I think you should think about surface contacts, simply.

When you transfer the plantlet, all root-media surface contacts are destroyed, therefore water, nutrient transfers are interrupted and these contacts must be reestablished on the new media surface. These new contacts are the most effectively formed by new (lateral) roots.

it may possibly be due to auto-toxicity of Arabidopsis in the existing medium (which may stimulate auto-toxicity and hence retard the emergence of lateral growth) or it may be due to chemical stress posed by the existing medium to root development. when such stress is removed or diluted as in case of transfer to fresh medium, the lateral growth increases

There could be many possible reasons, if it is a nutritional effect, maybe this paper can give you some ideas: http://www.public.iastate.edu/~bot.512/papers/Lopez-Bucio.pdf

For example, they propose that a nitrate-starved plant, upon contact with a nitrate-rich region, grows faster because of the abundance of nitrate and an increased consumption of photosynthates. However, I think that would be unlikely in this case, given the high concentration of salts in MS medium, so I don't think Arabidopsis could deplete any major nutrient.

I think you should think about surface contacts, simply.

When you transfer the plantlet, all root-media surface contacts are destroyed, therefore water, nutrient transfers are interrupted and these contacts must be reestablished on the new media surface. These new contacts are the most effectively formed by new (lateral) roots.

I like janos's answer. Removing seedlings from the plate they are on damages roots and root hairs necessitating generation of new roots.

root damage is certainly an issue

but this you can easily test by transferring seedling to the same plate.

could it also be connected to the action of opening the plate and closing it? did you try to expose the "control" plate to air for a certain time as well, as it is happening while transfer. I think there are several factors you should consider - plates dry a little, even when sealed, maybe your fresh ones simply contain more water; exposure to air might have an effect (in terms of CO2 and O2 ratio); and also maybe the sugar concentration of the new plate has in impact.

maybe this paper gives you an idea what I mean

http://www.ncbi.nlm.nih.gov/pubmed/22899086

If you bend a root, it will induce lateral root formation. So the transfer could induce lateral roots just by changing shape of the primary root. Have a look here:

http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0060307

Is there sucrose in your media? And, are the aerial tissues contacting the media? If so, the sucrose in the media can be taken up by the aerial tissue and used to make the root system larger (see http://www.plantcell.org/content/20/10/2643.abstract),... when you transfer to new media, then the aerial tissue has a fresh source of sucrose and the root system will get larger.

Hope this helps!

You did not mention whether you have hormones in your MS, but I am assuming that you do. Photo-autolysis of indole compounds such as auxin or 2,4D occurs in the light. You have long light periods so the concentration of these compounds declines during the first week. I'm guessing that the boost in effective hormone concentration upon re-plating probably does quite a few things, including increasing lateral root initiation, a known effect of auxin. To overcome this, you should use half-strength MS without hormones or sucrose for growing young seedlings. Exogenous hormones and sugars are not necessary for seedlings grown in the light.

I have the same behaviour when transferred 3, 5 or 7 days-old seedlings to new plates, whitout hormones in the media. I always use fresh media, I pick the seedlings with sterile toothpicks (under the cotyledon) and proceed carefully.

I associated it with the stress which you are generating when you transfer the plant. I mean, as was indicated when you pick the plant you are breaking the medium-plant-aerial continuum, also if you aren't delicate you can break the root or the shoot (first time I did), or when you try to place the root you bent the root and that change hormonal transport... The aerial interchange can easily solved using micropore tape. Depending on your topic this behaviour hasn't to be a problem, because you can transfer plants to control and treatment plates. If the phenotype is significant you'll obtain enought evidences. Another option in your work coud be split root system.

Thank you everyone for your inputs. I agree with fresh root media contacts being established as a possible reason. I try and keep other variables low by pouring out the same volume of media (allowing similar air volume above the seedlings), using same sucrose concentrations and trying to keep the root as straight as possible (especially the tip). My mutant is showing a subtle phenotype, hence the need to transfer to be able to ascertain the defect better. I don't use hormones in my media but i think 2,4 D is used to increase lateral root formation. I am thinking of using a 30nM concentration, do you have any suggestions on that?

I think that the surface contacts could be involved, but also higher availability of nutrients in comparison to an old substrate, that could be a little dry. Nutrient avalability induces in many plants an increase of branching. Also a possible damage to root apical meristems caused by the tranfer could be involved.

Plant morphology is dramatically influenced by environmental signals. The growth and development of the root system is an excellent example of this developmental plasticity. Both the number and placement of lateral roots are highly responsive to nutritional cues. This indicates that there must be a signal transduction pathway that interprets complex environmental conditions and makes the “decision” to form a lateral root at a particular time and place. Lateral roots originate from differentiated cells in adult tissues. These cells must reenter the cell cycle, proliferate, and redifferentiate to produce all of the cell types that make up a new organ. Almost nothing is known about how lateral root initiation is regulated or coordinated with growth conditions. Here, a report of growth assay that allows this regulatory mechanism to be dissected in Arabidopsis (from American Society of Plant Physiologists, Environmental Regulation of Lateral Root Initiation in Arabidopsis1 by Jocelyn E. Malamy * and Katherine S. Ryan). When Arabidopsis seedlings are grown on nutrient media with a high sucrose to nitrogen ratio, lateral root initiation is dramatically repressed. Auxin localization appears to be a key factor in this nutrient-mediated repression of lateral root initiation. We have isolated a mutant, lateral root initiation 1 (lin1), that overcomes the repressive conditions. This mutant produces a highly branched root system on media with high sucrose to nitrogen ratios. The lin1 phenotype is specific to these growth conditions, suggesting that thelin1 gene is involved in coordinating lateral root initiation with nutritional cues. Therefore, these studies provide novel insights into the mechanisms that regulate the earliest steps in lateral root initiation and that coordinate plant development with the environment.