All three of them.

1. Local domestication of the African aurochs (Bos primigenius mauretanicus) from North Africa.

2. Introduction of Eurasian aurochs (B. p. primigenius) from the Middle East via Egypt.

3. Introduction of zebus (domestic form of B. p. namadicus) from India by sea but also from Egypt where they were introduced by land relatively soon.

Most breeds of African cattle are thus a mix of all three subspecies of wild aurochs (all of them extinct today). There are places where pure or nearly pure zebu exist though, most notably in Madagascar and the Swahili Coast.

/u/masiakasaurus is correct. Modern cattle stock in Africa feature genetic markers from African aurochs, Eurasian aurochs, or zebus.

As with many subjects in African archaeology, it is a fiercely debated topic whether domestication happened independently in Africa before the introduction of cattle from Western Asia. (A quick note, I don't really address Zebu from here on out. Sorry Zebu fans!)

Recent genetic studies ( by Hanotte et al in 2002) concluded that breeding populations of Aurochs in Asia and Africa separated beginning 22,000 years ago. Supporters of African domestication theory have taken this to support their belief that domestication occurred independently in the western Sahara region.

Furthermore, there have been several sites of cattle bones around the Hoggar mountains in southern Algeria, which have been dated to the mid-8th millenium before present. (more precisely, the finds at Ti-n-Torha are estimated to be 7440 +/- 220 before present. At Uan Muhuggiag at 7438 +/- 220 before present, and at Ti-n-Hanakaten some time between Mid-eighth and mid-sixth millenium bp). Other finds in the Tibesti mountains in northern Chad, and the Emmedi mountains in central Chad have also been dated between 7400 and 7000 years before present.

On the other hand, along the Nile Valley, the earliest remains are all dated between 5800 and 5400 years before present, with two exceptions. The remains found at the oasis of Bir Keseiba in southern Egypt are dated to 9800 bp, and at Nabta to 8800 bp. However, the identification of these remains as domesticated cattle is very controversial. Wendorf and his colleagues who discovered the remains claim that the presence of tortoise, jackal, and hare remains at the site indicate a climate too arid for wild aurochs to survive without human care, indicating domestication. Others claim that the climate was in-fact much more hospitable than Wendorf claims, and that the Keseiba and Nabta bones are of wild Aurochs.

What is not disputed is that Sheep and Goats are not native to Africa, and were brought from West Asia, through Egypt. The earliest evidence of sheep and cattle domestication in Africa is dated between 8500-7500 years before present (sheep corrals in coastal Libya).

Supporters domestication coming from West Asia point to that fact, and argue that it circumstantially supports a belief that cattle arrived from West Asia to Egypt around the same time. They argue that separating the arrival of domesticated Asiatic cattle to a later period would not fit the pastoralist lifestyle that is shown.

So, which camp is correct? Did earliest domestication arrive from West Asia or occur earlier in the Sahara?

The picture is really too murky to tell. Again, there is some evidence to suggest early sedentism in the Sahara. For instance, finds of ceramic pottery and cereal cultivation occur earlier than in central and eastern saharan contexts. On the other hand, within the Sahara evidence has not yet been shown of a pattern of increased hunting and rudimentary domestication that could be expected in a trend of domesticating cattle.

Really, the lesson is that the picture is murky, and will only be cleared up through more scholarship, and hopefully more archaeological evidence.

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I relied heavily on Savino di Lerna's essay the emergence and spread of herding in Northern Africa: a critical reappraisal, which is chapter 36 in the Oxford Handbook of African Archaeology