A 1.8-kb insertion in the 3'-UTR of RXFP2 is associated with polledness in sheep

Genomic insights into demographic history, structural variation landscape, and complex traits from 514 Hu sheep genomes

Hu sheep is an indigenous breed from the Taihu Lake Plain in China, known for its high fertility. Although Hu sheep belong to the Mongolian group, their demographic history and genetic architecture remain inconclusive. Here, we analyze 697 sheep genomes from representatives of Mongolian sheep breeds. Our study suggests that the ancestral Hu sheep first separated from the Mongolian group approximately 3000 years ago. As Hu sheep migrated from the north and flourished in the Taihu Lake Plain around 1000 years ago, they developed a unique genetic foundation and phenotypic characteristics, which are evident in the genomic footprints of selective sweeps and structural variation landscape. Genes associated with reproductive traits (BMPR1B and TDRD10) and horn phenotype (RXFP2) exhibit notable selective sweeps in the genome of Hu sheep. A genome-wide association analysis reveals that structural variations at LOC101110773, MAST2, and ZNF385B may significantly impact polledness, teat number, and early growth in Hu sheep, respectively. Our study offers insights into the evolutionary history of Hu sheep and may serve as a valuable genetic resource to enhance the understanding of complex traits in Hu sheep.

The role of G protein-coupled receptors and their ligands in animal domestication

The domestication of plants and animals has resulted in one of the most significant cultural and socio-economical transitions in human history. Domestication of animals, including human-supervised reproduction, largely uncoupled particular animal species from their natural, evolutionary history driven by environmental and ecological factors. The primary motivations for domesticating animals were, and still are, producing food and materials (e.g. meat, eggs, honey or milk products, wool, leather products, jewelry and medication products) to support plowing in agriculture or in transportation (e.g. horse, cattle, camel and llama) and to facilitate human activities (for hunting, rescuing, therapeutic aid, guarding behavior and protecting or just as a companion). In recent years, decoded genetic information from more than 40 domesticated animal species have become available; these studies have identified genes and mutations associated with specific physiological and behavioral traits contributing to the complex genetic background of animal domestication. These breeding-altered genomes provide insights into the regulation of different physiological areas, including information on links between e.g. endocrinology and behavior, with important pathophysiological implications (e.g. for obesity and cancer), extending the interest in domestication well beyond the field. Several genes that have undergone selection during domestication and breeding encode specific G protein-coupled receptors, a class of membrane-spanning receptors involved in the regulation of a number of overarching functions such as reproduction, development, body homeostasis, metabolism, stress responses, cognition, learning and memory. Here we summarize the available literature on variations in G protein-coupled receptors and their ligands and how these have contributed to animal domestication.

Segregation GWAS to linearize a non-additive locus with incomplete penetrance: an example of horn status in sheep

BACKGROUND

The objective of this study was to introduce a genome-wide association study (GWAS) in conjunction with segregation analysis on monogenic categorical traits. Genotype probabilities calculated from phenotypes, mode of inheritance and pedigree information, are expressed as the expected allele count (EAC) (range 0 to 2), and are inherited additively, by definition, unlike the original phenotypes, which are non-additive and could be of incomplete penetrance. The EAC are regressed on the single nucleotide polymorphism (SNP) genotypes, similar to an additive GWAS. In this study, horn phenotypes in Merino sheep are used to illustrate the advantages of using the segregation GWAS, a trait believed to be monogenic, affected by dominance, sex-dependent expression and likely affected by incomplete penetrance. We also used simulation to investigate whether incomplete penetrance can cause prediction errors in Merino sheep for horn status.

RESULTS

Estimated penetrance values differed between the sexes, where males showed almost complete penetrance, especially for horned and polled phenotypes, while females had low penetrance values for the horned status. This suggests that females homozygous for the 'horned allele' have a horned phenotype in only 22% of the cases while 78% will be knobbed or have scurs. The GWAS using EAC on 4001 animals and 510,174 SNP genotypes from the Illumina Ovine high-density (600k) chip gave a stronger association compared to using actual phenotypes. The correlation between the EAC and the allele count of the SNP with the highest -log10(p-value) was 0.73 in males and 0.67 in females. Simulations using penetrance values found by the segregation analyses resulted in higher correlations between the EAC and the causative mutation (0.95 for males and 0.89 for females, respectively), suggesting that the most predictive SNP is not in full LD with the causative mutation.

CONCLUSIONS

Our results show clear differences in penetrance values between males and female Merino sheep for horn status. Segregation analysis for a trait with mutually exclusive phenotypes, non-additive inheritance, and/or incomplete penetrance can lead to considerably more power in a GWAS because the linearized genotype probabilities are additive and can accommodate incomplete penetrance. This method can be extended to any monogenic controlled categorical trait of which the phenotypes are mutually exclusive.

Whole-genome scan for selection signature associated with temperature adaptation in Iranian sheep breeds

The present study aimed to identify the selection signature associated with temperature adaptation in Iranian sheep breeds raised in cold and hot environments. The Illumina HD ovine SNP600K BeadChip genomic arrays were utilized to analyze 114 animals from eight Iranian sheep breeds, namely Ghezel, Afshari, Shall, Sanjabi, Lori-Bakhtiari, Karakul, Kermani, and Balochi. All animals were classified into two groups: cold-weather breeds and hot-weather breeds, based on the environments to which they are adapted and the regions where they have been raised for many years. The unbiased FST (Theta) and hapFLK tests were used to identify the selection signatures. The results revealed five genomic regions on chromosomes 2, 10, 11, 13, and 14 using the FST test, and three genomic regions on chromosomes 10, 14, and 15 using the hapFLK test to be under selection in cold and hot groups. Further exploration of these genomic regions revealed that most of these regions overlapped with genes previously identified to affect cold and heat stress, nervous system function, cell division and gene expression, skin growth and development, embryo and skeletal development, adaptation to hypoxia conditions, and the immune system. These regions overlapped with QTLs that had previously been identified as being associated with various important economic traits, such as body weight, skin color, and horn characteristics. The gene ontology and gene network analyses revealed significant pathways and networks that distinguished Iranian cold and hot climates sheep breeds from each other. We identified positively selected genomic regions in Iranian sheep associated with pathways related to cell division, biological processes, cellular responses to calcium ions, metal ions and inorganic substances. This study represents the initial effort to identify selective sweeps linked to temperature adaptation in Iranian indigenous sheep breeds. It may provide valuable insights into the genomic regions involved in climate adaptation in sheep.

Genome-wide association study for polledness, horn shape, and wool traits in Original Valachian sheep

Abstract. The Original Valachian sheep is an endangered Slovak national breed that is well adapted to high-altitude pastures. The sheep can be horned with various shapes and can have multi-coloured or completely white or black wool. Breeders are interested in learning about the genetic basis of these traits. We conducted a genome-wide association study based on the genomic information of 96 sheep genotyped by the GeneSeek GGP Ovine 50K SNP (single-nucleotide polymorphism) chip and on the following traits: polledness (presence or absence of horns), horn shape, and wool colour (completely white and completely black). The univariate linear mixed model was used to discover genetic variants significantly associated with tested traits. The Bonferroni correction and the false-discovery rate were used as significance thresholds. The RXFP2 gene (chromosome 10, 29.5 Mb) was identified as a strong candidate for polledness. In addition, when compared to animals with sideways-turned horns vs. polled, the region around the ADAMTS3 gene (chromosome 6, 88.47 Mb) was significant. A total of nine significant genomic regions were found when comparing the sideways-turned spiral horns with the backwards-curled horns, the two most frequent horn types in Original Valachian sheep. The RXFP2 may also contribute to the genetic control of horn shape. Genes identified in other regions were involved to osteogenic differentiation and osteoblast proliferation (PCP4, chromosome 1, 260.7 Mb), bone mineral density and mineral content (NKX1-2, chromosome 22, 43.75 Mb). The significant genetic variants close to the region of MC1R (chromosome 14, at 14.2 Mb) were associated with the wool colour of sheep that were fully white or fully black animals. The results of this study will contribute to a better understanding of the phenotypic variability of the Original Valachian sheep, especially regarding traits that are very important for breeders of this endangered breed.

Genetic diversity of United States Rambouillet, Katahdin and Dorper sheep

BACKGROUND

Managing genetic diversity is critically important for maintaining species fitness. Excessive homozygosity caused by the loss of genetic diversity can have detrimental effects on the reproduction and production performance of a breed. Analysis of genetic diversity can facilitate the identification of signatures of selection which may contribute to the specific characteristics regarding the health, production and physical appearance of a breed or population. In this study, breeds with well-characterized traits such as fine wool production (Rambouillet, N = 745), parasite resistance (Katahdin, N = 581) and environmental hardiness (Dorper, N = 265) were evaluated for inbreeding, effective population size (Ne), runs of homozygosity (ROH) and Wright's fixation index (FST) outlier approach to identify differential signatures of selection at 36,113 autosomal single nucleotide polymorphisms (SNPs).

RESULTS

Katahdin sheep had the largest current Ne at the most recent generation estimated with both the GONe and NeEstimator software. The most highly conserved ROH Island was identified in Rambouillet with a signature of selection on chromosome 6 containing 202 SNPs called in an ROH in 50 to 94% of the individuals. This region contained the DCAF16, LCORL and NCAPG genes that have been previously reported to be under selection and have biological roles related to milk production and growth traits. The outlier regions identified through the FST comparisons of Katahdin with Rambouillet and Dorper contained genes with known roles in milk production and mastitis resistance or susceptibility, and the FST comparisons of Rambouillet with Katahdin and Dorper identified genes related to wool growth, suggesting these traits have been under natural or artificial selection pressure in these populations. Genes involved in the cytokine-cytokine receptor interaction pathways were identified in all FST breed comparisons, which indicates the presence of allelic diversity between these breeds in genomic regions controlling cytokine signaling mechanisms.

CONCLUSIONS

In this paper, we describe signatures of selection within diverse and economically important U.S. sheep breeds. The genes contained within these signatures are proposed for further study to understand their relevance to biological traits and improve understanding of breed diversity.

Genome-Wide Association Analyses and Population Verification Highlight the Potential Genetic Basis of Horned Morphology during Polled Selection in Tibetan Sheep

The types and morphology of sheep horns have been extensively researched, yet the genetic foundation underlying the emergence of diverse horn characteristics during the breeding of polled Tibetan sheep has remained elusive. Genome-wide association analysis (GWAS) was performed on 103 subtypes (normal large horn, scurs, and polled) differentiated from G2 (offspring (G2) of parent (G1) of polled) of the polled core herd. Six single nucleotide polymorphisms (SNPs) located on chromosome 10 of the relaxin family peptide receptor 2 (RXFP2) gene exhibited positive correlations with horn length, horn base circumference, and horn base interval. Furthermore, in genotyping 382 G2 individuals, significant variations were observed for each specific horn type. Three additional mutations were identified near the target SNP upstream of the amplification product. Finally, the RXFP2-specific haplotype associated with the horned trait effectively maintained horn length, horn base circumference, and horn base interval in Tibetan sheep, as confirmed by population validation of nine loci in a sample size of 1125 individuals. The present study offers novel insights into the genetic differentiation of the horned type during improvement breeding and evolution, thereby establishing a robust theoretical foundation for polled Tibetan sheep breeding and providing valuable guidance for practical production.

Integration of selective sweeps across the sheep genome: understanding the relationship between production and adaptation traits

BACKGROUND

Livestock populations are under constant selective pressure for higher productivity levels for different selective purposes. This pressure results in the selection of animals with unique adaptive and production traits. The study of genomic regions associated with these unique characteristics has the potential to improve biological knowledge regarding the adaptive process and how it is connected to production levels and resilience, which is the ability of an animal to adapt to stress or an imbalance in homeostasis. Sheep is a species that has been subjected to several natural and artificial selective pressures during its history, resulting in a highly specialized species for production and adaptation to challenging environments. Here, the data from multiple studies that aim at mapping selective sweeps across the sheep genome associated with production and adaptation traits were integrated to identify confirmed selective sweeps (CSS).

RESULTS

In total, 37 studies were used to identify 518 CSS across the sheep genome, which were classified as production (147 prodCSS) and adaptation (219 adapCSS) CSS based on the frequency of each type of associated study. The genes within the CSS were associated with relevant biological processes for adaptation and production. For example, for adapCSS, the associated genes were related to the control of seasonality, circadian rhythm, and thermoregulation. On the other hand, genes associated with prodCSS were related to the control of feeding behaviour, reproduction, and cellular differentiation. In addition, genes harbouring both prodCSS and adapCSS showed an interesting association with lipid metabolism, suggesting a potential role of this process in the regulation of pleiotropic effects between these classes of traits.

CONCLUSIONS

The findings of this study contribute to a deeper understanding of the genetic link between productivity and adaptability in sheep breeds. This information may provide insights into the genetic mechanisms that underlie undesirable genetic correlations between these two groups of traits and pave the way for a better understanding of resilience as a positive ability to respond to environmental stressors, where the negative effects on production level are minimized.

High-throughput DNA sequence analysis elucidates novel insight into the genetic basis of adaptation in local sheep

Understanding how evolutionary factors related to climate adaptation and human selection have influenced the genetic architecture of domesticated animals is of great interest in biology. In the current study, by using 304 whole genomes from different geographical regions (including Europe, north Africa, Southwest Asia, east Asia, west Africa, south Asia, east Africa, Australia and Turkey), We evaluate global sheep population dynamics in terms of genetic variation and population structure. We further conducted comparative population analysis to study the genetic underpinnings of climate adaption to local environments and also morphological traits. In order to identify genomic signals under selection, we applied fixation index (FST) and also nucleotide diversity (θπ) statistical measurements. Our results revealed several candidate genes on different chromosomes under selection for local climate adaptation (e.g. HOXC12, HOXC13, IRF1, FGD2 and GNAQ), body size (PDGFA, HMGA2, PDE3A) and also morphological related traits (RXFP2). The discovered candidate genes may offer newel insights into genetic underpinning of regional adaptation and commercially significant features in local sheep.

Searching for homozygous haplotype deficiency in Manech Tête Rousse dairy sheep revealed a nonsense variant in the MMUT gene affecting newborn lamb viability

BACKGROUND

Recessive deleterious variants are known to segregate in livestock populations, as in humans, and some may be lethal in the homozygous state.

RESULTS

We used phased 50 k single nucleotide polymorphism (SNP) genotypes and pedigree data to scan the genome of 6845 Manech Tête Rousse dairy sheep to search for deficiency in homozygous haplotypes (DHH). Five Manech Tête Rousse deficient homozygous haplotypes (MTRDHH1 to 5) were identified, with a homozygous deficiency ranging from 84 to 100%. These haplotypes are located on Ovis aries chromosome (OAR)1 (MTRDHH2 and 3), OAR10 (MTRDHH4), OAR13 (MTRDHH5), and OAR20 (MTRDHH1), and have carrier frequencies ranging from 7.8 to 16.6%. When comparing at-risk matings between DHH carriers to safe matings between non-carriers, two DHH (MTRDHH1 and 2) were linked with decreased insemination success and/or increased stillbirth incidence. We investigated the MTRDHH1 haplotype, which substantially increased stillbirth rate, and identified a single nucleotide variant (SNV) inducing a premature stop codon (p.Gln409*) in the methylmalonyl-CoA mutase (MMUT) gene by using a whole-genome sequencing approach. We generated homozygous lambs for the MMUT mutation by at-risk mating between heterozygous carriers, and most of them died within the first 24 h after birth without any obvious clinical symptoms. Reverse transcriptase-qPCR and western blotting on post-mortem liver and kidney biological samples showed a decreased expression of MMUT mRNA in the liver and absence of a full-length MMUT protein in the mutant homozygous lambs.

CONCLUSIONS

We identified five homozygous deficient haplotypes that are likely to harbor five independent deleterious recessive variants in sheep. One of these was detected in the MMUT gene, which is associated with lamb lethality in the homozygous state. A specific management of these haplotypes/variants in the MTR dairy sheep selection program would help enhance the overall fertility and lamb survival.

Pan-Omics in Sheep: Unveiling Genetic Landscapes

Multi-omics-integrated analysis, known as panomics, represents an advanced methodology that harnesses various high-throughput technologies encompassing genomics, epigenomics, transcriptomics, proteomics, and metabolomics. Sheep, playing a pivotal role in agricultural sectors due to their substantial economic importance, have witnessed remarkable advancements in genetic breeding through the amalgamation of multiomics analyses, particularly with the evolution of high-throughput technologies. This integrative approach has established a robust theoretical foundation, enabling a deeper understanding of sheep genetics and fostering improvements in breeding strategies. The comprehensive insights obtained through this approach shed light on diverse facets of sheep development, including growth, reproduction, disease resistance, and the quality of livestock products. This review primarily focuses on the application of principal omics analysis technologies in sheep, emphasizing correlation studies between multiomics data and specific traits such as meat quality, wool characteristics, and reproductive features. Additionally, this paper anticipates forthcoming trends and potential developments in this field.

Recent advances in the genomic resources for sheep

Sheep (Ovis aries) provide a vital source of protein and fibre to human populations. In coming decades, as the pressures associated with rapidly changing climates increase, breeding sheep sustainably as well as producing enough protein to feed a growing human population will pose a considerable challenge for sheep production across the globe. High quality reference genomes and other genomic resources can help to meet these challenges by: (1) informing breeding programmes by adding a priori information about the genome, (2) providing tools such as pangenomes for characterising and conserving global genetic diversity, and (3) improving our understanding of fundamental biology using the power of genomic information to link cell, tissue and whole animal scale knowledge. In this review we describe recent advances in the genomic resources available for sheep, discuss how these might help to meet future challenges for sheep production, and provide some insight into what the future might hold.

Novel Heredity Basis of the Four-Horn Phenotype in Sheep Using Genome-Wide Sequence Data

Horns are an important breeding trait for sheep. However, no widely recognized viewpoint on the regulatory genes and mechanisms of horns is available, and the genetic basis of the four-horn phenotype (FHP) is unclear. This work conducted a genome-wide association study with 100 sheep genomes from multiple breeds to investigate the genetic basis of the FHP. The results revealed three significant associations (corrected as p < 1.64 × 10-8) of the InDels (CHR2: g.133,742,709delA, g.133,743,215insC, and g.133,743,940delT) for FHP in the intergenic sequence (IGS) between the MTX2 and the LOC105609047 of CHR2. Moreover, 14 significant associations (corrected as p < 1.42 × 10-9) of SNPs with the FHP phenotype were identified in CHR2 and CHR16, including five (e.g., CHR16: g.40,351,378G > A and g.40,352,577G > A) located in the intron of the ADAMTS12 gene, eight (e.g., CHR2: g.133,727,513C > T and g.133,732,145T > G) in the IGS between MTX2 and LOC105609047, and only one (CHR2: g.133,930,761A > G) in the IGS between HOXD1 and MTX2. Obvious divergence was also observed in genotype patterns between the FHP and others (two horns and hornless) in the HOXD1 and ADAMTS12 gene regions. An extremely significant linkage also occurred between Loci I and Loci II within 100 individuals (LD = -156.02186, p < 0.00001). In summary, our study indicated that the genomic sequences from CHR2 and CHR16 contributed to the FHP in sheep, specifically the key candidate genes HOXD1 and ADAMTS12. These results improved our understanding of the Mendelian genetic basis of the FHP in sheep.

Identification of Critical Genes for Ovine Horn Development Based on Transcriptome during the Embryonic Period

Horns, also known as headgear, are a unique structure of ruminants. As ruminants are globally distributed, the study of horn formation is critical not only for increasing our understanding of natural and sexual selection but also for the breeding of polled sheep breeds to facilitate modern sheep farming. Despite this, a significant number of the underlying genetic pathways in sheep horn remain unclear. In this study, to clarify the gene expression profile of horn buds and investigate the key genes in horn bud formation, RNA-sequencing (RNA-seq) technology was utilized to investigate differential gene expression in the horn buds and adjacent forehead skin of Altay sheep fetuses. There were only 68 differentially expressed genes (DEGs) identified, consisting of 58 up-regulated genes and 10 down-regulated genes. RXFP2 was differentially up-regulated in the horn buds and had the highest significance (p-value = 7.42 × 10^-14). In addition, 32 DEGs were horn-related genes identified in previous studies, such as RXFP2, FOXL2, SFRP4, SFRP2, KRT1, KRT10, WNT7B, and WNT3. Further, Gene Ontology (GO) analysis showed that the DEGs were mainly enriched with regard to growth, development, and cell differentiation. Pathway analysis revealed that the Wnt signaling pathway may be responsible for horn development. Further, through combining the protein-protein interaction networks of the DEGs, it was found that the top five hub genes, namely, ACAN, SFRP2, SFRP4, WNT3, and WNT7B, were also associated with horn development. Our results suggest that only a few key genes, including RXFP2, are involved in bud formation. This study not only validates the expression of candidate genes identified at the transcriptome level in previous studies but also provides new possible marker genes for horn development, which may promote our understanding of the genetic mechanisms of horn formation.

A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes

Structural variations (SVs) are a major contributor to genetic diversity and phenotypic variations, but their prevalence and functions in domestic animals are largely unexplored. Here we generated high-quality genome assemblies for 15 individuals from genetically diverse sheep breeds using Pacific Biosciences (PacBio) high-fidelity sequencing, discovering 130.3 Mb nonreference sequences, from which 588 genes were annotated. A total of 149,158 biallelic insertions/deletions, 6531 divergent alleles, and 14,707 multiallelic variations with precise breakpoints were discovered. The SV spectrum is characterized by an excess of derived insertions compared to deletions (94,422 vs. 33,571), suggesting recent active LINE expansions in sheep. Nearly half of the SVs display low to moderate linkage disequilibrium with surrounding single-nucleotide polymorphisms (SNPs) and most SVs cannot be tagged by SNP probes from the widely used ovine 50K SNP chip. We identified 865 population-stratified SVs including 122 SVs possibly derived in the domestication process among 690 individuals from sheep breeds worldwide. A novel 168-bp insertion in the 5' untranslated region (5' UTR) of HOXB13 is found at high frequency in long-tailed sheep. Further genome-wide association study and gene expression analyses suggest that this mutation is causative for the long-tail trait. In summary, we have developed a panel of high-quality de novo assemblies and present a catalog of structural variations in sheep. Our data capture abundant candidate functional variations that were previously unexplored and provide a fundamental resource for understanding trait biology in sheep.

Long divergent haplotypes introgressed from wild sheep are associated with distinct morphological and adaptive characteristics in domestic sheep

The worldwide sheep population comprises more than 1000 breeds. Together, these exhibit a considerable morphological diversity, which has not been extensively investigated at the molecular level. Here, we analyze whole-genome sequencing individuals of 1,098 domestic sheep from 154 breeds, and 69 wild sheep from seven Ovis species. On average, we detected 6.8%, 1.0% and 0.2% introgressed sequence in domestic sheep originating from Iranian mouflon, urial and argali, respectively, with rare introgressions from other wild species. Interestingly, several introgressed haplotypes contributed to the morphological differentiations across sheep breeds, such as a RXFP2 haplotype from Iranian mouflon conferring the spiral horn trait, a MSRB3 haplotype from argali strongly associated with ear morphology, and a VPS13B haplotype probably originating from urial and mouflon possibly associated with facial traits. Our results reveal that introgression events from wild Ovis species contributed to the high rate of morphological differentiation in sheep breeds, but also to individual variation within breeds. We propose that long divergent haplotypes are a ubiquitous source of phenotypic variation that allows adaptation to a variable environment, and that these remain intact in the receiving population probably due to reduced recombination.

Selection signature analysis and genome-wide divergence of South African Merino breeds from their founders

Merino sheep are a breed of choice across the world, popularly kept for their wool and mutton value. They are often reared as a pure breed or used in crossbreeding and are a common component in synthetic breed development. This study evaluated genetic diversity, population structure, and breed divergence in 279 animals of Merino and Merino-based sheep breeds in South Africa using the Illumina Ovine SNP 50K BeadChip. The sheep breeds analysed included the three Merino-derived breeds of Dohne Merino (n = 50); Meatmaster (n = 47); and Afrino (n = 52) and five presumed ancestral populations of Merinos (Merino (n = 46); South African Merino (n = 10); and South African Mutton Merino (n = 8)); and the non-Merino founding breeds of Damara (n = 20); Ronderib Afrikaner (n = 17); and Nguni (n = 29). Highest genetic diversity values were observed in the Dohne Merino (DM), with H _o = 0.39 ± 0.01, followed by the Meatmaster and South African Merino (SAM), with H _o = 0.37 ± 0.03. The level of inbreeding ranged from 0.0 ± 0.02 (DM) to 0.27 ± 0.05 (Nguni). Analysis of molecular variance (AMOVA) showed high within-population variance (>80%) across all population categories. The first principal component (PC1) separated the Merino, South African Mutton Merino (SAMM), DM, and Afrino (AFR) from the Meatmaster, Damara, Nguni, and Ronderib Afrikaner (RDA). PC2 aligned each Merino-derived breed with its presumed ancestors and separated the SAMM from the Merino and SAM. The iHS analysis yielded selection sweeps across the AFR (12 sweeps), Meatmaster (four sweeps), and DM (29 sweeps). Hair/wool trait genes such as FGF12; metabolic genes of ICA1, NXPH1, and GPR171; and immune response genes of IL22, IL26, IFNAR1, and IL10RB were reported. Other genes include HMGA, which was observed as selection signatures in other populations; WNT5A, important in the development of the skeleton and mammary glands; ANTXR2, associated with adaptation to variation in climatic conditions; and BMP2, which has been reported as strongly selected in both fat-tailed and thin-tailed sheep. The DM vs. SAMM shared all six sweep regions on chromosomes 1, 10, and 11 with AFR vs. SAMM. Genes such as FGF12 on OAR 1:191.3-194.7 Mb and MAP2K4 on OAR 11:28.6-31.3 Mb were observed. The selection sweep on chromosome 10 region 28.6-30.3 Mb harbouring the RXFP2 for polledness was shared between the DM vs. Merino, the Meatmaster vs. Merino, and the Meatmaster vs. Nguni. The DM vs. Merino and the Meatmaster vs. Merino also shared an Rsb-based selection sweep on chromosome 1 region 268.5-269.9 Mb associated with the Calpain gene, CAPN7. The study demonstrated some genetic similarities between the Merino and Merino-derived breeds emanating from common founding populations and some divergence driven by breed-specific selection goals. Overall, information regarding the evolution of these composite breeds from their founding population will guide future breed improvement programs and management and conservation efforts.

Genetics of the phenotypic evolution in sheep: a molecular look at diversity-driving genes

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.

The Complex and Diverse Genetic Architecture of the Absence of Horns (Polledness) in Domestic Ruminants, including Goats and Sheep

Horns are the most obvious common feature of Bovidae. The naturally occurring absence of horns in these species, also known as polledness, is of surprisingly heterogeneous nature, although they are Mendelian traits. This review compares in detail the molecular differences among the causes of inherited polledness in the domestic ruminant species of cattle, yak, sheep, and goat based on the causal gene variants that have been discovered in recent years. The genetic causes for the lack of horns in small ruminants seem not only to be more complex, e.g., in sheep, breed-specific characteristics are still unexplained, but in goats, there is also the associated disorder of intersexuality—polled intersex syndrome (PIS). In connection with animal welfare and the associated discussion about a legal ban on the dehorning of all farm animals, naturally hornless animals and the causal genetic variants are of increasing research interest in the age of genome editing. However, the low acceptance of genetic engineering in livestock, especially in European societies, limits its use in food-producing animals. Therefore, genotype-based targeted selection of naturally occurring variants is still a widely used method for spreading this desired trait within and across populations, at least in cattle and sheep.

Review: Balancing Selection for Deleterious Alleles in Livestock

Harmful alleles can be under balancing selection due to an interplay of artificial selection for the variant in heterozygotes and purifying selection against the variant in homozygotes. These pleiotropic variants can remain at moderate to high frequency expressing an advantage for favorable traits in heterozygotes, while harmful in homozygotes. The impact on the population and selection strength depends on the consequence of the variant both in heterozygotes and homozygotes. The deleterious phenotype expressed in homozygotes can range from early lethality to a slightly lower fitness in the population. In this review, we explore a range of causative variants under balancing selection including loss-of-function variation (i.e., frameshift, stop-gained variants) and regulatory variation (affecting gene expression). We report that harmful alleles often affect orthologous genes in different species, often influencing analogous traits. The recent discoveries are mainly driven by the increasing genomic and phenotypic resources in livestock populations. However, the low frequency and sometimes subtle effects in homozygotes prevent accurate mapping of such pleiotropic variants, which requires novel strategies to discover. After discovery, the selection strategy for deleterious variants under balancing selection is under debate, as variants can contribute to the heterosis effect in crossbred animals in various livestock species, compensating for the loss in purebred animals. Nevertheless, gene-assisted selection is a useful tool to decrease the frequency of the harmful allele in the population, if desired. Together, this review marks various deleterious variants under balancing selection and describing the functional consequences at the molecular, phenotypic, and population level, providing a resource for further study.

Genome-wide association study reveals 14 new SNPs and confirms two structural variants highly associated with the horned/polled phenotype in goats

Background

There is a long-term interest in investigating the genetic basis of the horned/polled phenotype in domestic goats. Here, we report a genome-wide association study (GWAS) to detect the genetic loci affecting the polled phenotype in goats.

Results

We obtained a total of 13,980,209 biallelic SNPs, using the genotyping-by-sequencing data from 45 Jintang Black (JT) goats, which included 32 female and nine male goats, and four individuals with the polled intersex syndrome (PIS). Using a mixed-model based GWAS, we identified two association signals, which were located at 150,334,857–150,817,260 bp (P = 5.15 × 10^− 119) and 128,286,704–131,306,537 bp (P = 2.74 × 10^− 15) on chromosome 1. The genotype distributions of the 14 most significantly associated SNPs were completely correlated with horn status in goats, based on the whole-genome sequencing (WGS) data from JT and two other Chinese horned breeds. However, variant annotation suggested that none of the detected SNPs within the associated regions were plausible causal mutations. Via additional read-depth analyses and visual inspections of WGS data, we found a 10.1-kb deletion (CHI1:g. 129424781_129434939del) and a 480-kb duplication (CHI1:150,334,286–150,818,098 bp) encompassing two genes KCNJ15 and ERG in the associated regions of polled and PIS-affected goats. Notably, the 10.1-kb deletion also served as the insertion site for the 480-kb duplication, as validated by PCR and Sanger sequencing. Our WGS genotyping showed that all horned goats were homozygous for the reference alleles without either the structural variants (SVs), whereas the PIS-affected goats were homozygous for both the SVs. We also demonstrated that horned, polled, and PIS-affected individuals among 333 goats from JT and three other Chinese horned breeds can be accurately classified via PCR amplification and agarose gel electrophoresis of two fragments in both SVs.

Conclusion

Our results revealed that two genomic regions on chromosome 1 are major loci affecting the polled phenotypes in goats. We provided a diagnostic PCR to accurately classify horned, polled, and PIS-affected goats, which will enable a reliable genetic test for the early-in-life prediction of horn status in goats.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08089-w.

Genome-Wide Detection of Structural Variations Reveals New Regions Associated with Domestication in Small Ruminants

During domestication processes, changes in selective pressures induce multiple phenotypical, physiological, and behavioral changes in target species. The rise of next-generation sequencing has provided a chance to study the genetics bases of these changes, most of the time based on single nucleotide polymorphisms (SNPs). However, several studies have highlighted the impact of structural variations (SVs) on individual fitness, particularly in domestic species. We aimed at unraveling the role of SVs during the domestication and later improvement of small ruminants by analyzing whole-genome sequences of 40 domestic sheep and 11 of their close wild relatives (Ovis orientalis), and 40 goats and 18 of their close wild relatives (Capra aegagrus). Using a combination of detection tools, we called 45,796 SVs in Ovis and 15,047 SVs in Capra genomes, including insertions, deletions, inversions, copy number variations, and chromosomal translocations. Most of these SVs were previously unreported in small ruminants. 69 and 45 SVs in sheep and goats, respectively, were in genomic regions with neighboring SNPs highly differentiated between wilds and domestics (i.e., putatively related to domestication). Among them, 25 and 20 SVs were close to or overlapping with genes related to physiological and morpho-anatomical traits linked with productivity (e.g., size, meat or milk quality, wool color), reproduction, or immunity. Finally, several of the SVs differentiated between wilds and domestics would not have been detected by screening only the differentiation of SNPs surrounding them, highlighting the complementarity of SVs and SNPs based approaches to detect signatures of selection.

The steroid-hormone ecdysone coordinates parallel pupariation neuromotor and morphogenetic subprograms via epidermis-to-neuron Dilp8-Lgr3 signal induction

Innate behaviors consist of a succession of genetically-hardwired motor and physiological subprograms that can be coupled to drastic morphogenetic changes. How these integrative responses are orchestrated is not completely understood. Here, we provide insight into these mechanisms by studying pupariation, a multi-step innate behavior of Drosophila larvae that is critical for survival during metamorphosis. We find that the steroid-hormone ecdysone triggers parallel pupariation neuromotor and morphogenetic subprograms, which include the induction of the relaxin-peptide hormone, Dilp8, in the epidermis. Dilp8 acts on six Lgr3-positive thoracic interneurons to couple both subprograms in time and to instruct neuromotor subprogram switching during behavior. Our work reveals that interorgan feedback gates progression between subunits of an innate behavior and points to an ancestral neuromodulatory function of relaxin signaling.

Selective Sweeps Uncovering the Genetic Basis of Horn and Adaptability Traits on Fine-Wool Sheep in China

Long-term natural and artificial selection leads to change in certain regions of the genome, resulting in selection signatures that can reveal genes associated with selected traits, such as horns (i.e., polled/horned), high-quality wool traits, and high-altitude hypoxia adaptability. These are complex traits determined by multiple genes, regulatory pathways, and environmental factors. A list of genes with considerable effects on horn and adaptability traits has not been found, although multiple quantitative trait loci (QTL) have been identified. Selection signatures could be identified using genetic differentiation (F_ST), polymorphism levels θπ, and Tajima’s D. This study aimed to identify selection signatures in fine-wool sheep and to investigate the genes annotated in these regions, as well as the biological pathways involved in horn and adaptability traits. For this purpose, the whole-genome sequence of 120 individuals from four breeds, which come from different elevations and habitats in China, was used to analyze selection signatures for horn and adaptability traits. Annotation of the consensus regions of F_ST and θπ ratios revealed a list of identified genes associated with polled/horned and high-altitude hypoxia adaptability traits, such as RXPF2, EERFC4, MSH6, PP1R12A, THBS1, ATP1B2, RYR2, and PLA2G2E. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified genes related primarily to mismatch repair, metabolism, vascular smooth muscle contraction, and cardiac muscle contraction. This is the first study to demonstrate that selection signatures play an important role in the polled/horned and high-altitude hypoxia adaptability traits of fine-wool sheep breeds that have undergone high-intensity selection and adapted to different ecological environments in China. Changes observed in the genome of fine-wool sheep may have acted on genomic regions that affect performance traits and provide a reference for genome design and breeding.

A global analysis of CNVs in Chinese indigenous fine-wool sheep populations using whole-genome resequencing

Background

Copy number variation (CNV) is an important source of genetic variation that has a significant influence on phenotypic diversity, economically important traits and the evolution of livestock species. In this study, the genome-wide CNV distribution characteristics of 32 fine-wool sheep from three breeds were analyzed using resequencing.

Results

A total of 1,747,604 CNVs were detected in this study, and 7228 CNV regions (CNVR) were obtained after merging overlapping CNVs; these regions accounted for 2.17% of the sheep reference genome. The average length of the CNVRs was 4307.17 bp. “Deletion” events took place more frequently than “duplication” or “both” events. The CNVRs obtained overlapped with previously reported sheep CNVRs to variable extents (4.39–55.46%). Functional enrichment analysis showed that the CNVR-harboring genes were mainly involved in sensory perception systems, nutrient metabolism processes, and growth and development processes. Furthermore, 1855 of the CNVRs were associated with 166 quantitative trait loci (QTL), including milk QTLs, carcass QTLs, and health-related QTLs, among others. In addition, the 32 fine-wool sheep were divided into horned and polled groups to analyze for the selective sweep of CNVRs, and it was found that the relaxin family peptide receptor 2 (RXFP2) gene was strongly influenced by selection.

Conclusions

In summary, we constructed a genomic CNV map for Chinese indigenous fine-wool sheep using resequencing, thereby providing a valuable genetic variation resource for sheep genome research, which will contribute to the study of complex traits in sheep.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07387-7.

Runs of homozygosity analysis of South African sheep breeds from various production systems investigated using OvineSNP50k data

Background

Population history, production system and within-breed selection pressure impacts the genome architecture resulting in reduced genetic diversity and increased frequency of runs of homozygosity islands. This study tested the hypothesis that production systems geared towards specific traits of importance or natural or artificial selection pressures influenced the occurrence and distribution of runs of homozygosity (ROH) in the South African sheep population. The Illumina OvineSNP50 BeadChip was used to genotype 400 sheep belonging to 13 breeds from South Africa representing mutton, pelt and mutton and wool dual-purpose breeds, including indigenous non-descript breeds that are reared by smallholder farmers. To get more insight into the autozygosity and distribution of ROH islands of South African breeds relative to global populations, 623 genotypes of sheep from worldwide populations were included in the analysis. Runs of homozygosity were computed at cut-offs of 1–6 Mb, 6–12 Mb, 12–24 Mb, 24–48 Mb and > 48 Mb, using the R package detectRUNS. The Golden Helix SVS program was used to investigate the ROH islands.

Results

A total of 121,399 ROH with mean number of ROH per animal per breed ranging from 800 (African White Dorper) to 15,097 (Australian Poll Dorset) were obtained. Analysis of the distribution of ROH according to their size showed that, for all breeds, the majority of the detected ROH were in the short (1–6 Mb) category (88.2%). Most animals had no ROH > 48 Mb. Of the South African breeds, the Nguni and the Blackhead Persian displayed high ROH based inbreeding (F_ROH) of 0.31 ± 0.05 and 0.31 ± 0.04, respectively. Highest incidence of common runs per SNP across breeds was observed on chromosome 10 with over 250 incidences of common ROHs. Mean proportion of SNPs per breed per ROH island ranged from 0.02 ± 0.15 (island ROH224 on chromosome 23) to 0.13 ± 0.29 (island ROH175 on chromosome 15). Seventeen (17) of the islands had SNPs observed in single populations (unique ROH islands). The MacArthur Merino (MCM) population had five unique ROH islands followed by Blackhead Persian and Nguni with three each whilst the South African Mutton Merino, SA Merino, White Vital Swakara, Karakul, Dorset Horn and Chinese Merino each had one unique ROH island. Genes within ROH islands were associated with predominantly metabolic and immune response traits and predomestic selection for traits such as presence or absence of horns.

Conclusions

Overall, the frequency and patterns of distribution of ROH observed in this study corresponds to the breed history and implied selection pressures exposed to the sheep populations under study.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07314-2.

Candidate genes for productivity identified by genome-wide association study with indicators of class in the Russian meat merino sheep breed

Genome-wide association studies allow identification of loci and polymorphisms associated with the formation of relevant phenotypes. When conducting a full genome analysis of sheep, particularly promising is the study of individuals with outstanding productivity indicators – exhibition animals, representatives of the super-elite class. The aim of this study was to identify new candidate genes for economically valuable traits based on the search for single nucleotide polymorphisms (SNPs) associated with belonging to different evaluation classes in rams of the Russian meat merino breed. Animal genotyping was performed using Ovine Infinium HD BeadChip 600K DNA, association search was performed using PLINK v. 1.07 software. Highly reliable associations were found between animals belonging to different evaluation classes and the frequency of occurrence of individual SNPs on chromosomes 2, 6, 10, 13, and 20. Most of the substitutions with high association reliability are concentrated on chromosome 10 in the region 10: 30859297–31873769. To search for candidate genes, 15 polymorphisms with the highest association reliability were selected (–log10(р) > 9). Determining the location of the analyzed SNPs relative to the latest annotation Oar_rambouillet_v1.0 allowed to identify 11 candidate genes presumably associated with the formation of a complex of phenotypic traits of animals in the exhibition group: RXFP2, ALOX5AP, MEDAG, OPN5, PRDM5, PTPRT, TRNAS-GGA, EEF1A1, FRY, ZBTB21-like, and B3GLCT-like. The listed genes encode proteins involved in the control of the cell cycle and DNA replication, regulation of cell proliferation and apoptosis, lipid and carbohydrate metabolism, the development of the inflammatory process and the work of circadian rhythms. Thus, the candidate genes under consideration can influence the formation of exterior features and productive qualities of sheep. However, further research is needed to confirm the influence of genes and determine the exact mechanisms for implementing this influence on the phenotype.

Genomic Scan for Selection Signature Reveals Fat Deposition in Chinese Indigenous Sheep with Extreme Tail Types

Simple Summary

According to the tail types, sheep can be briefly classified into three groups (fat-tailed, fat-rumped, and thin-tailed sheep). In this study, we used these three typical breeds from Chinese indigenous sheep breeds to perform a genome scan for selective sweeps using Ovine Infinium HD SNP BeadChip genotype data. Results showed that 25 genomic regions exhibited selection signals and harbored 73 positional candidate genes. These genes were documented not only to be associated with tail fat formation, but also be related to reproduction, body conformation, and appearance. Our findings contributed to understanding genetic basis of fat deposition in sheep tail and provide a reference for developing new sheep breeds with an ideal tail type.

Abstract

It is a unique feature that fat can be deposited in sheep tails and rumps. To elucidate the genetic mechanism underlying this trait, we collected 120 individuals from three Chinese indigenous sheep breeds with extreme tail types, namely large fat-tailed sheep (n = 40), Altay sheep (n = 40), and Tibetan sheep (n = 40), and genotyped them using the Ovine Infinium HD SNP BeadChip. Then genomic scan for selection signatures was performed using the hapFLK. In total, we identified 25 genomic regions exhibiting evidence of having been under selection. Bioinformatic analysis of the genomic regions showed that selection signatures related to multiple candidate genes had a demonstrated role in phenotypic variation. Nine genes have documented association with sheep tail types, including WDR92, TBX12, WARS2, BMP2, VEGFA, PDGFD, HOXA10, ALX4, and ETAA1. Moreover, a number of genes were of particular interest, including RXFP2 associated with the presence/absence and morphology of horns; MITF involved in coat color; LIN52 and SYNDIG1L related to the number of teats; MSRB3 gene associated with ear sizes; LTBP2 considered as a positional candidate genes for number of ribs; JAZF1 regulating lipid metabolism; PGRMC2, SPAG17, TSHR, GTF2A1, and LARP1B implicated with reproductive traits. Our findings provide insights into fat tail formation and a reference for carrying out molecular breeding and conservation in sheep.

Genetic basis of ruminant headgear and rapid antler regeneration

Ruminants are the only extant mammalian group possessing bony (osseous) headgear. We obtained 221 transcriptomes from bovids and cervids and sequenced three genomes representing the only two pecoran lineages that convergently lack headgear. Comparative analyses reveal that bovid horns and cervid antlers share similar gene expression profiles and a common cellular basis developed from neural crest stem cells. The rapid regenerative properties of antler tissue involve exploitation of oncogenetic pathways, and at the same time some tumor suppressor genes are under strong selection in deer. These results provide insights into the evolutionary origin of ruminant headgear as well as mammalian organ regeneration and oncogenesis.

Optimized Genetic Testing for Polledness in Multiple Breeds of Cattle

Many breeds of modern cattle are naturally horned, and for sound husbandry management reasons the calves frequently undergo procedures to physically remove the horns by disbudding or dehorning. These procedures are however a welfare concern. Selective breeding for polledness - absence of horns - has been effective in some cattle breeds but not in others (Bos indicus genotypes) due in part to the complex genetics of horn phenotype. To address this problem different approaches to genetic testing which provide accurate early-in-life prediction of horn phenotype have been evaluated, initially using microsatellites (MSAT) and more recently single nucleotide polymorphism (SNP). A direct gene test is not effective given the genetic heterogeneity and large-sized sequence variants associated with polledness in different breeds. The current study investigated 39,943 animals of multiple breeds to assess the accuracy of available poll testing assays. While the standard SNP-based test was an improvement on the earlier MSAT haplotyping method, 1999 (9.69%) out of 20,636 animals tested with this SNP-based assay did not predict a genotype, most commonly associated with the Indicus-influenced breeds. The current study has developed an optimized poll gene test that resolved the vast majority of these 1999 unresolved animals, while the predicted genotypes of those previously resolved remained unchanged. Hence the optimized poll test successfully predicted a genotype in 99.96% of samples assessed. We demonstrated that a robust set of 5 SNPs can effectively determine P_C and P_F alleles and eliminate the ambiguous and undetermined results of poll gene testing previously identified as an issue in cattle.

Understanding the effects of the bovine POLLED variants

Horns are paired appendages on the head of bovine species, comprising an inner bony core and outer keratin sheath. The horn bud forms during early fetal development but ossification of the developing horn does not occur until approximately 1 month after birth. Little is known about the genetic pathways that lead to horn growth. Hornless, or polled, animals are found in all domestic bovids. Histological studies of bovine fetuses have shown that the horn bud does not form in polled individuals. There are currently four known genetic variants for polledness in cattle on BTA1. All of the variants are intergenic, but probably affect regulation of nearby genes or long non-coding RNAs. Transcriptomic studies suggest that the expression of two nearby long non-coding RNAs are affected by the Celtic POLLED variant, but further studies are required to confirm these data. Candidate genes located elsewhere in the genome are involved in regulating bone formation and epithelial-to-mesenchymal transition. Expression of one of these candidate genes, RXFP2, appears to be reduced in the fetal horn bud of polled animals carrying the Celtic variant compared with horned individuals. Investigating horn ontogenesis and the genetic pathway by which the POLLED variants prevent horn development has implications for cattle breeding. If the genetic basis of horn bud formation and polledness is better understood, then new targets may be identified for precision genome editing to create polled individuals.

Review on Genomic Regions and Candidate Genes Associated with Economically Important Production and Reproduction Traits in Sheep (Ovies aries)

Sheep (Ovis aries) is one of the most economically, culturally, and socially important domestic animals. They are reared primarily for meat, milk, wool, and fur production. Sheep were reared using natural selection for a long period of time to offer these traits. In fact, this production system has been slowing the productivity and production potential of the sheep. To improve production efficiency and productivity of this animal through genetic improvement technologies, understanding the genetic background of traits such as body growth, weight, carcass quality, fat percent, fertility, milk yield, wool quality, horn type, and coat color is essential. With the development and utilization of animal genotyping technologies and gene identification methods, many functional genes and genetic variants associated with economically important phenotypic traits have been identified and annotated. This is useful and presented an opportunity to increase the pace of animal genetic gain. Quantitative trait loci and genome wide association study have been playing an important role in identifying candidate genes and animal characterization. This review provides comprehensive information on the identified genomic regions and candidate genes associated with production and reproduction traits, and gene function in sheep.

Comparative genome analyses reveal the unique genetic composition and selection signals underlying the phenotypic characteristics of three Chinese domestic goat breeds

BACKGROUND

As one of the important livestock species around the world, goats provide abundant meat, milk, and fiber to fulfill basic human needs. However, the genetic loci that underlie phenotypic variations in domestic goats are largely unknown, particularly for economically important traits. In this study, we sequenced the whole genome of 38 goats from three Chinese breeds (Chengdu Brown, Jintang Black, and Tibetan Cashmere) and downloaded the genome sequence data of 30 goats from five other breeds (four non-Chinese and one Chinese breed) and 21 Bezoar ibexes to investigate the genetic composition and selection signatures of the Chinese goat breeds after domestication.

RESULTS

Based on population structure analysis and FST values (average FST = 0.22), the genetic composition of Chengdu Brown goats differs considerably from that of Bezoar ibexes as a result of geographic isolation. Strikingly, the genes under selection that we identified in Tibetan Cashmere goats were significantly enriched in the categories hair growth and bone and nervous system development, possibly because they are involved in adaptation to high-altitude. In particular, we found a large difference in allele frequency of one novel SNP (c.-253G>A) in the 5'-UTR of FGF5 between Cashmere goats and goat breeds with short hair. The mutation at this site introduces a start codon that results in the occurrence of a premature FGF5 protein and is likely a natural causal variant that is involved in the long hair phenotype of cashmere goats. The haplotype tagged with the AGG-allele in exon 12 of DSG3, which encodes a cell adhesion molecule that is expressed mainly in the skin, was almost fixed in Tibetan Cashmere goats, whereas this locus still segregates in the lowland goat breeds. The pigmentation gene KITLG showed a strong signature of selection in Tibetan Cashmere goats. The genes ASIP and LCORL were identified as being under positive selection in Jintang Black goats.

CONCLUSIONS

After domestication, geographic isolation of some goat breeds has resulted in distinct genetic structures. Furthermore, our work highlights several positively selected genes that likely contributed to breed-related traits in domestic goats.

Runs of homozygosity and signatures of selection: a comparison among eight local Swiss sheep breeds

A dataset consisting of 787 animals with high-density SNP chip genotypes (346 774 SNPs) and 939 animals with medium-density SNP chip genotypes (33 828 SNPs) from eight indigenous Swiss sheep breeds was analyzed to characterize population structure, quantify genomic inbreeding based on runs of homozygosity and identify selection signatures. In concordance with the recent known history of these breeds, the highest genetic diversity was observed in Engadine Red sheep and the lowest in Valais Blacknose sheep. Correlation between F_PED and F_ROH was around 0.50 and thereby lower than that found in similar studies in cattle. Mean F_ROH estimates from medium-density data and HD data were highly correlated (0.95). Signatures of selection and candidate gene analysis revealed that the most prominent signatures of selection were found in the proximity of genes associated with body size (NCAPG, LCORL, LAP3, SPP1, PLAG1, ALOX12, TP53), litter size (SPP1), milk production (ABCG2, SPP1), coat color (KIT, ASIP, TBX3) and horn status (RXFP2). For the Valais Blacknose sheep, the private signatures in proximity of genes/QTL influencing body size, coat color and fatty acid composition were confirmed based on runs of homozygosity analysis. These private signatures underline the genetic uniqueness of the Valais Blacknose sheep breed. In conclusion, we identified differences in the genetic make-up of Swiss sheep breeds, and we present relevant candidate genes responsible for breed differentiation in locally adapted breeds.

The Genome Landscape of Tibetan Sheep Reveals Adaptive Introgression from Argali and the History of Early Human Settlements on the Qinghai-Tibetan Plateau

Tibetan sheep are the most common and widespread domesticated animals on the Qinghai-Tibetan Plateau (QTP) and have played an essential role in the permanent human occupation of this high-altitude region. However, the precise timing, route, and process of sheep pastoralism in the QTP region remain poorly established, and little is known about the underlying genomic changes that occurred during the process. Here, we investigate the genomic variation in Tibetan sheep using whole-genome sequences, single nucleotide polymorphism arrays, mitochondrial DNA, and Y-chromosomal variants in 986 samples throughout their distribution range. We detect strong signatures of selection in genes involved in the hypoxia and ultraviolet signaling pathways (e.g., HIF-1 pathway and HBB and MITF genes) and in genes associated with morphological traits such as horn size and shape (e.g., RXFP2). We identify clear signals of argali (Ovis ammon) introgression into sympatric Tibetan sheep, covering 5.23-5.79% of their genomes. The introgressed genomic regions are enriched in genes related to oxygen transportation system, sensory perception, and morphological phenotypes, in particular the genes HBB and RXFP2 with strong signs of adaptive introgression. The spatial distribution of genomic diversity and demographic reconstruction of the history of Tibetan sheep show a stepwise pattern of colonization with their initial spread onto the QTP from its northeastern part ∼3,100 years ago, followed by further southwest expansion to the central QTP ∼1,300 years ago. Together with archeological evidence, the date and route reveal the history of human expansions on the QTP by the Tang-Bo Ancient Road during the late Holocene. Our findings contribute to a depth understanding of early pastoralism and the local adaptation of Tibetan sheep as well as the late-Holocene human occupation of the QTP.

Deer antler stem cells are a novel type of cells that sustain full regeneration of a mammalian organ-deer antler

Deer antlers are extraordinary mammalian organs that can fully regenerate annually. Antler renewal is a stem cell-based epimorphic process and antler stem (AS) cells can initiate de novo generation of antlers in postnatal mammals. However, although being called stem cells, the AS cells have not been characterized at molecular level based on the stem cell criteria. Comprehensive characterization of the AS cells would undoubtedly help to decipher the mechanism underlying the full regeneration of deer antlers, the only case of stem cell-based epimorphic regeneration in mammals. In the present study, three types of AS cells (antlerogenic periosteal cells APCs, for initial pedicle and first antler formation; pedicle periosteal cells PPC, for annual antler regeneration; and reserve mesenchyme cells RMCs, for rapid antler growth), were isolated for comprehensive molecular characterization. A horn-growth-related gene, RXFP2, was found to be expressed only in AS cells lineages but not in the facial periosteal cells (FPCs, locates geographically in the vicinity of the APCs or PPCs), suggesting the RXFP2 might be a specific marker for the AS cell lineage in deer. Our results demonstrated that AS cells expressed classic MSC markers including surface markers CD73, CD90, CD105 and Stro-1. They also expressed some of the markers including Tert, Nestin, S100A4, nucleostemin and C-Myc, suggesting that they have some attributes of the ESCs. Microinjection of male APC into deer blastocysts resulted in one female foetus (110 days gestation) recovered with obvious pedicle primordia with both male and female genotype detected in the ovary. In conclusion, the AS cells should be defined as MSCs but with partial attributes of ESCs.

Genome-Wide Variation, Candidate Regions and Genes Associated With Fat Deposition and Tail Morphology in Ethiopian Indigenous Sheep

Variations in body weight and in the distribution of body fat are associated with feed availability, thermoregulation, and energy reserve. Ethiopia is characterized by distinct agro-ecological and human ethnic farmer diversity of ancient origin, which have impacted on the variation of its indigenous livestock. Here, we investigate autosomal genome-wide profiles of 11 Ethiopian indigenous sheep populations using the Illumina Ovine 50 K SNP BeadChip assay. Sheep from the Caribbean, Europe, Middle East, China, and western, northern and southern Africa were included to address globally, the genetic variation and history of Ethiopian populations. Population relationship and structure analysis separated Ethiopian indigenous fat-tail sheep from their North African and Middle Eastern counterparts. It indicates two main genetic backgrounds and supports two distinct genetic histories for African fat-tail sheep. Within Ethiopian sheep, our results show that the short fat-tail sheep do not represent a monophyletic group. Four genetic backgrounds are present in Ethiopian indigenous sheep but at different proportions among the fat-rump and the long fat-tail sheep from western and southern Ethiopia. The Ethiopian fat-rump sheep share a genetic background with Sudanese thin-tail sheep. Genome-wide selection signature analysis identified eight putative candidate regions spanning genes influencing growth traits and fat deposition (NPR2, HINT2, SPAG8, INSR), development of limbs and skeleton, and tail formation (ALX4, HOXB13, BMP4), embryonic development of tendons, bones and cartilages (EYA2, SULF2), regulation of body temperature (TRPM8), body weight and height variation (DIS3L2), control of lipogenesis and intracellular transport of long-chain fatty acids (FABP3), the occurrence and morphology of horns (RXFP2), and response to heat stress (DNAJC18). Our findings suggest that Ethiopian fat-tail sheep represent a uniquely admixed but distinct genepool that presents an important resource for understanding the genetic control of skeletal growth, fat metabolism and associated physiological processes.

Whole-genome sequences of 89 Chinese sheep suggest role of RXFP2 in the development of unique horn phenotype as response to semi-feralization

Background

Animal domestication has been extensively studied, but the process of feralization remains poorly understood.

Results

Here, we performed whole-genome sequencing of 99 sheep and identified a primary genetic divergence between 2 heterogeneous populations in the Tibetan Plateau, including 1 semi-feral lineage. Selective sweep and candidate gene analysis revealed local adaptations of these sheep associated with sensory perception, muscle strength, eating habit, mating process, and aggressive behavior. In particular, a horn-related gene, RXFP2, showed signs of rapid evolution specifically in the semi-feral breeds. A unique haplotype and repressed horn-related tissue expression of RXFP2 were correlated with higher horn length, as well as spiral and horizontally extended horn shape.

Conclusions

Semi-feralization has an extensive impact on diverse phenotypic traits of sheep. By acquiring features like those of their wild ancestors, semi-feral sheep were able to regain fitness while in frequent contact with wild surroundings and rare human interventions. This study provides a new insight into the evolution of domestic animals when human interventions are no longer dominant.

Proteomic Analysis of Plasma Membrane Proteins of Antler Stem Cells Using Label-Free LC⁻MS/MS

Deer antlers are unusual mammalian organs that can fully regenerate after annual shedding. Stem cells resident in the pedicle periosteum (PPCs) provide the main cell source for antler regeneration. Central to various cellular processes are plasma membrane proteins, but the expression of these proteins has not been well documented in antler regeneration. In the present study, plasma membrane proteins of PPCs and facial periosteal cells (FPCs) were analyzed using label-free liquid chromatography⁻mass spetrometry (LC⁻MS/MS). A total of 1739 proteins were identified. Of these proteins, 53 were found solely in the PPCs, 100 solely in the FPCs, and 1576 co-existed in both PPCs and FPCs; and 39 were significantly up-regulated in PPCs and 49 up-regulated in FPCs. In total, 226 gene ontology (GO) terms were significantly enriched from the differentially expressed proteins (DEPs). Five clusters of biological processes from these GO terms comprised responses to external stimuli, signal transduction, membrane transport, regulation of tissue regeneration, and protein modification processes. Further studies are required to demonstrate the relevancy of these DEPs in antler stem cell biology and antler regeneration.

Genomic prediction of the polled and horned phenotypes in Merino sheep

BACKGROUND

In horned sheep breeds, breeding for polledness has been of interest for decades. The objective of this study was to improve prediction of the horned and polled phenotypes using horn scores classified as polled, scurs, knobs or horns. Derived phenotypes polled/non-polled (P/NP) and horned/non-horned (H/NH) were used to test four different strategies for prediction in 4001 purebred Merino sheep. These strategies include the use of single 'single nucleotide polymorphism' (SNP) genotypes, multiple-SNP haplotypes, genome-wide and chromosome-wide genomic best linear unbiased prediction and information from imputed sequence variants from the region including the RXFP2 gene. Low-density genotypes of these animals were imputed to the Illumina Ovine high-density (600k) chip and the 1.78-kb insertion polymorphism in RXFP2 was included in the imputation process to whole-genome sequence. We evaluated the mode of inheritance and validated models by a fivefold cross-validation and across- and between-family prediction.

RESULTS

The most significant SNPs for prediction of P/NP and H/NH were OAR10_29546872.1 and OAR10_29458450, respectively, located on chromosome 10 close to the 1.78-kb insertion at 29.5 Mb. The mode of inheritance included an additive effect and a sex-dependent effect for dominance for P/NP and a sex-dependent additive and dominance effect for H/NH. Models with the highest prediction accuracies for H/NH used either single SNPs or 3-SNP haplotypes and included a polygenic effect estimated based on traditional pedigree relationships. Prediction accuracies for H/NH were 0.323 for females and 0.725 for males. For predicting P/NP, the best models were the same as for H/NH but included a genomic relationship matrix with accuracies of 0.713 for females and 0.620 for males.

CONCLUSIONS

Our results show that prediction accuracy is high using a single SNP, but does not reach 1 since the causative mutation is not genotyped. Incomplete penetrance or allelic heterogeneity, which can influence expression of the phenotype, may explain why prediction accuracy did not approach 1 with any of the genetic models tested here. Nevertheless, a breeding program to eradicate horns from Merino sheep can be effective by selecting genotypes GG of SNP OAR10_29458450 or TT of SNP OAR10_29546872.1 since all sheep with these genotypes will be non-horned.

Genomic analysis of morphometric traits in bighorn sheep using the Ovine Infinium® HD SNP BeadChip

Elucidating the genetic basis of fitness-related traits is a major goal of molecular ecology. Traits subject to sexual selection are particularly interesting, as non-random mate choice should deplete genetic variation and thereby their evolutionary benefits. We examined the genetic basis of three sexually selected morphometric traits in bighorn sheep (Ovis canadensis): horn length, horn base circumference, and body mass. These traits are of specific concern in bighorn sheep as artificial selection through trophy hunting opposes sexual selection. Specifically, horn size determines trophy status and, in most North American jurisdictions, if an individual can be legally harvested. Using between 7,994–9,552 phenotypic measures from the long-term individual-based study at Ram Mountain (Alberta, Canada), we first showed that all three traits are heritable (h² = 0.15–0.23). We then conducted a genome-wide association study (GWAS) utilizing a set of 3,777 SNPs typed in 76 individuals using the Ovine Infinium^® HD SNP BeadChip. We found suggestive association for body mass at a single locus (OAR9_91647990). The absence of strong associations with SNPs suggests that the traits are likely polygenic. These results represent a step forward for characterizing the genetic architecture of fitness related traits in sexually dimorphic ungulates.

Revealing the selection history of adaptive loci using genome-wide scans for selection: an example from domestic sheep

Background

One of the approaches to detect genetics variants affecting fitness traits is to identify their surrounding genomic signatures of past selection. With established methods for detecting selection signatures and the current and future availability of large datasets, such studies should have the power to not only detect these signatures but also to infer their selective histories. Domesticated animals offer a powerful model for these approaches as they adapted rapidly to environmental and human-mediated constraints in a relatively short time. We investigated this question by studying a large dataset of 542 individuals from 27 domestic sheep populations raised in France, genotyped for more than 500,000 SNPs.

Results

Population structure analysis revealed that this set of populations harbour a large part of European sheep diversity in a small geographical area, offering a powerful model for the study of adaptation. Identification of extreme SNP and haplotype frequency differences between populations listed 126 genomic regions likely affected by selection. These signatures revealed selection at loci commonly identified as selection targets in many species (“selection hotspots”) including ABCG2, LCORL/NCAPG, MSTN, and coat colour genes such as ASIP, MC1R, MITF, and TYRP1. For one of these regions (ABCG2, LCORL/NCAPG), we could propose a historical scenario leading to the introgression of an adaptive allele into a new genetic background. Among selection signatures, we found clear evidence for parallel selection events in different genetic backgrounds, most likely for different mutations. We confirmed this allelic heterogeneity in one case by resequencing the MC1R gene in three black-faced breeds.

Conclusions

Our study illustrates how dense genetic data in multiple populations allows the deciphering of evolutionary history of populations and of their adaptive mutations.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4447-x) contains supplementary material, which is available to authorized users.

High-resolution analysis of selection sweeps identified between fine-wool Merino and coarse-wool Churra sheep breeds

BACKGROUND

With the aim of identifying selection signals in three Merino sheep lines that are highly specialized for fine wool production (Australian Industry Merino, Australian Merino and Australian Poll Merino) and considering that these lines have been subjected to selection not only for wool traits but also for growth and carcass traits and parasite resistance, we contrasted the OvineSNP50 BeadChip (50 K-chip) pooled genotypes of these Merino lines with the genotypes of a coarse-wool breed, phylogenetically related breed, Spanish Churra dairy sheep. Genome re-sequencing datasets of the two breeds were analyzed to further explore the genetic variation of the regions initially identified as putative selection signals.

RESULTS

Based on the 50 K-chip genotypes, we used the overlapping selection signals (SS) identified by four selection sweep mapping analyses (that detect genetic differentiation, reduced heterozygosity and patterns of haplotype diversity) to define 18 convergence candidate regions (CCR), five associated with positive selection in Australian Merino and the remainder indicating positive selection in Churra. Subsequent analysis of whole-genome sequences from 15 Churra and 13 Merino samples identified 142,400 genetic variants (139,745 bi-allelic SNPs and 2655 indels) within the 18 defined CCR. Annotation of 1291 variants that were significantly associated with breed identity between Churra and Merino samples identified 257 intragenic variants that caused 296 functional annotation variants, 275 of which were located across 31 coding genes. Among these, four synonymous and four missense variants (NPR2_His847Arg, NCAPG_Ser585Phe, LCORL_Asp1214Glu and LCORL_Ile1441Leu) were included.

CONCLUSIONS

Here, we report the mapping and genetic variation of 18 selection signatures that were identified between Australian Merino and Spanish Churra sheep breeds, which were validated by an additional contrast between Spanish Merino and Churra genotypes. Analysis of whole-genome sequencing datasets allowed us to identify divergent variants that may be viewed as candidates involved in the phenotypic differences for wool, growth and meat production/quality traits between the breeds analyzed. The four missense variants located in the NPR2, NCAPG and LCORL genes may be related to selection sweep regions previously identified and various QTL reported in sheep in relation to growth traits and carcass composition.

Unveiling genomic regions that underlie differences between Afec-Assaf sheep and its parental Awassi breed

BACKGROUND

Sheep production in Israel has improved by crossing the fat-tailed local Awassi breed with the East Friesian and later, with the Booroola Merino breed, which led to the formation of the highly prolific Afec-Assaf strain. This strain differs from its parental Awassi breed in morphological traits such as tail and horn size, coat pigmentation and wool characteristics, as well as in production, reproductive and health traits. To identify major genes associated with the formation of the Afec-Assaf strain, we genotyped 41 Awassi and 141 Afec-Assaf sheep using the Illumina Ovine SNP50 BeadChip array, and analyzed the results with PLINK and EMMAX software. The detected variable genomic regions that differed between Awassi and Afec-Assaf sheep (variable genomic regions; VGR) were compared to selection signatures that were reported in 48 published genome-wide association studies in sheep. Because the Afec-Assaf strain, but not the Awassi breed, carries the Booroola mutation, association analysis of BMPR1B used as the test gene was performed to evaluate the ability of this study to identify a VGR that includes such a major gene.

RESULTS

Of the 20 detected VGR, 12 were novel to this study. A ~7-Mb VGR was identified on Ovies aries chromosome OAR6 where the Booroola mutation is located. Similar to other studies, the most significant VGR was detected on OAR10, in a region that contains candidate genes affecting horn type (RXFP2), climate adaptation (ALOX5AP), fiber diameter (KATNAl1), coat pigmentation (FRY) and genes associated with fat distribution. The VGR on OAR2 included BNC2, which is also involved in controlling coat pigmentation in sheep. Six other VGR contained genes that were shown to be involved in coat pigmentation by analyzing their mammalian orthologues. Genes associated with fat distribution in humans, including GRB14 and COBLL1, were located in additional VGR. Sequencing DNA from Awassi and Afec-Assaf individuals revealed non-synonymous mutations in some of these candidate genes.

CONCLUSIONS

Our results highlight VGR that differentiate the Awassi breed from the Afec-Assaf strain, some of which may include genes that confer an advantage to Afec-Assaf and Assaf over Awassi sheep with respect to intensive sheep production under Mediterranean conditions.

The 1.78-kb insertion in the 3'-untranslated region of RXFP2 does not segregate with horn status in sheep breeds with variable horn status

BACKGROUND

The mode of inheritance of horn status in sheep is far more complex than a superficial analysis might suggest. Observations, which were mostly based on crossbreeding experiments, indicated that the allele that results in horns is dominant in males and recessive in females, and some authors even speculated about the involvement of more than two alleles. However, all recent genome-wide association analyses point towards a very strong effect of a single autosomal locus on ovine chromosome 10, which was narrowed down to a putatively causal insertion polymorphism in the 3'-untranslated region of the relaxin/insulin-like family peptide receptor 2 gene (RXFP2). The main objective of this study was to test this insertion polymorphism as the causal mutation in diverse sheep breeds, including breeds with a variable and/or sex-dependent horn status.

RESULTS

After re-sequencing a region of about 246 kb that covered the RFXP2 gene and its flanking regions for 24 sheep from six completely horned and six completely polled breeds, we identified the same insertion polymorphism that was previously published as segregating with horn status in these breeds. Multiplex PCR genotyping of 489 sheep from 34 breeds and some crosses between sheep breeds showed a nearly perfect segregation of the insertion polymorphism with horn status in sheep breeds of Central and Western European origin. In these breeds and their crossings, heterozygous males were horned and heterozygous females were polled. However, this segregation pattern was not, or at least not completely, reproducible in breeds with sex-dependent and/or variable horn status, especially in sheep that originated from even more southern European regions and from Africa. In such breeds, we observed almost all possible combinations of genotype, sex and horn status phenotype.

CONCLUSIONS

The 1.78-kb insertion polymorphism in the 3'-untranslated region of RXFP2 and SNPs in the 3'-UTR, exon 14 and intron 11 of this gene that we analyzed in this study cannot be considered as the only cause of polledness in sheep and are not useful as a universal marker to define the genetic horn status in sheep.

Mapping the four-horned locus and testing the polled locus in three Chinese sheep breeds

Four-horned sheep are an ideal animal model for illuminating the genetic basis of horn development. The objective of this study was to locate the genetic region responsible for the four-horned phenotype and to verify a previously reported polled locus in three Chinese breeds. A genome-wide association study (GWAS) was performed using 34 two-horned and 32 four-horned sheep from three Chinese indigenous breeds: Altay, Mongolian and Sishui Fur sheep. The top two significant single nucleotide polymorphisms (SNPs) associated with the four-horned phenotype were both located in a region spanning positions 132.6 to 132.7 Mb on sheep chromosome 2. Similar locations for the four-horned trait were previously identified in Jacob, Navajo-Churro, Damara and Sishui Fur sheep, suggesting a common genetic component underlying the four-horned phenotype. The two identified SNPs were both downstream of the metaxin 2 (MTX2) gene and the HOXD gene cluster. For the top SNP-OAR2:g.132619300G>A-the strong associations of the AA and AG genotypes with the four-horned phenotype and the GG genotype with the two-horned phenotype indicated the dominant inheritance of the four-horned trait. No significant SNPs for the polled phenotype were identified in the GWAS analysis, and a PCR analysis for the detection of the 1.8-kb insertion associated with polled sheep in other breeds failed to verify the association with polledness in the three Chinese breeds. This study supports the hypothesis that two different loci are responsible for horn existence and number. This study contributes to the understanding of the molecular regulation of horn development and enriches the knowledge of qualitative traits in domestic animals.

A genome-wide association study identifies a genomic region for the polycerate phenotype in sheep (Ovis aries)

Horns are a cranial appendage found exclusively in Bovidae, and play important roles in accessing resources and mates. In sheep (Ovies aries), horns vary from polled to six-horned, and human have been selecting polled animals in farming and breeding. Here, we conducted a genome-wide association study on 24 two-horned versus 22 four-horned phenotypes in a native Chinese breed of Sishui Fur sheep. Together with linkage disequilibrium (LD) analyses and haplotype-based association tests, we identified a genomic region comprising 132.0–133.1 Mb on chromosome 2 that contained the top 10 SNPs (including 4 significant SNPs) and 5 most significant haplotypes associated with the polycerate phenotype. In humans and mice, this genomic region contains the HOXD gene cluster and adjacent functional genes EVX2 and KIAA1715, which have a close association with the formation of limbs and genital buds. Our results provide new insights into the genetic basis underlying variable numbers of horns and represent a new resource for use in sheep genetics and breeding.

Genome-wide association reveals the locus responsible for four-horned ruminant

Phenotypic variability in horn characteristics, such as their size, number and shape, offers the opportunity to elucidate the molecular basis of horn development. The objective of this study was to map the genetic determinant controlling the production of four horns in two breeds, Jacob sheep and Navajo-Churro, and examine whether an eyelid abnormality occurring in the same populations is related. Genome-wide association mapping was performed using 125 animals from the two breeds that contain two- and four-horned individuals. A case-control design analysis of 570 712 SNPs genotyped with the ovine HD SNP Beadchip revealed a strong association signal on sheep chromosome 2. The 10 most strongly associated SNPs were all located in a region spanning Mb positions 131.9-132.6, indicating the genetic architecture underpinning the production of four horns is likely to involve a single gene. The closest genes to the most strongly associated marker (OAR2_132568092) were MTX2 and the HOXD cluster, located approximately 93 Kb and 251 Kb upstream respectively. The occurrence of an eyelid malformation across both breeds was restricted to polled animals and those carrying more than two horns. This suggests the eyelid abnormality may be associated with departures from the normal developmental production of two-horned animals and that the two conditions are developmentally linked. This study demonstrated the presence of separate loci responsible for the polled and four-horned phenotypes in sheep and advanced our understanding of the complexity that underpins horn morphology in ruminants.