Genetics

Background:

Homunculus in Sperm One question that has always intrigued us humans is “Where did we come from?” Long ago, Hippocrates and Aristotle proposed the idea of what they called pangenes, which they thought were tiny pieces of body parts. They thought that pangenes came together to make up the homunculus, a tiny pre-formed human that people thought grew into a baby. In the 1600s, the development of the microscope brought the discovery of eggs and sperm. Antonie van Leeuwenhoek, using a primitive microscope, thought he saw the homunculus curled up in a sperm cell. His followers believed that the homunculus was in the sperm, the father “planted his seed,” and the mother just incubated and nourished the homunculus so it grew into a baby. On the other hand, Regnier de Graaf and his followers thought that they saw the homunculus in the egg, and the presence of semen just somehow stimulated its growth. In the 1800s, a very novel, “radical” idea arose: both parents contribute to the new baby, but people (even Darwin, as he proposed his theory) still believed that these contributions were in the form of pangenes.

Modern genetics traces its beginnings to Gregor Mendel, an Austrian monk, who grew peas in a monastery garden. Mendel was unique among biologists of his time because he sought quantifiable data, and actually counted the results of his crosses. He published his findings in 1865, but at that time, people didn’t know about mitosis and meiosis, so his conclusions seemed unbelievable, and his work was ignored until it was rediscovered in 1900 by a couple of botanists who were doing research on something else. Peas are an ideal organism for this type of research because they are easy to grow and it is easy to control mating.

We will be looking at the sorts of genetic crosses Mendel did, but first, it is necessary to introduce some terminology:

Alleles

alternate forms for genes

Dominant Allele

the one that’s fully expressed; symbolized by a capital letter, often the first letter of the word for which it stands

Recessive Allele

the one that’s completely masked; symbolized by the SAME letter, but lower case

Homozygote

an individual with a pair of two of the same allele (BB or bb)

Heterozygote

an individual with a pair of two different alleles (Bb)

Genotype

the organism’s actual genetic make-up: for example, is it BB, Bb, or bb?

Phenotype

the organism’s expressed traits, what it looks like, how the genes are expressed: for example, does it have brown or blue eyes?

Monohybrid Cross and Probabilities:

A monohybrid cross is a genetic cross where only one gene/trait is being studied. P stands for the parental generation, while F₁ and F₂ stand for the first filial generation (the children) and second filial generation (the grandchildren). Each parent can give one chromosome of each pair, therefore one allele for each trait, to the offspring. Thus, when figuring out what kind(s) of gametes an individual can produce, it is necessary to choose one of the two alleles for each gene (which presents no problem if they are the same).

Purple Pea Flower
White Pea Flower For example, a true-breeding purple-flowered plant (the dominant allele for this gene) would have the genotype PP, and be able to make gametes with either P or P alleles. A true-breeding white-flowered plant (the recessive allele for this gene) would have the genotype pp, and be able to make gametes with either p or p alleles. Note that both of these parent plants would be homozygous. If one gamete from each of these parents got together to form a new plant, that plant would receive a P allele from one parent and a p allele from the other parent, thus all of the F₁ generation will be genotype Pp, they will be heterozygous, and since purple is dominant, they will look purple. What if two individuals from the F₁ generation are crossed with each other (Pp × Pp)? Since gametes contain one allele for each gene under consideration, each of these individuals could contribute either a P or a p in his/her gametes. Each of these gametes from each parent could pair with each from the other, thus yielding a number of possible combinations for the offspring. We need a way, then, to predict what the possible offspring might be. Actually, there are two ways of doing this. The first is to do a Punnett square (named after Reginald Crandall Punnett). The possible eggs from the female are listed down the left side, and there is one row for each possible egg. The possible sperm from the male are listed across the top, and there is one column for each possible sperm. The boxes at the intersections of these rows and columns show the possible offspring resulting from that sperm fertilizing that egg. The Punnett square from this cross would look like this:

	P	p
P	PP	Pp
p	Pp	pp

Note that the chance of having a gamete with a P allele is ½ and the chance of a gamete with a p allele is ½, so the chance of an egg with P and a sperm with P getting together to form an offspring that is PP is ½ × ½ = ¼, just like the probabilities involved tossing coins. Thus, the possible offspring include:
¼ PP,
(¼ Pp + ¼ pP, which are the same (Pp), since P is dominant over p), so = ½ Pp, and
¼ pp.

Another way to calculate this is to use a branching, tree diagram:

Choices for 1st allele		Choices for 2nd allele		Resulting Offspring	Probability
P (½)		P (½)	=	PP	¼
	↗
	↘
		p (½)	=	Pp	}  ²⁄₄ = ½
p (½)		P (½)	=	Pp
	↗
	↘
		p (½)	=	pp	¼

Note, again, that the chance of Pp is ¼ + ¼ = ½. A shorter way of telling how many PP, Pp, and pp could be expected, would be to say that there is a 1:2:1 genotype ratio (that comes from the ¼, ²⁄₄, and ¼, above, and by the way, notice that they add up to ⁴⁄₄, so we know we have accounted for everything). The chance of getting at least one dominant allele (either PP or Pp) necessary for purple color (this can be written as P–) is ¼ + ²⁄₄ = ¾, so we could say that there’s a 3:1 phenotype ratio. These two ratios are classic genotype and phenotype ratios for a monohybrid cross between two heterozygotes.

Mendel’s Four-Part Theory:

Based on his data, Mendel came up with a four-part theory of how genetics works:

1. There are alternate forms for genes called alleles.
2. Each adult organism has two alleles for each inherited trait (one from each parent).
3. Eggs and sperm have only one allele for each trait and unite to form an offspring with two again.
4. When the two alleles of a pair are different, one is fully expressed (the dominant allele), and the other completely masked (the recessive allele).

Some special cases:

Testcross:

If an organism has the dominant phenotype, but an unknown genotype, cross that individual with a homozygous recessive individual. If all offspring are dominant, the individual in question probably has two dominant alleles, but if any recessive offspring show up, the individual is a heterozygote.
Either:

	D	D
d	Dd	Dd
d	Dd	Dd

	D	d
d	Dd	dd
d	Dd	dd

or  

Incomplete Dominance:

Incomplete Dominance

A red-flowered plant × white-flowered will give heterozygotes that are pink. The red allele is not completely dominant, so the heterozygote is intermediate. In many other genes, the dominant allele is instructions for “do this” while the recessive allele is instructions for “we don’t know how to do this.” However, in incomplete dominance, both the instructions for (in this case) “make red” and the instructions for “make white” are carried out. The same is true in a person who is heterozygous for sickle-cell anemia: instructions for both “make normal hemoglobin” and “make abnormal hemoglobin” are carried out, so that person’s blood has some of each.

	R	r
R	RR	Rr
r	Rr	rr

Thus, ¼ are red (RR), ½ are pink (Rr), and ¼ are white (rr).

Multiple Alleles:

Blood Cell Antigens

Many genes only have two alleles. An interesting exception to this (there are others) is the human ABO blood group. The alleles are I^A, I^B, and i, so the possible genotypes/phenotypes are I^AI^A or I^Ai = type A blood, I^BI^B or I^Bi = type B blood, I^AI^B = type AB blood, and ii = type O blood. These phenotypes are not all equally-distributed in all populations of humans. In the U. S., about 45% of the population is type O, 42% type A, 10% type B, and only 3% type AB. However, other cultures/ethnic groups exist in which 75% of the people are type A and 25% type 0 (no B or AB), or where 40% of the people have type B with a mixture of the other types also present.

(Rh factor, by the way, is a totally separate gene with Rh⁺ [R] and Rh^– [r] alleles [actually, that gene also has multiple alleles, but the vast majority of people are positive or negative for one particular allele called “D”]. In the U. S., about 85% of the population is Rh⁺ [RR and Rr] and 15% Rh^– [rr], thus the chances of someone being O^– [having both ii and rr] would be 45% × 15% = 6.75%. The rarest blood type in the U. S. would be AB^–, about 0.45% of the population.]

This is discussed in more depth in the human genetics notes.

Pleiotropy:

The ability of one gene to have multiple effects: for example, a deaf white cat or a cross-eyed white tiger.

Polygenic trait:

A trait controlled by several genes: for example, human skin color is controlled by about three or four genes (depending on which book you read), each of which has two alleles. The various skin colors arise from various combinations of the alleles in these several genes. Note that skin color also is influenced by environment, and exposure to sunlight will stimulate synthesis of the pigment melanin in skin.

Dihybrid Cross:

This is a cross where two traits/genes are under consideration. For example, in peas if R = round, so r = wrinkled, and Y = yellow, so y = green, in a cross between RRYY × rryy, the gametes must have ONE ALLELE FOR EACH GENE, so in this case, RRYY could produce gametes with one R AND one Y, or RY, and rryy could produce gametes with one r AND one y, or ry. The F₁ would get RY from one parent and ry from the other, thus would all be RrYy. Note that it is necessary to keep the alleles for the same gene together and put the dominant allele (capital letter) first for EACH GENE. In calculating what the F₂ generation would be, you must first figure out what gametes (eggs or sperm) each parent can make. It is very important to remember that gametes must have ONE ALLELE FOR EACH GENE, so figure out the possibilities this way:

Choices for 1st allele		Choices for 2nd allele		Resulting Gametes	Probability
R (½)		Y (½)	=	RY	¼
	↗
	↘
		y (½)	=	Ry	¼
r (½)		Y (½)	=	rY	¼
	↗
	↘
		y (½)	=	ry	¼

Thus, each parent could make four kinds of gametes, so the Punnett square would be 4 × 4 cells.

	RY	Ry	rY	ry
RY	RRYY	RRYy	RrYY	RrYy
Ry	RRYy	RRyy	RrYy	Rryy
rY	RrYY	RrYy	rrYY	rrYy
ry	RrYy	Rryy	rrYy	rryy

This would give the following possible offspring:

Possible Offspring:	Genotype Ratio		Phenotypes	Phenotype Ratio
RRYY	1		R–Y–	9
RRYy	2		R–yy	3
RRyy	1		rrY–	3
RrYY	2		rryy	1
RrYy	4		TOTAL	16
Rryy	2
rrYY	1
rrYy	2
rryy	1
TOTAL	16

Thus the genotype ratio is 1:2:1:2:4:2:1:2:1 and the phenotype ratio is 9:3:3:1. Notice the “shorthand” used to represent the phenotypes. Since both RR and Rr will look round, rather than writing “round pea seeds,” we can use R– to say “it’s got at least one R, so it’ll be round.”

Try This:

On your own, try I^AiRr × I^BiRr, a cross involving both the ABO blood group and Rh factor. Note, a little later, we will discuss what those blood groups actually are/do.

Genotype and Phenotype Are Not the Same:

It is important to understand the difference between genotype and phenotype. For example, for most of the genes we will be discussing, an organism with the genotype of, say, BB and an organism who is Bb both have at least one dominant allele for that gene, and thus, would both express/show/be the dominant phenotype. If, for example, this was a gene for human eye color, then “B” would represent the dominant allele which codes for “make brown eyes,” and “b” would represent the recessive allele which codes for blue eyes (technically, more like, “we don’t know how to make brown,” so blue is the “default”). Thus, people whose genotypes are either BB or Bb both have instructions for “make brown,” so the phenotypes of both are brown eye color.

As another example where many people get confused, an individual’s sex is a phenotype, not a genotype! We can talk of a person as having either two X chromosomes (XX) or one X and one Y chromosome (XY). Those are, essentially, genotypes, and there are also a few people who have genotypes such as X (also called XO), XXX, or XXY. Those X and Y chromosomes contain/consist of a number of genes, and factors such as what alleles a person has for each of those genes, how those alleles are expressed, and how that gene expression affects/influences various body processes will all come together to produce that phenotype which we call a person’s sex. In humans, if all those alleles are expressed in what we like to think of as being “normal,” then, usually, X, XX, and XXX are expressed as a “female” phenotype (with X and XXX producing some other physical characteristics considered to be “typical” for those genotypes), while the result of how the XY combination is expressed usually results in what we refer to as a “male” phenotype.

However, while uncommon, it is entirely possible that due to a mutation in some gene, somewhere, that codes for some enzyme or hormone, a person with 2 X chromosomes (XX) can have a male phenotype; can, clearly and unambiguously, be male. Similarly, while also not very common, it is also possible, due to a mutation in some gene, somewhere, that codes for some hormone or enzyme, that a person with an X and a Y chromosome (XY) can have a female phenotype; can, clearly and unambiguously, be female. Interestingly, because of differences in how the genes/alleles are expressed, the XXY combination typically results in a male in humans but results in a female in fruit flies.

Our culture, our way of thinking, is so locked into having/needing to choose between male and female as the only two options, that while in the “unambiguous” cases just mentioned where a person’s expressed phenotype obviously fits our preconception of maleness or femaleness even if their genotype/chromosomes are different from what we might think (and of which we would not even be aware unless we were that person’s doctor — and maybe not even then), on the other hand, people whose bodies don’t exactly and neatly fit into one of those two categories are lumped together in a group and labeled as “intersex.” Typically, at birth, their parents are advised by medical personnel to choose whether they wish to bring this child up as a “boy” or a “girl,” and may even be pressured into having cosmetic surgery performed on the child to make the child look more like the chosen sex assignment, yet it frequently happens as the child grows up, due to the influence of internal factors such as hormones, etc., that “he” or “she” does not “feel like” the sex which the doctors assigned/labeled at birth. On the other hand, if parents try to be more neutral and let the child make that choice when and if the child decides to do so, that tends to expose the child to a lot of ridicule from classmates and even other adults.

Pedigrees:

Sample Pedigree In pedigrees, a circle represents a female and a square represents a male. Filled-in vs. open symbols are used to distinguish between two phenotypes for the gene in question, and a half-filled symbol may be used to designate a carrier (a heterozygous individual who has a recessive allele for some gene, but is not showing that phenotype). Here is a sample pedigree for eye color. If the people with filled-in (dark) symbols have brown eyes and those with open (light) symbols have blue eyes, can you figure out the genotypes of the people marked with *?

Genetic Basis of Behavior, Polyploids:

Some further notes on genetics: We tend to think of genes that control what an organism looks like, etc., but genes can also control behavior of animals. For example, bird songs and other courtship rituals are under genetic control. The most successful competitors live and mate and pass on their genes. On a different subject, many of our horticultural plant varieties are polyploid plants. Typically, like us, plants are diploid. Horticulturists have figured out ways to manipulate plants and make triploid or tetraploid plants. Typically these plants are larger and/or have bigger or more ruffled flowers and/or larger seeds. While triploid plants are usually sterile (with three sets of chromosomes they have trouble doing meiosis), tetraploid plants are usually fertile and can reproduce. I believe I read somewhere that the wheat we eat is actually a hexaploid, resulting in seeds that are quite a bit larger than its grass-like ancestor.

References:

Borror, Donald J. 1960. Dictionary of Root Words and Combining Forms. Mayfield Publ. Co.

Campbell, Neil A., Lawrence G. Mitchell, Jane B. Reece. 1999. Biology, 5^th Ed.   Benjamin/Cummings Publ. Co., Inc. Menlo Park, CA. (plus earlier editions)

Campbell, Neil A., Lawrence G. Mitchell, Jane B. Reece. 1999. Biology: Concepts and Connections, 3^rd Ed.   Benjamin/Cummings Publ. Co., Inc. Menlo Park, CA. (plus earlier editions)

Marchuk, William N. 1992. A Life Science Lexicon. Wm. C. Brown Publishers, Dubuque, IA.