Hi! Did you sterilize the peat moss and perlite? In our lab we sterilize their in a plastic packaging bag by microwave oven (max power; 10 min, two time with break). Another way is sterilize at 150C for 3-4 h in autoclave (if you have a big volume, for example,10 liters). It keeps in a bag until using. 

Arabidopsis incubation temperatures are 18-20C. The growth inhibited at 25C (25-28C use for study temperature-sensitive mutants). 

Photoperiod is 16:8. (http://molbiol.ru/forums/lofiversion/index.php/t228883.html)

I hope it will be useful for you.

We sterilize the soil by autoclaving. I will try changing some sowing factors, as soil and sugar. Maybe, the sugar stress plus trespassing, are too much for these seedlings. Thanks for your help! :)

I might recommend checking out this website as it seems to be a compilation of research material on your study genus. 

https://www.arabidopsis.org/index.jsp

This problem has happened to me before. I think it is because of damage to the root when the plants are transferred. Is there a reason to sterilize the seeds? If not, I would use a toothpick and place the seeds directly into soil in pots. Place 6-8 seeds per pot and later when they are 2 weeks old, you can thin them. Hope this helps.

If 16:8 photoperiod means 16h light, then everything is as you would expect. Arabidopsis flowers in long days. Use 8:16.

Thanks to all of you! I will try some of your advices. Regards.

I also encountered a similar situation, that because there were several aseptic operation tables outside the greenhouse. when we removed the operation tables, the Arabidopsis was back to normal, thus we think it was the  ultraviolet rays and ozone problem. you can check.

Generally the fungus problem comes and affect the growth of root. while transferring the seedlings to soil you can wash the root by water, remove agar pieces from root. If the media contents remains on root then chances that the fungus will grow on roots. Also attached picture indicates that the soils you have used you soil is not tightly packed in pot. In loose soil the root/root hairs does not come in contact of soil properly and plant can not uptake nutrient. Also loose soil does not hold water for a long time. keep soil in pot and make it tight packing and while putting seedling make a small hole in soil by forceps or anything and do planting.

good luck

Hi.

The amount of sucrose you are using in your plates seems a little high and could be causing your seedlings to arrest before you have transferred them to soil. If they are wildtype columbia, they should not need sucrose to germinate and we usually would germinate them directly on soil. If they are a mutant which requires sucrose for establishment, try 0.5%. Also, 2 weeks on plates before transfer to soil is a bit longer than I would recommend leaving them. If you transfer them smaller, there is less root to damage and they usually transfer better (about 9 or 10 days on plates) especially if you make sure the soil is wet and  protect them with a propagator lid for a couple of days after transfer so they do not dry out.

Good luck

Hi，it seems that the soil water content is too high to arabidopsis growth. the watering method might be changed. 

Arabidopsis is sensitive for excessive water and temperature. Try to maintain 18-22oC for growth condition. Also, for the better germination, treat the seeds with Gibberlic acid during stratification. I normally keep the seeds moistured with GA and keep them in dark and cold condition for 48 hrs. It worked well for me.