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PART 1. GENETICS
CHAPTER 1
Genes
„The genes are the atoms of heredity”
Seymour Benzer 1960
Theory
The beauty and diversity of modern World has been formed through multiple climate changes, huge
landmasses movements and continuous evolution of endless number of living creatures during
million years of the Earth history. Today, people come to walk in the forest, by the lake or in the countryside and
they can see that some plants are more similar. Pines and spruces have needles; barley and wheat have long
narrow leaves. For other people physical differences are more evident. Pines and spruces are differentiated by
shape of cones, stature, needle length and colour, to name just a few. Similarly, barley and wheat are
characterized by a number of morphological traits. This pattern of similarities and differences between
organisms is explained by the science called genetics. Before this science emerged, people had intuitively
known that pines, spruces, barley and wheat represented different types of organisms (species). They
understood that a kind of hereditary material determined appearance and function of organisms. This knowledge
was used by ancient farmers when they sown cereal grains to obtain plants alike the parent. However, the
discovery of rules governing the inheritance of traits has occurred only recently, in 1866 when Gregor Mendel, a
monk published his work about trait inheritances in peas, which led him to postulate the existence of “discrete
units of inheritance”. Today Mendel is regarded as the father of genetics and his work is one of the best examples
how to carry research in the entire history of science. Mendel's hereditary units are now called genes while
genetics is the science of heredity and variation.
What are Genes?
The hereditary material must have properties enabling from one side transmitting unchanging
information from parents to offspring, and provide variation responsible for differences between organisms. All
these features are within the scope of substances called nucleic acids. Deoxyribonucleic acid (DNA) is the
hereditary material in all life forms except of some viruses, in which ribonucleic acid (RNA) is the hereditary
material. Both acids are biopolymers made of elementary units – nucleotides (for structure see genetic,
biochemistry books and Internet sources). In plant cells, DNA molecules are found in nucleus (nDNA),
chloroplasts (cpDNA) and mitochondria (mtDNA). Traditionally, a segment of DNA encoding a single feature,
PART 1. GENETICS
14
with the specific sequence of nucleotides makes a gene. For instance, the classical pea R gene described by
Mendel as affecting seed forms (rounded vs. wrinkled, see Fig. 1.4) consists of 3546 bp. The whole pea genome
is about 4 300 x 106 bp, thus roughly estimating, a DNA molecule may contain about million different genes.
However, it is not a case; genes are often only a tiny proportion of plant genomes (Table 1.1). The DNA contains
all information about structures and functions of organisms such as leaf shape, stem height, flower colors and
many others. These observable characteristics are referred as a phenotype while the genetic constitutions, e.g.,
genes controlling leaves, stems and flowers are called a genotype. In a given example of the Mendel's R gene,
the pea phenotype is “rounded” while the genotype can be RR (double R as pea is a diploid, for tetraploid would
be RRRR, for haploid R).
TABLE 1.1 Number of genes in selected plant species
Species
Genome
Genome size
Genes number
Arabidopsis thaliana
nDNA
157 Mb
26 819
Arabidopsis thaliana
cpDNA
155 kb
87
Modern
understanding of a
Arabidopsis thaliana
mtDNA
367 kb
117
gene, covers not only a
Hordeum vulgare
nDNA
5 300 Mb
~20 000
coding part but also
Oryza sativa
nDNA
490 Mb
~32 000
associated regulatory
Physcomitrella patens
nDNA
~30 000
511 Mb
regions. Plant genes,
Populus trichocarpa
nDNA
45 555
485 Mb
like all Eukaryotic
Zea mays
nDNA
~20 000
~2 500 Mb
genes, are built from
Based on Lang et al. 2008
both coding sequences
.– exons and non-coding parts – introns (Fig. 1.1). A set of all genes of an organism makes a genome – a kind of
a database storing data files (genes) and programmes for their execution (regulatory sequences; non-coding).
Regulation of
transcription
5’
Signals for termination
of transcription
Cap
AUG
poly A
UAA
3’
FIGURE 1.1 Modern structure of the gene - Cat1 encoding catalase in Zea mays
Yellow boxes - exons, navy blue - introns
How do Genes Function?
The function of genetic material is, first, to copy information from parents to offspring in a process of
replication and second, to provide information for growth and development of an individual. Beyond our
awareness, genes start to execute programmes that translate the DNA sequence into red flowers, growth, seed
development etc. This process is called gene expression (Fig. 1.2). This is described elsewhere. Here, suffice is
to say that structural proteins or enzymes are produced then. In a first step of gene expression called
transcription the DNA sequence in a gene (e.g., pea R gene) acts as a template for the synthesis of a
complementary strand of the RNA called transcript. Then, the RNA undergoes several modifications to produce
a final molecule - messenger RNA (mRNA). A collection of all different transcripts is referred as transcriptome.
Finally, nucleotides in the RNA are read as triplets calling codons in the process of translation – synthesis of a
protein using the gene's mRNA template. This way the pea R gene leads to the starch branching enzyme
(Accession N° CAA56319). The collection of all the different proteins in an organism is its proteome. Enzymes
control the synthesis of different metabolites, e.g., starch, alkaloids etc. A set of all metabolites is often referred as
metaboleome. Along with the technology developments, methods enabling analysis of many genes, transcripts,
proteins, metabolites developed and have become a foundation of a holistic approach in research referred as
“omics”with appropriate prefix.
CHAPTER 1. GENES
15
How do Genes Change?
GENETICS
INTEGRATED
GENOMICS
Genes from one side are reasonable
stable to preserve functions; from the other they can
change in a process called mutagenesis, in which
Genome
Gene
new forms of genes are produced (Chapters 4 and
16). For many years, biologists have observed that
each trait can exist in different forms – white and red
Transciptome
mRNA
flowers, round or wrinkle seeds, dwarf or high
plants. Mendel discovered that these different trait
stages are associated with different forms of the
same gene, which we now called alleles Protein
Proteome
alternative forms of a gene. Alleles are denoted by
the same basic symbol as R for round pea seeds
and r for wrinkled seeds. Sequencing of the
Structure
Mendel's R gene proved that the difference in the
Function
pea seed shapes is controlled by insertion of 800 bp
Organism
in the r allele. Another example involved a mutation
FIGURE 1.2 Key steps of gene expression - relation
within tb1 gene (teosinte branched), responsible for
between genetics and “omics” sciences
transition of a bushy grass (teosinte) into a modern
cereal – maize, thus being an important element of domestication and speciation. The pea example
demonstrates that mutations are responsible for variation among individuals within a species while the maize
example is unequivocal proof that mutations are the raw material for evolution. Without mutations alleles would
not exist, genetic analysis would not be possible and the most important, evolution would not be possible
(Chapter 4, 13).
Practical Examples
The genius of Mendel was that despite hundred years and the entire technical progress today, no
genetic analysis is possible without application of the Mendel's methodology based on hybridization and
statistics. Segregation analyses have still been the most important data about inheritance and differentiation. No
transgenic plant can be registered without confirming the Mendelian inheritance of a transgene. Comparing
segregation in different taxa informs about existence of reproductive barriers and their evolutionary divergence.
Monohybrid Crosses (Mono-factor) – Dominance and Segregation
Let us take two pea plants, the first with violet flowers and the second with white (Fig. 1.3). Both plants
are true-bred i.e., they have been stable with respect to the flower colour through several generations. Let us
assign the plants as P for parental. The resulted generation, F1 (First filial generation) will have only violet flowers.
Next fertilization will produce second filial generation, F2, in which 75% of plants will have violet flowers and 25%
white flowers, i.e., violet to white flowers ratio 3:1. This is a consequence of alleles' segregation during production
of gametes. Each diploid plant has two copies of a gene (two alleles). The plant is homozygous if both alleles are
identical and the plant is heterozygous if the alleles are different. Parental plants are homozygous with
respective genotypes AA for violet and aa for white flowers. Each parental plant produces one kind of gamete.
They merged in F1 giving a heterozygous plant, Aa with violet flowers. It is obvious that the A allele encoding violet
flowers control the phenotype even it is in a single copy. The phenomenon is called dominance, and the
„stronger” allele is called dominant while the a allele for white flowers is called recessive. The heterozygous F1
plants produce two kinds of gametes that can merge in four combinations giving the F2 generation. The first
Mendel principle says that alleles of a gene segregate from each other during the formation of gametes.
PART 1. GENETICS
16
Each parental
homozygote
produces one
kind of gamete
P2 (aa)
P1 (AA)
X
a
A
Heterozygote
produces two
kinds of gamets
in equal
proportions
F1 (Aa)
Self-fertilized
F2
Phenotypic ratio:
red - 3
white - 1
A
Genotypic ratio:
AA - 1
Aa - 2
aa - 1
a
A
a
AA
Aa
Aa
aa
FIGURE 1.3 Symbolic representation of a cross between peas. The first Mendel principle
Dihybrid (Two- factor) Crosses
After crossing plants differed in two traits e.g., a plant with yellow, round seeds and a plant with green,
wrinkled seeds, four phenotypic classes are observed in F2 (Fig. 1.4). They represent all possible combinations
of these two traits with the ratio of 9 yellow, round, 3 green and round, 3 yellow and wrinkled, and finally 1 green
and wrinkled. In this case each trait is controlled by a different gene segregating two alleles. We denote each
gene with an uppercase for dominant allele and lowercase for the recessive. For the seed color, the two alleles
are G for yellow and g for green. For the seed texture, R for rounded and r for wrinkled. The F1 produces haploid
gametes with one copy of each gene. It is possible to write down all the gametes and combine them
systematically in a form of the Punnet Square. This is the Principle of Independent Assortment – alleles of
two different genes segregate or assort independently of each other.
Formulating and Testing Genetic Hypotheses
In reality, the exact Mendelian ratios are rarely obtained. We rather observe numbers close to
expected ratio e.g., 1562 violet and 493 white flowers, 1000 round and 350 wrinkled seeds. How might we
explain the data? Let us to formulate a hypothesis that the traits are inherited according to the Mendel Principle
and the expected ratio is 3:1. Do our data really support this hypothesis? One procedure for testing the fit
between the predictions and the actual data uses chi-square statistics (χ2). The χ2 statistics allows to compare
obtained data with their predicted values. If the data are not in line with the predicted values, the statistics will
exceed a critical number and the genetic hypothesis will be rejected. Chi-square statistics is calculated as a
square of a difference between observed and expected number for each phenotypic class dividing by expected
number. Then the sum is computed over all phenotypic classes and the result is compared with the critical value,
which is typically a value for 5% of probability. If our chi-square value is lower than the critical value our
hypothesis about phenotypic distribution is correct.
CHAPTER 1. GENES
17
Yellow, Round
Green, Wrinkled
Yellow, Wrinkled
X
P1 (GGRR)
G - yellow
g - green
R - rounded
r - wrinkled
P2 (ggrr)
gw
GR
F1 (GgRr)
Self-fertilized
F2
Phenotypic ratio:
yellow, rounded - 9
yellow, wrinkled - 3
green, rounded - 3
green, wrinkled - 1
Genotypic ratio:
GGRR - 1
GgRR - 2
GGRr - 2
GgRr - 4
ggrr - 1
Gr
gR
gr
GGRR
GGRr
GgRR
GgRr
GGRr
GGrr
GgRr
Ggrr
GgRR
GgRr
ggRR
ggRr
GgRr
Ggrr
ggRr
ggrr
GR
Gr
gR
GGrr - 1
Ggrr - 2
ggRR - 1
ggRr - 2
GR
gr
FIGURE 1.4 Symbolic representation of a cross between peas. The second Mendel principle
PART 1. GENETICS
18
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Technological Links
http://www.ncbi.nlm.nih.gov
The NCBI database. Probable the biggest and the most used data base of DNA, protein and genomic sequences. For instance,
the Mendel's R gene sequence has the X8009 accession number. Except of huge scientific resources there are educational resources
including on line Mendelian inheritance in Animals (OMIA) and in Man (OMIN) – NCBI database of genes, inherited disorders and traits
with references and links to PubMed and Gene.
http://www.mendelweb.org/
The Web dedicated to Mendel and his work
http://www.ndsu.edu/pubweb/~mcclean/plsc431/mendel/mendel1.htm
Basic concepts of Mendelian genetics with examples
http://www.uwm.edu.pl/katgenbiol
•Photos of mutants: pea, barley, black oat – examples of allelic variation and characters controlling by a single gene. Also a good
demonstration of the efficiency of chemical mutagenesis. The collection can serve as a warning to some botanists against rash
delimitation of species based on just a few characters.
•Genetic problem book with sample solutions.
?
Challenging Questions
1. Explain how advances in genetics
influence life quality, social behavior and
politics.
2. Based on the NCBI database find a DNA sequence of a
plant gene, transcribe and translate it. How many
amino acids are in a putative protein?. How many
possibilities of sequence reading can you predict?
3. Compare DNA and RNA chemical structure. How the
DNA structure is connected with its function.
4. Compare plant and prokaryotic genes.
5. How can you explain Mendel laws by meiosis? Prepare
models of two non-homologous chromosomes (e.g.,
one blue, one red); locate one gene on each
chromosome (e.g., for height, and flower color), use
your desktop as a dividing cell of a diploid organism that
is heterozygous for each gene, simulate both meiotic
divisions.
6. Scientific papers contain four main sections of text –
Introduction, Material and Methods, Results and
Discussion. Imagine that you are Mendel and use the
scientific paper format to describe results of
experiments in pea and discovered laws.
7. Mendel seems to have done his research without any
government grant. Likely, he had no knowledge about
project management. Nevertheless, his experiments
enabled to formulate general laws. What do these
circumstances say about Mendel and his personality?
Compare his manner of work with scientists working on
research projects today.
8. In the chapter simple examples of interactions among
two genes were presented. Find examples of other
interactions that influence the distribution of
phenotypes in F2. Do these examples mean that
Mendel principles are not universal?
Problems to Solve
1. After crossing of two peas, a total of 125
plants with red flowers and 130 plants with white
flowers were obtained. What are genotypes and
phenotypes of crossed plants?
4. A breeder crossed two snapdragon plants with pink
flowers. He obtained 53 pink plants, 25 white plants and
27 red plants. What is the inheritance of flower color in
snapdragons?
2. What would be the frequency of six rowed barley plants
with long awns in F2 generation after crossing of six
rowed, awnless plant with two rowed plant with long
awns if F1 has two rows and long awns?
5. A geneticist crossed two true bred pea lines with white
flowers and he received only F1 plants with red flowers.
After self-fertilizing F1 he obtained 320 seeds that were
sown in a field. During flowering 180 plants appeared to
have red flowers and 140 white flowers. How to explain
results. Did a geneticist make a mistake? Might he mix
the seeds?
3. In the F2 of pea, a total 1 761 plants with tendrils and
round seeds were obtained, 628 plants with tendrils
and wrinkled seeds, 596 plants without tendrils and with
round seeds and 203 plants without tendrils and with
wrinkled seeds. Which characters are dominant? What
is the phenotype of F1? Describe all possible genotypes
and phenotypes of parents. How do both characters
inherit? Check the hypothesis using chi- square test.
6. The colour of a grape skin can be dark red, white and
pink. A single gene control these differences and the
allele for dark red skin is partially dominant over the
allele for white skin. Find in literature available in
Internet what the basis of differences in skin color is .
Further Reading
Gregor Mendel. 1909. Experiments in plant hybridisation. 2008 edition. New York: Cosimo, Inc. 54 p.
Gregor Mendel's experiments on plant hybrids: a guided study. Corcos AF, Monagham F editors. 1993.
The Mendel's original work as well as the work with editors explanations. It is the description of one of the best experiments in the science
history. It is very rare for one individual to carry out the whole process of science so completely and elegantly. It is a pioneering work not
only in genetics but also in integrating scientific disciplines – botany, physics and mathematics.
Snustad DP, Simmons MJ. 2006. Principles of genetics. Fourth Edition. John Willey & Sons, Inc. 866 p.
One of the best books in genetics, covers all topics, excellent pedagogy of the book.