scholarly journals Genetic signatures of high-altitude adaptation and geographic distribution in Tibetan sheep

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Jianbin Liu ◽  
Chao Yuan ◽  
Tingting Guo ◽  
Fan Wang ◽  
Yufeng Zeng ◽  
...  
Keyword(s):  
Bos Taurus ◽  
Body Height ◽  
Hypoxia Tolerance ◽  
Adaptive Responses ◽  
Sheep Breeds ◽  
Tibetan Sheep ◽  
Altitude Adaptation ◽  
Genomic Regions ◽  
The Tropics ◽  
Indel Variation

Abstract Most sheep breeding programs designed for the tropics and sub-tropics have to take into account the impacts of environmental adaptive traits. However, the genetic mechanism regulating the multiple biological processes driving adaptive responses remains unclear. In this study, we applied a selective sweep analysis by combing 1% top values of Fst and ZHp on both altitude and geographic subpopulations (APS) in 636 indigenous Tibetan sheep breeds. Results show that 37 genes were identified within overlapped genomic regions regarding Fst significantly associated with APS. Out of the 37 genes, we found that 8, 3 and 6 genes at chromosomes (chr.) 13, 23 and 27, respectively, were identified in the genomic regions with 1% top values of ZHp. We further analyzed the INDEL variation of 6 genes at chr.27 (X chromosome) in APS together with corresponding orthologs of 6 genes in Capra, Pantholops, and Bos Taurus. We found that an INDEL was located within 5′UTR region of HAG1 gene. This INDEL of HAG1 was strongly associated with the variation of APS, which was further confirmed by qPCR. Sheep breeds carrying “C-INDEL” of HAG1 have significantly greater body weight, shear amount, corpuscular hemoglobin and globulin levels, but lower body height, than those carrying “CA-INDEL” of HAG1. We concluded that “C-INDEL” variation of HAG1 gene confers better hypoxia tolerance in the highlands of Tibetan and explains well geographic distributions in this population. These results contribute to our understanding of adaptive responses to altitude and geographic adaptation in Tibetan sheep populations and will help to guide future conservation programs for Tibetan sheep native to Qinghai-Tibetan Plateau.

scholarly journals Whole genome sequences reveal multiple functions of PAT1 gene on environment adaptation and coat coloration in Tibetan sheep populations

2019 ◽  
Author(s):  
Jianbin Liu ◽  
Xuezhi Ding ◽  
Chao Yuan ◽  
Yufeng Zeng ◽  
Tingting Guo ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Coat Color ◽  
Body Height ◽  
Multiple Traits ◽  
Adaptive Traits ◽  
Environment Adaptation ◽  
Tibetan Sheep ◽  
Genomic Regions ◽  
The Tropics ◽  
Productive Trait

Abstract Background: Most sheep breeding programs designed for the tropics and sub-tropics have to take into account the impacts of both productive and adaptive traits. However, the genetic mechanism regulating the multiple biological process remain unclear. Results: In this study, we report a novel PAT1 gene that simultaneously explained the variations of productive trait (coat color), adaptive traits (altitude and geography response) in 15 indigenous Tibetan sheep populations. Overlapped genomic regions harboring 6 candidate genes across three traits were identified at 27 chromosomes, with the top 1% of Fst and |Zph| values. The SNP/INDELs and expression of these candidate genes were further analyzed, and we find that only PAT1 gene, a CSDE1 homologue was consistent with the variation of multiple traits regarding. Haplotype analysis of PAT1 reveal that Tibetan sheep breeds with C-type of PAT1 have significantly greater body weight, shear amount, chest width and body length, but have lower body height, than those with CA-type of PAT1. Conclusions: We emphasized that PAT1 gene could be a potentially selective target used for the improvements of environmental adaption and coat coloration in the future. These results contribute to the knowledge of adaptive response in Tibetan sheep populations and will help to guide future conservation programs for Tibetan sheep native to Qinghai-Tibetan Plateau.

scholarly journals Analysis of selection signatures reveals important insights into the adaptability of high-altitude Indian sheep breed Changthangi

2020 ◽  
Author(s):  
Sheikh Firdous Ahmad ◽  
Arnav Mehrotra ◽  
Sona Charles ◽  
Nazir Ahmad Ganai
Keyword(s):  
High Altitude ◽  
Sheep Breed ◽  
Selection Signatures ◽  
Sheep Breeds ◽  
Functional Regions ◽  
Population Comparisons ◽  
Genetic Mechanisms ◽  
Altitude Adaptation ◽  
Genomic Regions ◽  
Indian Sheep

AbstractChangthangi is a high-altitude sheep breed of India that is adapted to cold and hypoxic climate of Himalayas. In the present study, we analysed population structure of Changthangi and contrasted it with selected Indian and European commercial sheep breeds to detect genomic regions under positive selection. The studied domesticated sheep breeds included Changthangi, Indian Garole, Deccani, Tibetan, Rambouillet and Australian Merino. While the PCA results revealed Changthangi clustered with Tibetan sheep; TREEMIX and ADMIXTURE results also detected the introgression of lowland Indian sheep inheritance in Changthangi. Cross-population comparisons of Changthangi using XP-EHH showed multiple functional regions present on OAR 7, 15 and 16, to be under selection in Changthangi sheep. These regions are related to adaptation to climatic and hypoxic stressors, nervous system and mitochondrial functioning. The genes present in these regions are suitable candidates for future studies on the genetic mechanisms underlying high-altitude adaptation.

scholarly journals Genome-wide selection scans integrated with association mapping reveal mechanisms of physiological adaptation across a salinity gradient in killifish

2018 ◽  
Author(s):  
Reid S. Brennan ◽  
Timothy M. Healy ◽  
Heather J. Bryant ◽  
Man Van La ◽  
Patricia M. Schulte ◽  
...  
Keyword(s):  
Natural Selection ◽  
Salinity Tolerance ◽  
Hypoxia Tolerance ◽  
Physiological Traits ◽  
Adaptive Divergence ◽  
Genome Wide ◽  
Native Populations ◽  
Genomic Regions ◽  
Insight Into ◽  
Freshwater Environments

AbstractAdaptive divergence between marine and freshwater environments is important in generating phyletic diversity within fishes, but the genetic basis of adaptation to freshwater habitats remains poorly understood. Available approaches to detect adaptive loci include genome scans for selection, but these can be difficult to interpret because of incomplete knowledge of the connection between genotype and phenotype. In contrast, genome wide association studies (GWAS) are powerful tools for linking genotype to phenotype, but offer limited insight into the evolutionary forces shaping variation. Here, we combine GWAS and selection scans to identify loci important in the adaptation of complex physiological traits to freshwater environments. We focused on freshwater (FW)-native and brackish water (BW)-native populations of the Atlantic killifish (Fundulus heteroclitus) as well as a population that is a natural admixture of these two populations. We measured phenotypes for multiple physiological traits that differ between populations and that may contribute to adaptation across osmotic niches (salinity tolerance, hypoxia tolerance, metabolic rate, and body shape) and used a reduced representation approach for genome-wide genotyping. Our results show patterns of population divergence in physiological capabilities that are consistent with local adaptation. Selection scans between BW-native and FW-native populations identified genomic regions that presumably aect fitness between BW and FW environments, while GWAS revealed loci that contribute to variation for each physiological trait. There was substantial overlap in the genomic regions putatively under selection and loci associated with the measured physiological traits, suggesting that these phenotypes are important for adaptive divergence between BW and FW environments. Our analysis also implicates candidate genes likely involved in physiological capabilities, some of which validate a priori hypotheses. Together, these data provide insight into the mechanisms that enable diversification of fishes across osmotic boundaries.Author SummaryIdentifying the genes that underlie adaptation is important for understanding the evolutionary process, but this is technically challenging. We bring multiple lines of evidence to bear for identifying genes that underlie adaptive divergence. Specifically, we integrate genotype-phenotype association mapping with genome-wide scans for signatures of natural selection to reveal genes that underlie phenotypic variation and that are adaptive in populations of killifish that are diverging between marine and freshwater environments. Because adaptation is likely manifest in multiple physiological traits, we focus on hypoxia tolerance, salinity tolerance, and metabolic rate; traits that are divergent between marine and freshwater populations. We show that each of these phenotypes is evolving by natural selection between environments; genetic variants that contribute to variation in these physiological traits tend to be evolving by natural selection between marine and freshwater populations. Furthermore, one of our top candidate genes provides a mechanistic explanation for previous hypotheses that suggest the adaptive importance of cellular tight junctions. Together, these data demonstrate a powerful approach to identify genes involved in adaptation and help to reveal the mechanisms enabling transitions of fishes across osmotic boundaries.

scholarly journals Highly parallel genomic selection response in replicated Drosophila melanogaster populations with reduced genetic variation

2021 ◽  
Author(s):  
Claire Burny ◽  
Viola Nolte ◽  
Marlies Dolezal ◽  
Christian Schl&oumltterer
Keyword(s):  
Drosophila Melanogaster ◽  
Experimental Evolution ◽  
Selection Response ◽  
Adaptive Responses ◽  
Genetic Redundancy ◽  
Powerful Approach ◽  
Polygenic Adaptation ◽  
Parallel Selection ◽  
Sufficient Variation ◽  
Genomic Regions

Many adaptive traits are polygenic and frequently more loci contributing to the phenotype than needed are segregating in populations to express a phenotypic optimum. Experimental evolution provides a powerful approach to study polygenic adaptation using replicated populations adapting to a new controlled environment. Since genetic redundancy often results in non-parallel selection responses among replicates, we propose a modified Evolve and Resequencing (E&R) design that maximizes the similarity among replicates. Rather than starting from many founders, we only use two inbred Drosophila melanogaster strains and expose them to a very extreme, hot temperature environment (29°C). After 20 generations, we detect many genomic regions with a strong, highly parallel selection response in 10 evolved replicates. The X chromosome has a more pronounced selection response than the autosomes, which may be attributed to dominance effects. Furthermore, we find that the median selection coefficient for all chromosomes is higher in our two-genotype experiment than in classic E&R studies. Since two random genomes harbor sufficient variation for adaptive responses, we propose that this approach is particularly well-suited for the analysis of polygenic adaptation.

scholarly journals EPAS1 Gain-of-Function Mutation Contributes to High-Altitude Adaptation in Tibetan Horses

2019 ◽  
Vol 36 (11) ◽  
pp. 2591-2603 ◽  
Author(s):  
Xuexue Liu ◽  
Yanli Zhang ◽  
Yefang Li ◽  
Jianfei Pan ◽  
Dandan Wang ◽  
...  
Keyword(s):  
High Altitude ◽  
Extreme Environments ◽  
Hypoxia Tolerance ◽  
Missense Mutations ◽  
Data Set ◽  
Genetic Changes ◽  
Genome Data ◽  
Hypoxic Conditions ◽  
Domestic Horses ◽  
Altitude Adaptation

Abstract High altitude represents some of the most extreme environments worldwide. The genetic changes underlying adaptation to such environments have been recently identified in multiple animals but remain unknown in horses. Here, we sequence the complete genome of 138 domestic horses encompassing a whole altitudinal range across China to uncover the genetic basis for adaptation to high-altitude hypoxia. Our genome data set includes 65 lowland animals across ten Chinese native breeds, 61 horses living at least 3,300 m above sea level across seven locations along Qinghai-Tibetan Plateau, as well as 7 Thoroughbred and 5 Przewalski’s horses added for comparison. We find that Tibetan horses do not descend from Przewalski’s horses but were most likely introduced from a distinct horse lineage, following the emergence of pastoral nomadism in Northwestern China ∼3,700 years ago. We identify that the endothelial PAS domain protein 1 gene (EPAS1, also HIF2A) shows the strongest signature for positive selection in the Tibetan horse genome. Two missense mutations at this locus appear strongly associated with blood physiological parameters facilitating blood circulation as well as oxygen transportation and consumption in hypoxic conditions. Functional validation through protein mutagenesis shows that these mutations increase EPAS1 stability and its hetero dimerization affinity to ARNT (HIF1B). Our study demonstrates that missense mutations in the EPAS1 gene provided key evolutionary molecular adaptation to Tibetan horses living in high-altitude hypoxic environments. It reveals possible targets for genomic selection programs aimed at increasing hypoxia tolerance in livestock and provides a textbook example of evolutionary convergence across independent mammal lineages.

scholarly journals The evolution of a tropical biodiversity hotspot

Science ◽  
2020 ◽  
Vol 370 (6522) ◽  
pp. 1343-1348 ◽  
Author(s):  
Michael G. Harvey ◽  
Gustavo A. Bravo ◽  
Santiago Claramunt ◽  
Andrés M. Cuervo ◽  
Graham E. Derryberry ◽  
...  
Keyword(s):  
Species Diversity ◽  
Biodiversity Hotspot ◽  
Tropical Biodiversity ◽  
Environmental Extremes ◽  
Speciation Rates ◽  
Gradual Accumulation ◽  
Using Data ◽  
Genomic Regions ◽  
The Tropics ◽  
Over Time

The tropics are the source of most biodiversity yet inadequate sampling obscures answers to fundamental questions about how this diversity evolves. We leveraged samples assembled over decades of fieldwork to study diversification of the largest tropical bird radiation, the suboscine passerines. Our phylogeny, estimated using data from 2389 genomic regions in 1940 individuals of 1287 species, reveals that peak suboscine species diversity in the Neotropics is not associated with high recent speciation rates but rather with the gradual accumulation of species over time. Paradoxically, the highest speciation rates are in lineages from regions with low species diversity, which are generally cold, dry, unstable environments. Our results reveal a model in which species are forming faster in environmental extremes but have accumulated in moderate environments to form tropical biodiversity hotspots.

scholarly journals Tick burden in Bos taurus cattle and its relationship with heat stress in three agroecological zones in the tropics of Colombia

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Juan Felipe Rocha ◽  
Rodrigo Martínez ◽  
Nicolas López-Villalobos ◽  
Steve Todd Morris
Keyword(s):  
Heat Stress ◽  
Bos Taurus ◽  
Agroecological Zones ◽  
The Tropics ◽  
Tick Burden

scholarly journals A novel hypothesis for histone-to-protamine transition in Bos taurus spermatozoa

Reproduction ◽  
2017 ◽  
Vol 153 (3) ◽  
pp. 241-251 ◽  
Author(s):  
Gerly Sillaste ◽  
Lauris Kaplinski ◽  
Riho Meier ◽  
Ülle Jaakma ◽  
Elo Eriste ◽  
...  
Keyword(s):  
Bos Taurus ◽  
Structural Information ◽  
Gene Clusters ◽  
Early Embryo ◽  
Sperm Chromatin ◽  
New Findings ◽  
Sperm Development ◽  
Dependent Protein ◽  
And Function ◽  
Genomic Regions

DNA compaction with protamines in sperm is essential for successful fertilization. However, a portion of sperm chromatin remains less tightly packed with histones, which genomic location and function remain unclear. We extracted and sequenced histone-associated DNA from sperm of nine ejaculates from three bulls. We found that the fraction of retained histones varied between samples, but the variance was similar between samples from the same and different individuals. The most conserved regions showed similar abundance across all samples, whereas in other regions, their presence correlated with the size of histone fraction. This may refer to gradual histone–protamine transition, where easily accessible genomic regions, followed by the less accessible regions are first substituted by protamines. Our results confirm those from previous studies that histones remain in repetitive genome elements, such as centromeres, and added new findings of histones in rRNA and SRP RNA gene clusters and indicated histone enrichment in some spermatogenesis-associated genes, but not in genes of early embryonic development. Our functional analysis revealed significant overrepresentation of cGMP-dependent protein kinase G (cGMP-PKG) pathway genes among histone-enriched genes. This pathway is known for its importance in pre-fertilization sperm events. In summary, a novel hypothesis for gradual histone-to-protamine transition in sperm maturation was proposed. We believe that histones may contribute structural information into early embryo by epigenetically modifying centromeric chromatin and other types of repetitive DNA. We also suggest that sperm histones are retained in genes needed for sperm development, maturation and fertilization, as these genes are transcriptionally active shortly prior to histone-to-protamine transition.

scholarly journals Genomic Uniqueness of Local Sheep Breeds From Morocco

2021 ◽  
Vol 12 ◽  
Author(s):  
Abdessamad Ouhrouch ◽  
Simon Boitard ◽  
Frédéric Boyer ◽  
Bertrand Servin ◽  
Anne Da Silva ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Demographic History ◽  
Large Set ◽  
Whole Genome ◽  
Selection Signatures ◽  
Effective Population ◽  
High Genetic Diversity ◽  
Sheep Breeds ◽  
Genome Data ◽  
Genomic Regions

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.

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