Difficulty: Introductory | Prerequisites: None (this is a foundation chapter).
Tags: Mendelian genetics, Gregor Mendel, alleles, genotype, phenotype, dominant, recessive, segregation, independent assortment, Punnett square, monohybrid cross, dihybrid cross, F1 generation, F2 generation, homozygous, heterozygous, pea plants, 3:1 ratio, 9:3:3:1 ratio, incomplete dominance, codominance, multiple alleles, polygenic inheritance, epistasis
This is the opening chapter of molecular biology, and it covers the rules of inheritance that Gregor Mendel worked out in the 1860s using pea plants. Everything else in genetics builds on what is here: how traits pass from parent to offspring, how alleles behave during reproduction, and why offspring ratios come out the way they do. If you are coming in cold, start here. If you already know the basics of DNA structure and replication from later chapters, this material gives you the historical and conceptual framework those later chapters assume.
Mendel discovered that inherited traits are controlled by discrete factors (genes) that come in pairs and separate during gamete formation. Crossing experiments in pea plants revealed predictable ratios (3:1 for single traits, 9:3:3:1 for two traits) explained by the laws of segregation and independent assortment. Later work showed that not all inheritance is simple dominance: incomplete dominance, codominance, multiple alleles, polygenic traits, and epistasis all add complexity.
Allele
Alternative forms of a gene at the same locus. Written as uppercase for dominant (R) and lowercase for recessive (r). In simple terms, alleles are the different "versions" of a gene that determine which variant of a trait you express.
Homozygous
Having two identical alleles for a gene (RR or rr). Think of it as both copies of the gene saying the same thing.
Heterozygous
Having two different alleles for a gene (Rr). One copy says one thing, the other says something different. The dominant allele typically determines the visible trait.
Dominant
The allele whose phenotype is expressed in a heterozygote. Written as a capital letter (R, Y) or with a + symbol. In simple terms, the version that "wins" when paired with a recessive allele.
Recessive
The allele whose phenotype is hidden in a heterozygote and only expressed when homozygous (rr). Think of it as the version that only shows up when there is no dominant copy to override it.
Genotype
The actual genetic makeup of an organism (e.g. RR, Rr, rr). This is what the DNA says.
Phenotype
The visible or measurable appearance of an organism. This is what you can observe. Two organisms with different genotypes (RR and Rr) can share the same phenotype if one allele is dominant.
Diploid
A cell containing two complete sets of chromosomes (2n). In humans, 2n = 46.
Haploid
A cell containing one set of chromosomes (n). In humans, n = 23. Gametes (sperm and egg) are haploid.
Segregation (Mendel's 1st Law)
The separation of the two alleles of a gene pair during gamete formation, so each gamete carries only one allele. Think of it as alleles being split apart when sex cells are made.
Independent assortment (Mendel's 2nd Law)
Genes for different traits sort independently of one another during gamete formation, provided they are on different chromosomes (or far apart on the same one). In simple terms, inheriting one trait does not force you to inherit another in a particular way.
Principle of dominance
When an organism has at least one dominant allele, it displays the dominant phenotype. The recessive phenotype only appears when both alleles are recessive.
True breeding / pure breeding
A strain that produces offspring identical to the parents for a given trait, generation after generation. These organisms are homozygous for the trait in question.
F1 generation (first filial)
The first generation of offspring from a cross between two true-breeding parents.
F2 generation (second filial)
The offspring produced by crossing F1 individuals with each other.
Incomplete dominance
A pattern where the heterozygote shows a phenotype intermediate between the two homozygotes. Think of it as blending: red (RR) crossed with white (rr) snapdragons gives pink (Rr).
Codominance
A pattern where both alleles in a heterozygote are fully expressed simultaneously, with no blending. Think of it as both traits appearing side by side, like a roan cow showing distinct red and white hairs.
Epistasis
When one gene modifies or masks the expression of another gene. Think of it as one gene acting as a gatekeeper for another gene's effect.
Polygenic inheritance
A trait controlled by two or more genes, producing a continuous range of phenotypes. Think of it as many genes each contributing a small amount to the final result, such as hair colour or eye colour.
Gregor Mendel (born 1822, Austrian Empire) became an Augustinian monk in Brno to gain access to education and scientific resources
He studied pea plant hybrids and tracked how traits passed from one generation to the next
His 1865 paper, "Experiments in Plant Hybridization," was presented to the Natural Society at Brno
Mendel recognised that discrete factors (what we now call genes) controlled inheritance, although his paper never used the word "gene" or the 9:3:3:1 ratio explicitly
His work was ignored for roughly 35 years, rediscovered independently around 1900 by Hugo de Vries, Carl Correns, and Erich von Tschermak
Darwin read and annotated Mendel's paper but apparently did not grasp its significance; had he done so, genetics might have advanced 30 years sooner
Pea plants had easily observed, contrasting traits (seven traits, each happening to be on a different chromosome)
Mendel kept meticulous records of at least 29,000 plant crosses
He could only infer genotype from phenotype and progeny; genetics relied entirely on phenotype until molecular techniques arrived in the 1970s
Mendel chose parental strains that bred true (homozygous) for a single contrasting trait
Crossing true-breeding yellow seeds (YY) with true-breeding green seeds (yy) produced F1 offspring that were all yellow (Yy), because Y is dominant over y
F1 x F1 (Yy x Yy) gave a 3:1 phenotypic ratio in the F2: three-quarters yellow, one-quarter green
Genotypic ratio: 1 YY : 2 Yy : 1 yy
The same 3:1 ratio held for all seven traits he studied
Yellow F2 plants (YY or Yy): one-third bred true (YY), two-thirds showed a 3:1 ratio when selfed (Yy)
Green F2 plants (yy): all bred true and only produced green offspring
For a monohybrid cross Rr x Rr:
Probability of RR = 1/4
Probability of Rr = 1/2
Probability of rr = 1/4
Probability of dominant phenotype (R_) = 3/4
Probability of recessive phenotype (rr) = 1/4
Mendel crossed round yellow seeds (RRYY) with wrinkled green seeds (rryy)
Round seeds have the starch branching enzyme SBE1; wrinkled seeds lost this enzyme through an 800 bp insertion, leaving them with higher water content and sweeter taste
Yellow seeds have the SGR enzyme that breaks down chlorophyll
F1: all round yellow (RrYy)
F1 x F1 gave a 9:3:3:1 phenotypic ratio in the F2:
9 round yellow (R_Y_), both enzymes present
3 round green (R_yy), SBE1 present, SGR absent
3 wrinkled yellow (rrY_), SGR present, SBE1 absent
1 wrinkled green (rryy), both enzymes absent
The 9:3:3:1 ratio holds because each trait segregates independently
Treat each gene pair separately, then multiply:
P(genotype RRYy) from RrYy x RrYy = 1/4 (RR) x 1/2 (Yy) = 1/8
P(genotype rryy) = 1/4 x 1/4 = 1/16
P(phenotype round yellow, R_Y_) = 3/4 x 3/4 = 9/16
P(phenotype wrinkled yellow, rrY_) = 1/4 x 3/4 = 3/16
For crosses with more loci, the same multiplication principle applies:
AaBbcc x AabbCC, probability of aaBbCc = 1/4 x 1/2 x 1 = 1/8
AaBbccDd x AabbCCDD, probability of aaBbCcdd = 1/4 x 1/2 x 1/2 x 0 = 0 (DD cannot produce dd)
Law of Segregation (1st Law): genes occur in pairs (alleles), and at the time of gamete formation one allele from each pair enters each gamete. Half the gametes carry one allele, half carry the other. Inferred from F1 x F1 crosses.
Law of Independent Assortment (2nd Law): genes for different traits assort independently of one another during gamete formation.
Principle of Dominance: some alleles are dominant while others are recessive. An organism with at least one dominant allele displays the dominant phenotype.
Incomplete dominance
Some alleles are neither fully dominant nor fully recessive
Snapdragons: red pigment (anthocyanin) is produced at 100% in RR, 50% in Rr (pink), and 0% in rr (white)
Pure red x pure white gives all pink F1
F1 x F1 gives 1 red : 2 pink : 1 white (1:2:1 phenotypic ratio, compared to 3:1 with complete dominance)
Sickle cell anaemia is incomplete dominance because the heterozygote (sickle cell trait) has an intermediate phenotype, though the presence of two distinct RBC shapes is technically codominance
Codominance
Both alleles are fully expressed simultaneously; traits do not blend
Example: roan cattle (red hairs + white hairs, not pink), erminette chickens (black + white feathers)
Codominance with multiple alleles: ABO blood types
Three alleles: A, B, and O (no enzyme)
A and B encode different glycosyltransferases (differing by just four amino acids) on chromosome 9
A and B are codominant (AB blood type); both are dominant over O
Everyone carries two alleles; possible genotypes: AA, AO, BB, BO, AB, OO
Multiple alleles
Mendel assumed only two alleles per gene, but many genes have more
Rabbit coat colour: four alleles in a dominance series C > c^ch > c^h > c, producing dark grey/brown, chinchilla, point restricted (Himalayan), and albino phenotypes
Each rabbit still carries only two alleles
Polygenic inheritance
Many traits are controlled by two or more genes, producing a continuum of phenotypes rather than discrete categories
Alleles in a series range from high enzyme activity (dominant) to low activity (recessive)
Hair colour: the ebony allele produces high levels of brown pigment (dominant to all others); swedish-blonde produces very little (recessive to all others); intermediate alleles (honey, mahogany, oak) fall between
Eye colour: at least 10 genes (OCA2, HERC2, SLC24A4, TYR, and others) explain roughly 50% of variation
Epistasis: dog coat colour
Determined by at least two genes:
B gene: dark pigment (eumelanin) via TYRP1
E gene: expression in hair via melanocortin 1 receptor (MCR1), epistatic to B
The E gene controls whether the B gene's pigment is deposited in hair, making it the gatekeeper
In 1936, the statistician Ronald Fisher analysed Mendel's results and concluded they were "too good," fitting the expected ratios more closely than chance would predict
Possible explanations include confirmation bias (Mendel may have continued collecting data until ratios matched expectation)
Recent analyses generally suggest Mendel's data was correct and unbiased
Monohybrid cross (Aa x Aa): 3:1 phenotypic ratio, 1:2:1 genotypic ratio
Dihybrid cross (AaBb x AaBb): 9:3:3:1 phenotypic ratio
Incomplete dominance (Aa x Aa): 1:2:1 phenotypic ratio (matches genotypic ratio)
Probability rule: for independent events, multiply individual probabilities. P(genotype) = P(allele combo at locus 1) x P(allele combo at locus 2) x ...
Mendel's laws underpin genetic counselling, crop breeding, and livestock selection. Any time a breeder predicts the proportion of offspring with a desired trait, they are using Mendelian ratios.
ABO blood typing (codominance with multiple alleles) is the basis of safe blood transfusion and is used in forensic identification.
Understanding epistasis is essential in pharmacogenomics: one gene may control whether another gene's drug-metabolising enzyme is active.
Students often think dominant means "more common" or "better." It does not. Dominant simply means the allele that is expressed in the heterozygote. A dominant allele can be rare and harmful.
Students frequently confuse incomplete dominance with codominance. Incomplete dominance produces a blend (pink from red + white). Codominance produces both traits side by side (red patches and white patches, not pink).
Students sometimes assume the 3:1 ratio means exactly three out of every four offspring will be dominant. The ratio is a probability, not a guarantee. Small sample sizes can deviate considerably.
Students often forget that independent assortment only applies to genes on different chromosomes (or far apart on the same chromosome). Linked genes do not follow the 9:3:3:1 ratio.
⚠️ Be able to calculate genotypic and phenotypic ratios for monohybrid (3:1) and dihybrid (9:3:3:1) crosses using both Punnett squares and the probability method.
⚠️ Know the difference between incomplete dominance (1:2:1 phenotypic ratio) and codominance (both alleles fully expressed, no blending).
⚠️ Understand that Mendel's Law of Independent Assortment has a major caveat: it only holds for genes on separate chromosomes or genes far enough apart on the same chromosome. Gene linkage (covered in Part 3) is the exception.
⚠️ Be prepared to apply the multiplication rule across multiple loci (e.g. probability of aaBbCcdd from a given cross).
True or False: A heterozygous organism (Rr) always shows the dominant phenotype under complete dominance.
Fill in the blank: The F2 phenotypic ratio from a monohybrid cross (Aa x Aa) with complete dominance is ______.
True or False: In codominance, the heterozygote shows a blended intermediate phenotype.
Fill in the blank: The F2 phenotypic ratio from a dihybrid cross (AaBb x AaBb) with complete dominance at both loci is ______.
True or False: If two parents are both AaBbcc x AabbCC, it is possible to produce offspring with genotype aaBbCc.
Q: In a cross between two heterozygous pea plants (Yy x Yy), what proportion of the F2 offspring will be true-breeding yellow?
A: 1/4. Only YY individuals are true-breeding yellow. The genotypic ratio is 1 YY : 2 Yy : 1 yy.
Q: A snapdragon cross between two pink flowers (Rr x Rr) produces what phenotypic ratio, and why does this differ from a standard monohybrid cross?
A: 1 red : 2 pink : 1 white (1:2:1). This differs from 3:1 because snapdragon flower colour shows incomplete dominance, so the heterozygote has a distinct intermediate phenotype rather than looking the same as the homozygous dominant.
Q: From the cross AaBbcc x AabbCC, what is the probability of offspring with genotype aaBbCc?
A: P(aa) = 1/4, P(Bb) = 1/2, P(Cc) = 1 (all offspring are Cc). 1/4 x 1/2 x 1 = 1/8.
Q: A couple both have blood type AB. Can they have a child with blood type O? Explain.
A: No. Each parent must pass either an A or a B allele. The child could be AA, AB, or BB, but never OO.
Q: How does epistasis differ from dominance?
A: Dominance describes the relationship between two alleles of the same gene (one masks the other). Epistasis describes the interaction between alleles at different genes, where one gene modifies or masks the expression of a separate gene entirely.
The laws of segregation and independent assortment are explained at the cellular level by meiosis (Part 2 of these notes). Alleles segregate because homologous chromosomes separate in meiosis I.
Gene linkage (Part 3) is the major exception to independent assortment and was discovered by Thomas Hunt Morgan using fruit flies.
The "one gene, one enzyme" concept introduced here is expanded in Chapter 2 (biochemistry and molecular biology), where gene expression, protein function, and metabolic pathways are covered in detail.
Related Terms / Search Tags: Mendelian genetics, Gregor Mendel, pea plant crosses, alleles, genotype vs phenotype, dominant recessive, homozygous heterozygous, monohybrid cross, dihybrid cross, F1 F2 generation, 3:1 ratio, 9:3:3:1 ratio, Punnett square, probability method, law of segregation, law of independent assortment, principle of dominance, incomplete dominance, codominance, ABO blood types, multiple alleles, polygenic inheritance, epistasis, true breeding, test cross