I need to display the entire rice genome on the form of chromossomes and mark down genes belonging to a specific gene family. The idea is to show how they are distributed throughout the rice genome. Something like what is available on the TAIR website for Arabidopsis
See http://www.gramene.org/ for the needs of rice genome and marker annotation on chromosomes. I don't think there is a automatic tool as such to make the diagram form you.
There is an easy way to get a map from the Oryzabase website (https://shigen.nig.ac.jp/rice/oryzabase/ )
If you go to Tools in the top bar there is a drop-down option called Chromosome Map Tool and you can input your gene names to automatically get them plotted onto a set of rice chromosomes. It is not too pretty and it will get messy if many are on one chromosome but I am writing it here because it did what I needed.
The attached image is an example and shows genes described in the literature that have been reported to be involved in improved zinc absorption in rice and/or rice grains.
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