Is there anyone who can supplement some good materials for linkage disequilibrium. I am trying to understand the base of LD, not by definition but by the concept. How LD is different from linkage and how LD is used for QTL mapping?
Please let me know about this topic.
Hi, I hope this helps you
Any deviation of the haplotype frequencies from 0.25 (four haplotypes each with 0.25 frequency) is linkage disequilibrium (LD).
LD means that genes are not in the random association but in non-random.
This definition assists to illustrate that the difference between linkage and linkage disequilibrium is somewhat artificial, in fact, linkage disequilibrium between a marker and a QTL is required if the QTL is to be detected in either linkage or linkage disequilibrium mapping.
The difference is:
The linkage analysis only considers the linkage disequilibrium that exists within families, which can extend for 10s of cM, and is broken down by recombination after only a few generations.
The linkage disequilibrium mapping requires a marker to be in LD with a QTL across the entire population. To be a property of the whole population, the association must have persisted for a considerable number of generations, so the marker(s) and QTL must, therefore, be closely linked ( Ben Hayes)
Thank you mam for your valuable answer. However, I would like to know, can we say all LD is a result of linkage? Peymaneh Davoodi
I would say it is the result of selection. Of course two genes, two markers or one marker and one gene that are in LD, are also linked.
Due to selection of both positive alleles of two closely linked different genes they are more often selected together if you look at an diverse set of breeding lines. The have a higher common frequnency than one would expect by random recombination.
You look at the LD in a panel of diverese Lines not in one population.
Thank you sir Stephan Schie . I really satisfied with your explanation.
Shantanu Das , Hi, LD is a slight misnomer. Dis equilibrium means not normal. But, LD is the normal thing observed and is only due to linkage. Imagine a situation where cross overs and recombinations compulsorily occur between two adjacent nucleotides/genes. That would lead to utter chaos. Certain stretches of the genetic material are CONSERVED INTACT, sequence wise, over generations/ages as that is the best configuration devised by nature (I dare say, God !) for the trait in question and its interactions with other genes/stretches of DNA. Hence, disequilibrium is normal.
The nearer a QTL to a gene/stretch of DNA housing trait control, the better it can be tracked as it suffers a lesser chance of recombination leading to a consequent loss in its connection with the trait of interest.
Imagine a situation where cross overs and recombinations compulsorily occur between two adjacent nucleotides/genes AND BETWEEN EVERY ADJACENT GENES.....
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