Genome-wide structure and dynamics of Nubian goats from Northeast Africa

Abstract

The Nubian goat breed-group includes the Algerian Mzabite, Egyptian Zaraibi and Nubian goats found in Ethiopia, Sudan and Eritrea, and is one of the ancestral founders of the Anglo-Nubian. Whether the breed-group comprises one or separate genepools remains unknown as is their genetic contribution to the Anglo-Nubian dairy traits. We used Caprine 52K SNP Beadchip generated data to investigate the genome structure of Nubian goats from Egypt, Sudan and Ethiopia. Population structure analysis revealed two genetic groups (A and B) in Egypt. These were distinct from the Ethiopian and Sudanese Nubians, which occurred, in close proximity suggesting close genetic relationship. TreeMix analysis however, revealed one weak migration event involving Egyptian group-A with Sudanese Nubian suggesting possible historical connections. From hapFLK analysis, eight selection sweeps were revealed on chromosomes 6, 8, 9, 11, 13, 18, 23 and 25, respectively. The one on chromosome 6 was present in both Egyptian groups, while the ones on chromosomes 9 and 18, and 11 and 25 were specific to group-A and -B, respectively. The sweeps on chromosomes 8, 13 and 23 were common to Sudanese and Ethiopian Nubians. Functional annotation of the candidate regions in the Egyptian groups revealed several genes implicated in dairy traits (ABCG2), fat metabolism (PPARGC1A, ACMS3) and reproduction (BMPR1B; LCORL) as well as ARL6IP1 and TNRC6A in group-A with roles in thermo-tolerance during lactation and climatic stress tolerance, respectively. The ones in Sudanese and Ethiopian Nubian were associated with adaptation and immune traits (RAP1, BPIFA/B gene family, HS3ST2, CDR2). Our findings suggest that the three genepools present in Northeast African Nubians, as a repository of diverse genes, are an integral component of agro-biodiversity that may be required at present, and in future, to respond to different production and climate change scenarios.