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Date	November 2019	Marks available	1	Reference code	19N.2.SL.TZ0.1
Level	Standard level	Paper	Paper 2	Time zone	TZ0 / no time zone
Command term	State	Question number	1	Adapted from	N/A

Question

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.

[Source: He Z, Zhai W, Wen H, Tang T, Wang Y, Lu X, et al. (2011) Two Evolutionary Histories in the Genome of Rice:
the Roles of Domestication Genes. PLoS Genet 7(6): e1002100. https://doi.org/10.1371/journal.pgen.1002100]

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.

[Source: reprinted by permission from Springer Nature: Nature, Huang, X., Kurata, N., Wei, X. et al. A map of rice
genome variation reveals the origin of cultivated rice. Nature 490, 497–501 (2012) doi:10.1038/nature11532]

State the reason that O. sativa and O. rufipogon are classified as different species.

[1]

Determine which type of rice has the lowest overall diversity index.

[1]

Compare and contrast the trends for O. rufipogon and O. sativa indica.

[2]

State the proportion of the ancestral allele for the gene GS3 in the O. rufipogon-III population.

[1]

Distinguish between the proportion of ancestral and derived alleles for all three genes in O. sativa indica and O. sativa japonica.

[2]

State one reason for having a control group.

[1]

Using all of the data, discuss whether there is evidence that the two sub-species of O. sativa might have evolved independently from O. rufipogon.

[4]

Markscheme

cannot interbreed to produce fertile offspring ✔

Accept converse or a good explanation.

«O. sativa» japonica ✔

Similarities
both show diversity
OR
similar pattern/peaks and troughs in the first part of the chromosome / up to «approximately» 1.5 megabases
OR
similar diversity between 2.4 to 2.7 mb
OR
both highest at 0.7 mb ✔

Differences
there are «two» major drops in diversity for O. sativa indica whereas none for O. rufipogon/much wider fluctuations in O. s. indica
OR
O.s. indica much lower at PROG1
OR
O.rufipogon does not drop < 2.5 whereas O. s. indica approaches 0
OR
O.rufipogon generally higher than O. s. indica after 1.4-1.5 ✔

One answer from mpa and one from mpb required for 2 [max].

Accept a statement of where the drops occur.

$\frac{3}{4}$ /0.75/75% ✔

Do not accept 0.75% or 75 or ratios

a. O.s. indica has more of the ancestral allele «for all three genes» ✔ Accept converse.

b. lower/higher values for ancestral/derived are not for the same genes ✔ Allow specific gene examples.

c. for O. s. indica the highest proportion is for DPL2 ancestral, but for O. s. japonica is GS3 derived allele ✔ Allow converse for smallest derived.

any reference to comparison ✔

a. large difference in diversity index between O. s. indica and O. s. japonica «suggests independent evolution» ✔

b. «some of the» peaks/troughs for O. s. indica and O. s. japonica in different positions «suggests independent evolution» ✔

c. O.s. indica has a similar diversity index to O. rufipogon «which suggests closer relationship/recent divergence» ✔
Allow converse for japonica

d. O.s. japonica has very different proportions of ancestral and derived alleles compared to O. s. indica ✔

e. O.s. indica has similar large number of ancestral alleles to O. rufipogon I/II ✔ Allow converse for derived

f. O.s. japonica has a large number of derived alleles similar to O. rufipogon III
OR
«but» the number of derived alleles is greater in O. s. japonica than in O.rufipogon III ✔ Allow converse for ancestral

g. O.s. indica and O. s. japonica are in different clades ✔
OR
O.s. indica and O. rufipogon I are in the same clade ✔

h. evidence from one chromosome/3 genes/2 studies is not sufficient to form a conclusion ✔

Examiners report

[N/A]

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Core » Topic 3: Genetics » 3.1 Genes

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