Meta-Analysis of Mitochondrial DNA Control Region Diversity to Shed Light on Phylogenetic Relationship and Demographic History of African Sheep (Ovis aries) Breeds.

George Wanjala,Szilvia Kusza,Zoltán Bagi

doi:10.3390/biology10080762

Abstract

Simple SummaryThe African continent is home to more than 400 million heads of sheep, the majority of which are classified as indigenous and raised primarily for subsistence. They live and thrive well in a wide range of climatic and production conditions, ranging from unfavorable to favorable environments. Recent molecular and archeological studies have hypothesized that these breeds harbor novel genomic regions that give them the ability to adapt to varied production environments. However, the genetic relationship among these populations is poorly understood. Knowledge about the population history and genetic relationships between populations provides an opportunity for the improvement of breeding and conservation programs. We meta-analyzed 399 African sheep breeds mtDNA control region sequences retrieved from the NCBI GenBank database to elucidate their diversity, phylogenetic relationship, and demographic history.To improve sheep breeding and conservation of genetic resources, the mitochondrial DNA control region (mtDNA CR) of 399 sequences of African indigenous sheep breeds from previously published research articles were meta-analyzed to elucidate their phylogenetic relationship, diversity, and demographic history. A total of 272 haplotypes were found, of which 207 were unique and a high level of mtDNA CR variability was observed. Generally, the number of polymorphic sites, nucleotide and haplotype diversity were high (284, 0.254 ± 0.012 and 0.993 ± 0.002, respectively). The median-joining (MJ) network of haplotypes produced three major haplogroups (A, B and C), with haplogroup B being dominant. A mixture of populations suggests a common matrilineal origin and lack of and/or a weak phylogeographic structure. Mismatch analysis showed recent expansion of North African breeds, whereas East African and continental populations exhibited selection pressures for adaptation. A slight historical genetic difference was also observed between the fat tail and thin tail sheep breeds. However, further investigations are required using more samples and long sequence segments to achieve deeper levels of conclusions on the African sheep phylogenetic relationship. The present meta-analysis results contribute to the general understanding of African native sheep populations for improved management of sheep genetic resources.

Highlights

Domestic animal agriculture plays a crucial role in maintaining food security, as envisioned in sustainable development goal two (“End hunger, achieve food security and improved nutrition and promote sustainable agriculture”) [1]
Haplotypes belonging to haplogroup B are descendants of European mouflon (Ovis aries musimon) and are more frequent in Europe [4,6,14], while haplogroup A descends from Asiatic mouflon (Ovis orientalis) which is mainly present in Asian breeds [4,15]
The scope of the present meta-analysis was to elucidate their mtDNA CR diversity and phylogenetic relationships as wells as the demographic history of African sheep breeds clustered in four regions

Summary

Introduction

Domestic animal agriculture plays a crucial role in maintaining food security, as envisioned in sustainable development goal two (“End hunger, achieve food security and improved nutrition and promote sustainable agriculture”) [1]. The estimated global sheep, goat and cattle populations are 1.2, 1.1, and 1.5 billion heads, respectively [2]. Diversity and adaptation under the current climate change challenges [3] in recent decades, researchers have extensively studied the origin, history, phylogenetic relationships and diversity of domestic animals within species and among populations such as in sheep [4,5,6,7], goats [8,9,10], and cattle [11]. Further studies have identified the existence of other sheep clades from C to E [4] These could have risen from post domestication selection leading to the emergence of varied phenotypes, for instance, meat production traits, wool characteristics, coat color, presence or absence of horns, body sizes and tail size [15]. Studies indicate that haplogroup C is present in China [4], whereas clades D and E are very rare spotted in near East sheep [14]

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