Mitogenomes from Egyptian Cattle Breeds: New Clues on the Origin of Haplogroup Q and the Early Spread of Bos taurus from the Near East

Abstract

BackgroundGenetic studies support the scenario that Bos taurus domestication occurred in the Near East during the Neolithic transition about 10 thousand years (ky) ago, with the likely exception of a minor secondary event in Italy. However, despite the proven effectiveness of whole mitochondrial genome data in providing valuable information concerning the origin of taurine cattle, until now no population surveys have been carried out at the level of mitogenomes in local breeds from the Near East or surrounding areas. Egypt is in close geographic and cultural proximity to the Near East, in particular the Nile Delta region, and was one of the first neighboring areas to adopt the Neolithic package. Thus, a survey of mitogenome variation of autochthonous taurine breeds from the Nile Delta region might provide new insights on the early spread of cattle rearing outside the Near East.MethodologyUsing Illumina high-throughput sequencing we characterized the mitogenomes from two cattle breeds, Menofi (N = 17) and Domiaty (N = 14), from the Nile Delta region. Phylogenetic and Bayesian analyses were subsequently performed.ConclusionsPhylogenetic analyses of the 31 mitogenomes confirmed the prevalence of haplogroup T1, similar to most African cattle breeds, but showed also high frequencies for haplogroups T2, T3 and Q1, and an extremely high haplotype diversity, while Bayesian skyline plots pointed to a main episode of population growth ~12.5 ky ago. Comparisons of Nile Delta mitogenomes with those from other geographic areas revealed that (i) most Egyptian mtDNAs are probably direct local derivatives from the founder domestic herds which first arrived from the Near East and the extent of gene flow from and towards the Nile Delta region was limited after the initial founding event(s); (ii) haplogroup Q1 was among these founders, thus proving that it underwent domestication in the Near East together with the founders of the T clades.

Whole Mitogenomes Reveal the History of Swamp Buffalo: Initially Shaped by Glacial Periods and Eventually Modelled by Domestication

“…Complete mitogenome sequences were obtained by using two different approaches: 1) PCR amplification (with 27 primer pairs, Supplementary Table S2A) 40 and Sanger sequencing; 2) Long-Range PCR amplification (Supplementary Table S2B) and Illumina sequencing 41 . GenBank accession number, sequencing method, coverage and depth of each sample are reported in Supplementary Dataset S1.…”

Complete mitochondrial genome sequences of Korean native horse from Jeju Island: uncovering the spatio-temporal dynamics

“…They thought the important factor of geographic structure of horse is geographic isolation by Silk Road, high mountain, and etc. In addition, geographic isolation of other domestic animals such as goat were reported [e.g., [35][36][37].…”

Early North African Cattle Domestication and Its Ecological Setting: A Reassessment

“…In conjunction with recent reviews of genetic data suggestive of introgression of Y-chromosomal data from African Bos primigenius into African Bos taurus descended from Near Eastern stock (Achilli et al 2010;Bonfiglio et al 2012;Olivieri et al 2015;Perez-Pardal et al 2010;Stock and Gifford-Gonzalez 2013), a re-examination of the archaeobotanical, faunal and geomorphological data from the early and middle Holocene periods in the Nabta Playa-Bir Kiseiba region is appropriate in order to determine whether the ecological underpinnings of the early African independent domestication model are valid.…”

“…These and other studies (Ajmone-Marsan et al 2010, Beja-Pereira et al 2006 show that the T1 haplogroup found in African Bos taurus originates in the Fertile Crescent. Olivieri et al (2015) undertook Bayesian and phylogenetic analyses on 31 mitogenomes from the Domiatry and Menofi cattle breeds in the Nile Delta. High haplotype and haplogroup affiliation diversity were detected.…”