At the end of the year 2009, India signed a civil nuclear agreement with Russia. This agreement was significant as it allowed for cooperation between the two countries in the field of nuclear energy.

Option 1, Brazil, is not the correct answer because India did not sign a civil nuclear agreement with Brazil at the end of 2009.

Option 2, China, is not the correct answer because India did not sign a civil nuclear agreement with China at the end of 2009.

Option 4, South Africa, is not the correct answer because India did not sign a civil nuclear agreement with South Africa at the end of 2009.

Therefore, the correct answer is option 3, Russia. The civil nuclear agreement signed with Russia in 2009 marked a significant development in India`s nuclear energy cooperation with other countries.