Mendel's Laws, Mapping, and Epistasis

Gene

portion of the DNA that codes for a phenotype

Allele

alternate forms of a gene

structural allele

transcription or protein codding changes

regulatory allele

effect expression

locus

location of gene (can be specific or general)

homozygous

alleles are the same at a specific locus (AA, BB)

heterozygous

alleles are different at a specific locus (Ab, Ba)

Dominant and recessive alleles

refers to the relationship between alleles where a dominant allele masks the expression of a recessive allele in a heterozygous genotype. dependent on heterozygous phenotype

selfing

the process of self-fertilization in plants, where pollen from a flower fertilizes its own ovules, leading to offspring that are genetically similar to the parent. pollen used for fertilization is from the same plant.

outcrossing

pollen use for fertilization is from a different plant

true breeding

refers to organisms that, when self-fertilized, produce offspring identical to themselves for a specific trait. This occurs because they are homozygous for that trait. Homozygous genotype, selfing a true breeding plant will yield progeny with the same genotypes (and there for phenotypes, as the parent)

trait or characteristic

roughly synonymous for phenotype

monohybrid cross

a cross between two individuals identically heterozygous at one gene pair (A/a crossed by A/a)

dihybrid cross

a cross between two individuals that are heterozygous for two gene pairs (A/a B/b crossed by A/a B/b).

mendel’s law of segregation

The principle stating that during the formation of gametes, the two alleles for a trait separate, so that each gamete carries only one allele for each gene.

Mendel’s law of independent assortment

The principle stating that alleles for different traits are distributed to gametes independently of one another, meaning the inheritance of one trait does not affect the inheritance of another.

sum rule

A principle used in probability that states the probability of either of two mutually exclusive events occurring is the sum of their individual probabilities.

product (multiplication) rule

Used when evaluating the probability of independent events occurring at the same time: for the word “and”

Chi-squared test (x² test)

(observed value-expected value)²/ expected value

Degrees of freedom

The number of independent variables in data, DoF= # classes-1

recombination frequency

the frequency of crossover events between two loci

genetic map unit

distance between loci which on product of meiosis in 100 recombinants, often shortened to “map units”

Centimorgans (cM)

another name for map units

Homolog

A member of a pair of homologous chromosomes

partial linkage

Some crossing over happens between two loci. This is helpful for creating linkage maps

Complete linkage

no crossing over occurs between two loci, so they fundamentally function as one locus

cis conformation

The two “dominant” alleles are present on the same homolog (AB/ab)

Trans conformation

The two “dominant” alleles are on opposite homologs (Ab/aB)

Map units

(#recominants/total # plants) x 100 (cM0

double recombination

Help determine the order of different loci and is relatively a rare phenomenon where crossing over happens twice within a relatively short genetic distance

Interference (I)

Measure of independence of cross overs from one another

Coefficient of coincidence (CoC)

Ratio of observed # of double crossovers to expected # double crossover events

Mapping principle

The best estimates of map distance are obtained from the sum of distances calculated for shorter intervals