Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data

Abstract

Since the time of their domestication, goats (Capra hircus) have evolved in a large variety of locally adapted populations in response to different human and environmental pressures. In the present era, many indigenous populations are threatened with extinction due to their substitution by cosmopolitan breeds, while they might represent highly valuable genomic resources. It is thus crucial to characterize the neutral and adaptive genetic diversity of indigenous populations. A fine characterization of whole genome variation in farm animals is now possible by using new sequencing technologies. We sequenced the complete genome at 12× coverage of 44 goats geographically representative of the three phenotypically distinct indigenous populations in Morocco. The study of mitochondrial genomes showed a high diversity exclusively restricted to the haplogroup A. The 44 nuclear genomes showed a very high diversity (24 million variants) associated with low linkage disequilibrium. The overall genetic diversity was weakly structured according to geography and phenotypes. When looking for signals of positive selection in each population we identified many candidate genes, several of which gave insights into the metabolic pathways or biological processes involved in the adaptation to local conditions (e.g., panting in warm/desert conditions). This study highlights the interest of WGS data to characterize livestock genomic diversity. It illustrates the valuable genetic richness present in indigenous populations that have to be sustainably managed and may represent valuable genetic resources for the long-term preservation of the species.

Genetic diversity of the Northern Morocco goat population assessed with microsatellite markers

“…These findings are very similar to those examining other Moroccan goat populations, i.e., Black, Draa and Northern (Benjelloun et al, 2015), for which three principal components explained only 5.8% of the variance among the three populations. Hilal et al (2016) reported weak differentiation in the Hamra goat population in two different locations of Morocco.…”

“…Genetic differentiation (FST) among the populations was not detected (2%), and 98% of the genetic variability of the studied subpopulations was due to differences among individuals of the total population and not to differences among the geographical subpopulations. Our FST values are notably inferior to those reported by Ouragh et al (2012) but are similar to those obtained with SNPs for other Moroccan goats (Black of the Atlas, Draa and Northern populations) by Benjelloun et al (2015).…”

“…The genetic characterization of Moroccan goats using microsatellites has been limited to studies of the Draa (Tadlaoui Ouafi et al, 2002), Black Rahalli breeds (Ouragh et al, 2012) and the Hamra population (Hilal et al, 2016). Previous studies reporting the genetic structure and diversity of Moroccan goat populations have been achieved using mitochondrial DNA markers (Benjelloun et al, 2011) and WGS data (Benjelloun et al, 2015).…”

Whole-genome sequencing of eight goat populations for the detection of selection signatures underlying production and adaptive traits

“…The genome of goats, which have diverse production potentials and extensive adaptation to diverse environments, provides a unique opportunity for identifying signatures associated with selection. Array- or sequencing-based detection of signatures during the selection process has been described in cattle456, chicken7, pigs8910, sheep1112, and recently in goats131415. By using whole-genome resequencing (WGS) data, Benjelloun et al .…”

Scanning of selection signature provides a glimpse into important economic traits in goats (Capra hircus)

“…But the morphologicaland behavioral characteristics of modern domestic goats have greatly changed compared with wild progenitor, the Bezoar goat ( Capra aegagrus )2. Compared with the Bezoar goat, modern goats exhibit a reduction in body size, a more docile demeanor, a series of coat color variants and the ability to adapt after domestication and breed formation, which have left detectable signatures of selection within the genomes34. Hence, scanning of selection signature can’t only provide straightforward insights into the mechanism of evolution events but also use for identifying functional genes of important economic traits or causative variations of phenotypic diversity.…”