Discovering novel clues of natural selection on four worldwide goat breeds

Abstract

In goat breeds, the domestication followed by artificial selection for economically important traits have shaped genetic variation within populations, leading to the fixation of specific alleles for specific traits. This led to the formation and evolution of many different breeds specialised and raised for a particular purpose. However, and despite the intensity of artificial selection, natural selection continues acting, possibly leaving a more diluted contribution over time, whose traces may be more difficult to capture. In order to explore selection footprints as response of environmental adaptation, we analysed a total of 993 goats from four transboundary goats breeds (Angora, Boer, Nubian and Saanen) genotyped with the SNP chip 50 K using outlier detection, runs of homozygosity and haplotype-based detection methods. Our results showed that all methods identified footprints on chromosome 6 (from 30 to 49 Mb) for two specific populations of Nubian goats sampled in Egypt. In Angora and Saanen breeds, we detected two selective sweeps using HapFLK, on chromosome 21 (from 52 to 55 Mb) and chromosome 25 (from 1 to 5 Mb) respectively. The analysis of runs of homozygosity showed some hotspots in all breeds. The overall investigation of the selected regions detected combining the different approaches and the gene ontology exploration revealed both novel and well-known loci related to adaptation, especially for heat stress. Our findings can help to better understand the balance between the two selective pressures in commercial goat breeds providing new insights on the molecular mechanisms of adaptation.

Genomic analysis revealed hotspots of genetic adaptation and risk of disappearance in the Brazilian goat populations

“…Analysis of ROH and HRR in the Marota and Anglo-Nubian breeds has revealed markers potentially under selection for adaptation to the semi-arid environment of Brazil. Our discoveries have led to the identification of target genes related to adaptation, specifically concerning the immune/inflammatory response, energy homeostasis, reproductive and production traits, and heat stress [18,22,40,54,55,57].…”

“…Thus, biological adaptation is essential to ensure that animals remain healthy and productive. Within their DNA, it is possible to find markers of natural selection that emerge in response to environmental pressures, identifiable through genomic and bioinformatics techniques [18,54,55].…”

“…Research into the specific functions of genes has unveiled an intricate panorama of biological processes, wherein genes play distinct and essential roles in cellular functions, contributing to a wide range of biological processes. For example, the GMCL1 and TEX12 genes are known to be involved in the regulation and/or participation of reproductive processes, specifically in sperm production [9,18,55,56]. The Zbtb11 gene, with its integrase-like HHCC zinc finger, serves as a crucial regulator in neutrophil differentiation, contributing significantly to the immune defense system.…”

Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat

“…In recent years, due to the extensive utilization of SNP microarray gene chip and whole-genome resequencing technologies [8][9][10][11], research into ROHs based on livestock and poultry genomic information has been increasing. This includes research on various species, such as goats [12][13][14], sheep [15][16][17], cattle [7,18,19], pigs [3,20,21], chickens [22][23][24] and so on. Genomic regions that were abundant with ROHs were defined as ROH islands, potentially signaling selection sweeps.…”

Editorial: Environmental and genomic strategies for conservation and selection in small ruminants

“…In the last decade, several studies aimed to investigate the adaptation to the local environmental conditions, most of them focused on local or indigenous populations, thus highlighting a probable population-specific selection footprint ( 4 ). Detecting regions under selection is a complex task, especially where the natural selection acts leaving detectable fingerprints.…”