Comparative genomics
The genome sequences of Arabidopsisand rice that became available in the year 2000 and 2002 respectively, can be utilized for understanding the functions of genes in a variety of crops. Comparative genomic analysis can be undertaken at different levels of organization. Such studies at the chromosome level have been undertaken in grasses, using rice genome as the anchor genome. It was shown that 30 rice linkage blocks can be used to construct genome of each of a number of species. It was also shown that the 'gene space' occupies about 50% of the Arabidopsis genomeand 24% of rice genome, the remaining genome being repetitive sequences and transposons.

There is also evidence for conservation of synteny (conserved clustering of genes unique sequences) and collinearity (conserved order of genes or markers) among both related and highly divergent plant species like the following: (i) rice and other grass species, (ii) Arabidopsisand Capsella rubella,(iii) Arabidopsis and Brassica, and (iv) tomato and Arabidopsis. While comparing genes, it has also been possible to distinguish between orthologous genes (derived due to speciation) and paralogous genes (derived due to gene duplication). The approach of micro-collinearity has also been used for study of gene function and for isolation of orthologous genes.