The genetic variation of lactase persistence alleles in northeast Africa

Lactase persistence (LP) is a well-studied example of a Mendelian trait under selection in some human groups due to gene-culture co-evolution. We investigated the frequencies of genetic variants linked to LP in Sudanese and South Sudanese populations. These populations have diverse subsistence patterns, and some are dependent on milk to various extents, not only from cows, but also from other livestock such as camels and goats. We sequenced a 316bp region involved in regulating the expression of the LCT gene on chromosome 2, which encompasses five polymorphisms that have been associated with LP. Pastoralist populations showed a higher frequency of LP-associated alleles compared to non-pastoralist groups, hinting at positive selection also in northeast African pastoralists. There was no incidence of the East African LP allele (-14010:C) in the Sudanese groups, and only one heterozygote individual for the European LP allele (-13910:T), suggesting limited recent admixture from these geographic regions. Among the LP variants, the -14009:G variant occurs at the highest frequency among the investigated populations, followed by the -13915:G variant, which is likely of Middle Eastern origin, consistent with Middle Eastern gene-flow to the Sudanese populations. The Beja population of the Beni Amer show three different LP-variants at substantial and similar levels, resulting in one of the greatest frequencies of LP-variants among all populations across the world.