Similarity Between Rice and Other Cereals

1. Rice has significant synteny with other cereals.

Synteny, or preservation of the order of genes on a chromosome, can be a marker for evolutionary history, or a key to functional relationships between genes. Over time, chromosomal rearrangements take place, and therefore the degree of synteny can give us information about shared ancestry. In organisms with a known shared ancestry, synteny can be used to predict the presence of genes in more than one species. Moreover, it means that genes present in one species are likely to be present in closely-related species. For example, the degree of synteny between rice and other cereals means that genes present in one or both rice species may well be present in other species.

But how great is the degree of synteny between rice and other cereals? Very great. In fact, if you look at any rice chromosome, the degree of synteny between it and, for example, maize is astounding (see Figure 1). This principle holds true for all the cereals, and means that genes present in one cereal will almost certainly be present in the same order in another. When Goff et al (2002 Science 296: 92-100) assessed the known proteins from maize, wheat and barley, 98% had homologues in the rice genome.

What is the significance of synteny between cereals? Why is this of concern when talking about patenting the rice genome? Depending on the language used in the patent, this could potentially mean that a patent on an important rice gene could cover, without separate patents, that gene in wheat, in corn, in sorghum, in rye, in sugar cane, etc. But is there significant homology between rice and other cereals at the level of individual genes?

2. Rice is homologous to other plants.

Just because the same “genes” exist in the same order on a chromosome in rice and wheat, for example, does not necessarily mean that the sequences of the individual genes or resulting proteins are identical or highly similar. There are examples of conserved genes that tolerate a great degree of diversity, and others that are virtually identical across a wide evolutionary range. Furthermore, many sequences that “drive” expression of important genes are patented. So what degree of homology exists between rice and other cereals? Homology is usually expressed in terms of “percent identity”, although “percent similarity” is also used. Percent identity is more precise, as it means the percent to which two genes or proteins match exactly over a given seqeuence. When we look, as an example, at the homology between rice and wheat (Figure 2), we see that many rice genes are present that share nucleotide identity of 80% or more with wheat.

The same is true for maize. As shown in Goff et al. (2002 Science 296: 92-100), the regions of homology between rice and maize of greater than 80% over 100 bp. Virtually every part of the maize genome finds a homologue in rice, where the sequence identity is greater than 80%.

Figure 1: Comparison of chromosome 3 of the rice variety
japonica with the maize species Zea mays.

Image re-printed from
Note that to a large extent, the rice genes (centre) are present
in the same order on one or more maize chromosomes.


Figure 2: Comparison of the rice genome (chromosomes 1-12) with the wheat genome.

Each coloured box represents a match of 80% or greater at the nucleotide level with a
wheat gene. The chromosomal location of the corresponding wheat gene is colour-coded
(wheat chromosome 1 is purple, wheat chromsome 4 is yellow and so on).
Image kindly provided by Dr Mark Sorrells, Department of Plant Breeding & Genetics,
Cornell, Ithaca, NY