What is gene,alleles and traits?

What is gene,alleles and traits?

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Gene is present on chromosomes so the alleles should be same as gene but what is difference between them and what is traits?

An allele is a variant of a gene. To understand what that means, the easiest is to consider a simplified example…

Simplified example

There is a gene for eye color. Eye color is a trait (aka. phenotypic trait). In the human population, there are different variants at the gene for eye color. These variants are called alleles. There is the allele 'blue eyes', the allele 'green eyes', the allele 'brown eyes', etc…


Above I wroteAn allele is a variant of a gene. It would actually be more correct to sayAn allele is a variant at a locusbut I did not want to introduce one extra word too early. A locus is a region of arbitrary size on a chromosome.

Genetic variation and phenotypic variation

If there are more than one allele at a given locus, then there is genetic variation in the population at this locus. This genetic variation can cause variation in various phenotypic traits.

Considering again the example of the gene for eye color, the fact that there are different alleles at the gene for eye color causes that there is variation in eye color in the population.

Although it may be too advanced for you, you can learn more about these concepts and how it related to heritability in this post.

Source of information

You can also have a look at the wikipedia articles

Or have a look at an intro course such as these ones at Khan Academy.

Diploid organisms typically have two alleles for a trait. When allele pairs are the same, they are homozygous. When the alleles of a pair are heterozygous, the phenotype of one trait may be dominant and the other recessive. The dominant allele is expressed and the recessive allele is masked. This is known as complete genetic dominance. In heterozygous relationships where neither allele is dominant but both are completely expressed, the alleles are considered to be co-dominant. Co-dominance is exemplified in AB blood type inheritance. When one allele is not completely dominant over the other, the alleles are said to express incomplete dominance. Incomplete dominance is exhibited in pink flower color inheritance from red and white tulips.

While most genes exist in two allele forms, some have multiple alleles for a trait. A common example of this in humans is ABO blood type. Human blood type is determined by the presence or absence of certain identifiers, called antigens, on the surface of red blood cells. Individuals with blood type A have A antigens on blood cell surfaces, those with type B have B antigens, and those with type O have no antigens. ABO blood types exist as three alleles, which are represented as (I A , I B , I O ). These multiple alleles are passed from parent to offspring such that one allele is inherited from each parent. There are four phenotypes (A, B, AB, or O) and six possible genotypes for human ABO blood groups.

Blood Groups Genotype
A (I A ,I A ) or (I A ,I O )
B (I B ,I B ) or (I B ,I O )
AB (I A ,I B )
O (I O ,I O )

The alleles I A and I B are dominant to the recessive I O allele. In blood type AB, the I A and I B alleles are co-dominant as both phenotypes are expressed. The O blood type is homozygous recessive containing two I O alleles.


Genes govern the traits of an organism. They do so by acting as instructions to make proteins. Proteins are the diverse molecules that play many critical roles in our bodies, such as producing hormones and creating antibodies.

Humans have two copies (or alleles) of each gene, one inherited from each parent. Alleles play a significant role in shaping each human’s individual features. Alleles are versions of the same gene with slight variations in their sequence of DNA bases. These small differences among alleles of the same gene contribute to each person’s unique characteristics.

Related Biology Terms

  • Polymerase – An enzyme used to bind monomers into polymers, or smaller molecules into large ones.
  • Mutation – When DNA polymerase makes a mistake, and places the wrong nucleic acid in a DNA chain.
  • Genotype – The alleles present at a specific locus in the DNA, which give rise to phenotypes through the production (or lack of production) of protein.
  • Phenotype – The physical manifestation of the DNA, expressed in terms of protein.

1. Red hair is a recessive trait. Both of your parents have red hair. You have brown hair, a dominant trait. You begin to suspect that you are adopted. Is it more likely that you are adopted or that your hair mutated.
A. Adopted more likely
B. Mutated more likely
C. Equally likely

2. Mendel, when breeding pea plants, noticed that when he would cross a tall plant and a short plant he would not get a medium plant as he expected. Instead, he would get some short plants, and some tall plants. Why is this?
A. Height is controlled by a gene, of which there are two alleles: tall and short.
B. Some plants were shadowing the others, not allowing them to get sunlight.
C. Medium plants are selected against by natural selection.

3. A pregnant mother gets skin cancer. The cancer forms a tumor, but has not metastasized, or traveled throughout the body, yet. Her baby is born. Does the baby have risk of inheriting the mutations that caused the cancer?
A. Yes
B. No
C. It depends

Mendel’s laws and meiosis

Mendel’s laws of segregation and independent assortment are both explained by the physical behavior of chromosomes during meiosis.

Segregation occurs because each gamete inherits only one copy of each chromosome. Each chromosome has only one copy, or allele, of each gene therefore each gamete only gets one allele. Segregation occurs when the homologous chromosomes separate during meiotic anaphase I . This principle is illustrated here:

Source: Adapted from Wikimedia Commons (

Independent assortment occurs because homologous chromosomes are randomly segregated into different gametes ie, one gamete does not only get all maternal chromosomes while the other gets all paternal chromosomes. Independent assortment occurs when homologous chromosomes align randomly at the metaphase plate during meiotic metaphase I . This principle is illustrated here, where the patterns on the left and right show two independent ways that the little r allele from the round gene can be matched with an allele (y or Y) from the yellow gene:

chromosomes. Source: Adapted from Wikimedia Commons ( and OpenStax Biology (

Random, independent assortment during metaphase I can be demonstrated by considering a cell with a set of two chromosomes (n = 2). In this case, there are two possible arrangements at the equatorial plane in metaphase I. The total possible number of different gametes is 2 to the power of n, where n equals the number of chromosomes in a set. In this example, there are four possible genetic combinations for the gametes. With n = 23 in human cells, there are over 8 million possible combinations of paternal and maternal genotypes in a potential offspring.

Here’s a quick summary of many of these ideas from Ted Ed:

and here is Khan Academy’s take:

The Test Cross Distinguishes the Dominant Phenotype

Beyond predicting the offspring of a cross between known homozygous or heterozygous parents, Mendel also developed a way to determine whether an organism that expressed a dominant trait was a heterozygote or a homozygote. Called the test cross , this technique is still used by plant and animal breeders. In a test cross, the dominant-expressing organism is crossed with an organism that is homozygous recessive for the same characteristic. If the dominant-expressing organism is a homozygote, then all F1 offspring will be heterozygotes expressing the dominant trait ([link]). Alternatively, if the dominant expressing organism is a heterozygote, the F1 offspring will exhibit a 1:1 ratio of heterozygotes and recessive homozygotes ([link]). The test cross further validates Mendel’s postulate that pairs of unit factors segregate equally.

In pea plants, round peas (R) are dominant to wrinkled peas (r). You do a test cross between a pea plant with wrinkled peas (genotype rr) and a plant of unknown genotype that has round peas. You end up with three plants, all which have round peas. From this data, can you tell if the round pea parent plant is homozygous dominant or heterozygous? If the round pea parent plant is heterozygous, what is the probability that a random sample of 3 progeny peas will all be round?

Many human diseases are genetically inherited. A healthy person in a family in which some members suffer from a recessive genetic disorder may want to know if he or she has the disease-causing gene and what risk exists of passing the disorder on to his or her offspring. Of course, doing a test cross in humans is unethical and impractical. Instead, geneticists use pedigree analysis to study the inheritance pattern of human genetic diseases ([link]).

What are the genotypes of the individuals labeled 1, 2 and 3?

Human Sex-linked Disorders

Sex-linkage studies provided the fundamentals for understanding X-linked recessive disorders in humans, including red-green color blindness, and Types A and B hemophilia. Because human males need to inherit only one recessive X allele to be affected, X-linked disorders are disproportionately observed in males. Females must inherit recessive X-linked alleles from both parents in order to express the trait. When they inherit one recessive X-linked allele and one dominant X-linked allele, they are carriers of the trait and are typically unaffected. However, female carriers can contribute the trait to their sons, resulting in the son exhibiting the trait. They can contribute the recessive allele to their daughters, resulting in the daughters being carriers of the trait (Figure 10). Although some Y-linked recessive disorders exist, typically they are associated with male infertility and are not transmitted to subsequent generations.

Figure 10. The son of a woman who is a carrier of a recessive X-linked disorder will have a 50 percent chance of being affected. A daughter will not be affected, but will have a 50 percent chance of being a carrier like her mother.

Link to Learning

Watch this video to learn more about sex-linked traits.

How Are Traits Inherited?

How are traits passed from one generation to the next? This happens when gametes unite. When an egg is fertilized by a sperm, for each chromosome pair, we receive one chromosome from our father and one from our mother.

For a particular trait, we receive what is known as an allele from our father and one allele from our mother. An allele is a different form of a gene. When a given gene controls a characteristic that is expressed in the phenotype, the different forms of a gene show as the different characteristics that are observed in the phenotype.

In simple genetics, alleles can be homozygous or heterozygous. Homozygous refers to having two copies of the same allele, while heterozygous refers to having different alleles.

Section Summary

When true-breeding or homozygous individuals that differ for a certain trait are crossed, all of the offspring will be heterozygotes for that trait. If the traits are inherited as dominant and recessive, the F1 offspring will all exhibit the same phenotype as the parent homozygous for the dominant trait. If these heterozygous offspring are self-crossed, the resulting F2 offspring will be equally likely to inherit gametes carrying the dominant or recessive trait, giving rise to offspring of which one quarter are homozygous dominant, half are heterozygous, and one quarter are homozygous recessive. Because homozygous dominant and heterozygous individuals are phenotypically identical, the observed traits in the F2 offspring will exhibit a ratio of three dominant to one recessive.

Alleles do not always behave in dominant and recessive patterns. Incomplete dominance describes situations in which the heterozygote exhibits a phenotype that is intermediate between the homozygous phenotypes. Codominance describes the simultaneous expression of both of the alleles in the heterozygote. Although diploid organisms can only have two alleles for any given gene, it is common for more than two alleles of a gene to exist in a population. In humans, as in many animals and some plants, females have two X chromosomes and males have one X and one Y chromosome. Genes that are present on the X but not the Y chromosome are said to be X-linked, such that males only inherit one allele for the gene, and females inherit two. Finally, some alleles can be lethal. Recessive lethal alleles are only lethal in homozygotes, but dominant lethal alleles are fatal in heterozygotes as well.

Additional Self Check Questions

1. In pea plants, round peas (R) are dominant to wrinkled peas (r). You do a test cross between a pea plant with wrinkled peas (genotype rr) and a plant of unknown genotype that has round peas. You end up with three plants, all which have round peas. From this data, can you tell if the round pea parent plant is homozygous dominant or heterozygous? If the round pea parent plant is heterozygous, what is the probability that a random sample of 3 progeny peas will all be round?

2. What are the genotypes of the individuals labeled 1, 2 and 3?

3. What ratio of offspring would result from a cross between a white-eyed male and a female that is heterozygous for red eye color?

4. The gene for flower position in pea plants exists as axial or terminal alleles. Given that axial is dominant to terminal, list all of the possible F1 and F2 genotypes and phenotypes from a cross involving parents that are homozygous for each trait. Express genotypes with conventional genetic abbreviations.

5. Use a Punnett square to predict the offspring in a cross between a dwarf pea plant (homozygous recessive) and a tall pea plant (heterozygous). What is the phenotypic ratio of the offspring?

6. Can a human male be a carrier of red-green color blindness?


1. You cannot be sure if the plant is homozygous or heterozygous as the data set is too small: by random chance, all three plants might have acquired only the dominant gene even if the recessive one is present. If the round pea parent is heterozygous, there is a one-eighth probability that a random sample of three progeny peas will all be round.

2. Individual 1 has the genotype aa. Individual 2 has the genotype Aa. Individual 3 has the genotype Aa.

3. Half of the female offspring would be heterozygous (X W X w ) with red eyes, and half would be homozygous recessive (X w X w ) with white eyes. Half of the male offspring would be hemizygous dominant (X W Y) withe red yes, and half would be hemizygous recessive (X w Y) with white eyes.

4. Because axial is dominant, the gene would be designated as A. F1 would be all heterozygous Aa with axial phenotype. F2 would have possible genotypes of AA, Aa, and aa these would correspond to axial, axial, and terminal phenotypes, respectively.

5. The Punnett square would be 2 × 2 and will have T and T along the top, and T and t along the left side. Clockwise from the top left, the genotypes listed within the boxes will be Tt, Tt, tt, and tt. The phenotypic ratio will be 1 tall:1 dwarf.

6. No, males can only express color blindness. They cannot carry it because an individual needs two X chromosomes to be a carrier.

What are Alleles? (with pictures)

Alleles are corresponding pairs of genes located at specific positions in the chromosomes. Together, they determine the genotype of their host organism. For example, the alleles for eye color are found on chromosomes 15 and 19, and depending on which ones someone has, he or she may have blue, brown, green, gray, or hazel eyes, and sometimes a mixture of these traits is present. Alleles that determine some aspect of the phenotype, the physical appearance of an organism, are said to be “coding alleles,” while “non-coding alleles” or “junk DNA” are those which do not appear to have an impact on phenotype.

There are numerous combinations of alleles, ranging from simple pairs to complex relationships between multiple ones that determine someone's appearance. When both of the alleles in a pair are the same, they are said to be “homozygous,” while if they are different, the situation is described as “heterozygous.” In the case of homozygous alleles, the expression of phenotype is usually very straightforward. In heterozygous instances, however, the phenotype of the organism is determined by which one is dominant, meaning that the one overrides the other.

In the case of eye color, if someone inherits a blue and a brown allele, his or her eyes will be brown, because brown is a dominant genetic trait, requiring only one allele for expression. However, if that person had a child with someone who also carried a blue allele and both parents passed the blue trait down, the child would have blue eyes. This explains why blue-eyed children sometimes randomly pop up in a brown-eyed family: because someone in the family's genetic history had blue eyes.

Researchers are constantly identifying new alleles, and developing specific tests to look for certain ones, especially those linked with genetic conditions or genetic predispositions to disease. In genetic testing for conditions like Huntington's Disease, a medical lab can search for the specific spot on chromosome four where the Huntington's allele resides. Unfortunately, Huntington's is a dominant trait, so it only takes one allele to develop the condition.

Alleles are also use in DNA tests used to establish a connection between a known DNA sample and an unknown sample. Crime labs, for example, test DNA evidence from crime scenes against known DNA databases and potential suspects, and DNA tests are also used to test the parentage of children. Such testing is often extremely accurate, as long as the samples are handled properly and they are of good quality.

Ever since she began contributing to the site several years ago, Mary has embraced the exciting challenge of being a InfoBloom researcher and writer. Mary has a liberal arts degree from Goddard College and spends her free time reading, cooking, and exploring the great outdoors.

Ever since she began contributing to the site several years ago, Mary has embraced the exciting challenge of being a InfoBloom researcher and writer. Mary has a liberal arts degree from Goddard College and spends her free time reading, cooking, and exploring the great outdoors.

What’s the Difference Between a Gene and an Allele?

A gene is a unit of hereditary information. Except in some viruses, genes are made up of DNA, a complex molecule that codes genetic information for the transmission of inherited traits. Alleles are also genetic sequences, and they too code for the transmission of traits. So, what it is the difference between a gene and an allele?

The short answer is that an allele is a variant form of a gene. Explained in greater detail, each gene resides at a specific locus (location on a chromosome) in two copies, one copy of the gene inherited from each parent. The copies, however, are not necessarily the same. When the copies of a gene differ from each other, they are known as alleles. A given gene may have multiple different alleles, though only two alleles are present at the gene’s locus in any individual.

Alleles can sometimes result in different phenotypes (observable traits), with certain alleles being dominant (overriding the traits of other alleles) or, in some cases, multiple alleles acting in a codominant fashion. An example of the latter is the human ABO blood group system, in which persons with type AB blood have one allele for A and one for B (persons with neither allele are type O). An example of dominant allele expression is flower color in pea plants. A plant with purple flowers actually has a genotype (genetic makeup) consisting of a gene with a dominant P and a recessive p allele.