Selection signature analysis reveals genes associated with tail type in Chinese indigenous sheep

Colon microbiota and metabolite potential impact on tail fat deposition of Altay sheep

Tail fat deposition of Altay sheep not only increased the cost of feeding but also reduced the economic value of meat. Currently, because artificial tail removal and gene modification methods cannot solve this problem, it is maybe to consider reducing tail fat deposition from the path of intestinal microbiota and metabolite. We measured body weight and tail fat weight, collected the serum for hormone detection by enzyme-linked immunosorbent assay, and collected colon contents to 16S rRNA sequence and liquid chromotography with mass spectrometry detection to obtain colon microbiota and metabolite information, from 12 3-month-old and 6-month-old Altay sheep. Subsequently, we analyzed the correlation between colon microbiota and tail fat weight, hormones, and metabolites, respectively. We identified that the tail fat deposition of Altay sheep increased significantly with the increase of age and body weight, and the main microbiota that changed were Verrucomicrobia, Cyanobacteria, Akkermansia, Bacteroides, Phocaeicola, Escherichia-Shigella, and Clostridium_sensu_stricto_1. The results indicated that the diversities of metabolites in the colon contents of 3-months old and 6-months old were mainly reflected in phosphocholine (PC) and phosphatidylethanolamine (PE) in the lipid metabolism pathway. The correlations analyzed showed that Verrucomicrobia, Chlamydiae, Akkermansia, Ruminococcaceae_UCG-005, Bacteroides, and Phocaeicola were negatively correlated with tail fat deposition. Verrucomicrobia, Akkermansia, and Bacteroides were negatively correlated with growth hormone (GH). Verrucomicrobia was positively correlated with L-a-lysophosphatidylserine and PE(18:1(9Z)/0:0). Our results showed that tail fat deposition of Altay sheep was probably correlated with the abundance of Verrucomicrobia, Akkermansia, Bacteroides of colon microbiota, PC, PE of metabolites, and GH of serum.

IMPORTANCE

Excessive tail fat deposition of Altay sheep caused great economic losses, and the current research results could not solve this problem well. Now, our research speculates that the tail fat deposition of Aletay sheep may be related to the abundance of Verrucomicrobia, Akkermansia, Bacteroides, metabolites phosphocholine, phosphatidylethanolamine, and growth hormone of serum. Further investigation of the interaction mechanism between these microbiota or metabolites and tail fat deposition is helpful in reducing tail fat deposition of Altay sheep and increasing the economic benefits of breeding farms.

Analysis of 206 whole-genome resequencing reveals selection signatures associated with breed-specific traits in Hu sheep

As an invaluable Chinese sheep germplasm resource, Hu sheep are renowned for their high fertility and beautiful wavy lambskins. Their distinctive characteristics have evolved over time through a combination of artificial and natural selection. Identifying selection signatures in Hu sheep can provide a straightforward insight into the mechanism of selection and further uncover the candidate genes associated with breed-specific traits subject to selection. Here, we conducted whole-genome resequencing on 206 Hu sheep individuals, each with an approximate 6-fold depth of coverage. And then we employed three complementary approaches, including composite likelihood ratio, integrated haplotype homozygosity score and the detection of runs of homozygosity, to detect selection signatures. In total, 10 candidate genomic regions displaying selection signatures were simultaneously identified by multiple methods, spanning 88.54 Mb. After annotating, these genomic regions harbored collectively 92 unique genes. Interestingly, 32 candidate genes associated with reproduction were distributed in nine genomic regions detected. Out of them, two stood out as star candidates: BMPR1B and GNRH2, both of which have documented associations with fertility, and a HOXA gene cluster (HOXA1-5, HOXA9, HOXA10, HOXA11 and HOXA13) had also been linked to fertility. Additionally, we identified other genes that are related to hair follicle development (LAMTOR3, EEF1A2), ear size (HOXA1, KCNQ2), fat tail formation (HOXA10, HOXA11), growth and development (FAF1, CCNDBP1, GJB2, GJA3), fat deposition (ACOXL, JAZF1, HOXA3, HOXA4, HOXA5, EBF4), immune (UBR1, FASTKD5) and feed intake (DAPP1, RNF17, NPBWR2). Our results offer novel insights into the genetic mechanisms underlying the selection of breed-specific traits in Hu sheep and provide a reference for sheep genetic improvement programs.

Insight into the current genomic diversity, conservation status and population structure of Tunisian Barbarine sheep breed

Local livestock breeds play a crucial role in global biodiversity, connecting natural and human-influenced environments and contributing significantly to ecosystem services. While commercial breeds dominate industrial systems, local livestock breeds in developing countries, like Barbarine sheep in Tunisia, are vital for food security and community maintenance. The Tunisian Barbarine sheep, known for its adaptability and distinctive fat-tailed morphology, faces challenges due to historical crossbreeding. In this study, the Illumina Ovine SNP50K BeadChip array was used to perform a genome-wide characterization of Tunisian Barbarine sheep to investigate its genetic diversity, the genome structure, and the relationship within the context of Mediterranean breeds. The results show moderate genetic diversity and low inbreeding. Runs of Homozygosity analysis find genomic regions linked to important traits, including fat tail characteristics. Genomic relationship analysis shows proximity to Algerian thin-tailed breeds, suggesting crossbreeding impacts. Admixture analysis reveals unique genetic patterns, emphasizing the Tunisian Barbarine's identity within the Mediterranean context and its closeness to African breeds. Current results represent a starting point for the creation of monitoring and conservation plans. In summary, despite genetic dilution due to crossbreeding, the identification of genomic regions offers crucial insights for conservation. The study confirms the importance of preserving unique genetic characteristics of local breeds, particularly in the face of ongoing crossbreeding practices and environmental challenges. These findings contribute valuable insights for the sustainable management of this unique genetic reservoir, supporting local economies and preserving sheep species biodiversity.

Refining the genomic profiles of North African sheep breeds through meta-analysis of worldwide genomic SNP data

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.

Signatures of selection in riverine buffalo populations revealed by genome-wide SNP data

The detection of selection signatures assists in understanding domestication, evolution, and the identification of genomic regions related to adaptation and production traits in buffaloes. The emergence of high-throughput technologies like Next Generation Sequencing and SNP genotyping had expanded our ability to detect these signatures of selection. In this study, we sought to identify signatures of selection in five buffalo populations (Brazilian Murrah, Bulgarian Murrah, Indian Murrah, Nili-Ravi, and Kundi) using Axiom Buffalo 90 K Genotyping Array data. Using seven different methodologies (Tajima's D, CLR, ROH, iHS, FST, FLK and hapFLK), we identified selection signatures in 374 genomic regions, spanning a total of 381 genes and 350 quantitative trait loci (QTLs). Among these, several candidate genes were associated with QTLs for milk production, reproduction, growth and carcass traits. The genes and QTLs reported in this study provide insight into selection signals shaping the genome of buffalo breeds. Our findings can aid in further genomic association studies, genomic prediction, and the implementation of breeding programmes in Indian buffaloes.

Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds

BACKGROUND

The importance of sheep breeding in the Mediterranean part of the eastern Adriatic has a long tradition since its arrival during the Neolithic migrations. Sheep production system is extensive and generally carried out in traditional systems without intensive systematic breeding programmes for high uniform trait production (carcass, wool and milk yield). Therefore, eight indigenous Croatian sheep breeds from eastern Adriatic treated here as metapopulation (EAS), are generally considered as multipurpose breeds (milk, meat and wool), not specialised for a particular type of production, but known for their robustness and resistance to certain environmental conditions. Our objective was to identify genomic regions and genes that exhibit patterns of positive selection signatures, decipher their biological and productive functionality, and provide a "genomic" characterization of EAS adaptation and determine its production type.

RESULTS

We identified positive selection signatures in EAS using several methods based on reduced local variation, linkage disequilibrium and site frequency spectrum (eROHi, iHS, nSL and CLR). Our analyses identified numerous genomic regions and genes (e.g., desmosomal cadherin and desmoglein gene families) associated with environmental adaptation and economically important traits. Most candidate genes were related to meat/production and health/immune response traits, while some of the candidate genes discovered were important for domestication and evolutionary processes (e.g., HOXa gene family and FSIP2). These results were also confirmed by GO and QTL enrichment analysis.

CONCLUSIONS

Our results contribute to a better understanding of the unique adaptive genetic architecture of EAS and define its productive type, ultimately providing a new opportunity for future breeding programmes. At the same time, the numerous genes identified will improve our understanding of ruminant (sheep) robustness and resistance in the harsh and specific Mediterranean environment.

A Functional Variant Alters the Binding of Bone morphogenetic protein 2 to the Transcription Factor NF-κB to Regulate Bone morphogenetic protein 2 Gene Expression and Chicken Abdominal Fat Deposition

In this study, we employed a dual-luciferase reporter assay and electrophoretic mobility shift analysis (EMSA) in vitro to explore whether a 12-base pair (bp) insertion/deletion (InDel) variant (namely g.14798187_14798188insTCCCTGCCCCCT) within intron 2 of the chicken BMP2 gene, which was significantly associated with chicken abdominal fat weight and abdominal fat percentage, is a functional marker and its potential regulatory mechanism. The reporter analysis demonstrated that the luciferase activity of the deletion allele was extremely significantly higher than that of the insertion allele (p < 0.01). A bioinformatics analysis revealed that compared to the deletion allele, the insertion allele created a transcription factor binding site of nuclear factor-kappa B (NF-κB), which exhibited an inhibitory effect on fat deposition. A dual-luciferase reporter assay demonstrated that the inhibitory effect of NF-κB on the deletion allele was stronger than that on the insertion allele. EMSA indicated that the binding affinity of NF-κB for the insertion allele was stronger than that for the deletion allele. In conclusion, the 12-bp InDel chicken BMP2 gene variant is a functional variant affecting fat deposition in chickens, which may partially regulate BMP2 gene expression by affecting the binding of transcription factor NF-κB to the BMP2 gene.

Genomic selection pressure discovery using site-frequency spectrum and reduced local variability statistics in Pakistani Dera-Din-Panah goat

BACKGROUND

Population geneticists have long sought to comprehend various selection traces accumulated in the goat genome due to natural or human driven artificial selection through breeding practices, which led the wild animals to domestication, so understanding evolutionary process may helpful to utilize the full genetic potential of goat genome.

METHODS AND RESULTS

As a step forward to pinpoint the selection signals in Pakistani Dera-Din-Panah (DDP) goat, whole-genome pooled sequencing (n = 12) was performed, and 618,236,192 clean paired-end reads were mapped against ARS1 reference goat assembly. Five different selection signature statistics were applied using four site-frequency spectrum (SFS) methods (Tajima's D ([Formula: see text]), Fay and Wu's H ([Formula: see text]), Zeng's E ([Formula: see text]), [Formula: see text]) and one reduced local variability approach named pooled heterozygosity ([Formula: see text]). The under-selection regions were annotated with significant threshold values of [Formula: see text]≥4.7, [Formula: see text]≥6, [Formula: see text]≥2.5, Pool-HMM ≥ 12, and [Formula: see text]≥5 that resulted in accumulative 364 candidate gene hits. The highest genomic selection signals were observed on Chr. 4, 6, 10, 12, 15, 16, 18, 20, and 27 and harbor ADAMTS6, CWC27, RELN, MYCBP2, FGF14, STIM1, CFAP74, GNB1, CALML6, TMEM52, FAM149A, NADK, MMP23B, OPN3, FH, MFHAS1, KLKB1, RRM1, KMO, SPEF2, F11, KIT, KMO, ERI1, ATP8B4, and RHOG genes. Next, the validation of our captured genomic hits was also performed by more than one applied statistics which harbor meat production, immunity, and reproduction associated genes to strengthen our hypothesis of under-selection traits in this Pakistani goat breed. Furthermore, common candidate genes captured by more than one statistical method were subjected to gene ontology and KEGG pathway analysis to get insights of particular biological processes associated with this goat breed.

CONCLUSION

Current perception of genomic architecture of DDP goat provides a better understanding to improve its genetic potential and other economically important traits of medium to large body size, milk, and fiber production by updating the genomic insight driven breeding strategies to boost the livestock and agriculture-based economy of the country.

The Effects of DDI1 on Inducing Differentiation in Ovine Preadipocytes via Oar-miR-432

Reducing fat deposition in sheep (Ovis aries) tails is one of the most important ways to combat rising costs and control consumer preference. Our previous studies have shown that oar-miR-432 is differentially expressed in the tail adipose tissue of Hu (a fat-tailed sheep breed) and Tibetan (a thin-tailed sheep breed) sheep and is a key factor in the negative regulation of fat deposition through BMP2 in ovine preadipocytes. This study investigated the effect of oar-miR-432 and its target genes in ovine preadipocytes. A dual luciferase assay revealed that DDI1 is a direct target gene of oar-miR-432. We transfected an oar-miR-432 mimic and inhibitor into preadipocytes to analyze the expression of target genes. Overexpression of oar-miR-432 inhibits DDI1 expression, whereas inhibition showed the opposite results. Compared with thin-tailed sheep, DDI1 was highly expressed in the fat-tailed sheep at the mRNA and protein levels. Furthermore, we transfected the overexpression and knockdown target genes into preadipocytes to analyze their influence after inducing differentiation. Knockdown of DDI1 induced ovine preadipocyte differentiation into adipocytes but suppressed oar-miR-432 expression. Conversely, the overexpression of DDI1 significantly inhibited differentiation but promoted oar-miR-432 expression. DDI1 overexpression also decreased the content of triglycerides. Additionally, DDI1 is a nested gene in intron 1 of PDGFD. When DDI1 was overexpressed, the PDGFD expression also increased, whereas DDI1 knockdown showed the opposite results. This is the first study to reveal the biological mechanisms by which oar-miR-432 inhibits preadipocytes through DDI1 and provides insight into the molecular regulatory mechanisms of DDI1 in ovine preadipocytes. These results have important applications in animal breeding and obesity-related human diseases.

Whole-body adipose tissue multi-omic analyses in sheep reveal molecular mechanisms underlying local adaptation to extreme environments

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.

Genomic Regions Associated with Wool, Growth and Reproduction Traits in Uruguayan Merino Sheep

The aim of this study was to identify genomic regions and genes associated with the fiber diameter (FD), clean fleece weight (CFW), live weight (LW), body condition score (BCS), pregnancy rate (PR) and lambing potential (LP) of Uruguayan Merino sheep. Phenotypic records of approximately 2000 mixed-age ewes were obtained from a Merino nucleus flock. Genome-wide association studies were performed utilizing single-step Bayesian analysis. For wool traits, a total of 35 genomic windows surpassed the significance threshold (PVE ≥ 0.25%). The proportion of the total additive genetic variance explained by those windows was 4.85 and 9.06% for FD and CFW, respectively. There were 42 windows significantly associated with LWM, which collectively explained 43.2% of the additive genetic variance. For BCS, 22 relevant windows accounted for more than 40% of the additive genetic variance, whereas for the reproduction traits, 53 genomic windows (24 and 29 for PR and LP, respectively) reached the suggestive threshold of 0.25% of the PVE. Within the top 10 windows for each trait, we identified several genes showing potential associations with the wool (e.g., IGF-1, TGFB2R, PRKCA), live weight (e.g., CAST, LAP3, MED28, HERC6), body condition score (e.g., CDH10, TMC2, SIRPA, CPXM1) or reproduction traits (e.g., ADCY1, LEPR, GHR, LPAR2) of the mixed-age ewes.

Whole-genome resequencing reveals genetic diversity and selection characteristics of dairy goat

The dairy goat is one of the earliest dairy livestock species, which plays an important role in the economic development, especially for developing countries. With the development of agricultural civilization, dairy goats have been widely distributed across the world. However, few studies have been conducted on the specific characteristics of dairy goat. In this study, we collected the whole-genome data of 89 goat individuals by sequencing 48 goats and employing 41 publicly available goats, including five dairy goat breeds (Saanen, Nubian, Alpine, Toggenburg, and Guanzhong dairy goat; n = 24, 15, 11, 6, 6), and three goat breeds (Guishan goat, Longlin goat, Yunshang Black goat; n = 6, 15, 6). Through compared the genomes of dairy goat and non-dairy goat to analyze genetic diversity and selection characteristics of dairy goat. The results show that the eight goats could be divided into three subgroups of European, African, and Chinese indigenous goat populations, and we also found that Australian Nubian, Toggenburg, and Australian Alpine had the highest linkage disequilibrium, the lowest level of nucleotide diversity, and a higher inbreeding coefficient, indicating that they were strongly artificially selected. In addition, we identified several candidate genes related to the specificity of dairy goat, particularly genes associated with milk production traits (GHR, DGAT2, ELF5, GLYCAM1, ACSBG2, ACSS2), reproduction traits (TSHR, TSHB, PTGS2, ESR2), immunity traits (JAK1, POU2F2, LRRC66). Our results provide not only insights into the evolutionary history and breed characteristics of dairy goat, but also valuable information for the implementation and improvement of dairy goat cross breeding program.

High-density SNP markers elucidate the genetic divergence and population structure of Noticiana sheep breed in the Mediterranean context

Among livestock species, sheep have played an early major role in the Mediterranean area. Italy has a long history of sheep breeding and, despite a dramatic contraction in numbers, still raise several local populations that may represent a unique source of genetic diversity. The Noticiana is a breed of the south-eastern part of Sicily appreciated both for its dairy products and for its resistance to harsh environment. In this study, the high-density Illumina Ovine SNP600K BeadChip array was used for the first genome-wide characterization of 48 individuals of Noticiana sheep to investigate its diversity, the genome structure and the relationship within the context of worldwide and Italian breeds. Moreover, the runs of homozygosity (ROH) pattern and the pairwise F_ST-outliers were examined. Noticiana reported moderate levels of genetic diversity. The high percentage of short and medium length ROH segments (93% under 4 Mb) is indicative of a within breed relatedness dating back to ancient times, despite the absence of management for the mating plans and the reduced population size. In the worldwide context, the Southern Italian, Spanish and Albanian breeds overlapped in a macro cluster which also included the Noticiana sheep. The results highlighted ancestral genetic components of Noticiana shared with Comisana breed, and showed the clear separation from the other Italian sheep. This is likely the consequence of the combined effects of genetic drift, small population size and reproductive isolation. ROH islands and F_ST-outliers approaches in Noticiana identified genes and QTLs involved in milk and meat production, as well as related to the local adaptation, and therefore are consistent with the phenotypic traits of the studied breed. Although a wider sampling could be useful to deepen the genomic survey on Noticiana, these results represent a crucial starting point for the characterization of an important local genetic resource, with a view of supporting the local economy and preserving the biodiversity of the sheep species.

Genome-Wide Genetic Diversity and Population Structure of Local Sudanese Sheep Populations Revealed by Whole-Genome Sequencing

Local Sudanese sheep populations inhabiting diverse environmental conditions and holding opposing morphologies provide opportunities for molecular-genetic research. Characterizing their genome is crucial for sustainable breeding improvement and targeting favorable genes in breeding programs. However, the genome of these sheep populations, which comprises several subtypes, remains uncharacterized using whole-genome sequence data. This study aimed to elucidate genome-wide genetic diversity and population structure of 11 local Sudanese sheep populations, namely, Hammari, Kabbashi, Meidobe, Ashgar, Dubasi, Watish, Bega, Naili, Fulani, Zagawi, and Garag. Ninety whole blood samples were collected, and we extracted DNA using a Qiagen DNeasy® extraction kit. We used the Illumina HiSeq 2000 platform to sequence all the DNA samples. We included whole-genome sequence data of three Ethiopian sheep (Doyogena, Kefis, and Gafera) and one Libyan sheep (Libyan Barbary) in the study to infer the genetic relationships of local Sudanese sheep populations from a continental perspective. A total of 44.8 million bi-allelic autosomal SNPs were detected; 28.5% and 63.3% occur in introns and intergenic regions, respectively. The mean genetic diversity ranged from 0.276 for Garag to 0.324 for Kabbashi sheep populations. The lowest FST estimates were observed between Kabbashi and Ashgar and the highest between Bega and Fulani local Sudanese sheep populations. The principal component and population structure analyses of the 11 local Sudanese sheep populations indicated three separate genetic groups categorized following their tail morphotype, geographical distribution, and population subtype. The thin-tailed local Sudanese sheep populations exhibited independent clustering from the fat-tailed Ethiopian and Libyan sheep. We also observed distinct clustering between the fat-tailed Ethiopian and Libyan sheep. The present study’s findings demonstrated the population structure and principal components related to tail morphotype, geographical distribution, and population subtype of local Sudanese sheep populations. A clear signature of admixture was observed among the studied local Sudanese sheep populations.

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.

Impact of Feeding Probiotics on Blood Parameters, Tail Fat Metabolites, and Volatile Flavor Components of Sunit Sheep

Sheep crude tail fat has unique nutritional values and is used as a raw material for high-quality natural oil. The purpose of this study was to investigate the effects of probiotics on the metabolites and flavor of sheep crude tail fat. In this study, 12 Sunit sheep were randomly divided into an experimental group (LTF, basal feed + Lactiplantibacillusplantarum powder) and a control group (CTF, basal feed). The results of sheep crude tail fat analysis showed that blood lipid parameters were significantly lower and the expression of fatty acid synthase and stearoyl-CoA desaturase genes higher in the LTF group than in the CTF group (p < 0.05). Metabolomic analysis via liquid chromatography−mass spectrometry showed that the contents of metabolites such as eicosapentaenoic acid, 16-hydroxypalmitic acid, and L-citrulline were higher in the LTF group (p < 0.01). Gas chromatography−mass spectrometry detection of volatile flavor compounds in the tail fat showed that nonanal, decanal, and 1-hexanol were more abundant in the LTF group (p < 0.05). Therefore, Lactiplantibacillus plantarum feeding affected blood lipid parameters, expression of lipid metabolism-related genes, tail fat metabolites, and volatile flavor compounds in Sunit sheep. In this study, probiotics feeding was demonstrated to support high-value sheep crude tail fat production.

Trajectory of livestock genomics in South Asia: A comprehensive review

Livestock plays a central role in sustaining human livelihood in South Asia. There are numerous and distinct livestock species in South Asian countries. Several of them have experienced genetic development in recent years due to the application of genomic technologies and effective breeding programs. This review discusses genomic studies on cattle, buffalo, sheep, goat, pig, horse, camel, yak, mithun, and poultry. The frontiers covered in this review are genetic diversity, admixture studies, selection signature research, QTL discovery, genome-wide association studies (GWAS), and genomic selection. The review concludes with recommendations for South Asian livestock systems to increasingly leverage genomic technologies, based on the lessons learned from the numerous case studies. This paper aims to present a comprehensive analysis of the dichotomy in the South Asian livestock sector and argues that a realistic approach to genomics in livestock can ensure long-term genetic advancements.

Natural adaptation and human selection of northeast African sheep genomes

African sheep manifest diverse but distinct physio-anatomical traits, which are the outcomes of natural- and human-driven selection. Here, we generated 34.8 million variants from 150 indigenous northeast African sheep genomes sequenced at an average depth of ∼54× for 130 samples (Ethiopia, Libya) and ∼20× for 20 samples (Sudan). These represented sheep from diverse environments, tail morphology and post-Neolithic introductions to Africa. Phylogenetic and model-based admixture analysis provided evidence of four genetic groups corresponding to altitudinal geographic origins, tail morphotypes and possible historical introduction and dispersal of the species into and across the continent. Running admixture at higher levels of K (6 ≤ K ≤ 25), revealed cryptic levels of genome intermixing as well as distinct genetic backgrounds in some populations. Comparative genomic analysis identified targets of selection that spanned conserved haplotype structures overlapping clusters of genes and gene families. These were related to hypoxia responses, ear morphology, caudal vertebrae and tail skeleton length, and tail fat-depot structures. Our findings provide novel insights underpinning morphological variation and response to human-driven selection and environmental adaptation in African indigenous sheep.

Using comparative genomics to detect mutations regulating plumage variations in graylag (A. anser) and swan geese (A. cygnoides)

Although graylag geese (A. anser) showed similar plumages of white, grey, and white with grey patches compared to those in swan geese (A. cygnoides), it was believed the substantial molecular mechanism for plumage variations were different. To date, studies on genes responsible for diverse plumages among graylag geese were limited and causal mutations remain unknown. In this study, genomes from 57 individuals belonging to six breeds showing different plumages were sequenced at ∼10X depth. Firstly, the allele frequency differences (AFD) of variants on the scaffold394 (NW_013185915.1) between grey and white goose breeds (A. anser) was calculated and a genomic region between 768,290-779,889 bp was detected to carry candidate variants associated with plumages, including one SNP (g. 775,151G > T, ∼18.6 kb upstream of EDNRB2) found to be fixed in white geese. This region was overlapped with the one detected by the haplotype-based sweep analysis, in which significant signals defined a candidate region of 736,610-820,622 bp on the same scaffold. Results from the transcriptomic data showed that expression levels of EDNRB2 and many other melanogenesis-related genes were significantly decreased among white geese compared to that in grey geese, especially at late embryonic stages (>E15). Modifications at transcriptional levels might result in abnormal melanocyte developments and thus the white plumages when they grow up. In addition, a frameshift mutation (C > -) in exon4 of MLANA gene on scaffold176 (NW_013185876.1) was suggested as the causal mutation for sex-linked dilution phenotype in graylag geese although this requires more demonstration experiments. Together with observed white plumages caused by EDNRB2 mutations in coding regions among swan geese and chicken, our study provided new examples to study the parallel evolution.

Analysis on the desert adaptability of indigenous sheep in the southern edge of Taklimakan Desert

The southern margin of the Taklimakan Desert is characterized by low rainfall, heavy sandstorms, sparse vegetation and harsh ecological environment. The indigenous sheep in this area are rich in resources, with the advantages of perennial estrus and good resistance to stress in most sheep. Exploring the molecular markers of livestock adaptability in this environment will provide the molecular basis for breeding research to cope with extreme future changes in the desert environment. In this study, we analyzed the population genetic structure and linkage imbalance of five sheep breeds with three different agricultural geographic characteristics using four complementary genomic selection signals: fixation index (FST), cross-population extended haplotype homozygosity (xp-EHH), Rsb (extended haplotype homozygosity between-populations) and iHS (integrated haplotype homozygosity score). We used Illumina Ovine SNP 50K Genotyping BeadChip Array, and gene annotation and enrichment analysis were performed on selected regions of the obtained genome. The ovary of Qira Black sheep (Follicular phase, Luteal phase, 30th day of pregnancy, 45th day of pregnancy) was collected, and the differentially expressed genes were screened by transcriptomic sequencing. Genome-wide selective sweep results and transcriptome data were combined for association analysis to obtain candidate genes associated with perennial estrus and stable reproduction. In order to verify the significance of the results, 15 resulting genes were randomly selected for fluorescence quantitative analysis. The results showed that Dolang sheep and Qira Black sheep evolved from Kazak sheep. Linkage disequilibrium analysis showed that the decay rate of sheep breeds in the Taklimakan Desert was higher than that in Yili grassland. The signals of FST, xp-EHH, Rsb and iHS detected 526, 332, 308 and 408 genes, respectively, under the threshold of 1% and 17 overlapping genes under the threshold of 5%. A total of 29 genes were detected in association analysis of whole-genome and transcriptome data. This study reveals the genetic mechanism of perennial estrus and environmental adaptability of indigenous sheep breeds in the Taklimakan Desert. It provides a theoretical basis for the conservation and exploitation of genetic resources of indigenous sheep breeds in extreme desert environment. This provides a new perspective for the quick adaptation of sheep and other mammals to extreme environments and future climate changes.

Transcriptome study digs out BMP2 involved in adipogenesis in sheep tails

Background

Hu sheep and Tibetan sheep in China are characterized by fat tails and thin tails, respectively. Several transcriptomes have been conducted in different sheep breeds to identify the differentially expressed genes (DEGs) underlying this trait. However, these studies identified different DEGs in different sheep breeds.

Results

Hence, RNA sequencing was performed on Hu sheep and Tibetan sheep. We obtained a total of 45.57 and 43.82 million sequencing reads, respectively. Two libraries mapped reads from 36.93 and 38.55 million reads after alignment to the reference sequences. 2108 DEGs were identified, including 1247 downregulated and 861 upregulated DEGs. GO and KEGG analyses of all DEGs demonstrated that pathways were enriched in the regulation of lipolysis in adipocytes and terms related to the chemokine signalling pathway, lysosomes, and glycosaminoglycan degradation. Eight genes were selected for validation by RT–qPCR. In addition, the transfection of BMP2 overexpression into preadipocytes resulted in increased PPAR-γ expression and expression. BMP2 potentially induces adipogenesis through LOX in preadipocytes. The number of lipid drops in BMP2 overexpression detected by oil red O staining was also greater than that in the negative control.

Conclusion

In summary, these results showed that significant genes (BMP2, HOXA11, PPP1CC and LPIN1) are involved in the regulation of adipogenesis metabolism and suggested novel insights into metabolic molecules in sheep fat tails.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08657-8.

Expression features of the ovine FTO gene and association between FTO polymorphism and tail fat deposition related-traits in Hu sheep

Fat mass and obesity associated (FTO) gene is a famous dominant predictor of obesity, and plays pivotal roles in the regulating fatty acid transport and fat metabolism. In the current study, the quantitative real-time PCR (qRT-PCR), DNA-pooled sequencing and KAspar assay were performed to detect the expression features of FTO and the polymorphisms of FTO associated with the tail fat weight related-traits of Hu sheep. The results indicated that the expression of FTO gene is widely expressed in the tissues tested, and the expression level of FTO in tail fat tissue was evidently higher compared with that in the other tissues. In addition, FTO showed the highest expression level in tail fat tissue at three months. The expression of FTO mRNA was lower in the large-tail fat group compared with that in the small-tail fat group in 6 months old. Subsequently, the polymorphism loci g. 23704451C > A detected in the FTO gene was confirmed to be significantly related to the tail length and the weight of tail fat. These results suggested that the polymorphism might be regarded as novel molecular marker for the breeding of small tail sheep.

Genetic polymorphisms within the ETAA1 gene associated with growth traits in Chinese sheep breeds

Ewing tumor-associated antigen 1 (ETAA1) is an important candidate gene for fat deposition in sheep. This study aimed to investigate the indel variations in the ETAA1 gene and their associations with growth traits in the 1619 sheep. The polymorphism information content of this indel ranged from 0.308 to 0.375, with medium genetic diversity (0.25 ≤ polymorphism information content ≤ 0.5). The correlation analysis showed that an 8-bp insertion within the ETAA1 gene was significantly associated with growth traits in Luxi Blackhead sheep (LXBH), Lanzhou fat-tailed sheep, Hu sheep, Tong sheep, and Tan sheep (p < 0.05). Furthermore, the ETAA1 gene was significantly associated with several growth traits (p < 0.01), such as chest width and paunch girth of LXBH, Tong, and Tan rams. It was significantly related to the body morphometric traits of LXBH, Lanzhou fat-tailed sheep, Hu, Tong, and Tan ewes. In conclusion, the detected 8-bp indel within the ETAA1 gene was confirmed in sheep, significantly affecting the growth traits, and might be a potential DNA marker for the selection of high-quality individuals in marker-assisted selection for sheep breeding.

Hitchhiking Mapping of Candidate Regions Associated with Fat Deposition in Iranian Thin and Fat Tail Sheep Breeds Suggests New Insights into Molecular Aspects of Fat Tail Selection

Simple Summary

Fatness-related traits are economically very important in sheep production and are associated with serious diseases in humans. Using a denser set of SNP markers and a variety of statistical approaches, our results were able to refine the regions associated with fat deposition and to suggest new insights into molecular aspects of fat tail selection. These results may provide a strong foundation for studying the regulation of fat deposition in sheep and do offer hope that the causal mutations and the mode of inheritance of this trait will soon be discovered by further investigation.

Abstract

The fat tail is a phenotype that divides indigenous Iranian sheep genetic resources into two major groups. The objective of the present study is to refine the map location of candidate regions associated with fat deposition, obtained via two separate whole genome scans contrasting thin and fat tail breeds, and to determine the nature of the selection occurring in these regions using a hitchhiking approach. Zel (thin tail) and Lori-Bakhtiari (fat tail) breed samples that had previously been run on the Illumina Ovine 50 k BeadChip, were genotyped with a denser set of SNPs in the three candidate regions using a Sequenom Mass ARRAY platform. Statistical tests were then performed using different and complementary methods based on either site frequency (F_ST and Median homozygosity) or haplotype (iHS and XP-EHH). The results from candidate regions on chromosome 5 and X revealed clear evidence of selection with the derived haplotypes that was consistent with selection to near fixation for the haplotypes affecting fat tail size in the fat tail breed. An analysis of the candidate region on chromosome 7 indicated that selection differentiated the beneficial alleles between breeds and homozygosity has increased in the thin tail breed which also had the ancestral haplotype. These results enabled us to confirm the signature of selection in these regions and refine the critical intervals from 113 kb, 201 kb, and 2831 kb to 28 kb, 142 kb, and 1006 kb on chromosome 5, 7, and X respectively. These regions contain several genes associated with fat metabolism or developmental processes consisting of TCF7 and PPP2CA (OAR5), PTGDR and NID2 (OAR7), AR, EBP, CACNA1F, HSD17B10,SLC35A2, BMP15, WDR13, and RBM3 (OAR X), and each of which could potentially be the actual target of selection. The study of core haplotypes alleles in our regions of interest also supported the hypothesis that the first domesticated sheep were thin tailed, and that fat tail animals were developed later. Overall, our results provide a comprehensive assessment of how and where selection has affected the patterns of variation in candidate regions associated with fat deposition in thin and fat tail sheep breeds.

Genome-wide identification of copy number variation and association with fat deposition in thin and fat-tailed sheep breeds

Copy number variants (CNVs) are a type of genetic polymorphism which contribute to phenotypic variation in several species, including livestock. In this study, we used genomic data of 192 animals from 3 Iranian sheep breeds including 96 Baluchi sheep and 47 Lori-Bakhtiari sheep as fat-tailed breeds and 47 Zel sheep as thin-tailed sheep breed genotyped with Illumina OvineSNP50K Beadchip arrays. Also, for association test, 70 samples of Valle del Belice sheep were added to the association test as thin-tailed sheep breed. PennCNV and CNVRuler software were, respectively, used to study the copy number variation and genomic association analyses. We detected 573 and 242 CNVs in the fat and thin tailed breeds, respectively. In terms of CNV regions (CNVRs), these represented 328 and 187 CNVRs that were within or overlapping with 790 known Ovine genes. The CNVRs covered approximately 73.85 Mb of the sheep genome with average length 146.88 kb, and corresponded to 2.6% of the autosomal genome sequence. Five CNVRs were randomly chosen for validation, of which 4 were experimentally confirmed using Real time qPCR. Functional enrichment analysis showed that genes harbouring CNVs in thin-tailed sheep were involved in the adaptive immune response, regulation of reactive oxygen species biosynthetic process and response to starvation. In fat-tailed breeds these genes were involved in cellular protein modification process, regulation of heart rate, intestinal absorption, olfactory receptor activity and ATP binding. Association test identified one copy gained CNVR on chromosomes 6 harbouring two protein-coding genes HGFAC and LRPAP1. Our findings provide information about genomic structural changes and their association to the interested traits including fat deposition and environmental compatibility in sheep.

Oar-miR-432 Regulates Fat Differentiation and Promotes the Expression of BMP2 in Ovine Preadipocytes

The fat tail is a unique characteristic of sheep that represents energy reserves and is a complex adaptative mechanism of fat-tailed sheep to environmental stress. MicroRNA plays a significant role as regulators at the posttranscriptional level, but no studies have explained the molecular mechanisms of miRNA which regulate fat deposition in sheep tails. In this study, mRNA and miRNA analysis examined tail fat tissue from three Hu fat-tailed and three Tibetan thin-tailed sheep. After aligning to the reference sequences, 2,108 differentially expressed genes and 105 differential expression miRNAs were identified, including 1,247 up- and 861 downregulated genes and 43 up- and 62 downregulated miRNAs. Among these differentially expressed miRNAs, oar-miR-432 was one of the most downregulated miRNAs between Hu sheep and Tibetan sheep, and 712 genes were predicted to be targeted by oar-miR-432, 80 of which overlapped with DEGs. The Gene Ontology analysis on these genes showed that BMP2, LEP, GRK5, BMP7, and RORC were enriched in fat cell differentiation terms. The genes for BMP2 targeted by oar-miR-432 were examined using dual-luciferase assay. The oar-miR-432 mimic transfected into preadipocytes resulted in increased expression of BMP2. The marker gene PPAR-γ of fat differentiation had a lower expression than the negative control on days 0, 2, and 4 after induced differentiation. The decrease in the number of lipids in the oar-miR-432 mimic group detected by oil red O stain was also less than that in the negative control. This is the first study to reveal the fat mechanisms by which oar-miR-432 inhibits fat differentiation and promotes the expression of BMP2 in sheep tails.

Transcriptome reveals key microRNAs involved in fat deposition between different tail sheep breeds

MicroRNA (miRNA) is a kind of noncoding RNA whose function involved in various biological processes in neuronal maturation and adipocyte cells, such as differentiation, proliferation, development, apoptosis, and metabolism. Herein, miRNA-Seq was used to identify miRNAs in the tail fat tissue of Hu sheep (short-fat-tailed) and Tibetan sheep (short-thin-tailed). In this study, 155 differentially expression miRNAs (DE miRNAs) were identified, including 78 up-regulated and 77 down-regulated. Among these DE miRNAs, 17 miRNAs were reported and related with lipid metabolism. MiRanda and RNAhybrid software were used to predict the target genes of DE miRNAs, obtaining the number of targeting relationships is 38553. Target genes were enriched by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). 742 terms and 302 single pathways are enriched, including lipid metabolic process, response to lipid, cellular lipid catabolic process, lipid catabolic process, cellular lipid metabolic process, inositol lipid-mediated signaling, calcium channel activity, PI3K-Akt signaling pathway, MAPK signaling pathway, ECM-receptor interaction, AMPK signaling pathway, Wnt signaling pathway and TGF-beta signaling pathway. Notably, miR-379-5p was associated with tail fat deposition of sheep. Dual-Luciferase reporter assays showed miR-379-5p and HOXC9 had targeted relationship. The result of RT-qPCR showed that the expression trend of miR-379-5p and HOXC9 was opposite. miR-379-5p was down-regulated and highly expressed in tail adipose tissue of Tibetan sheep. HOXC9 was highly expressed in adipose tissue of Hu sheep. These results could provide a meaningful theoretical basis for studying the molecular mechanisms of sheep tail adipogenesis.

Identification of Copy Number Variations and Genetic Diversity in Italian Insular Sheep Breeds

Copy number variants (CNVs) are one of the major contributors to genetic diversity and phenotypic variation in livestock. The aim of this work is to identify CNVs and perform, for the first time, a CNV-based population genetics analysis with five Italian sheep breeds (Barbaresca, Comisana, Pinzirita, Sarda, and Valle del Belìce). We identified 10,207 CNVs with an average length of 1.81 Mb. The breeds showed similar mean numbers of CNVs, ranging from 20 (Sarda) to 27 (Comisana). A total of 365 CNV regions (CNVRs) were determined. The length of the CNVRs varied among breeds from 2.4 Mb to 124.1 Mb. The highest number of shared CNVRs was between Comisana and Pinzirita, and only one CNVR was shared among all breeds. Our results indicated that segregating CNVs expresses a certain degree of diversity across all breeds. Despite the low/moderate genetic differentiation among breeds, the different approaches used to disclose the genetic relationship showed that the five breeds tend to cluster in distinct groups, similar to the previous studies based on single-nucleotide polymorphism markers. Gene enrichment was described for the 37 CNVRs selected, considering the top 10%. Out of 181 total genes, 67 were uncharacterized loci. Gene Ontology analysis showed that several of these genes are involved in lipid metabolism, immune response, and the olfactory pathway. Our results corroborated previous studies and showed that CNVs represent valuable molecular resources for providing useful information for separating the population and could be further used to explore the function and evolutionary aspect of sheep genome.

Unravelling the effect of environment on the genome of Sarda breed ewes using Runs of Homozygosity

Natural adaptation and artificial selection have shaped the genome of modern livestock breeds. Among SNP-based metrics that are used to detect signatures of selection at genome-wide level, runs of homozygosity (ROH) are getting increasing popularity. In this paper, ROH distribution and features of a sample of 823 Sarda breed ewes farmed at different levels of altitude are analysed to investigate the effect of the environment on the patterns of homozygosity. A total of 46,829 (33,087 unique) ROH were detected. OAR2 exhibited the largest average number of ROH per animal. The most frequent ROH (OAR27, 38.9-44.2 Mb) was shared by 327. ROH length was statistically affected (p < 0.001) by both the altitude and temperature of the place where the flock was located. The highest probability of a SNP falling in a ROH was observed for hill ewes, whereas the smallest one for mountain. A total of 457 SNP exceeded the 99th percentile of the ROH count per SNP distribution and were considered significant. These markers mapped in eight chromosomes and they clustered into 17 ROH islands, where 80 candidate genes were mapped. Results of this study highlighted differences in the ROH distribution and features among sheep farmed in flocks located at different levels of altitude, confirming the role of environmental adaptability in shaping the genome of this breed.

Genome-Wide Selective Signatures Reveal Candidate Genes Associated with Hair Follicle Development and Wool Shedding in Sheep

Hair follicle development and wool shedding in sheep are poorly understood. This study investigated the population structures and genetic differences between sheep with different wool types to identify candidate genes related to these traits. We used Illumina ovine SNP 50K chip genotyping data of 795 sheep populations comprising 27 breeds with two wool types, measuring the population differentiation index (Fst), nucleotide diversity (θπ ratio), and extended haplotype homozygosity among populations (XP-EHH) to detect the selective signatures of hair sheep and fine-wool sheep. The top 5% of the Fst and θπ ratio values, and values of XP-EHH < −2 were considered strongly selected SNP sites. Annotation showed that the PRX, SOX18, TGM3, and TCF3 genes related to hair follicle development and wool shedding were strongly selected. Our results indicated that these methods identified important genes related to hair follicle formation, epidermal differentiation, and hair follicle stem cell development, and provide a meaningful reference for further study on the molecular mechanisms of economically important traits in sheep.

Whole-genome sequence analysis unveils different origins of European and Asiatic mouflon and domestication-related genes in sheep

The domestication and subsequent development of sheep are crucial events in the history of human civilization and the agricultural revolution. However, the impact of interspecific introgression on the genomic regions under domestication and subsequent selection remains unclear. Here, we analyze the whole genomes of domestic sheep and their wild relative species. We found introgression from wild sheep such as the snow sheep and its American relatives (bighorn and thinhorn sheep) into urial, Asiatic and European mouflons. We observed independent events of adaptive introgression from wild sheep into the Asiatic and European mouflons, as well as shared introgressed regions from both snow sheep and argali into Asiatic mouflon before or during the domestication process. We revealed European mouflons might arise through hybridization events between a now extinct sheep in Europe and feral domesticated sheep around 6000-5000 years BP. We also unveiled later introgressions from wild sheep to their sympatric domestic sheep after domestication. Several of the introgression events contain loci with candidate domestication genes (e.g., PAPPA2, NR6A1, SH3GL3, RFX3 and CAMK4), associated with morphological, immune, reproduction or production traits (wool/meat/milk). We also detected introgression events that introduced genes related to nervous response (NEURL1), neurogenesis (PRUNE2), hearing ability (USH2A), and placental viability (PAG11 and PAG3) into domestic sheep and their ancestral wild species from other wild species.

Integrative analysis of Iso-Seq and RNA-seq data reveals transcriptome complexity and differentially expressed transcripts in sheep tail fat

Background

Nowadays, both customers and producers prefer thin-tailed fat sheep. To effectively breed for this phenotype, it is important to identify candidate genes and uncover the genetic mechanism related to tail fat deposition in sheep. Accumulating evidence suggesting that post-transcriptional modification events of precursor-messenger RNA (pre-mRNA), including alternative splicing (AS) and alternative polyadenylation (APA), may regulate tail fat deposition in sheep. Differentially expressed transcripts (DETs) analysis is a way to identify candidate genes related to tail fat deposition. However, due to the technological limitation, post-transcriptional modification events in the tail fat of sheep and DETs between thin-tailed and fat-tailed sheep remains unclear.

Methods

In the present study, we applied pooled PacBio isoform sequencing (Iso-Seq) to generate transcriptomic data of tail fat tissue from six sheep (three thin-tailed sheep and three fat-tailed sheep). By comparing with reference genome, potential gene loci and novel transcripts were identified. Post-transcriptional modification events, including AS and APA, and lncRNA in sheep tail fat were uncovered using pooled Iso-Seq data. Combining Iso-Seq data with six RNA-sequencing (RNA-Seq) data, DETs between thin- and fat-tailed sheep were identified. Protein protein interaction (PPI) network, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were implemented to investigate the potential functions of DETs.

Results

In the present study, we revealed the transcriptomic complexity of the tail fat of sheep, result in 9,001 potential novel gene loci, 17,834 AS events, 5,791 APA events, and 3,764 lncRNAs. Combining Iso-Seq data with RNA-Seq data, we identified hundreds of DETs between thin- and fat-tailed sheep. Among them, 21 differentially expressed lncRNAs, such as ENSOART00020036299, ENSOART00020033641, ENSOART00020024562, ENSOART00020003848 and 9.53.1 may regulate tail fat deposition. Many novel transcripts were identified as DETs, including 15.527.13 (DGAT2), 13.624.23 (ACSS2), 11.689.28 (ACLY), 11.689.18 (ACLY), 11.689.14 (ACLY), 11.660.12 (ACLY), 22.289.6 (SCD), 22.289.3 (SCD) and 22.289.14 (SCD). Most of the identified DETs have been enriched in GO and KEGG pathways related to extracellular matrix (ECM). Our result revealed the transcriptome complexity and identified many candidate transcripts in tail fat, which could enhance the understanding of molecular mechanisms behind tail fat deposition.

Local adaptations of Mediterranean sheep and goats through an integrative approach

Small ruminants are suited to a wide variety of habitats and thus represent promising study models for identifying genes underlying adaptations. Here, we considered local Mediterranean breeds of goats (n = 17) and sheep (n = 25) from Italy, France and Spain. Based on historical archives, we selected the breeds potentially most linked to a territory and defined their original cradle (i.e., the geographical area in which the breed has emerged), including transhumant pastoral areas. We then used the programs PCAdapt and LFMM to identify signatures of artificial and environmental selection. Considering cradles instead of current GPS coordinates resulted in a greater number of signatures identified by the LFMM analysis. The results, combined with a systematic literature review, revealed a set of genes with potentially key adaptive roles in relation to the gradient of aridity and altitude. Some of these genes have been previously implicated in lipid metabolism (SUCLG2, BMP2), hypoxia stress/lung function (BMPR2), seasonal patterns (SOX2, DPH6) or neuronal function (TRPC4, TRPC6). Selection signatures involving the PCDH9 and KLH1 genes, as well as NBEA/NBEAL1, were identified in both species and thus could play an important adaptive role.

Trends towards revealing the genetic architecture of sheep tail patterning: Promising genes and investigatory pathways

Different sheep breeds have evolved after initial domestication, generating various tail phenotypic patterns. The phenotypic diversity of sheep tail patterns offers ideal materials for comparative analysis of its genetic basis. Evolutionary biologists, animal geneticists, breeders, and producers have been curious to clearly understand the underlying genetics behind phenotypic differences in sheep tails. Understanding the causal gene(s) and mutation(s) underlying these differences will help probe an evolutionary riddle, improve animal production performance, promote animal welfare, and provide lessons that help comprehend human diseases related to fat deposition (i.e., obesity). Historically, fat tails have served as an adaptive response to aridification and climate change. However, the fat tail is currently associated with compromised mating and animal locomotion, fat distribution in the animal body, increased raising costs, reduced consumer preference, and other animal welfare issues such as tail docking. The developing genomic approaches provide unprecedented opportunities to determine causal variants underlying phenotypic differences among populations. In the last decade, researchers have performed several genomic investigations to assess the genomic causality underlying phenotypic variations in sheep tails. Various genes have been suggested with the prominence of several potentially significant causatives, including the BMP2 and PDGFD genes associated with the fat tail phenotype and the TBXT gene linked with the caudal vertebrae number and tail length. Although the potential genes related to sheep tail characteristics have been revealed, the causal variant(s) and mutation(s) of these high-ranking candidate genes are still elusive and need further investigation. The review discusses the potential genes, sheds light on a knowledge gap, and provides possible investigative approaches that could help determine the specific genomic causatives of sheep tail patterns. Besides, characterizing and revealing the genetic determinism of sheep tails will help solve issues compromising sheep breeding and welfare in the future.

Life in Deserts: The Genetic Basis of Mammalian Desert Adaptation

Deserts are among the harshest environments on Earth. The multiple ages of different deserts and their global distribution provide a unique opportunity to study repeated adaptation at different timescales. Here, we summarize recent genomic research on the genetic mechanisms underlying desert adaptations in mammals. Several studies on different desert mammals show large overlap in functional classes of genes and pathways, consistent with the complexity and variety of phenotypes associated with desert adaptation to water and food scarcity and extreme temperatures. However, studies of desert adaptation are also challenged by a lack of accurate genotype-phenotype-environment maps. We encourage development of systems that facilitate functional analyses, but also acknowledge the need for more studies on a wider variety of desert mammals.

Genome-wide analyses reveal population structure and identify candidate genes associated with tail fatness in local sheep from a semi-arid area

Under a climate change perspective, the genetic make-up of local livestock breeds showing adaptive traits should be explored and preserved as a priority. We used genotype data from the ovine 50 k Illumina BeadChip for assessing breed autozygosity based on runs of homozygosity (ROH) and fine-scale genetic structure and for detecting genomic regions under selection in 63 Tunisian sheep samples. The average genomic inbreeding coefficients based on ROH were estimated at 0.017, 0.021, and 0.024 for Barbarine (BAR, n = 26), Noire de Thibar (NDT, n = 23), and Queue fine de l'Ouest (QFO, n = 14) breeds, respectively. The genomic relationships among individuals based on identity by state (IBS) distance matrix highlighted a recent introgression of QFO into the BAR and a genetic differentiation of NDT samples, possibly explained by past introgression of European gene pools. Genome-wide scan for ROH across breeds and within the BAR sample set identified an outstanding signal on chromosome 13 (46.58-49.61 Mbp). These results were confirmed using F_ST index, differentiating fat vs. thin-tailed individuals. Candidate genes under selection pressure (CDS2, PROKR1, and BMP2) were associated to lipid storage and probably preferentially selected in fat-tailed BAR animals. Our findings suggest paying more attention to preserve the genetic integrity and adaptive alleles of local sheep breeds.

Genomic scans for selective sweeps through haplotype homozygosity and allelic fixation in 14 indigenous sheep breeds from Middle East and South Asia

The performance and productivity of livestock have consistently improved by natural and artificial selection over the centuries. Both these selections are expected to leave patterns on the genome and lead to changes in allele frequencies, but natural selection has played the major role among indigenous populations. Detecting selective sweeps in livestock may assist in understanding the processes involved in domestication, genome evolution and discovery of genomic regions associated with economically important traits. We investigated population genetic diversity and selection signals in this study using SNP genotype data of 14 indigenous sheep breeds from Middle East and South Asia, including six breeds from Iran, namely Iranian Balochi, Afshari, Moghani, Qezel, Zel, and Lori-Bakhtiari, three breeds from Afghanistan, namely Afghan Balochi, Arabi, and Gadik, three breeds from India, namely Indian Garole, Changthangi, and Deccani, and two breeds from Bangladesh, namely Bangladeshi Garole and Bangladesh East. The SNP genotype data were generated by the Illumina OvineSNP50 Genotyping BeadChip array. To detect genetic diversity and population structure, we used principal component analysis (PCA), admixture, phylogenetic analyses, and Runs of homozygosity. We applied four complementary statistical tests, FST (fixation index), xp-EHH (cross-population extended haplotype homozygosity), Rsb (extended haplotype homozygosity between-populations), and FLK (the extension of the Lewontin and Krakauer) to detect selective sweeps. Our results not only confirm the previous studies but also provide a suite of novel candidate genes involved in different traits in sheep. On average, FST, xp-EHH, Rsb, and FLK detected 128, 207, 222, and 252 genomic regions as candidates for selective sweeps, respectively. Furthermore, nine overlapping candidate genes were detected by these four tests, especially TNIK, DOCK1, USH2A, and TYW1B which associate with resistance to diseases and climate adaptation. Knowledge of candidate genomic regions in sheep populations may facilitate the identification and potential exploitation of the underlying genes in sheep breeding.

Quantitative proteomic analysis identified differentially expressed proteins with tail/rump fat deposition in Chinese thin- and fat-tailed lambs

Tail adipose as one of the important functional tissues can enhance hazardous environments tolerance for sheep. The objective of this study was to gain insight into the underlying development mechanisms of this trait. A quantitative analysis of protein abundance in ovine tail/rump adipose tissue was performed between Chinese local fat- (Kazakh, Hu and Lanzhou) and thin-tailed (Alpine Merino, Tibetan) sheep in the present study by using lable-free approach. Results showed that 3400 proteins were identified in the five breeds, and 804 were differentially expressed proteins, including 638 up regulated proteins and 83 down regulated proteins in the tail adipose tissues between fat- and thin-tailed sheep, and 8 clusters were distinguished for all the DEPs’ expression patterns. The differentially expressed proteins are mainly associated with metabolism pathways and peroxisome proliferator activated receptor signaling pathway. Furthermore, the proteomics results were validated by quantitative real-time PCR and Western Blot. Our research has also suggested that the up-regulated proteins ACSL1, HSD17β4, FABP4 in the tail adipose tissue might contribute to tail fat deposition by facilitating the proliferation of adipocytes and fat accumulation in tail/rump of sheep. Particularly, FABP4 highly expressed in the fat-tail will play an important role for tail fat deposition. Our study might provide a novel view to understanding fat accumulation in special parts of the body in sheep and other animals.

Genomic analysis of worldwide sheep breeds reveals PDGFD as a major target of fat-tail selection in sheep

Background

Fat tail is a unique trait in sheep acquired during domestication. Several genomic analyses have been conducted in sheep breeds from limited geographic origins to identify the genetic factors underlying this trait. Nevertheless, these studies obtained different candidates. The results of these regional studies were easily biased by the breed structures.

Results

To minimize the bias and distinguish the true candidates, we used an extended data set of 968 sheep representing 18 fat-tailed breeds and 14 thin-tailed breeds from around the world, and integrated two statistical tests to detect selection signatures, including Genetic Fixation Index (F_ST) and difference of derived allele frequency (ΔDAF). The results showed that platelet derived growth factor D (PDGFD) exhibited the highest genetic differentiation between fat- and thin-tailed sheep breeds. Analysis of sequence variation identified that a 6.8-kb region within the first intron of PDGFD is likely the target of positive selection and contains regulatory mutation(s) in fat-tailed sheep. Histological and gene expression analyses demonstrated that PDGFD expression is associated with maturation and hemostasis of adipocytes. Further retrospective analysis of public transcriptomic datasets revealed that PDGFD expression is down-regulated during adipogenesis in both human and mouse, and is higher in fat tissues of obese individuals than that in lean individuals.

Conclusions

These results reveal that PDGFD is the predominant factor for the fat tail phenotype in sheep by contributing to adiopogenesis and maintaining the hemostasis of mature adipocytes. This study provides insights into the selection of fat-tailed sheep and has important application to animal breeding, as well as obesity-related human diseases.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07210-9.

Genetic Signatures of Selection for Cashmere Traits in Chinese Goats

Simple Summary

Cashmere goats are a unique husbandry resource in China. These goats are well known for producing the highest cashmere yield and best fiber quality in the world. Although cashmere is highly valued and also known as “fiber gem” and “soft gold”, few studies have examined the genetic basis of cashmere traits in cashmere goats. Here, we identified selection signals by comparing Fst and XP-EHH (the cross population extend haplotype homozygosity test) of a non-cashmere breed (Huanghuai goat) with those of two cashmere breeds (Inner Mongolia and Liaoning cashmere goats). Two genes (WNT10A and CSN3) were potentially associated with cashmere traits. This information may be valuable for studying the genetic uniqueness of cashmere goats and elucidating the mechanisms underlying cashmere traits in cashmere goats.

Abstract

Inner Mongolia and Liaoning cashmere goats in China are well-known for their cashmere quality and yield. Thus, they are great models for identifying genomic regions associated with cashmere traits. Herein, 53 Inner Mongolia cashmere goats, Liaoning cashmere goats and Huanghuai goats were genotyped, and 53,347 single-nucleotide polymorphisms (SNPs) were produced using the Illumina Caprine 50K SNP chip. Additionally, we identified some positively selected SNPs by analyzing Fst and XP-EHH. The top 5% of SNPs had selection signatures. After gene annotation, 222 and 173 candidate genes were identified in Inner Mongolia and Liaoning cashmere goats, respectively. Several genes were related to hair follicle development, such as TRPS1, WDR74, LRRC14, SPTLC3, IGF1R, PADI2, FOXP1, WNT10A and CSN3. Gene enrichment analysis of these cashmere trait-associated genes related 67 enriched signaling pathways that mainly participate in hair follicle development and stem cell pluripotency regulation. Furthermore, we identified 20 overlapping genes that were selected in both cashmere goat breeds. Among these overlapping genes, WNT10A and CSN3, which are associated with hair follicle development, are potentially involved in cashmere production. These findings may improve molecular breeding of cashmere goats in the future.

Genome-wide insights of Ethiopian indigenous sheep populations reveal the population structure related to tail morphology and phylogeography

BACKGROUND

Ethiopian sheep living in different climatic zones and having contrasting morphologies are a most promising subject of molecular-genetic research. Elucidating their genetic diversity and genetic structure is critical for designing appropriate breeding and conservation strategies.

OBJECTIVE

The study was aimed to investigate genome-wide genetic diversity and population structure of eight Ethiopian sheep populations.

METHODS

A total of 115 blood samples were collected from four Ethiopian sheep populations that include Washera, Farta and Wollo (short fat-tailed) and Horro (long fat-tailed). DNA was extracted using Quick-DNA™ Miniprep plus kit. All DNA samples were genotyped using Ovine 50 K SNP BeadChip. To infer genetic relationships of Ethiopian sheep at national, continental and global levels, genotype data on four Ethiopian sheep (Adilo, Arsi-Bale, Menz and Black Head Somali) and sheep from east, north, and south Africa, Middle East and Asia were included in the study as reference.

RESULTS

Mean genetic diversity of Ethiopian sheep populations ranged from 0.352 ± 0.14 for Horro to 0.379 ± 0.14 for Arsi-Bale sheep. Population structure and principal component analyses of the eight Ethiopian indigenous sheep revealed four distinct genetic cluster groups according to their tail phenotype and geographical distribution. The short fat-tailed sheep did not represent one genetic cluster group. Ethiopian fat-rump sheep share a common genetic background with the Kenyan fat-tailed sheep.

CONCLUSION

The results of the present study revealed the principal component and population structure follows a clear pattern of tail morphology and phylogeography. There is clear signature of admixture among the study Ethiopian sheep populations.

Selection Signatures Analysis Reveals Genes Associated with High-Altitude Adaptation in Tibetan Goats from Nagqu, Tibet

Simple Summary

In the process of domestication, goats have undergone long-term artificial and natural selection, leading to differences among goat breeds and leaving different selection traces on the genome. However, the genetic components underlying high-altitude adaptation remain largely unknown. Here, we genotyped four goat breeds using the Illumina Caprine 50K single nucleotide polymorphism (SNP) Chip. One highland breed (Tibetan goat) compared with three lowland breeds (Huanghuai goat, Taihang goat and Xinjiang goat) to identify the molecular basis of high-altitude adaptation. So, we investigated selection signatures using the di statistic of four goat breeds and some genes in Tibetan goats related to high-altitude adaptation were identified. In addition, q-PCR validated the gene expression level in Tibetan goats and Huanghuai goats. This information may be valuable for the study of the genetic uniqueness of Tibetan goats and increased understanding of the hypoxic adaptation mechanism of Tibetan goats on the plateau.

Abstract

Tibetan goat is an ancient breed, which inhabits the adverse conditions of the plateaus in China. To investigate the role of selection in shaping its genomes, we genotyped Tibetan goats (Nagqu Prefecture, above 4500 m) and three lowland populations (Xinjiang goats, Taihang goats and Huanghuai goats). The result of PCA, neighbor-joining (N-J) tree and model-based clustering showed that the genetic structure between the Tibetan goat and the three lowland populations has significant difference. As demonstrated by the di statistic, we found that some genes were related to the high-altitude adaptation of Tibetan goats. Functional analysis revealed that these genes were enriched in the VEGF (vascular endothelial growth factor) signaling pathway and melanoma, suggesting that nine genes (FGF2, EGFR, AKT1, PTEN, MITF, ENPEP, SIRT6, KDR, and CDC42) might have important roles in the high-altitude adaptation of Nagqu Tibetan goats. We also found that the LEPR gene was under the strongest selection (di value = 16.70), and it could induce upregulation of the hypoxic ventilatory response. In addition, five genes (LEPR, LDB1, EGFR, NOX4 and FGF2) with high di values were analyzed using q-PCR. Among them, we found that LEPR, LDB1 and FGF2 exhibited higher expression in the lungs of the Tibetan goats; LEPR, EGFR and LDB1 exhibited higher expression in the hearts of the Huanghuai goat. Our results suggest that LEPR, LDB1, EGFR and FGF2 genes may be related to the high-altitude adaptation of the goats. These findings improve our understanding of the selection of the high-altitude adaptability of the Nagqu Tibetan goats and provide new theoretical knowledge for the conservation and utilization of germplasm resources.

Identification of markers associated with estimated breeding value and horn colour in Hungarian Grey cattle

OBJECTIVE

This study was conducted to estimate effect of single nucleotide polymorphisms (SNP) on the estimated breeding value of Hungarian Grey (HG) bulls and to find markers associated with horn colour.

METHODS

Genotypes 136 HG animals were determined on Geneseek high-density Bovine SNP 150K BeadChip. A multi-locus mixed-model was applied for statistical analyses.

RESULTS

Six SNPs were identified to be associated (-log10P>10) with green and white horn. These loci are located on chromosome 1, 3, 9, 18, and 25. Seven loci (on chromosome 1, 3, 6, 9, 10, 28) showed considerable association (-log10P>10) with the estimated breeding value.

CONCLUSION

Analysis provides markers for further research of horn colour and supplies markers to achieve more effective selection work regarding estimated breeding value of HG.

RNA-Seq based genetic variant discovery provides new insights into controlling fat deposition in the tail of sheep

Genetic basis of fat deposition in sheep tail have not been completely elucidated yet. Understanding the genetic mechanisms controlling fat-tail size can improve breeding strategies to modulate fat deposition. RNA sequencing has made it possible to discover genetic variants that may underlie various phenotypic differences. Hence, to identify genetic variants that are important for describing different fat-tail phenotypes in sheep, RNA sequencing was used for single nucleotide polymorphism (SNP) calling in two Iranian sheep breeds (Lori-Bakhtiari, fat-tailed; n = 4, vs Zel, thin-tailed; n = 4). Using a stringent pipeline, a total of 112,344 known SNPs were genotyped, of which 30,550 and 42,906 SNPs were shared by at least two Lori-Bakhtiari and Zel, respectively. Comparing these SNPs showed 2,774 (including 209 missense and 25 deleterious SNPs) and 10,470 (including 1,054 missense and 116 deleterious SNPs) breed-specific SNPs in Lori-Bakhtiari and Zel sheep, respectively. Potential breed-specific SNPs were detected by considering those located in QTL regions associated with fatness or reported as important candidates in previous similar studies. Of the breed-specific SNPs, 724 and 2,905 were located in the QTL regions. Functional enrichment analysis of the affected genes revealed several enriched gene ontologies and KEGG pathways related to fat metabolism. Based on the results, several affected genes were proposed to be strongly linked with fat deposition such as DGAT2, ACSL1, ACACA, ADIPOQ, ACLY, FASN, CPT2, SCD, ADCY6, PER3, CSF1R, SLC22A4, GFPT1, CDS2, BMP6, ACSS2, ELOVL6, HOXA10 and FABP4. Moreover, several SNPs were found in the candidate genes related to fatty acid oxidation introducing them as promising candidates responsible for lower fat content in tail of Zel. Our findings provided new insights into the genetic mechanisms of fat deposition in sheep, which can serve to designing appropriate breeding programs.

On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools

Background

In the Neolithic, domestic sheep migrated into Europe and subsequently spread in westerly and northwesterly directions. Reconstruction of these migrations and subsequent genetic events requires a more detailed characterization of the current phylogeographic differentiation.

Results

We collected 50 K single nucleotide polymorphism (SNP) profiles of Balkan sheep that are currently found near the major Neolithic point of entry into Europe, and combined these data with published genotypes from southwest-Asian, Mediterranean, central-European and north-European sheep and from Asian and European mouflons. We detected clines, ancestral components and admixture by using variants of common analysis tools: geography-informative supervised principal component analysis (PCA), breed-specific admixture analysis, across-breed \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$f_{4}$$\end{document}f4 profiles and phylogenetic analysis of regional pools of breeds. The regional Balkan sheep populations exhibit considerable genetic overlap, but are clearly distinct from the breeds in surrounding regions. The Asian mouflon did not influence the differentiation of the European domestic sheep and is only distantly related to present-day sheep, including those from Iran where the mouflons were sampled. We demonstrate the occurrence, from southeast to northwest Europe, of a continuously increasing ancestral component of up to 20% contributed by the European mouflon, which is assumed to descend from the original Neolithic domesticates. The overall patterns indicate that the Balkan region and Italy served as post-domestication migration hubs, from which wool sheep reached Spain and north Italy with subsequent migrations northwards. The documented dispersal of Tarentine wool sheep during the Roman period may have been part of this process. Our results also reproduce the documented 18th century admixture of Spanish Merino sheep into several central-European breeds.

Conclusions

Our results contribute to a better understanding of the events that have created the present diversity pattern, which is relevant for the management of the genetic resources represented by the European sheep population.

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.

Association Between BMP2 Functional Polymorphisms and Sheep Tail Type

Bone morphogenetic protein 2 (BMP2) is strongly selected in both fat-tailed and thin-tailed sheep and may be a candidate gene for sheep tail type selection. However, the mechanism of action of BMP2 in sheep tail fat deposition remains unclear. This study investigated genetic variation and haplotype combinations of the BMP2 gene in sheep with different tail types, aiming to reveal the molecular mechanism of BMP2 in sheep tail fat deposition. We detected a total of three single nucleotide polymorphisms (SNPs) (g.48401619 T > A, g.48401272 C > A, and g.48401136 C > T) among 533 sheep. The alleles and genotype frequencies of these SNPs were in Hardy-Weinberg equilibrium and showed significant correlations with tail length. Linkage disequilibrium existed between the g.48401272 C > A and g.48401136 C > T sites, where CACT was the predominant genotype. At the cellular level, the expression levels of peroxisome proliferator-activated receptor gamma (PPARγ) and lipoprotein lipase (LPL) were upregulated after BMP2 overexpression; there were significantly higher levels of PPARγ than controls at 0 d and 1 d, and of LPL than controls at 1 d and 7 d. These results indicate that the BMP2 gene may participate in sheep tail fat deposition and could be used for molecular-marker-assisted selection of sheep tail type.