Question

When studying a specific trait, what does having a good linkage disequilibrium mean when looking at different SNPs in a chromosome?

Answer 1

Single nucleotide polymorphism & Linkage disequilibrium:

1. Single nucleotide polymorphism (SNP) occurs due to the difference in a single nucleotide at a specific site. SNP is a site in the genome with a base-pair difference among chromosomes that is present at least one in every 50 individuals. SNP’s do not produce deleterious effects. Examples of SNP’s include differences among the alleles of haemoglobin (A, S and C).

2. The concept of single nucleotide polymorphism is applied in detecting the source of an unknown DNA (deoxyribonucleic acid) sample. In situations like crime scenes and natural disasters, only small pieces of DNA will be available. In such cases, DNA microarray technique is used to detect the SNP of suspects with the DNA samples that were collected from crime scene. If the SNPs of any Suspect and Crime scene SNPs are matched, then he will be considered as an accused.

3. Lod score method is used widely in plant and human genetic linkage analysis and also in confirming the recombination maps based on the recombination frequencies. This frequency is considered as a measure of genetic linkage during the crossover of the homologous chromosomes.

4. Linkage disequilibrium is defined as the existence of alleles at different loci with the absence of genetic linkage between them even though there is no equilibrium with allelic frequencies independently. The recombination frequency is the measure of genetic linkage at different loci. The value of recombination frequency is 50% if the chromosomal genes are located at different regions on the different chromosome as a result of independent assortment. If the genes are located closely together on the same chromosome then those genes are considered to be as genetically linked and as they are not assorted independently then the recombination frequency value is less than 50%.

5. Major advantage is that we can easily or indirectly examine the considerable variation in the total genome by assaying and assessing a subset of merely total SNPs. Major disadvantage is heterozygosity rate at a SNP locus is normally < 50% .

6. In the eukaryotic cells at the time meitotic cell division or mitotic cell division, sometimes double stranded DNA break is due to presence of a protein reffered as Spo11, and this protein is a precursor for the chromosomal crossover. Base pair dense regions where double strand DNA breakage occurs mainly such as guanine and cytosine rich with 1000 to 2000 base pair length possess very higher ability of recombination and these are the heritable genes equally pass through genetic linkage and independent assortment further result in abnormal phenotypic offspring.

Major steps of homologous recombination: Predominantly there total two crucial homologous recombination repairs are existing in order to renovate the harmful broken double strand DNA on the chromosome