@M.Sidhu there is no constant ratio to convert between cM and bp. CentiMorgan (cM) distances are usually defined as between genetic markers on a linkage map, and are an estimate of likelihood of recombinations occurring in that interval. There are some regions of the genome where recombinations are frequent, so there are fewer bp per cM and some regions where recombinations are rare (e.g. centromeres), so more bp per cM.

Probably the best approach is to take the most detailed genetic map you can find, get the sequence for each marker in the map, and BLAST these markers against the genome.

The genetic map already has the cM distances between each pair of adjacent markers. From the BLAST analysis you will be able to translate each of these cM distances into a bp distance between the points of alignment from the markers to the chromosome. In that way you will have a 'patchwork' map converting between bp and cM distances. The relationship between the two measurements is highly non-linear, depends on the population in question, and varies from place to place within the genome.

When the genome was originally assembled, it is likely that the team assembling it already had a detailed genetic map and used this to assemble their scaffolds - you might be able to get the map from them.

It will depend on species you are working with. For human being you may want to check following link; http://www.isogg.org/wiki/CentiMorgan .

@Asjad,

One cM contains 1,000,000 base pairs. Ten base pairs has length is 3.4 nanometer. Therefore, 1,000,000 base pairs is equal to 340000nm. This is equal to 0.034 centimeter. This is equal to 0.00034 meter.

1cM=1Mbp=1000Kbp=1,000,000bp.

The distance between the base pairs in DNA is also depends upon the type of DNA. So the length may change accordingly.

in my case it is Brassica rapa.

@M.Sidhu there is no constant ratio to convert between cM and bp. CentiMorgan (cM) distances are usually defined as between genetic markers on a linkage map, and are an estimate of likelihood of recombinations occurring in that interval. There are some regions of the genome where recombinations are frequent, so there are fewer bp per cM and some regions where recombinations are rare (e.g. centromeres), so more bp per cM.

Probably the best approach is to take the most detailed genetic map you can find, get the sequence for each marker in the map, and BLAST these markers against the genome.

The genetic map already has the cM distances between each pair of adjacent markers. From the BLAST analysis you will be able to translate each of these cM distances into a bp distance between the points of alignment from the markers to the chromosome. In that way you will have a 'patchwork' map converting between bp and cM distances. The relationship between the two measurements is highly non-linear, depends on the population in question, and varies from place to place within the genome.

When the genome was originally assembled, it is likely that the team assembling it already had a detailed genetic map and used this to assemble their scaffolds - you might be able to get the map from them.

@Jonathan,

Thanks for your highly informative words.

I read in an article that 1 cM is equal to 500 Kbp but according to you guys it varies in different regions.

It depends a lot even within the same genome. Generally in plants the ends of chromosomes have a higher # of centimorgans per bp as compared to the center of the chromosome. In one plant I work with I have a region that may be 100 MBP that is 1 centimorgan long.

Centimorgans also depend on the cross involved and a large inversion can prevent recombination so large regions can be 0 centimorgans long in one cross, but many centimorgans long in another cross.

My metaphor is centimorgans events correlated to distance but not related at the same ratio. It is similar to compare driving time to distance on a long road trip. Parts of the genome are freeways, and others are congested, and on a long trip you might spend some of the time driving 200 km an hour and other places you may be driving 10 km an hour or slower.

For most plants the chromosomes tend to be 50-150 centimorgans long. Generally this is because 1 recombination event occurs per chromosome pair in meiosis. This is regardless of the genome size, and the generalization is true for Arabidopsis with an chromsomes of 20-40MBP and wheat with chromosomes 700-1000 MBP.

@John, Thank you for detailed reply

Detailed information has been provided about relation between cM and Mbp. I will like to add that you can have an estimate of Mbp by using FISH. If you have markers for which cM distance is known, you can localize them through FISH to estimate size in Mbp. It will not be an exact but an approximate estimate. You need a big enough piece of DNA to localize through FISH (appox. 5Kb). You can genome walk to get a big enough piece, this is a useful exercise for species where no sequence information is available.

Based on your comments, my next project will now be designed with the objective of translating genetic maps into physical maps for a number of important species, allowing people to easily work back and forth  between cM  and  Bp. 

is it possible to use the syntenic block regions in order to do the conversion from cM to bp, if the comparison was done between genetic and physical map.

Your question is not clear to me since information is scanty. I will still try to answer. You can compare genetic and physical map, which will be indicative of distances but it should not be considered absolute. If the order of markers is same, it will provide you some information. Centimorgan distances between markers will not be same as in physical map. The differences will be even more pronounced if different species/genus are being considered.

Genetic map and physical map are synonymously used to define the distance between genes and markers. 1cM may be variable depending upon the particular genome and organism in question.

whereas base pair is actually the nucleotide sequence segment at DNA level. that determines the length of chromosome, resulting into whole genome.