# data[].attributes.body
In bio, the Marker system is used to distinguish individuals, populations, varieties and species.

# data[].attributes.body
AMEER HAKIM
LIM KHANG NING
NURUL FARYANA

# data[].attributes.body
- Population is a group of individuals of a same species that routinely interbreed
- Evolution did not happen in individual but happen among the group

# data[].attributes.body
-The study of evolution from genetic point of view
-When evolution in population occurs at the genetic level, it is sometimes called micro evolution. It's change in the collective genetic material of a population

# data[].attributes.headline
Importantance of studying population genetics

# data[].attributes.subject
Importantance of studying population genetics

# data[].attributes.body
1.  Learn about human migration and history

2. To identify and localize disease genes

3. Difference in linkage disequilibrium for fine mapping

4. Avoid false positive date

5. Mapping of disease

6. Signature of natural selection

# data[].attributes.body
Stabilizing selection

Natural selection will stabilise the population if it favours an average phenotype by selecting against extreme variation. Natural selection will favour individuals who blend in best with the forest floor and are less likely to be detected by predators in a population of mice living in the woods, for example. Assuming the ground is a fairly consistent shade of brown, mice with fur that is the most nearly matched to that colour will most likely survive and breed, passing on their brown coat genes. Mice with alleles that make them somewhat lighter or darker stand out against the ground and are more likely to be eaten by predators. The genetic variation of the population will diminish as a result of this stabilising selection.

Directional selection

When the environment changes, populations frequently go through directional selection, which favours phenotypes on one extreme of the current variation spectrum. The evolution of the peppered moth in eighteenth- and nineteenth-century England is a typical example of this form of selection. Prior to the Industrial Revolution, moths were mostly light in colour, allowing them to blend in with nearby light-colored trees and lichens. As industries began to spew soot, the trees darkened, making light-colored moths easier to spot for predatory birds.

Disruptive/diversifying selection

Natural selection can sometimes favour two or more unique phenotypes, each with its own set of advantages. The intermediate genotypes are generally less suited than their extreme counterparts in these situations. Diversifying or disruptive selection is evident in many populations of animals, such as lobsters, that have numerous male mating techniques. Large, dominant alpha males gain mates by brutal force, whereas little males can slip in for furtive copulations with the females in an alpha male’s domain.Both dominant males and “sneaking” men will be picked in this circumstance, but medium-sized males, who cannot surpass alpha males and are too large to sneak copulations, will be rejected.

# data[].attributes.body
1. Phenotypic/Morphological Marker

First-generation of marker

Distinguishes based on morphological/physical characteristics.

Eg：

Height (tall/short plant）

Resistance (resistant/susceptible plant to the certain environment)

2. Biochemical Marker

The second generation of marker

Distinguish based on variation in the expressed product

Eg:

Proteins

Isozymes

Disease resistant protein (A biochemical marker distinguishes individual)

Major limitation 1st and 2nd marker:

1. They are influenced by the environmental changes(very unstable)

2. The number of characters/proteins are very less.

3. Genetic markers/ DNA markers

The third generation of marker

Distinguish based on variation in the DNA sequence/genome

Eg:

RAPD, RFLP, AFLP, SSR & SNP

The variation detected by this marker:

Deletion

Insertion

Duplication

Inversion

Advantage:

1. They are not influenced by the environment (very stable)

2. The number of markers is almost unlimited

# data[].attributes.headline
RFLP (Restriction Fragment Length Polymorphism)

# data[].attributes.subject
RFLP (Restriction Fragment Length Polymorphism)

# data[].attributes.body
1. First generation marker

2. Exploits variation in restriction sites of DNA

3. RFLP is a site in genome where the distance of 2 restriction site varies in every individuals

4. Process:

1. Restriction enzymes recognised the restriction site

2. Restriction Site is cut/cleaved- become fragmented DNA

3. 2 restriction fragments are separated on Gel Electrophoresis-forming bands pattern.

4. Fragments transferred to nitrocellulose membrane

5. DNA hybridization- Radiolabelled probes are applied at Southern Blot (Probes bind to complementary DNA on membrane)

6. X-ray film is applied to the blot- To visualise DNA fingerprint pattern

7. Allowed the probes to develop

8. Extra columns shows the restriction fragment pattern of 2 individuals

5. Application:

Identifying Parentage

Criminal Identification

Diversity/Phylogeny Analysis

Breeding

Marker assisted selection

Mapping

6. Pros:

Codominant- Can distinguish Homozygous & Heterozygous DNA

Sequense specific- Probe is developed with sequence specifications

Genomic abundance- Restriction site are distributed throughout the genome

Reproducible & Stable- Results are highly reproducible even across different labs

Simple—given the availability of suitable probes, the technique can readily be applied to plant

7. Cons:

Requires high quality & large amount of DNA- Restriction enzymes activity is highly affected by impurities

Radiolabeled Probe is costly and working requires caution

Not automated

Tedious

Time Consuming

Low level of polymorphism

# data[].attributes.headline
RAPD (Randomly Amplified POlymorphic DNA)

# data[].attributes.subject
RAPD (Randomly Amplified POlymorphic DNA)

# data[].attributes.body
10 nucleotides long arbitrary sequences added forwards/reversed

Amplify complimentary region in genome

RAPD amplification depends on template

2 other variants of RAPD:

1. AP-PCR (Arbitrary Primed PCR)

2. DAF (DNA Amplification Fingerprint)

Pros:

Fast & Easy Assay-can be completed with 4-5 hours

Sequence info not required for primer designing

Can be performed with few nanograms of DNA

High genomic abundance

Cheap

Cons:

Low reproducibility

Dominant markers

High quality of template DNA is required

Highly sensitive to reaction conditions.

# data[].attributes.headline
AFLP (Amplified Fragment Length Polymorphism)

# data[].attributes.subject
AFLP (Amplified Fragment Length Polymorphism)

# data[].attributes.body
PCR amplification based

Combination of both restriction based & PCR based method

Process：

1. Involve in the digestion of genomic DNA using Restriction Endonucleases (Eco R1- 6bp cutter & Mse I-4bp cutter)

2. Followed by Adapter Ligation and PCR Amplification

3. Amplified products are visualized on high-resolution polyacrylamide gels.

4. Amplification (2 phases)

1. Pre-selective amplification

The first round of amplification

Few fragments are selectively amplified

20 PCR cycle is set

2. Selective amplification

The second round of amplification

More primers + 3 extra nucleotide bases are used

Few cycles of Touch Down PCR is set - to improve the amplification efficiency

5. Fragment separation- Bending pattern of the fragment is analyzed manually/with analytical software

Pros:

Multilocus-Restriction sites are present across the whole genome, can analyze multiple-locus at once

Universal primers- sequence information is not essential as primers complementary to adapter sequences are designed.

Simplicity

Low temperature

Can detect Polymorphisms

Cons:

High-quality DNA is required

Dominant- Cannot detect homozygous/heterozygous

Locus unknown

Expensive

Time consuming

# data[].attributes.body
Short Tandem Repeats of 1-6 base

Others name:

STR (Short Tandem Repeat)

Microsatellites

SSLP (Simple Sequence Length Polymorphism)

Types of SSR:

Genomic SSR

Found in coding, intronic/intergenic regions

More variability

Less cross- transferability

Genic SSR

Only found in the coding region

Lesser Variability

High cross-transferability

Cause of SSR:

1. Replication slippage is a major cause for SSR

2. Mutations & Recombination during meiosis

Pros:

Co-dominant

Hyper variable

Stable

Low quantity of DNA required

Sequence-specific

Automation, Fast , multiplexing

Transferable between species

Cons：

High cost

Shadow/shutter bands appear

Presence of null alleles

Too many alleles at certain loci

Microsatellite flanking regions contain the length mutation (sometimes)

# data[].attributes.body
Latest Generation markers

Types of SNP:

1. Transition & Transversion: Purine mutated to Purine & Purine mutated to Pyrimidine

2. Coding: Synonymous (Do not alter the amino acids) & Non-synonymous

3. Non-coding

4. Homozygous

5. Heterozygous

Protocols of SNPs:

1. Amplification of target fragment (PCR & Strand displacement amplification)

2. Allele discrimination reaction (DNA polymerases, DNA ligases, hybridization)

3. Detection & Identification (Fluorescence intensity, Microarray, Mass spectrometry, Gel Electrophoresis)

*To improve resolution & accuracy of results, most SNP technologies separate protocols 2 & 3

Pros:

PCR products can be very small (markers work with degraded DNA)

Many possibly multiplex hundreds/thousands on a chip

Reproducible

Sequence-Specific

Genome-wide detection

Cons:

Less allele- marker less informative

Need more SNP- to get the same level of information about DNA

Hard to use

Expensive