Whole-Genome Resequencing Reveals Genetic Diversity and Wool Trait-Related Genes in Liangshan Semi-Fine-Wool Sheep.

Understanding the genetic makeup of local sheep breeds is essential for their scientific conservation and sustainable utilization. The Liangshan semi-fine-wool sheep (LSS), a Chinese semi-fine-wool breed renowned for its soft wool, was analyzed using whole-genome sequencing data including 35 LSS, 84 sheep from other domestic breeds, and 20 Asiatic mouflons. We investigated the genetic composition of LSS by conducting analyses of the population structure, runs of homozygosity, genomic inbreeding coefficients, and selection signature. Our findings indicated that LSS shares greater genetic similarity with Border Leicester and Romney sheep than with Tibetan (TIB), Yunnan (YNS), and Chinese Merino sheep. Genomic analysis indicated low to moderate inbreeding coefficients, ranging from 0.014 to 0.154. In identifying selection signals across the LSS genome, we pinpointed 195 candidate regions housing 74 annotated genes (e.g., IRF2BP2, BVES, and ALOX5). We also found the overlaps between the candidate regions and several known quantitative trait loci related to wool traits, such as the wool staple length and wool fiber diameter. A selective sweep region, marked by the highest value of cross-population extended haplotype homozygosity, encompassed IRF2BP2-an influential candidate gene affecting fleece fiber traits. Furthermore, notable differences in genotype frequency at a mutation site (c.1051 + 46T > C, Chr25: 6,784,190 bp) within IRF2BP2 were observed between LSS and TIB and YNS sheep (Fisher's exact test, p < 2.2 × 10-16). Taken together, these findings offer insights crucial for the conservation and breeding enhancement of LSS.

Integrated metabolomics and transcriptomics analyses reveal the key genes regulating differential metabolites of longissimus dorsi muscle in castrated South Sichuan black goats (Capra hircus).

The main aim of the current work was to explore the differential metabolites and differentially expressed genes of longissimus dorsi muscle (LDM) between castrated and uncastrated fattening male South Sichuan black goats (Capra hircus). Then, the key genes regulating important differential metabolites (DMs) in castrated male goats were observed by integrated metabolomics and transcriptomics analyses. In addition, we evaluated the effects of castration on blood constituents, dressing percentage, and water holding capacity of LDM in male black goats. The results showed that the concentrations of alkaline phosphatase (ALP), total cholesterol (TC), triglyceride (TG), and low-density lipoprotein cholesterol (LDL-C) were significantly increased and testosterone was significantly decreased in castrated male goats compared with the uncastrated male goats, while dressing percentage of black goats and water holding capacity of longissimus dorsi muscle were not significant differences. Through metabolomics and transcriptomics analyses, 23 important KEGG pathways, 13 important DMs, 32 important differentially expressed genes (DEGs), and 13 key genes related to the "Metabolism" and "Organismal systems" pathways were screened. Lipid accumulation may be elevated in the blood of fattening South Sichuan black goats after castration. Castration might play a positive role in energy provision, intercellular signaling, muscle function, softening of meat, disease reduction, and anti-oxidation of LDM. P4HA2, AKR1B1, GPT2, L2HGDH, ENSCHIG00000021660, ENSCHIG00000023861, DGAT2, ULK1, SLC38A3, PLA2G4A, SLC6A1, ENSCHIG00000026624, and ND2 might be the key genes regulating important DMs in the KEGG pathways related to "Metabolism" and "Organismal systems" of castrated male goats compared with the uncastrated male goats.

Transcriptome analysis reveals the regulatory effects of Bacillus amyloliquefaciens and Bacillus pumilus on immune and digestive related genes in the spleen of weanling black goats.

The aim of the present study was to evaluate the effects of Bacillus amyloliquefaciens fsznc-06 and Bacillus pumilus fsznc-09 on the expressions of spleen genes in weanling Jintang black goats. Bacillus amyloliquefaciens fsznc-06 (BA-treated group) and Bacillus pumilus fsznc-09 (BP-treated group) were directly fed to goats, and the spleens were harvested for transcriptome analysis. The KEGG pathway analysis showed that the differentially expressed genes (DEGs) in BA-treated vs CON group were mainly involved in digestive system and immune system, while those in BP-treated vs CON group were mainly involved in immune system, and those in BA-treated vs BP-treated group were mainly involved in digestive system. In conclusion, Bacillus amyloliquefaciens fsznc-06 might promote the expressions of genes related to immune system and digestive system, reduce the expressions of disease genes related to digestive system and might promote mutual accommodation of some immune genes in weanling black goat. Bacillus pumilus fsznc-09 might promote the expressions of genes related to immune system and mutual accommodation of some immune genes in weanling black goat. Bacillus amyloliquefaciens fsznc-06 has advantages over Bacillus pumilus fsznc-09 in promoting the expressions of genes related to digestive system and mutual accommodation of some immune genes.

Analysis of spleen of mice (Mus musculus) infected with Aspergillus nidulans identifies immune-related genes.

Aspergillus nidulans (A. nidulans) is an ascomycetous fungus that can cause disseminated infection in humans or animals. The present study aimed to explore the pathogenesis and host spleen immune response after infection with A. nidulans. Thirty KM mice were divided into control group (C) and treated group (T). Serum was collected for the detection of inflammatory markers. Spleens were collected for histopathological examination, fungal culture and transcriptomic analysis. Compared with the control group, the concentrations of serum total protein (TP), globulin (GLO) and C-reactive protein (CRP) were significantly increased (P < 0.01), but the concentration of albumin (ALB) and the ratio of albumin/globulin (A/G) were significantly decreased in the treated group (P < 0.01). In addition, the splenic red pulp was hyperemic, and the white pulp was infiltrated by inflammatory cells in treated group. The chromatin was aggregated, and the mitochondria were swollen in the spleen lymphocytes of treated group. Transcriptome sequencing results showed that 47.2 million and 44.9 million clean reads were obtained in the control group and treated group, respectively. 946 differentially expressed genes (DEGs) were obtained, including 372 up-regulated genes and 574 down-regulated genes. GO analysis showed that these DEGs were mainly involved in the immune responses, antigen binding, immunoglobulin receptor binding, bacterial defence responses, endopeptidase activity and so on. Moreover, KEGG analysis showed that these DEGs were mainly enriched in the following pathways: complement and coagulation cascades, retinol metabolism, cytochrome p450, IL-17 signalling pathway and so on. Additionally, 9 DEGs was validated by qRT-PCR approach. In summary, this study revealed the immune response mechanism of spleen in A. nidulan-infected mice. It will benefit for a better understanding of the pathogenic mechanisms of A. nidulans.

Goat CCL5 promotes cell viability and inflammatory factors production in lung fibroblasts and macrophages.

Inflammatory chemokine CCL5 can mediate the occurrence of inflammatory reactions and participate in various disease processes. (Ch)CCL5 gene of Jintang black goat (Capra hircus, C. hircus) was cloned. The CDS (coding sequences) was 276 bp in length and encoded 91 amino acids. The 26.5 kDa recombinant protein was expressed by Escherichia coli system and purified by Ni-Agarose. The viabilities of primary goat lung fibroblasts could be enhanced after treating with ChCCL5 protein (12.5, 25, 50 µg/mL) (P < 0.05). The expression levels of interleukin-1beta (IL-1ß), interleukin 6 (IL-6), tumor necrosis factor (TNF-α), C-C motif chemokine ligand 2 (CCL2) and heat-shock proteins (Hsp70) genes were upregulated after treating with ChCCL5 protein (12.5, 25, 50 µg/mL). Besides, the viabilities and phagocytic abilities of primary mouse peritoneal macrophages could be enhanced after treating with ChCCL5 protein (12.5, 25, 50 µg/mL) (P < 0.05). The expression levels of IL-1ß, IL-6, toll-like receptor 4 (TLR4), inducible nitric oxide synthase (iNOs) and TNF-α genes were upregulated after treating with ChCCL5 protein (12.5, 25, 50 µg/mL) (P < 0.05). These results indicated that goat CCL5 might play a role in the inflammatory response by regulating the inflammatory cytokines produced by lung fibroblasts and macrophages.

Excessive manganese alters serum biochemical indices, induces histopathological alterations, and activates apoptosis in liver and cerebrum of Jianzhou Da'er goat (Capra hircus).

The present study aimed to explore the toxic effects of excessive dietary Mn in livers and cerebrums of Jianzhou Da'er goat (Capra hircus). Three-month old goats were assigned into three groups: control group, fed on basal diet; Mn I group, fed on the basal diet mixed with MnCl2 (2.5 g/kg); Mn II group, fed on the basal diet mixed with MnCl2 (5 g/kg). Compared with the control group, the activities of serum alkaline phosphatase (ALP), alanine aminotransferase (ALT), aspartate aminotransferase (AST) and the concentrations of interferon-γ (IFN-γ) in Mn I and Mn II groups were significantly increased, but the concentrations of IgG in Mn I and Mn II groups were significantly decreased (p < 0.05). The activities of superoxide dismutase (T-SOD), glutathione peroxidase (GSH-Px), and the concentrations of glutathione (GSH) in Mn I and Mn II groups were significantly decreased, whereas the concentrations of malondialdehyde (MDA) in Mn I and Mn II groups were significantly increased in livers and cerebrums (p < 0.05). Moreover, the hepatocytes necrosed, inflammatory cells infiltrated, chromatin concentrated, mitochondrial cristae reduced in Mn I and Mn II groups. The nerve cells necrosed, blood vessels congested, inflammatory cells infiltrated, mitochondrial electron density and mitochondrial cristae decreased, and vacuolization increased in Mn I and Mn II groups. Furthermore, the mRNA expressions of tumor necrosis factor alpha (TNF-α), tumor necrosis factor receptor type 1 (TNFR1), fas-associated protein via a death domain (FADD), Bcl2-associated X (Bax), cysteinyl aspartate specific proteinase 3, 8, 9 (Caspase-3, 8, 9) in Mn I and Mn II groups were significantly increased (p < 0.05), but the mRNA expressions of B-cell lymphoma-2 (Bcl-2) in Mn I and Mn II groups were significantly decreased (p < 0.05) in livers. The mRNA expressions of Bcl-2, Bax, Caspase-3, 9, 7, 12 in Mn I and Mn II groups were significantly increased (p < 0.05), however, the ratio of Bcl-2/Bax in Mn I and Mn II groups was significantly decreased (p < 0.05) in cerebrums. In summary, our results provided new insights for better understanding the mechanisms of Mn toxicity in Capra hircus.

Grazing and Supplementation of Dietary Yeast Probiotics Shape the Gut Microbiota and Improve the Immunity of Black Fattening Goats (Capra hircus).

This study aimed to investigate the effects of different feeding modes on the growth performance, gut microbiota, and immunity of Black Fattening Goat (Capra hircus). A total of 30 goats were grouped in three groups by their feeding modes (pasture grazing group, PG; barn feeding group, BF; barn feeding + probiotics, BF + P; n = 10) and the study was performed for 114 days. After a 2-week adaptation period, the first growth performance test was conducted, and the blood and fecal samplings (day 0) were collected on January 17, 2020, while the second and third test and samplings were conducted on days 53 and 100 of feeding. The species-composition of fecal microbiota was analyzed by 16S ribosomal RNA gene-sequencing using PacBio single molecule real time (SMRT) sequencing technology. Both the BF and BF + P groups had the highest (P < 0.05) body's weight and length, and chest circumference at days 53 and 100, especially at day 100, the body's weight of both the BF groups were more than 18 kg. The levels of immunoglobulin A (IgA) and immunoglobulin G (IgG) were found to be significantly higher (P < 0.05) in the PG and BF + P groups at day 100. The PG group exhibited the highest number of operational taxonomic unit (OTUs) and alpha diversity. Firmicutes, Bacteroidetes, and Verrucomicrobia were the predominant phyla in all the fecal samples. The relative abundance of Akkermansia muciniphila and Ruminococcus flavefaciens were found to be significantly higher (P < 0.05) in PG group and BF + P group at day 100, respectively, which might partially explain the significantly higher (P < 0.05) levels of IgA and IgG in these two groups. These findings suggested that BF supplemented with 5 g probiotics (Saccharomyces cerevisiae and mannan oligosaccharides) per day has the potential to enhance the growth and immunity of Black Fattening Goats.

miR-214-5p Regulating Differentiation of Intramuscular Preadipocytes in Goats via Targeting KLF12.

Intramuscular fat (i.m.) is an adipose tissue that is deposited between muscle bundles. An important type of post-transcriptional regulatory factor, miRNAs, has been observed as an important regulator that can regulate gene expression and cell differentiation through specific binding with target genes, which is the pivotal way determining intramuscular fat deposition. Thus, this study intends to use RT-PCR, cell culture, liposome transfection, real-time fluorescent quantitative PCR (qPCR), dual luciferase reporter systems, and other biological methods clarifying the possible mechanisms on goat intramuscular preadipocyte differentiation that is regulated by miR-214-5p. Ultimately, our results showed that the expression level of miR-214-5p peaked at 48 h after the goat intramuscular preadipocytes were induced for adipogenesis. Furthermore, after inhibition of the expression of miR-214-5p, the accumulation of lipid droplets and adipocyte differentiation in goat intramuscular adipocytes were promoted by the way of up-regulation of the expression level of lipoprotein lipase (LPL) (p < 0.05) and peroxisome proliferator-activated receptor gamma (PPARγ) (p < 0.01) but inhibited the expression of hormone-sensitive lipase (HSL) (p < 0.01). Subsequently, our study confirmed that Krüppel-like factor 12 (KLF12) was the target gene of miR-214-5p. Inhibition of the expression of KLF12 promoted adipocyte differentiation and lipid accumulation by upregulation of the expression of LPL and CCAAT/enhancer binding protein (C/EBPα) (p < 0.01). Overall, these results indicated that miR-214-5p and its target gene KLF12 were negative regulators in progression of goat preadipocyte differentiation. Our research results provided an experimental basis for finally revealing the mechanism of miR-214-5p in adipocytes.