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. 2021 Dec 2:12:723599.
doi: 10.3389/fgene.2021.723599. eCollection 2021.

Genomic Uniqueness of Local Sheep Breeds From Morocco

Abdessamad Ouhrouch  1   2 , Simon Boitard  3 , Frédéric Boyer  4 , Bertrand Servin  5 , Anne Da Silva  6 , François Pompanon  4 , Abdelmajid Haddioui  2 , Badr Benjelloun  1
Affiliations

Genomic Uniqueness of Local Sheep Breeds From Morocco

Abdessamad Ouhrouch et al. Front Genet. .

Abstract

Sheep farming is a major source of meat in Morocco and plays a key role in the country's agriculture. This study aims at characterizing the whole-genome diversity and demographic history of the main Moroccan sheep breeds, as well as to identify selection signatures within and between breeds. Whole genome data from 87 individuals representing the five predominant local breeds were used to estimate their level of neutral genetic diversity and to infer the variation of their effective population size over time. In addition, we used two methods to detect selection signatures: either for detecting selective sweeps within each breed separately or by detecting differentially selected regions by contrasting different breeds. We identified hundreds of genomic regions putatively under selection, which related to several biological terms involved in local adaptation or the expression of zootechnical performances such as Growth, UV protection, Cell maturation or Feeding behavior. The results of this study revealed selection signatures in genes that have an important role in traits of interest and increased our understanding of how genetic diversity is distributed in these local breeds. Thus, Moroccan local sheep breeds exhibit both a high genetic diversity and a large set of adaptive variations, and therefore, represent a valuable genetic resource for the conservation of sheep in the context of climate change.

Keywords: demography; local breeds; selection signatures; sheep; whole genome sequences.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Variation of the effective population size in five Moroccan breeds in comparison with the wild Asiatic mouflon and a multi-breed group of cosmopolitan sheep. Estimates were obtained independently for each group by the popsizeABC algorithm.
FIGURE 2
FIGURE 2
Selective sweeps detected by hapFLK and plots for an example candidate region. (A) Manhattan plot depicting hapFLK scores in five Moroccan sheep breeds along autosomal chromosomes. Each dot represents a SNP. The horizontal red line represents the 0.1% FDR threshold of significance. (B) Local tree for the example region on Chromosome 10 in Dman. (C) Haplotype cluster plot of the same example region on chromosome 10 in Dman (Cluster frequencies plot).
FIGURE 3
FIGURE 3
Selective sweeps, SNPs and genes identified by both freqHMM and hapFLK methods. (A) Venn diagram of candidate regions under selection. (B) Venn diagram of genes under selection. (C) Venn diagram of SNPs under selection.
See this image and copyright information in PMC

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