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Chinese indigenous sheep can be classified into three types based on tail morphology: fat-tailed, fat-rumped, and thin-tailed sheep, of which the typical breeds are large-tailed Han sheep, Altay sheep, and Tibetan sheep, respectively. To unravel the molecular genetic basis underlying the phenotypic differences among Chinese indigenous sheep with th...
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Citations
... In fact, a comparison of Afec-Assaf sheep and its parental Awassi breed revealed variation in or near PDGFD, VEGFA, and RXFP2 (36). The BMP2 and PDGFD (platelet-derived growth factor D) genes are considered plausible candidate genes for the sheep fat-tail phenotype (10, 56,[57][58][59][60][61][62]. The VEGFA (vascular endothelial growth factor A) gene is in endothelial cells involved in angiogenesis by targeting lipids to peripheral tissues and may thus influence the expansion and loss of adipose tissue (63) and fat distribution in humans (64). ...
Introduction
The development of reproducible tools for the rapid genotyping of thousands of genetic markers (SNPs) has promoted cross border collaboration in the study of sheep genetic diversity on a global scale.
Methods
In this study, we collected a comprehensive dataset of 239 African and Eurasian sheep breeds genotyped at 37,638 filtered SNP markers, with the aim of understanding the genetic structure of 22 North African (NA) sheep breeds within a global context.
Results and discussion
We revealed asubstantial enrichment of the gene pool between the north and south shores of the Mediterranean Sea, which corroborates the importance of the maritime route in the history of livestock. The genetic structure of North African breeds mirrors the differential composition of genetic backgrounds following the breed history. Indeed, Maghrebin sheep stocks constitute a geographically and historically coherent unit with any breed-level genetic distinctness among them due to considerable gene flow. We detected a broad east–west pattern describing the most important trend in NA fat-tailed populations, exhibited by the genetic closeness of Egyptian and Libyan fat-tailed sheep to Middle Eastern breeds rather than Maghrebin ones. A Bayesian FST scan analysis revealed a set of genes with potentially key adaptive roles in lipid metabolism (BMP2, PDGFD VEGFA, TBX15, and WARS2), coat pigmentation (SOX10, PICK1, PDGFRA, MC1R, and MTIF) and horn morphology RXFP2) in Tunisian sheep. The local ancestry method detected a Merino signature in Tunisian Noire de Thibar sheep near the SULF1gene introgressed by Merino’s European breeds. This study will contribute to the general picture of worldwide sheep genetic diversity.
... Comparative analyses conducted on fat-tailed and thin-tailed sheep breeds highlighted the bone morphogenetic protein 2 gene as a potential causative gene for the tail phenotype [87][88][89]. Another gene probably involved in sheep tail fat deposition is the platelet-derived growth factor D (PDGF-D) gene [49,[89][90][91][92][93][94][95], with the recent investigation of Dong et al. [90] reporting a correlation between mutations that occur within the first intron of the PDGF-D gene and the fat tail phenotype. In another study, which includes more than 200 sequenced whole-genomes of wild and domestic sheep, Li et al. [91] found that tail fat deposition is correlated with the level of PDGF-D protein in adipose tissues. ...
The domestication of animals started around 12,000 years ago in the Near East region. This “endless process” is characterized by the gradual accumulation of changes that progressively marked the genetic, phenotypic and physiological differences between wild and domesticated species. The main distinctive phenotypic characteristics are not all directly attributable to the human-mediated selection of more productive traits. In the last decades, two main hypotheses have been proposed to clarify the emergence of such a set of phenotypic traits across a variety of domestic species. The first hypothesis relates the phenotype of the domesticated species to an altered thyroid hormone-based signaling, whereas the second one relates it to changes in the neural crest cells induced by selection of animals for tameness. These two hypotheses are not necessarily mutually exclusive since they may have contributed differently to the process over time and space. The adaptation model induced by domestication can be adopted to clarify some aspects (that are still controversial and debated) of the long-term evolutionary process leading from the wild Neolithic mouflon to the current domestic sheep. Indeed, sheep are among the earliest animals to have been domesticated by humans, around 12,000 years ago, and since then, they have represented a crucial resource in human history. The aim of this review is to shed light on the molecular mechanisms and the specific genomic variants that underlie the phenotypic variability between sheep and mouflon. In this regard, we carried out a critical review of the most recent studies on the molecular mechanisms that are most accredited to be responsible for coat color and phenotype, tail size and presence of horns. We also highlight that, in such a complicate context, sheep/mouflon hybrids represent a powerful and innovative model for studying the mechanism by which the phenotypic traits related to the phenotypic responses to domestication are inherited. Knowledge of these mechanisms could have a significant impact on the selection of more productive breeds. In fact, as in a journey back in time of animal domestication, the genetic traits of today’s domestic species are being progressively and deliberately shaped according to human needs, in a direction opposite to that followed during domestication.
... Selection signal and genome-wide association studies (GWAS) on wild ancestors were conducted, and they identified some selected regions and genes that may be affected by domestication . To date, a series of nonsynonymous mutations and significant differences in allele frequen-cies among different breeds were also found, among which PDGFD may be an important gene affecting fat deposition in the sheep tail Zhu et al., 2021). In addition, based on comparative genomic analysis of sheep habitats in different environments, some candidate genes were detected to be associated with extreme environments, like the adaptability to high altitude hypoxia and water reservation in arid environments (Yang et al., 2016). ...
As one of the most successful domesticated animals in the Neolithic age, sheep gradually migrated all over the world with human activities. During the domestication process, remarkable changes have taken place in morphology, physiology, and behavior, resulting in different breeds with different characters via artificial and natural selection. However, the genetic background responsible for these phenotypic variations remains largely unclear. Here, we used whole genome resequencing technology to compare and analyze the genome differences between Asiatic mouflon wild sheep (Ovis orientalis) and Hu sheep (Ovis aries). A total of 755 genes were positively selected in the process of domestication and selection, and the genes related to sensory perception had directional evolution in the autosomal region, such as OPRL1, LEF1, TAS1R3, ATF6, VSX2, MYO1A, RDH5, and some novel genes. A missense mutation of c.T722C/p.M241T in exon 4 of RDH5 existing in sheep were found, and the T allele was completely fixed in Hu sheep. In addition, the mutation with the C allele reduced the retinol dehydrogenase activity encoding by RDH5, which can impair retinoic acid metabolism and further influenced the visual cycle. Overall, our results showed significant enrichment for positively selected genes involved in sensory perception development during sheep domestication; RDH5 and its variants may be related to the retinal degeneration in sheep. We infer that the wild sheep ancestors with weaker visual sensitivity were weeded out by humans, and the mutation was selective, swept by the dual pressures of natural and artificial selection.
... Understanding the underlying energy homeostasis in response to environmental challenges could have applications for adapting to climate change. Previous studies revealed a few candidate genes associated with the fat tail phenotype using multiomics [13][14][15][16][17] . For example, candidate genes PDGFD, BMP2, TBXT, and HOXB13 were detected by selective sweep or GWAS analysis 15,[18][19][20][21][22] , which are involved in preadipocyte differentiation and associated with fat deposition in sheep 5,23 . ...
The fat tail of sheep is an important organ that has evolved to adapt to extreme environments. However, the genetic mechanisms underlying the fat tail phenotype remain poorly understood. Here, we characterize transcriptome and lipidome profiles and morphological changes in 250 adipose tissues from two thin-tailed and three fat-tailed sheep populations in summer and winter. We implement whole-genome selective sweep tests to identify genetic variants related to fat-tails. We identify a set of functional genes that show differential expression in the tail fat of fat-tailed and thin-tailed sheep in summer and winter. These genes are significantly enriched in pathways, such as lipid metabolism, extracellular matrix (ECM) remodeling, molecular transport, and inflammatory response. In contrast to thin-tailed sheep, tail fat from fat-tailed sheep show slighter changes in adipocyte size, ECM remodeling, and lipid metabolism, and had less inflammation in response to seasonal changes, indicating improved homeostasis. Whole-genome selective sweep tests identify genes involved in preadipocyte commitment (e.g., BMP2, PDGFD) and terminal adipogenic differentiation (e.g., VEGFA), which could contribute to enhanced adipocyte hyperplasia. Altogether, we establish a model of regulatory networks regulating adipose homeostasis in sheep tails. These findings improve our understanding of how adipose homeostasis is maintained, in response to extreme environments in animals.
... We used the four first PCA vectors as covariates to account for population structure in the analysis using the following model: Y = μ = + G + Q + e, with Y being the tail shape phenotype, μ the overall population mean, G the genotype matrix vector, Q the covariance of the first four PCA effect and e the residual. This method was previously used in GWASs related to fat deposition-related traits (Cui et al., 2022;Zhu et al., 2019Zhu et al., , 2021. The genomewide marker threshold was defined as the top 0.05% ranked −log 10 (p) values. ...
In developing countries, the use of simple and cost‐efficient molecular technology is crucial for genetic characterization of local animal resources and better development of conservation strategies. The genotyping by sequencing (GBS) technique, also called restriction enzyme‐ reduced representational sequencing, is an efficient, cost‐effective method for simultaneous discovery and genotyping of many markers. In the present study, we applied a two‐enzyme GBS protocol (PstI/MspI) to discover and genotype SNP markers among 197 Tunisian sheep samples. A total of 100 333 bi‐allelic SNPs were discovered and genotyped with an SNP call rate of 0.69 and mean sample depth 3.33. The genomic relatedness between 183 samples grouped the samples perfectly to their populations and pointed out a high genetic relatedness of inbred subpopulation reflecting the current adopted reproductive strategies. The genome‐wide association study contrasting fat vs. thin‐tailed breeds detected 41 significant variants including a peak positioned on OAR20. We identified FOXC1, GMDS, VEGFA, OXCT1, VRTN and BMP2 as the most promising for sheep tail‐type trait. The GBS data have been useful to assess the population structure and improve our understanding of the genomic architecture of distinctive characteristics shaped by selection pressure in local sheep breeds. This study successfully investigates a cost‐efficient method to discover genotypes, assign populations and understand insights into sheep adaptation to arid area. GBS could be of potential utility in livestock species in developing/emerging countries.
... Selective sweep studies are now widely used across livestock species with the aim of explaining the molecular mechanisms of inheritance hidden beneath complex economic traits. Many scholars have done extensive sequencing and selection signals in different sheep and goat breeds and have identified many candidate genes associated with the trait (Guan et al., 2016;Yuan et al., 2019;Guo et al., 2018;Zhu et al., 2021). It is clear from the above description that the vast majority of studies have been based on a genome-wide selective sweep of extreme traits, including altitude, reproductive traits, tail type, in indigenous sheep breeds. ...
Background: Many genomic imprinting left during long-term selective evolution may drive the formation of important economical traits of introduced and indigenous sheep breeds. Methods: In this study, OvineSNP50 BeadChip data of the introduced breeds GMM and DOR and the indigenous breed Sunit were downloaded from public databases. Selective sweep base on Pi and Fst strategy initially screened for a number of candidate genes that could explain the genetic mechanism elucidated the genetic-molecular mechanisms underlying the differentiation of growth development and reproductive traits between introduced and indigenous breeds. Result: In the DOR_VS_GMM group, 32 genes were identified. In the DOR_VS_SUN group, 26 genes were identified. In the GMM_VS_SUN group, 25 genes were identified. GO, KEGG enrichment analysis showed that these genes are mainly involved in the pathways of muscle development and reproductive regulation. We speculate that EHBP1, CSRP1, TNNI1, MBNL1, AADACL3, RDH13, TNNI3, BMP2, Wfdc8, PPP1CC2 and MOV10L1 may have left deep marks on the genome during long-term domestication and evolution and may be responsible for the productive and reproductive performance in the Merino and Sunit sheep. These genes have played an important role in the evolution of selection in the three breeds. It is expected that the selected candidate genes will provide some insights for future sheep germplasm mining and foreign introductions.
... A significant association between TGFBRAP1 and meat quality traits was also revealed in DU pigs [78]. FRMD6, ITGA8, ITGB8, MYO1G, KLHDC2 [79], and SMC2 [80] genes are associated with growth and meat production traits, whereas CALCR is involved in osteoclast differentiation and associated with body conformation traits [81]. These genes could be important in muscle and fat tissue formation in pigs, including VAT, SAT, and IMF, and thus influence the quality of meat raw materials. ...
Indigenous pig breeds are mainly associated with the adaptive capacity that is necessary to respond adequately to climate change, food security, and livelihood needs, and natural resources conservation. Livni pigs are an indigenous fat-type breed farmed in a single farm in the Orel region and located in the Central European part of the Russian Federation. To determine the genomic regions and genes that are affected by artificial selection, we conducted the comparative study of two pig breeds with different breeding histories and breeding objectives, i.e., the native fat-type Livni and meat-type Duroc breeds using the Porcine GGP HD BeadChip, which contains ~80,000 SNPs. To check the Livni pigs for possible admixture, the Landrace and the Large White breeds were included into the study of genetic diversity as these breeds participated in the formation of the Livni pigs. We observed the highest level of genetic diversity in Livni pigs compared to commercial breeds (UHE = 0.409 vs. 0.319–0.359, p < 0.001; AR = 1.995 vs. 1.894–1.964, p < 0.001). A slight excess of heterozygotes was found in all of the breeds. We identified 291 candidate genes, which were localized within the regions under putative selection, including 22 and 228 genes, which were specific for Livni and Duroc breeds, respectively, and 41 genes common for both breeds. A detailed analysis of the molecular functions identified the genes, which were related to the formation of meat and fat traits, and adaptation to environmental stress, including extreme temperatures, which were different between breeds. Our research results are useful for conservation and sustainable breeding of Livni breed, which shows a high level of genetic diversity. This makes Livni one of the valuable national pig genetic resources.
... They reported that the fat-tailed trait is consistent with a recessive mode of inheritance (Moradi et al., 2012) even if fat tail appears to be under a polygenic determinism. Currently, fat tail is not conducive to breeding programs (Li et al., 2018;Moradi et al., 2012;Zhu et al., 2021), because: (1) most of the fat is deposited in the tail, leading to decreased carcass and intermuscular fat deposits, which affects carcass percentage and meat quality (Alizadeh et al., 2013;Khaldari et al., 2007;Yousefi et al., 2012); (2) more feed is needed for fat deposition than for meat production (Sillence, 2004); and (3) large fat tail is a critical obstacle for ram fertility. However, it has been reported the size of fat tail does not have an effect on growth rate in sheep (Khaldari et al., 2020). ...
Sheep is a major contributor to global food production among livestock and one of the great sources of red meat for human consumption. Several QTL and numerous genes with major and minor effects have been identified in association with the muscle characteristics in sheep breeds worldwide. Understanding the genetic background of growth and carcass‐related traits in sheep is a major factor in increasing muscle growth, muscle hypertrophy and, eventually, meat production. This review concisely shows how major signaling pathways control skeletal muscle growth. Herein we aimed to discuss and summarize different research findings on genomic regions related to carcass traits and meat production in sheep. Several causative mutations with major effects on different muscle‐related traits have been reported in various sheep breeds. A general overview of the studies on main candidate genes showed that some alleles have major phenotypic effects in different breeds with commercial and farm level usability. However, numerous genes with minor effects were also reported regarding the polygenic nature of muscle‐related traits. The knowledge of the candidate genes involved in growth traits and their effects provides valuable information for breeding and selection of muscularity traits.
... Additional file 2: Table S1. Additional genomic investigations on sheep tails [159,[218][219][220][221][222][223][224][225][226]. Table S2. ...
Background
After domestication, the evolution of phenotypically-varied sheep breeds has generated rich biodiversity. This wide phenotypic variation arises as a result of hidden genomic changes that range from a single nucleotide to several thousands of nucleotides. Thus, it is of interest and significance to reveal and understand the genomic changes underlying the phenotypic variation of sheep breeds in order to drive selection towards economically important traits.
Review
Various traits contribute to the emergence of variation in sheep phenotypic characteristics, including coat color, horns, tail, wool, ears, udder, vertebrae, among others. The genes that determine most of these phenotypic traits have been investigated, which has generated knowledge regarding the genetic determinism of several agriculturally-relevant traits in sheep. In this review, we discuss the genomic knowledge that has emerged in the past few decades regarding the phenotypic traits in sheep, and our ultimate aim is to encourage its practical application in sheep breeding. In addition, in order to expand the current understanding of the sheep genome, we shed light on research gaps that require further investigation.
Conclusions
Although significant research efforts have been conducted in the past few decades, several aspects of the sheep genome remain unexplored. For the full utilization of the current knowledge of the sheep genome, a wide practical application is still required in order to boost sheep productive performance and contribute to the generation of improved sheep breeds. The accumulated knowledge on the sheep genome will help advance and strengthen sheep breeding programs to face future challenges in the sector, such as climate change, global human population growth, and the increasing demand for products of animal origin.
... Currently, with the improvement of people's living standards and diet structure, consumers are paying increased attention to their own health and meat quality. However, for fat-tailed sheep, most of the fat is deposited in the tail, leading to the reduction of fat deposition in other parts of the body, which affects meat quality (7). In modern mutton sheep production systems, tail fat deposition requires higher energy costs. ...
Fat deposition is an important economic trait that is closely related to feed efficiency and carcass performance in livestock. In this study, the fat deposition-related traits of 1,293 Hu sheep were measured and descriptive statistical analysis was conducted. The results showed that the coefficient of variation of all fat deposition-related traits was higher than 24%. In addition, single nucleotide polymorphisms and the expression characteristics of TRAPPC9 (encoding trafficking protein particle complex subunit 9) and BAIAP2 (encoding brain-specific Angiogenesis inhibitor 1-associated protein 2) genes in Hu sheep were detected using PCR amplification, Sanger sequencing, KASPar genotyping, and quantitative real-time reverse transcription PCR (qRT-PCR). The associations between SNPs and fat deposition-related traits were also analyzed. Two intronic mutations, TRAPPC9 g.57654 A > G and BAIAP2 g.46061 C > T, were identified in Hu sheep. The result of association analysis showed that TRAPPC9 g.57654 A > G and BAIAP2 g.46061 C > T were both significantly associated with the weight of tail fat, tail fat relative weight (body weight), and tail fat relative weight (carcass) (P < 0.05). Comprehensive effects analysis showed that there were significant differences between the combined genotypes and tail fat and perirenal fat deposition. Moreover, qRT-PCR analysis showed that TRAPPC9 and BAIAP2 are widely expressed, and their expression levels were significantly higher in the small-tail group compared with those in the big-tail group (P < 0.01). These results provided important candidate molecular markers that could be used in strategies to reduce tail fat deposition in Hu sheep.
