Endophytic Streptomyces sp. NEAU-DD186 from Moss with Broad-Spectrum Antimicrobial Activity: Biocontrol Potential Against Soilborne Diseases and Bioactive Components.

Soilborne diseases cause significant economic losses in agricultural production around the world. They are difficult to control because a host plant is invaded by multiple pathogens, and chemical control often does not work well. In this study, we isolated and identified an endophytic Streptomyces sp. NEAU-DD186 from moss, which showed broad-spectrum antifungal activity against 17 soilborne phytopathogenic fungi, with Bipolaris sorokiniana being the most prominent. The strain also exhibited strong antibacterial activity against soilborne phytopathogenic bacteria Ralstonia solanacearum. To evaluate its biocontrol potential, the strain was prepared into biofertilizer by solid-state fermentation. Response surface methodology was employed to optimize the fermentation conditions for maximizing spore production and revealed that the 1:1 ratio of vermicompost to wheat bran, a temperature of 28°C, and 50% water content with an inoculation amount of 15% represented the optimal parameters. Pot experiments showed that the application of biofertilizer with a spore concentration of 108 CFU/g soil could effectively suppress the occurrence of tomato bacterial wilt caused by R. solanacearum and wheat root rot caused by B. sorokiniana, and the biocontrol efficacy was 81.2 and 72.2%, respectively. Chemical analysis of strain NEAU-DD186 extracts using nuclear magnetic resonance spectrometry and mass analysis indicated that 25-O-malonylguanidylfungin A and 23-O-malonylguanidylfungin A were the main active constituents, which showed high activity against R. solanacearum (EC50 of 2.46 and 2.58 µg ml-1) and B. sorokiniana (EC50 of 3.92 and 3.95 µg ml-1). In conclusion, this study demonstrates that Streptomyces sp. NEAU-DD186 can be developed as biofertilizer to control soilborne diseases.

Whole-Genome Resequencing of Worldwide Wild and Domestic Sheep Elucidates Genetic Diversity, Introgression, and Agronomically Important Loci.

Domestic sheep and their wild relatives harbor substantial genetic variants that can form the backbone of molecular breeding, but their genome landscapes remain understudied. Here, we present a comprehensive genome resource for wild ovine species, landraces and improved breeds of domestic sheep, comprising high-coverage (∼16.10×) whole genomes of 810 samples from 7 wild species and 158 diverse domestic populations. We detected, in total, ∼121.2 million single nucleotide polymorphisms, ∼61 million of which are novel. Some display significant (P < 0.001) differences in frequency between wild and domestic species, or are private to continent-wide or individual sheep populations. Retained or introgressed wild gene variants in domestic populations have contributed to local adaptation, such as the variation in the HBB associated with plateau adaptation. We identified novel and previously reported targets of selection on morphological and agronomic traits such as stature, horn, tail configuration, and wool fineness. We explored the genetic basis of wool fineness and unveiled a novel mutation (chr25: T7,068,586C) in the 3'-UTR of IRF2BP2 as plausible causal variant for fleece fiber diameter. We reconstructed prehistorical migrations from the Near Eastern domestication center to South-and-Southeast Asia and found two main waves of migrations across the Eurasian Steppe and the Iranian Plateau in the Early and Late Bronze Ages. Our findings refine our understanding of genome variation as shaped by continental migrations, introgression, adaptation, and selection of sheep.

Mumia quercus sp. nov., isolated from the root of Quercus variabilis.

A novel endophytic actinomycete, designated strain NEAU-365T, was isolated from the root of Quercus variabilis collected from Nanjing, Jiangsu, PR China. Comparative 16S rRNA gene sequencing showed that strain NEAU-365T belonged to the genus Mumia but clearly differs from the currently recognized species Mumia zhuanghuii Z350T (99.31 %), Mumia xiangluensis NEAU-KD1T (98.82 %) and Mumia flava MUSC 201T (97.78 %). Phylogenetic tree analysis revealed that strain NEAU-365T clustered with the type strains of the genus Mumia. The genome size was 4.1 Mbp with a DNA G+C content of 71.2 mol%. Digital DNA-DNA hybridization and average nucleotide identity values between the genome sequence of strain NEAU-365T and those of M. zhuanghuii Z350T(27.5 and 84.0 %), M. xiangluensis NEAU-KD1T(23.4 and 80.9 %) and M. flava MUSC 201T(20.9 and 77.7 %) were below the recommended thresholds for species delineation. Cells were observed to be irregular cocci shaped. The cell wall contained ll-diaminopimelic acid and the whole-cell sugars were galactose and rhamnose. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid and three unidentified phospholipids. The predominant menaquinone was detected as MK-9(H4). The major fatty acids were C16 : 0, C18 : 0, C18 : 1 ω9c and 10-methyl C18 : 0. On the basis of genotypic and phenotypic differences from members of the genus Mumia, a novel species, Mumia quercus sp. nov. is proposed. The type strain is NEAU-365T (=CCTCC AA 2021033T=JCM 35005T).

Sphaerisporangium perillae sp. nov., isolated from the root of Perilla frutescens (Linn.) Britt.

A novel protease-producing actinomycete, designated strain NEAU-ZS1T, was isolated from the root of Perilla frutescens (Linn.) Britt collected from Jiamusi, Heilongjiang, PR China. Comparative 16S rRNA gene sequencing showed that strain NEAU-ZS1T belonged to the genus Sphaerisporangium and was most closely related to 'Sphaerisporangium corydalis' NEAU-YHS15T (99.2%) and Sphaerisporangium cinnabarinum JCM 3291T (99.0%). Phylogenetic tree analysis revealed that strain NEAU-ZS1T formed a monophyletic clade with 'S. corydalis' NEAU-YHS15T. The genome size was 9.3 Mbp with a DNA G+C content of 70.3 mol%. Digital DNA-DNA hybridization, average nucleotide identity and average amino acid identity values between the genome sequence of strain NEAU-ZS1T and those of 'S. corydalis' NEAU-YHS15T (28.6, 83.9 and 79.1 %) and S. cinnabarinum JCM 3291T (18.5, 70.6 and 50.2 %) were below the recommended thresholds for species delineation. The strain formed spherical spore vesicles produced on the aerial hyphae. The cell wall contained meso-diaminopimelic acid and the whole-cell sugars were glucose and madurose. The polar lipids consisted of diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylinositol, an unidentified phospholipid and an unidentified glycolipid. The menaquinones were MK-9(H4), MK-9(H6) and MK-9(H2). The major fatty acids were iso-C16 : 0, C16 : 1 ω5c, 10-methy C17 : 0 and C17 : 1 ω7c. On the basis of the results of a polyphasic taxonomic study, it is concluded that strain NEAU-ZS1T represents a novel species of the genus Sphaerisporangium, for which the name Sphaerisporangium perillae sp. nov. is proposed. The type strain is NEAU-ZS1T (=CCTCC AA 2021019T= JCM 35655T).

Historical Introgression from Wild Relatives Enhanced Climatic Adaptation and Resistance to Pneumonia in Sheep.

How animals, particularly livestock, adapt to various climates and environments over short evolutionary time is of fundamental biological interest. Further, understanding the genetic mechanisms of adaptation in indigenous livestock populations is important for designing appropriate breeding programs to cope with the impacts of changing climate. Here, we conducted a comprehensive genomic analysis of diversity, interspecies introgression, and climate-mediated selective signatures in a global sample of sheep and their wild relatives. By examining 600K and 50K genome-wide single nucleotide polymorphism data from 3,447 samples representing 111 domestic sheep populations and 403 samples from all their seven wild relatives (argali, Asiatic mouflon, European mouflon, urial, snow sheep, bighorn, and thinhorn sheep), coupled with 88 whole-genome sequences, we detected clear signals of common introgression from wild relatives into sympatric domestic populations, thereby increasing their genomic diversities. The introgressions provided beneficial genetic variants in native populations, which were significantly associated with local climatic adaptation. We observed common introgression signals of alleles in olfactory-related genes (e.g., ADCY3 and TRPV1) and the PADI gene family including in particular PADI2, which is associated with antibacterial innate immunity. Further analyses of whole-genome sequences showed that the introgressed alleles in a specific region of PADI2 (chr2: 248,302,667-248,306,614) correlate with resistance to pneumonia. We conclude that wild introgression enhanced climatic adaptation and resistance to pneumonia in sheep. This has enabled them to adapt to varying climatic and environmental conditions after domestication.

Expression profile analysis of microRNAs during hair follicle development in the sheep foetus.

MicroRNAs (miRNAs) regulate the development and growth cycle of hair follicles (HFs). The molecular mechanism by which miRNAs determine the development of HFs in the sheep foetus remains elusive. In this study, the expression profiles of miRNAs at 11 development periods (45, 55, 65, 75, 85, 95, 105, 115, 125, 135 and 145 d) in sheep foetus skin were analysed by high-throughput sequencing and bioinformatics analysis. A total of 72 conserved miRNAs, 44 novel miRNAs and 32 known miRNAs were significantly differentially expressed. qRT-PCR results for 18 miRNAs were consistent with the sequencing data. 85 d of foetal development was the starting point for secondary hair follicle (SF) development according to tissue morphology and cluster analysis. In SF development, the prolactin signalling pathway and platelet activation played important roles, and 10 miRNAs were potential candidate miRNAs in SF initiation.

Individual Treatment of Delayed Distal Biceps Tendon Rupture: Case Report and Literature Review.

INTRODUCTION: Complicated elbow injuries (elbow injuries with bone and soft tissue injury) with distal biceps tendon ruptures (DBTRs) are not uncommon. There are several treatment modalities in different situations of injuries. In this article, we reported 3 successful individual treatments of delayed DBTR with complicated elbow injuries. MATERIALS AND METHODS: Three cases of complicated elbow injuries treated between 2010 and 2016 were reviewed. The delayed DBTR cases were summarized and treated. Mayo Elbow Performance Score value, range of motion, and visual analog scale score were used to assess outcomes after a minimum follow-up of 12 months. RESULTS: All 3 patients were male, aged 47 to 54 years (mean, 49.6 years). Patients received surgical treatments. After a mean follow-up of 13.7 months, in cases 1 and 2, Mayo Elbow Performance Score values improved by 50% and 100%, elbow flexion-extension arc were 115 degrees and 110 degrees, pronation-supination arc were 130 degrees and 120 degrees. Arthrodesis case reported pain relief; visual analog scale score for pain was 0 to 1. No postoperative complications were observed, and all patients were satisfied with the results. CONCLUSIONS: Individual treatment is advised in DBTR with complicated elbow injuries. Secondary treatment of DBTR can achieve satisfactory results using individual strategies depending on patients' overall condition.

[Molecular cloning and tissue expression of the CCNG1 gene in sheep].

The CCNG1 gene encodes cyclin G1, which is an important cell cycle regulator and has been reported to be involved in reproductive biological processes, such as oocyte maturation and granule cell proliferation in mammals. But the study of CCNG1 in sheep has been rarely reported. To examine the effects of CCNG1 on estrous control and seasonal breeding in sheep, we first cloned and characterized the expression level of the sheep CCNG1 gene. Then by Real-time PCR, we detected and analyzed the expressions of CCNG1 gene at mRNA levels in the hypothalamus-pituitary-ovary (HPO) axis in different stages of an estrous cycle in Duo Lang sheep (non-seasonal breeding) and Merino sheep (seasonal breeding). The results showed that the open reading frame of the sheep CCNG1 gene is 885 bp in length and encodes 294 amino acids. Bioinformatic analysis indicated that the secondary structure of the sheep CCNG1 protein contained multiple phosphorylation sites and some Protein Kinase C phosphorylation sites. CCNG1 mRNA was identified in all tissues tested, with the levels in ovary and kidney higher than others. The expression profiles of CCNG1 in the HPO axis in different stages of an estrous cycle were similar in different sheep breeds: the expression levels of CCNG1 in the ovary, uterus, pineal gland and pituitary gland all peaked in the estrus phase. But there were significant differences for expression change extent of CCNG1 in ovaries in the oestrus and metestrus phase between different sheep breeds. The results suggested that CCNG1 probably participated in the regulation of estrous behavior and seasonal reproduction through controling the growth and development of follicles in sheep.

NADPH oxidase-2 is a key regulator of human dermal fibroblasts: a potential therapeutic strategy for the treatment of skin fibrosis.

The proliferation of human skin dermal fibroblasts (HDFs) is a critical step in skin fibrosis, and transforming growth factor-beta1 (TGF-ß1) exerts pro-oxidant and fibrogenic effects on HDFs. In addition, the oxidative stress system has been implicated in the pathogenesis of skin disease. However, the role of NADPH oxidase as a mediator of TGF-ß1-induced effects in HDFs remains unknown. Thus, our aim was to investigate the role of NADPH in human skin dermal fibroblasts. Primary fibroblasts were cultured and pretreated with various stimulants. Real-time Q-PCR and Western blotting analyses were used for mRNA and protein detection. In addition, siRNA technology was applied for gene knock-down analysis. Hydrogen peroxide production and 2',7'-dichlorofluorescein diacetate (DCFDA) measurement assay were performed. Here, our findings demonstrated that HDFs express key components of non-phagocytic NADPH oxidase mRNA. TGF-ß1 induced NOX2 and reactive oxygen species formation via NADPH oxidase activity. In contrast, NOX3 was barely detectable, and other NOXs did not display significant changes. In addition, TGF-ß1 phosphorylated MAPKs and increased activator protein-1 (AP-1) in a redox-sensitive manner, and NOX2 suppression inhibited baseline and TGF-ß1-mediated stimulation of Smad2 phosphorylation. Moreover, TGF-ß1 stimulated cell proliferation, migration, collagen I and fibronectin expression, and bFGF and PAI-1 secretion: these effects were attenuated by diphenylene iodonium (DPI), an NADPH oxidase inhibitor, and NOX2 siRNA. Importantly, NOX2 siRNA suppresses collagen production in primary keloid dermal fibroblasts. These findings provide the proof of concept for NADPH oxidase as a potential target for the treatment of skin fibrosis.

[Detection and analysis of polymorphisms of 59571364 and 59912586 loci on X chromosome in fat-tail and thin-tail sheep flocks].

In order to analyze the correlation of tail fat deposition and two SNP loci on Ovis arise chromosome X and provide a theoretical basis for using molecular assisted selection technology in further low-fat sheep breeding, the breeds with extreme differences in tail types (Altay, Small Tail Han Sheep, Hu, Chinese Merino and Suffolk) were used to detect the polymorphisms of two SNP loci on X chromosome and the haplotypes with PCR-RFLP method. The results showed that the TT genotype at 59571364 locus and GG genotype at 59912586 locus were preponderant genotypes in thin-tailed Chinese Merino and Suffolk sheep flocks, while the percentage of the two genotypes in fat-tailed (fat-rmup) Altay and Hu flocks is less than 2%. Haplotype analysis showed that CA haplotype is the main haplotype, the percentage of CA is up to 55%, and the percentage of CA and TA haplotypes together was 88.33% in Altay sheep flock. These results suggest that there are great differences in the SNP distribution of the 59571364 and 59912586 loci among different tail-typed sheep flocks, which can be used as molecular markers in high or low fat sheep breeding.

[Correlation analysis between polymorphism of the 59383635th locus on X chromosome and fat-tail trait in sheep].

Fat tail or fat rump is one of essential traits for surviving in harsh environments, and the mechanism of fat deposition and its inheritable characters in sheep are still unclear. Therefore, the 59383635th locus on X chromosome in our unpublished chip data was chosen as candidate SNP, PCR-SSCP method was used to detect genotypes in five sheep breeds which have extreme differences in tail types (Altay, Small Tail Han Sheep, Hu, Chinese Merino and Suffolk), and the mathematical model was employed to analyze the correlation between the polymorphism and the trait of fat tail or fat rump. The results in this study showed that the high frequency of allele T exists in Altay flock, and the frequency of allele C appears to be particularly high in the thin tail sheep breeds. The result of mathematical model showed that the ratio of T/C increased exponentially with the increase of phenotype score. These results suggest that there is a big difference in the SNP distribution between fat tail (rump) and thin tail sheep populations, and the SNP can be used as an ideal molecular marker in high-fat or low-fat sheep breeding. However, the biological function of the SNP remains to be further studied.

Endophytic Streptomyces sp. NEAU-ZSY13 from the leaf of Perilla frutescens, as a promising broad-spectrum biocontrol agent against soil-borne diseases.

Soil-borne diseases cause significant economic losses in global agricultural production. These diseases are challenging to control due to the invasion of multiple pathogens into host plants, and traditional chemical control methods often yield unsatisfactory results. In this study, we isolated and identified an endophytic Streptomyces, designated as NEAU-ZSY13, from the leaf of Perilla frutescens. This isolate exhibited broad-spectrum antifungal activity against 17 soil-borne phytopathogenic fungi, with Bipolaris sorokiniana being the most prominent. Additionally, it displayed strong antibacterial activity against the soil-borne phytopathogenic bacterium Ralstonia solanacearum. To assess its biocontrol potential, the isolate was utilized to produce a biofertilizer through solid-state fermentation. The fermentation conditions were optimized using response surface methodology to maximize the spore production. The results revealed that more abundant spores were produced with a 1:2 ratio of vermicompost to wheat bran, 60% water content, 20% inoculation amount and 28°C. Subsequent pot experiments demonstrated that the application of the biofertilizer with a spore concentration of 108 CFU/g soil effectively suppressed the occurrence of tomato bacterial wilt caused by R. solanacearum and wheat root rot caused by B. sorokiniana, with biocontrol efficacies of 72.2 and 78.3%, respectively. Chemical analysis of NEAU-ZSY13 extracts, using nuclear magnetic resonance spectrometry and mass analysis, identified niphimycin C and niphimycin A as the primary active constituents. These compounds exhibited high activity against R. solanacearum (EC50 of 3.6 and 2.4 µg mL-1) and B. sorokiniana (EC50 of 3.9 and 3.4 µg mL-1). In conclusion, this study demonstrates the potential of Streptomyces sp. NEAU-ZSY13 as a biofertilizer for the control of soil-borne diseases.

[Cloning and expression in follicle anagen of ILK gene in sheep].

Integrin linked kinase (ILK) is a scaffold protein, which plays important roles in hair follicle development. The cDNA sequence of novel ILK gene in sheep was cloned by PCR method and analyzed by bioinformatics. Tissue expression profiling in eight tissues and temporal profiling at different wool follicle anagen stages in skin was analyzed. The results showed that the whole open reading frame (ORF) of ILK gene was 1 359 bp in length, which encoded 452 amino acids. Bioinformatic analysis indicated that the secondary structure of ILK gene was mainly made up of three ankyrin repeats and a kinase domain, and there were multiple phosphorylation and Protein Kinase C sites in this gene. The RT-PCR result confirmed that ILK mRNA was expressed in heart, liver, spleen, lung, skeletal muscle, skin, and small intestine, and the expression level was much higher in skin, spleen, and liver than others. The q-PCR analysis demonstrated that the ex-pression level of ILK was significantly increased from March to May (early follicle anagen initiation) in both sheep breeds, Chinese Merino and Kazakh sheep, and there were certain differences from June to October between the two breeds. The above results indicated that ILK gene may play key roles in regulating secondary follicle growth.

Glycogen Synthase Kinase 3ß (GSK3ß) Regulates Myogenic Differentiation in Skeletal Muscle Satellite Cells of Sheep.

Glycogen synthase kinase 3ß (GSK3ß) has a vital role in the regulation of many cellular processes. However, the role of GSK3ß in muscle cell differentiation in sheep remains unknown. In this study, we investigated the function of GSK3ß in skeletal muscle satellite cells (SMSCs) of sheep. An overexpression of GSK3ß significantly inhibited myotube formation as well as the mRNA levels of myogenic genes (MyoD, MyoG, MyHC1, and MyHC2a) in sheep SMSCs. SB216763 treatment had a time-course effect on the phosphorylation levels of sheep GSK3ß. In addition, reducing the activity of GSK3ß lead to the promotion of sheep SMSCs differentiation as well as the mRNA levels of myogenic genes (MyoD, MyoG, MyHC1, and MyHC2a). This study illustrated the function of GSK3ß to inhibit myogenesis in sheep SMSCs, which provided evidence for studying the mechanisms involved in the regulation of sheep SMSCs differentiation by GSK3ß.

Dorsal pentagonal local flap: a new technique of web reconstruction for syndactyly without skin graft.

BACKGROUND: Many techniques for web space reconstruction have been described over the years. However, few techniques are completely satisfactory in terms of cosmetic requirement and functional recovery due to scar contracture, web creep, or conspicuous scarring resulting from skin grafting or additional incisions on the dorsal palm. Based on the anatomy of the dorsal metacarpal artery, the authors describe a local pentagonal advancement flap including perforators of the dorsal metacarpal artery to optimize web reconstruction and facilitate direct closure in the syndactyly treatment. METHODS: A local dorsal pentagonal advancement flap was used to reconstruct 17 web spaces in ten patients. The skin of the syndactylized fingers was brought to the web space from the dorsum of the two adjacent syndactylized fingers to cover the web area, facilitating a skin graft-free procedure for web reconstruction. RESULTS: All 17 web releases were successfully reconstructed. During the follow-up period of 23-35 months, the appearance of all the reconstructed webs was similar to that of the adjacent normal webs, and all the patients had full functional recovery. No case of web creep was reported during this period, and none of the patients required a secondary operation. CONCLUSION: The dorsal pentagonal advancement flap is a dependable flap based on known perforators from the dorsal metacarpal arteries. The reported technique is a simple and effective technique for the correction of simple syndactyly and is especially suitable for reconstruction of two webs in multiple syndactyly simultaneously, avoiding the need for skin grafts and leaving acceptable scars on the dorsum of the hand for web reconstruction.

[Effect of ginsenoside Rg1 on the spatial learning-memory ability in dementia rats after transplanted with bone marrow mesenchymal stem cells].

OBJECTIVE: To study the effect and mechanism of ginsenoside Rg1 on the spatial learning-memory ability in rats with Alzheimer's disease after transplanted with bone marrow mesenchymal stem cells (BMSCs). METHODS: Using digital randomization table method, seventy-five male SD rats were divided into the bilateral FF transection model group (as the model group: ambi-hippocampal fimbria-fomix transected), the sham-operative control group (the SOC group: receiving the same modeling process as the model group, but without ambi-hippocampal fimbria-fomix transected), the ginsenoside Rg1 treatment group (as the treatment group: Two weeks after modeling ginsenoside Rg1 was peritoneally injected at the dose of 5 mg/kg, once daily for four weeks in total), the BMSCs transplanted treatment group [as the control group: Two weeks after modeling every rat received transplantation of BMSCs (10 microL, 1 x 10(6) cells)], and the ginsenoside Rg1 + BMSCs treatment group (as the combination group: They received both transplantation of BMSCs and peritoneal injection of ginsenoside Rgl). The spatial learning-memory ability of rats was detected by Morris water maze and the escape latency (s) was recorded, mRNA expression of nerve growth factor (NGF) was detected using Real-time PCR. RESULTS: Six weeks after the hippocampal fimbria-fomix (FF) transection, the escape latency o feach medication group was obviously shorter than that of the model group, and the spatial learning-memory ability of dementia rats was somewhat improved. The spatial learning-memory ability of rats in the combination group was (29.95 +/- 2.03) and the mRNA expression level of NGF was (1.13 +/- 0.15), better than those in the BMSCs group (44.36 +/- 1.43, 0.78 +/- 0.09, P<0.05). CONCLUSIONS: Ginsenoside Rg1 could strengthen the spatial learning-memory ability in dementia rats after transplanted with BMSCs. Its mechanism might be possibly correlated with up-regulating mRNA expression of NGF in basal forebrain after BMSCs transplantation.

Hematogenous Macrophages: A New Therapeutic Target for Spinal Cord Injury.

Spinal cord injury (SCI) is a devastating disease leading to loss of sensory and motor functions, whose pathological process includes mechanical primary injury and secondary injury. Macrophages play an important role in SCI pathology. According to its origin, it can be divided into resident microglia and peripheral monocyte-derived macrophages (hematogenous Mφ). And it can also be divided into M1-type macrophages and M2-type macrophages on the basis of its functional characteristics. Hematogenous macrophages may contribute to the SCI process through infiltrating, scar forming, phagocytizing debris, and inducing inflammatory response. Although some of the activities of hematogenous macrophages are shown to be beneficial, the role of hematogenous macrophages in SCI remains controversial. In this review, following a brief introduction of hematogenous macrophages, we mainly focus on the function and the controversial role of hematogenous macrophages in SCI, and we propose that hematogenous macrophages may be a new therapeutic target for SCI.

Comparative Transcriptome Analysis of Key Genes and Pathways Activated in Response to Fat Deposition in Two Sheep Breeds With Distinct Tail Phenotype.

Fat tail in sheep presents a valuable energy reserve that has historically facilitated adaptation to harsh environments. However, in modern intensive and semi-intensive sheep industry systems, breeds with leaner tails are more desirable. In the present study, RNA sequencing (RNA-Seq) was applied to determine the transcriptome profiles of tail fat tissues in two Chinese sheep breeds, fat-rumped Altay sheep and thin-tailed Xinjiang fine wool (XFW) sheep, with extreme fat tail phenotype difference. Then the differentially expressed genes (DEGs) and their sequence variations were further analyzed. In total, 21,527 genes were detected, among which 3,965 displayed significant expression variations in tail fat tissues of the two sheep breeds (P < 0.05), including 707 upregulated and 3,258 downregulated genes. Gene Ontology (GO) analysis disclosed that 198 DEGs were related to fat metabolism. In Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, the majority of DEGs were significantly enriched in "adipocytokine signaling," "PPAR signaling," and "metabolic pathways" (P < 0.05); moreover, some genes were involved in multiple pathways. Among the 198 DEGs, 22 genes were markedly up- or downregulated in tail fat tissue of Altay sheep, indicating that these genes might be closely related to the fat tail trait of this breed. A total of 41,724 and 42,193 SNPs were detected in the transcriptomic data of tail fat tissues obtained from Altay and XFW sheep, respectively. The distribution of seven SNPs in the coding regions of the 22 candidate genes was further investigated in populations of three sheep breeds with distinct tail phenotypes. In particular, the g.18167532T/C (Oar_v3.1) mutation of the ATP-binding cassette transporter A1 (ABCA1) gene and g.57036072G/T (Oar_v3.1) mutation of the solute carrier family 27 member 2 (SLC27A2) gene showed significantly different distributions and were closely associated with tail phenotype (P < 0.05). The present study provides transcriptomic evidence explaining the differences in fat- and thin-tailed sheep breeds and reveals numerous DEGs and SNPs associated with tail phenotype. Our data provide a valuable theoretical basis for selection of lean-tailed sheep breeds.

Paternal Origins and Migratory Episodes of Domestic Sheep.

The domestication and subsequent global dispersal of livestock are crucial events in human history, but the migratory episodes during the history of livestock remain poorly documented [1-3]. Here, we first developed a set of 493 novel ovine SNPs of the male-specific region of Y chromosome (MSY) by genome mapping. We then conducted a comprehensive genomic analysis of Y chromosome, mitochondrial DNA, and whole-genome sequence variations in a large number of 595 rams representing 118 domestic populations across the world. We detected four different paternal lineages of domestic sheep and resolved, at the global level, their paternal origins and differentiation. In Northern European breeds, several of which have retained primitive traits (e.g., a small body size and short or thin tails), and fat-tailed sheep, we found an overrepresentation of MSY lineages y-HC and y-HB, respectively. Using an approximate Bayesian computation approach, we reconstruct the demographic expansions associated with the segregation of primitive and fat-tailed phenotypes. These results together with archaeological evidence and historical data suggested the first expansion of early domestic hair sheep and the later expansion of fat-tailed sheep occurred ∼11,800-9,000 years BP and ∼5,300-1,700 years BP, respectively. These findings provide important insights into the history of migration and pastoralism of sheep across the Old World, which was associated with different breeding goals during the Neolithic agricultural revolution.

Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits.

Understanding the genetic changes underlying phenotypic variation in sheep (Ovis aries) may facilitate our efforts towards further improvement. Here, we report the deep resequencing of 248 sheep including the wild ancestor (O. orientalis), landraces, and improved breeds. We explored the sheep variome and selection signatures. We detected genomic regions harboring genes associated with distinct morphological and agronomic traits, which may be past and potential future targets of domestication, breeding, and selection. Furthermore, we found non-synonymous mutations in a set of plausible candidate genes and significant differences in their allele frequency distributions across breeds. We identified PDGFD as a likely causal gene for fat deposition in the tails of sheep through transcriptome, RT-PCR, qPCR, and Western blot analyses. Our results provide insights into the demographic history of sheep and a valuable genomic resource for future genetic studies and improved genome-assisted breeding of sheep and other domestic animals.