No abstract

Long non-coding RNAs (lncRNAs), >200 nt in length, are transcribed from mammalian genomes. They play important regulatory roles in various biological processes; However, the function and expression profile of lncRNAs involved in the development of hair follicles in the fetus, have been relatively under-explored area. To investigate the specific role of lncRNAs and mRNAs that regulate hair follicle development, we herein performed a comprehensive study on the lncRNA and mRNA expression profiles of sheep at multiple embryonic days (E65, E85, E105, and E135) and six lambs aged one week (D7) and one month (D30) using RNA-seq technology. The number of genes (471 lncRNAs and 12,812 mRNAs) differentially expressed and potential targets of differentially expressed lncRNAs were predicted. Differentially expressed lncRNAs were grouped into 10 clusters based on their expression pattern by K-means clustering. Moreover, Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that some differentially expressed mRNAs, such as DKK1 , DSG4 , FOXE1 , Hoxc13 , SFRP1 , SFRP2 , and Wnt10A overlapped with lncRNAs targets, and enriched in important hair follicle developmental pathways, including Wnt, TNF, and MAPK signaling pathways. In addition, 9 differentially expressed lncRNAs and 4 differentially expressed mRNAs were validated using quantitative real-time PCR (qRT-PCR). This study helps enrich the Ovis lncRNA databases and provides a comprehensive lncRNA transcriptome profile of fetal and postnatal skin of sheep. Additionally, it provides a foundation for further experiments on the role of lncRNAs in the regulation of hair growth in sheep.

Tibetan cashmere goats are famous for producing the finest, softest and lightest cashmere fiber in China. The growth and development of skin are closely related to fineness and are the key factors affecting the quality of cashmere. To investigate the specific role of long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) in regulating cashmere fineness of Tibetan Cashmere goats in the anagen phase, we conducted high-throughput RNA sequencing of fine-type and coarse-type skin tissues. We identified 2,059 lncRNA candidates (1,589 lncRNAs annotated, 470 lncRNAs novel), and 80 differentially expressed (DE) lncRNAs and their potential targets were predicted. We also identified 384 DE messenger RNAs (mRNAs) out of 29,119 mRNAs. Several key genes in KRT26, KRT28, KRT39, IFT88, JAK3, NOTCH2 and NOTCH3 and a series of lncRNAs, including ENSCHIT00000009853, MSTRG.16794.17, MSTRG.17532.2, were shown to be potentially important for regulating cashmere fineness. GO and KEGG enrichment analyses of DE mRNAs and DE lncRNAs targets significantly enriched in positive regulation of the canonical Wnt signaling pathway, regulation of protein processing and metabolism processes. The mRNA-mRNA and lncRNA-mRNA regulatory networks further revealed potential transcripts involved in cashmere fineness. We further validated the expression patterns of DE mRNAs and DE lncRNAs by quantitative real-time PCR (qRT-PCR), and the results were consistent with the sequencing data. This study will shed new light on selective cashmere goat breeding, and these lncRNAs and mRNAs that were found to be enriched in Capra hircus RNA database.

BackgroundEssential Oils (EO) are complex mixtures of plant secondary metabolites that have been proposed as promising feed additives for mitigating methane and ammonia emissions. We have previously demonstrated that Essential Oil-Cobalt (EOC) supplementation resulted in increased average daily gain and improved phenotypes (cashmere fiber traits, carcass weight, and meat quality) when cashmere goats received supplementation at approximately 2 mg/kg of body weight. However, the ruminal microbiological effects of EO remain poorly understood with regard to the extent to which ruminal populations can adapt to EO presence as feed ingredients. The effects of varying levels of EO require additional study.ResultsIn this study, we conducted metagenomic analyses using ruminal fluid samples from three groups (addition of 0, 52, and 91 mg) to evaluate the influence of dietary EOC supplementation on goat rumen bacterial community dynamics. EOC addition resulted in changes of ruminal fermentation types and the EOC dose strongly impacted the stability of ruminal microbiota. The Bacteroides sp. and Succinivibrio sp. type bacterial community was positively associated with improved volatile fatty acid production when the diet was supplemented with EOC.ConclusionsA clear pattern was found that reflected rapid fermentative improvement in the rumen, subsequent to butyrate metabolism and EOC based feed additives may affect rumen microbes to further improve feed conversion. This observation indicates that EOC can be safely used to enhance animal productivity and to reduce ammonia and waste gas emissions, thus positively impacting the environment.Electronic supplementary materialThe online version of this article (10.1186/s12866-019-1400-3) contains supplementary material, which is available to authorized users.

Beef cattle are often fed high-concentrate diet (HCD) to achieve high growth rate. However, HCD feeding is strongly associated with metabolic disorders. Mild acid treatment of grains in HCD with 1% hydrochloric acid (HA) followed by neutralization with sodium bicarbonate (SB) might modify rumen fermentation patterns and microbiota, thereby decreasing the negative effects of HCD. This study was thus aimed to investigate the effects of treatment of corn with 1% HA and subsequent neutralization with SB on rumen fermentation and microbiota, inflammatory response and growth performance in beef cattle fed HCD. Eighteen beef cattle were randomly allocated to three groups and each group was fed different diets: low-concentrate diet (LCD) (concentrate : forage = 40 : 60), HCD (concentrate : forage = 60 : 40) or HCD based on treated corn (HCDT) with the same concentrate to forage ratio as the HCD. The corn in the HCDT was steeped in 1% HA (wt/wt) for 48 h and neutralized with SB after HA treatment. The animal trial lasted for 42 days with an adaptation period of 7 days. At the end of the trial, rumen fluid samples were collected for measuring ruminal pH values, short-chain fatty acids, endotoxin (or lipopolysaccharide, LPS) and bacterial microbiota. Plasma samples were collected at the end of the trial to determine the concentrations of plasma LPS, proinflammatory cytokines and acute phase proteins (APPs). The results showed that compared with the LCD, feeding the HCD had better growth performance due to a shift in the ruminal fermentation pattern from acetate towards propionate, butyrate and valerate. However, the HCD decreased ruminal pH and increased ruminal LPS release and the concentrations of plasma proinflammatory cytokines and APPs. Furthermore, feeding the HCD reduced bacterial richness and diversity in the rumen. Treatment of corn increased resistant starch (RS) content. Compared with the HCD, feeding the HCDT reduced ruminal LPS and improved ruminal bacterial microbiota, resulting in decreased inflammation and improved growth performance. In conclusion, although the HCD had better growth performance than the LCD, feeding the HCD promoted the pH reduction and the LPS release in the rumen, disturbed the ruminal bacterial stability and increased inflammatory response. Treatment of corn with HA in combination with subsequent SB neutralization increased the RS content and helped counter the negative effects of feeding HCD to beef steers.

Background Characterization of the molecular mechanisms underlying hair follicle development is of paramount importance in the genetic improvement of wool-related traits in sheep and skin-related traits in humans. The Merino is the most important breed of fine-wooled sheep in the world. In this study, we systematically investigated the complexity of sheep hair follicle development by integrating transcriptome and methylome datasets from Merino sheep skin. Results We analysed 72 sequence datasets, including DNA methylome and the whole transcriptome of four gene types, i.e. protein-coding genes (PCGs), lncRNAs, circRNAs, and miRNAs, across four embryonic days (E65, E85, E105, and E135) and two postnatal days (P7 and P30) from the skin tissue of 18 Merino sheep. We revealed distinct expression profiles of these four gene types across six hair follicle developmental stages, and demonstrated their complex interactions with DNA methylation. PCGs with stage-specific expression or regulated by stage-specific lncRNAs, circRNAs, and miRNAs were significantly enriched in epithelial differentiation and hair follicle morphogenesis. Regulatory network and gene co-expression analyses identified key transcripts controlling hair follicle development. We further predicted transcriptional factors (e.g. KLF4, LEF1, HOXC13, RBPJ, VDR, RARA, and STAT3) with stage-specific involvement in hair follicle morphogenesis. Through integrating these stage-specific genomic features with results from genome-wide association studies (GWAS) of five wool-related traits in 7135 Merino sheep, we detected developmental stages and genes that were relevant with wool-related traits in sheep. For instance, genes that were specifically upregulated at E105 were significantly associated with most of wool-related traits. A phenome-wide association study (PheWAS) demonstrated that candidate genes of wool-related traits (e.g. SPHK1, GHR, PPP1R27, CSRP2, EEF1A2, and PTPN1) in sheep were also significantly associated with dermatological, metabolic, and immune traits in humans. Conclusions Our study provides novel insights into the molecular basis of hair follicle morphogenesis and will serve as a foundation to improve breeding for wool traits in sheep. It also indicates the importance of studying gene expression in the normal development of organs in understanding the genetic architecture of economically important traits in livestock. The datasets generated here are useful resources for functionally annotating the sheep genome, and for elucidating early skin development in mammals, including humans.

Background Merino sheep are the most famous fine wool sheep in the world. They have high wool production and excellent wool quality and have attracted worldwide attention. The fleece of the Merino sheep is composed predominantly of wool fibers grown from secondary wool follicles. Therefore, it is necessary to study the development of hair follicles to understand the mechanism of wool production. The hair follicle is a complex biological system involved in a dynamic process governed by gene regulation. The hair follicle development process is very complex and poorly understood. The purpose of our research is to identify candidate genes related to hair follicle development, provide a theoretical molecular breeding basis for the cultivation of fine wool sheep, and provide a reference for the problems of hair loss and alopecia areata that affect human beings. Results We analyzed mRNAs data in skin tissues of 18 Merino sheep at four embryonic days (E65, E85, E105 and E135) and two postnatal days (P7 and P30). G1 to G6 represent hair follicles developmental at six stages (i.e. E65 to P30). We identified 7879 differentially expressed genes (DEGs) and 12623 novel DEGs, revealed different expression patterns of these DEGs at six stages of hair follicle development, and demonstrated their complex interactions. DEGs with stage-specific expression were significantly enriched in epidermal differentiation and development, hair follicle development and hair follicle morphogenesis and were enriched in many pathways related to hair follicle development. The key genes (LAMA5, WNT10A, KRT25, SOSTDC1, ZDHHC21, FZD1, BMP7, LRP4, TGFβ2, TMEM79, SOX10, ITGB4, KRT14, ITGA6, and GLI2) affecting hair follicle morphogenesis were identified by network analysis. Conclusion This study provides a new reference for the molecular basis of hair follicle development and lays a foundation for further improving sheep hair follicle breeding. Candidate genes related to hair follicular development were found, which provided a theoretical basis for molecular breeding for the culture of fine wool sheep. These results are a valuable resource for biological investigations of fleece evolution in animals.

Background Genetic improvement of wool and growth traits is a major goal in the sheep industry, but their underlying genetic architecture remains elusive. To improve our understanding of these mechanisms, we conducted a weighted single-step genome-wide association study (WssGWAS) and then integrated the results with large-scale transcriptome data for five wool traits and one growth trait in Merino sheep: mean fibre diameter (MFD), coefficient of variation of the fibre diameter (CVFD), crimp number (CN), mean staple length (MSL), greasy fleece weight (GFW), and live weight (LW). Results Our dataset comprised 7135 individuals with phenotype data, among which 1217 had high-density (HD) genotype data (n = 372,534). The genotypes of 707 of these animals were imputed from the Illumina Ovine single nucleotide polymorphism (SNP) 54 BeadChip to the HD Array. The heritability of these traits ranged from 0.05 (CVFD) to 0.36 (MFD), and between-trait genetic correlations ranged from − 0.44 (CN vs. LW) to 0.77 (GFW vs. LW). By integrating the GWAS signals with RNA-seq data from 500 samples (representing 87 tissue types from 16 animals), we detected tissues that were relevant to each of the six traits, e.g. liver, muscle and the gastrointestinal (GI) tract were the most relevant tissues for LW, and leukocytes and macrophages were the most relevant cells for CN. For the six traits, 54 quantitative trait loci (QTL) were identified covering 81 candidate genes on 21 ovine autosomes. Multiple candidate genes showed strong tissue-specific expression, e.g. BNC1 (associated with MFD) and CHRNB1 (LW) were specifically expressed in skin and muscle, respectively. By conducting phenome-wide association studies (PheWAS) in humans, we found that orthologues of several of these candidate genes were significantly (FDR < 0.05) associated with similar traits in humans, e.g. BNC1 was significantly associated with MFD in sheep and with hair colour in humans, and CHRNB1 was significantly associated with LW in sheep and with body mass index in humans. Conclusions Our findings provide novel insights into the biological and genetic mechanisms underlying wool and growth traits, and thus will contribute to the genetic improvement and gene mapping of complex traits in sheep.