess of cytokinin
produces shoots, and a balanced mixture allows the
cells to multiply as an undifferentiated mass of cells
called a callus.
• Pieces of the callus can be cut out and propagated
indefinitely.

6. Sexual Reproduction
• Diploid: having 2 copies of each chromosome, one set from each
parent.
– Humans have 46 chromosomes, 23 from each parent.
– Almost any organisms you can see: plant, animal, fungus, is diploid.
• Haploid: having only 1 copy of each chromosome.
– Sperm and eggs (=gametes) are haploid
– moss, a primitive plant, is haploid for most of its life
• Plants, animals, and other eukaryotes alternate between haploid and
diploid phases. This is called alternation of generations.

7. Life Cycle
• Diploid organism generates haploid
gametes using the process of meiosis.
The gametes combine during the process
of fertilization to form a new diploid
organism.
• In animals, the haploid phase is just one
cell generation, the gametes, which
immediately do fertilization to produce a
diploid zygote, the first cell of the new
individual.
• In plants, the haploid phase is several cell
generations at least.
– Lower plants are mostly haploid
– Higher plants are haploid for only a few
cell generations
• The diploid plant is called the sporophyte,
and the haploid plant is called the
gametophyte.

8. Genetics
• The science of genetics is devoted to understanding the patterns of how
traits are inherited during sexual reproduction. It was founded by Gregor
Mendel in the 1850's, using pea plants. Despite the obvious differences,
humans and peas have very similar inheritance patterns.
• The fundamental observation of genetics: within a species, there are a fixed
number of genes, and each gene has a fixed location on one of the
chromosomes.
– This allows genes to be mapped: a gene's neighbors are always the same.
– Most species of higher organism have about 25,000 different genes distributed
onto 10-30 different chromosomes.

9. Genetics
• Alleles. Many genes have several variant forms, which are called
alleles.
– For example, a gene the produces color in the flower might have a purple
allele and a white allele. These alleles are designated P and p.
– Differences in alleles are what makes each human different from all
others
• True-breeding lines. If you cross close relatives with each other for
many generations, eventually all the offspring look alike.
– Mendel started with several true-breeding lines, which differed from
each other in 7 distinctive characteristics

10. Genetics
• In many plants, you can self-pollinate: cross the
male parts of a plant with the female parts of the
same plant.
– In this case, both copies of any given gene are
identical. This is called homozygous. The plants are
homozygotes, either PP (purple) or pp (white).
– The closest cross you can do in animals is brother x
sister.
• Hybrids. If you cross two true-breeding lines with
each other and examine some trait where the
parents had different alleles, you produce a
heterozygote: the two copies of the gene are
different.
– Surprisingly, you often find that the heterozygote
looks just like one of the parents. The Pp
heterozygote is purple, just like its PP parent.
– This is the F1 generation in the diagram.

11. Genetics
• Dominant and recessive. If a heterozygote is
identical to one parent, the allele from that
parent is dominant. The allele from the other
parent is recessive. That is, the heterozygote
looks like the dominant parent.
– This is why we say purple is dominant to white,
and give purple the capital letter P.
• Phenotype and genotype. Phenotype is the
physical appearance, and genotype is the
genetic constitution.
– The heterozygote in the previous paragraph
has the same phenotype as the homozygous
dominant parent (i.e. purple flowers), but a
different genotype (the heterozygote is Pp and
the parent is PP).

12. Genetics
• Now we want to move to the next
generation, by self-pollinating the
heterozygotes.
• When a heterozygote undergoes
meiosis to produce the haploid
gametes, half are P and half are p.
– These gametes combine randomly,
producing 1/4 PP, 1/2 Pp, and 1/4
pp offspring.
• Since PP and Pp have the same
phenotype, 3/4 of the offspring are
purple and 1/4 are white.

13. Independent Assortment
• Much of Mendel’s work involved pairs of genes:
how do they affect each other when forming
the gametes and combining the gametes to
form the next generation?
• Simple answer: in most cases pairs of genes act
completely independently of each other. Each
gamete gets 1 copy of each gene, chosen
randomly.
• Two genes:
• 1. seed shape. Dominant allele S is smooth;
recessive allele s is wrinkled.
• 2. seed color. Dominant allele Y is yellow;
recessive allele y is green.
• Heterozygous for both has genotype Ss Yy,
which is smooth and yellow. Gametes are
formed by taking 1 copy of each gene randomly,
giving ¼ SY, ¼ Sy, ¼ sY, and ¼ sy.
• These gametes can be put into a Punnett square
to show the types of offspring that arise.
– Comes out to 9/16 smooth yellow, 3/16 smooth
green, 3/16 wrinkled yellow, and 1/16 wrinkled
green.
– 3/4 are yellow, 1/4 are green, and 3/4 are round,
1/4 are wrinkled

14. Continuous Variation
• Many traits don’t seem to fall
into discrete categories: height,
for example. Tall parents usually
have tall children. Short parents
have short children, and tall x
short often gives intermediate
height. In all cases, wide
variations occur.
• Simple interactions between
several genes can give rise to
continuous variation. Also:
variations caused by
environment, and our inability to
distinguish fine distinctions lead
us to see continuous variation
where there actually are discrete
classes.

15. Linkage
• Most pairs of genes assort
independently.
• However, if two genes are close
together on the same
chromosome, they are said to be
linked, which means the genes
don’t do into the gametes
independently of each other.
• The closer two genes are, the
more the parental combination
of alleles stays together. This
relationship can be used to make
maps of genes on chromosomes.

16. Lessons from Genetics
• Inheritance is controlled by a relatively small number of distinct objects:
the genes
• Genes are in fixed locations on chromosomes, and they are inherited by
a few simple rules:
– Each gamete gets one of the two copies of each genes, chosen randomly
– Most genes are inherited independently of each other
– Genes close together on chromosomes are usually inherited together
(linkage)
• Genes are usually passed from parent to offspring without change
– They are not affected by the events of our lives: there is no “inheritance of
acquired characteristics” (Lamarck)
– But, sometimes random changes (=mutations) occur in individual genes
• The physical characteristics (phenotype) of an individual is determined
by the interaction of genes with each other and with the environment
– Dominant vs. recessive, for example
– But often in more complex ways

17. Methods of Crop Improvement
• The idea that we can improve the inherited characteristics of crop
species is fundamental. Very few of the plants we use are unmodified
wild plants: most of them have been modified to make them easier to
grow and harvest, and to increase the quality and quantity of the
desired product.
• We will see many examples of crop improvement this semester. Here
are some of the basic methods used.

18. When Asexual Reproduction is Impossible
• Maize ( and other cereal grains) only
reproduces sexually. How can good
combinations of traits be preserved?
• The simplest approach: inbreeding.
– Self-pollinate for many generations: the plants
become almost completely homozygous
– They are now a pure-breeding line, in which all
plants are genetically identical.
• Problem: inbred plants are low yielding,
sickly, small, and weak. This is called
inbreeding depression.
– Many genes have alleles that are recessive and
which cause bad effects when they become
homozygous : recessive deleterious alleles.
– The positive side of inbreeding depression: the
plants that survive inbreeding have had most
of their bad alleles bred out.
gen litter
size
% dead
by 4
weeks
0 7.50 3.9
6 7.14 4.4
12 7.71 5.0
18 6.58 8.7
24 4.58 36.4
30 3.20 45.5

19. Hybrid Vigor
• Inbreeding doesn’t work as a method to
preserve good sets of genetic traits, because of
inbreeding depression.
• However, if you make a hybrid between 2
inbreds, the resulting offspring are genetically
uniform.
– Each hybrid offspring gets the exact same alleles from
the inbred parents as every other hybrid offspring.
– The hybrids are genetically identical, but heterozygous
• Hybrids show hybrid vigor. They are stronger
and healthier than the inbred parents.
• So, by first inbreeding to purify the genes, then
crossing inbred to make a hybrid, you get the
benefits of genetic uniformity as well as the
benefits of being heterozygous.
Left: elite inbred B73;
Right: elite inbred Mo17
Center: B73 x Mo17 hybrid

20. Hybrid Corn
• One of the major developments in agriculture during the early 20th century was
scientific plant breeding based on Mendel's genetic principles.
– Corn yield has increased 5-10 fold since 1900 because of this.
– Traditional method: save the best seed to plant the previous year. Leads to slow
improvement.
•

21. Single Gene Traits and Mutation
• Single gene traits. Many useful traits are controlled
by a single gene. Spontaneous mutations can lead to
important, abrupt changes
– A good example: sweet corn. The recessive mutation su
(sugary) produces kernels that are 5-10% sugar. But,
only when homozygous: the non-sugary allele (Su) is
dominant.
• Single gene mutations occur rarely, but often enough
so that observant people notice and propagate them.
– Sweet corn was recognized and propagated by several
Native American tribes. The Iroquois introduced it to
European settlers.
– Mutation rate: 1 in 10,000 to 1 in 1,000,000 plants.
– Artificially-induced mutation occasionally works, but
most are spontaneous.
• Single gene traits are inherited in a Mendelian
fashion:
– each individual carries one copy of the gene from each
parent,
– the relationship between phenotype (sweet vs. starchy
corn) and genotype (homozygous or heterozygous) is
determined by dominance vs. recessiveness.
Genotype Phenotype
Su Su Starchy
Su su Starchy
su su Sweet

22. Polygenic Traits and
Selection
• Polygenic traits. Many traits are controlled
by many genes, each of which contributes a
small amount to the phenotype. Grain yield
is a good example: lots of genes contribute
to this.
• Such traits respond well to selection. In the
simplest sense, selection means using the
best seeds to start the next generation. If
this is done consistently, the crop slowly
improves over many generations.
• Genetic research has led to an
understanding of what happens during
selection. This allows much faster and
more effective selection than just saving the
best seeds.
• This is often called “conventional breeding”
or “traditional plant breeding”. It has been
the main way crops have been improved for
a long time.

23. Polyploidy
• Normal diploids have 2 copies of every
chromosome. Sometimes it is possible to double
this number, making a tetraploid, 4 copies of
every chromosome.
• Can occur spontaneously
– The drug colchicine does this by causing meiosis to
produce diploid gametes instead of the normal
haploids. Then, diploid sperm + diploid egg =
tetraploid embryo.
• Tetraploids are often bigger, healthier, more
nourishing than their diploid parents.
– Examples: cotton, durum wheat, potato, daylily
• Tetraploid is a form of polyploid, which means
having more than 2 sets of chromosomes (2 sets =
diploid).
• There are triploid (e.g. banana and watermelon),
hexaploid (bread wheat, chrysanthemum), and
octoploid (strawberry, sugar cane) crops
• Triploids are sterile
Diploid vs. tetraploid daylilies
Diploid vs. octoploid strawberries

24. Hybridization
• Plants are not as rigid in maintaining species boundaries as
animals are. It is often possible to produce hybrids between two
different, but closely related species.
– Members of the same genus will often hybridize
• The resulting plants often have characteristics different
from both parents
– Often sterile, but many plants can be propagated vegetatively
• The grapefruit is a naturally-occurring hybrid between a
pomelo (native to Indonesia) and a sweet orange (native to
Asia). It was discovered in Barbados in 1750, then brought to
Florida and propagated.
• Hybrids have an “x” in their species name: Citrus x paradisi
• Sometimes, a hybrid will spontaneously double its chromosomes,
so you end up with a tetraploid . These interspecies tetraploids
are usually fertile, and they benefit from the general effect of
tetraploidy: bigger, healthier plants. Interspecies hybrid of
Drosera (sundew), a
Carnivorous plant

25. Genetic Engineering
• In the last 30 years it has become possible to take a gene out of one
organism and put it into the DNA of another organism. This process is
called genetic engineering. The resulting organisms are genetically
modified organisms (GMOs) and the gene that has been transplanted is
a transgene.
• There are no real interspecies barriers here: all organisms use the same
genetic code, so genes from bacteria (for example) will produce the
correct protein in a corn plant.
– However, some modifications must be made to the signals that control gene
expression, since these are more species-specific.
• A few examples:
– Bt corn. Bacillus thuringiensis, a soil bacterium, produces a protein that kills
many insect pests, especially the corn earworm. The gene for this protein
has been transplanted into much of the US corn crop.
– Roundup Ready soybeans (plus other crops). Roundup is the Monsanto
brand name for the herbicide glyphosate. A bacterial gene that confers
resistance to this herbicide has been transplanted to many crops. The
farmer can then spray the fields with glyphosate and kill virtually all the
weeds without harming the crop. About 87% of the US soybean crop is now
Roundup Ready transgenic plants.
• Some cultural issues here: are GMOs safe to eat? (Most scientific
opinion is that they are probably harmless)
Blue rose, with blue
pigment gene from
delphinium
Dead volunteer corn
in a glyphosate-resistant
soybean field

26. Molecular Cloning
• The first step in genetic engineering is
molecular cloning.
• Molecular cloning means taking a gene, a piece
of DNA, out of the genome and growing it in
bacteria. The bacteria (usually E. coli) produce
large amounts of this particular gene.
• The cloned gene can then be used for further
research, or to produce large amounts of
protein, or to be inserted into cells of another
species (to confer a useful trait).
• The basic tools:
• 1. plasmid vector: small circle of DNA that
grows inside the bacteria. It carries the gene
being cloned
• 2. Restriction enzymes: cut the DNA at
specific spots, allowing the isolation of specific
genes.
• 3. DNA ligase, an enzyme that attached
pieces of DNA together.
• 4. transformation. Putting the DNA back
into living cells and having it function.

27. The Cloning Process
• 1. Cut genomic DNA with a
restriction enzyme.
• 2. Cut plasmid vector with
the same restriction
enzyme.
• 3. Mix the two DNAs
together and join them with
DNA ligase.
• 4. Put the recombinant DNA
back into E. coli by
transformation.
• 5. Grow lots of the E. coli
containing your gene.
• The real trick, however, is to find
the gene that confers your
desired trait.

28. Transgenic Plants
• Once a gene of interest has been identified and cloned, it
must be put into the plant.
• Usually done with plant tissue culture. Small pieces of a
plant can be grown as an undifferentiated mass of cells
on an artificial growth medium.
– Then, when treated with the proper plant hormones, these
cells develop roots and shoots. They can then be
transferred to soil and grown as regular plants.
• To make transgenic plants, DNA gets put into the tissue
culture cells, by one of several methods:
• One method is the gene gun: tiny gold particles are
coated with the DNA, and then shot at high speed into
the cells. The gold particles penetrate the cell wall and
membrane. Some end up in the nucleus, where the DNA
gets incorporated into the chromosomes.
• An important issue: the proteins produced by transgenes
are identical to those produced in the original species,
because the genetic code is universal.
• However, the signals needed to express these genes are
plant-specific, not universal.

29. Centers of Domestication
• Primary theory came from Nikolay Vavilov,
– Vavilov was a Russian who came to a bad end in one of
Stalin’s prison camps in Siberia. He believed in
Mendelian genetics, which was considered “bourgeois”
and thus evil by the Communist Party. (Lysenko)
• “Centers of domestication”. The idea is that a
plant was probably first domesticated where there
are many wild relatives living and where there is a
lot of variation in the domesticated plant. Lots of
diversity near a domestication center.
• Eight major centers:
– Southern Mexico and Central America: maize, beans,
cotton, pepper, sweet potato
– South America (mostly Peru): potato, common bean,
tomato, cocoa, tobacco
– Mediterranean: pea, mustard, flax, cabbage, asparagus,
clover, olive
– Middle East (Turkey and eastward): wheat, alfalfa, rye,
lentil, melon, fig
– Ethiopia: barley, millet, coffee, indigo, sorghum
– Central Asia: onion, apple, carrot, almond, grape
– India: sugar cane, yam, cucumber, chickpea, orange,
coconut, banana, pepper
– China: rice, soybean, buckwheat, peach, opium poppy, tea
Diversity of maize from Mexico
Diversity of potatoes from Peru

30. Centers of Origin

31. More Domestication
• More recently, Jack Harlan (from U of Illinois)
examined genetic data and found that many
crops were domesticated multiple times in
multiple locations. Also, some were
domesticated over very wide areas that don’t
seem much like “centers”.
• Nevertheless, our current crops come from many
different areas of the world. We will look at the
origins of specific crops as we study them.