If you have the list of genes and their positions you can use the R package karyoploteR to create the plot (still in Bioconductor devel only, though). It can create karyoplots for various organisms including Rice. In this case you'll need to have the rice BSGenome package installed. Unfortunatelly since it relies on UCSC to get the cytobands and they are not available for MSU7, it will plot the chromosomes without banding. If you have this information youself you can provide it to karyoploteR.
library(karyoploteR) library(regioneR) #Create 50 regions as mock genes genes <- createRandomRegions(50, length.mean=10000, genome="MSU7",non.overlapping = TRUE) mcols(genes) <- data.frame(symbol=paste0("Gene", 1:50)) #Or read them from a BED file if available #genes <- toGRanges("genes.file.bed") kp <- plotKaryotype(genome="MSU7") kpPlotRegions(kp, data=genes, r0=0, r1=0.3) #plot the genes kpText(kp, data = genes, y=0.5, labels = genes$symbol, r0=0.3, r1=1, cex=0.5, srt=45) #and add the gene symbols