A genome is all the genetic information in an organism. Members of a species share most of their genome but differ at variants; common single-base differences called SNPs can be used as biological markers.
Cultivated rice, Oryza sativa, is one of the most important human foods. The two main sub-species of cultivated rice are O. sativa indica and O. sativa japonica. O. rufipogon is a wild species from which they probably evolved.
To investigate whether the sub-species of cultivated rice evolved independently from the wild species, scientists analysed their chromosomes to find areas with similar DNA base sequences. Wild species tend to have many different alleles of genes present on each chromosome, but during the development of a crop plant by artificial selection from a wild species, this diversity drops considerably, increasing the base sequence similarity.
The number of different alleles of the genes on a chromosome can be represented by a diversity index. The following graph of part of chromosome 7 shows the diversity index of O. rufipogon and two varieties of cultivated rice, O. sativa indica and O. sativa japonica. The gene PROG1 allows the plant to stand upright, which is typical of cultivated rice. Its position is indicated by the vertical arrow on the graph.
Determine which type of rice has the lowest overall diversity index.
Compare and contrast the trends for O. rufipogon and O. sativa indica.
In another experiment, scientists retrieved genome sequences of the wild rice O. rufipogon taken from a wide range of geographical sites (I, II and III) and those of the two sub-species of O. sativa from gene banks.
The pie charts, presented along with a cladogram, show the proportion of alleles for three genes which confer specific characteristics to O . sativa. Mutations can produce derived alleles that are different from the original ancestral alleles. The control group represents wild rice species other than O. rufipogon.
State the proportion of the ancestral allele for the gene GS3 in the O. rufipogon-III population.
Distinguish between the proportion of ancestral and derived alleles for all three genes in O. sativa indica and O. sativa japonica.