1. PLANT BIOTECHNOLOGY & GENETIC ENGINEERING (3 CREDIT HOURS)
LECTURE 12
HAPLOTYPE
ALLELE FREQUENCY
POPULATION GENETICS
FITNESS
GENOTYPE FREQUENCY
LINKAGE
LINKAGE EQUILIBRIUM & DISEQUILIBRIUM
MORGAN

2. HAPLOTYPE
A haplotype is a group of genes within an organism that is inherited together from a single plant.
The word “haplotype” is derived from the word “haploid”, which describes cells with only one set of chromosomes, and from the word “genotype”, which refers to the genetic makeup of an organism.
A haplotype can describe a pair of genes inherited together from one parent on one chromosome, or it can describe all the genes on a chromosome that were inherited together from a single parent.
This group of genes is inherited together because of genetic linkage, or the phenomenon by which genes that are close to each other on the same chromosome are often inherited together.

3. HAPLOTYPE
In addition, the term “haplotype” can also refer to the inheritance of a cluster of single nucleotide polymorphisms (SNPs), which are variations at single positions in the DNA sequence among individuals.
By examining haplotypes, scientists can identify patterns of genetic variation that are associated with health and disease states. For instance, if a haplotype is associated with a certain disease, then scientists can examine stretches of DNA near the SNP cluster to try to identify the gene or genes responsible for causing the disease.

4. ALLELE FREQUENCY
Allele frequency or gene frequency is the proportion of a particular allele (variant of a gene) among all allele copies being considered.
It can be formally defined as the percentage of all alleles at a given locus in a population gene pool represented by a particular allele.
In other words, it is the number of copies of a particular allele divided by the number of copies of all alleles at the genetic place (locus) in a population.
It is usually expressed as a percentage.
In population genetics, allele frequencies are used to depict the amount of genetic diversity at the individual, population and species level. It is also the relative proportion of all alleles of a gene that are of a designated type.

5. ALLELE FREQUENCY
A particular locus on a chromosome and the gene occupying that locus
A population of N individuals carrying n loci in each of their somatic cells (e.g., two loci in the cells of diploid species, which contain 2 sets of chromosomes)
Different alleles of the gene exist
One allele exists in copies

6. GENOTYPE FREQUENCY
Genotype frequencies are the frequencies of the homozygous dominant (AA), heterozygous (Aa) and the homozygous recessive (aa). In population genetics, they are p2, 2pq and q2.
Allele frequencies are the frequencies of each allele, dominant (A) and recessive (a). In population genetics, these are p and q.
Gamete frequencies refer to the proportion of gametes made that have each allele. So, a heterozygous individual (Aa) makes ½ A and ½ a gametes. A homozygous individual makes only one kind of gamete.

7. POPULATION GENETICS Based on Darwin’s 4 principles:
Heritable differences among individuals in population
Heritable differences passed to offspring.
More offspring are born that survive.
Some offsprings are more “fit” than others in a given environment.

8. POPULATION GENETICS
Population genetics is the study of allele and genotype frequencies in population
Population: Group of individuals of one species that actually or potentially interbreed
Genotype Frequency: Fraction of population with given genotype
Allele Frequency: Fraction of gametes with given allele
Gene Pool: All gametes made by breeding members in a generation (i.e., all inherited genes)

9. FITNESS
The quantifiable measure of an individual’s genetic contribution to the future.
High Fitness
Genotypes with high rate of survival and/or high level of reproduction (genes are passed on)
Low Fitness
Genotypes with low rate of survival and/or low level of reproduction (genes are NOT passed on)
Lethal genotype is WORST CASE SCENARIO – extremely low fitness

10. LINKAGE
Two genes are said to be linked if they are located on the same chromosome. We assume that different chromosomes segregate independently during meiosis. Therefore, for two genes located at different chromosomes, we may assume that their alleles also segregate independently. The chance that an allele at one locus co-inherits with an allele at another locus of the same parental origin is then 0.5 and such genes are unlinked.
Parent 1 x Parent 2
AABB aabb
AbBb (100%)
F1 gametes AB Ab aB ab
A & B are unlinked: frequency%
A & B linked:
A & B tightly linked:

11. LINKAGE EQUILIBRIUM & LINKAGE DISEQUILIBRIUM
If two genes/traits/loci are in linkage equilibrium, it means that they are inherited completely independently in each generation.
An example would be loci that are on two different chromosomes and encode unrelated, non-interacting proteins.
If two genes are in linkage disequilibrium, it means that certain alleles of each gene are inherited together more often that would be expected by chance.
This may be due to actual genetic linkage – that is the genes are closely located on the same chromosome.
Or it could be due to some form of functional interaction where some combinations of alleles at the two loci affect the viability of potential offspring.

12. LINKAGE DISEQUILIBRIUM
Linkage equilibrium and its opposite; linkage disequilibrium, are terms used for the chance of co-inheritance of alleles at different loci.
Alleles that are in random association are said to be in linkage equilibrium.
The chance of finding one allele at one locus is independent of finding another allele at another locus.
If the chance of finding either the B-allele or the b-allele is 50%, the genes are in linkage equilibrium.
Hence, if we look at the gamete frequencies, then we speak of linkage equilibrium if the
Freq (AB) = Freq (Ab) = Freq (aB) = Freq (ab)
And the amount of disequilibrium is measured as:
D = Freq (AB). Freq (ab) – Freq (Ab). Freq (aB)

13. LINKAGE DISEQUILIBRIUM
Linkage disequilibrium is the result of physical linkage of genes.
However, if the genes are even on the different chromosomes, there can be linkage disequilibrium.
This can be due to selection.
If A and B both affect a characteristic positively, and the characteristic is selected for, then in the selected offspring there will be a negative association between A and B.

14. LINKAGE DISEQUILIBRIUM
Linkage disequilibrium can also be the result of crossing or migration. If a new individual with AB gametes come into a population with ab gametes, then in the offsprings there will be more AB and ab gametes if the genes are linked. However, after a number of generations, the number of AB and ab gametes will approach that of the recombinant aB and Ab gametes, indicating linkage equilibrium. If the linkage is closer, the process will take longer. But ultimately, even if the distance between two genes is less that 1cM, genes will become in linkage equilibrium (with no selection).

15. LINKAGE DISEQUILIBRIUM
Hence, linkage disequilibrium is due to:
Recent migration or crossing
Selection
Recent mutation

16. MORGAN
The distance between two genes is determined by their recombination fraction. The map units are Morgans. One Morgan is the distance over which, on average, one crossover occurs per meiosis.
The distances on the genetic map are mapped using a mapping function. A mapping function translates recombination frequencies between two loci into a map distance in cM.
A mapping function gives the relationship between the distance between two chromosomal locations on the genetic map (in cM) and their recombination frequency.

17. MORGAN Two properties of a good mapping function is that:
Distances are additive, i.e., the distance AC should be equal to AB + BC if the order is ABC
A distance of more than 50cM should translate into a recombination fraction of 50%.

18. RECOMBINATION FREQUENCY
Genetic mapping is also known as gene mapping or chromosome mapping
1% recombination = 1 map unit (m.u) = 1 cM
Recombination Frequency between 2 genes = No. of recombinant offspring/Total no. of offsprings

19. THE END