Delineating molecular regulatory network of meat quality of longissimus dorsi indicated by transcriptomic, proteomic, and metabolomics analysis in rabbit.

This study aims to investigate the potential regulatory network responsible for the meat quality using multi-omics to help developing better varieties. Slaughter performance and meat quality of Shuxing No.1 rabbit outperformed IRA rabbit according to the tested rabbit parameters. Differentially expressed genes (DEGs) and differentially abundance proteins (DAPs) were involved in meat quality-related pathways, such as PI3K - Akt and MAPK signaling pathways. Only SMTNL1 and PM20D2 shared between DEGs and DAPs. Olfactory-sensitive undecanal, a differentially abundant metabolite (DAM) in volatilomics (vDAMs), correlated with all of the remaining 11 vDAMs, and most of 12 vDAMs were associated with amino acid metabolism. Integration revealed that 829 DEGs/DAPs were associated with 15 DAMs in four KEGG pathways, such as melatonin (a DAM in widely targeted metabolomics) was significantly positively correlated with ALDH and negatively correlated with RAB3D and CAT in the tryptophan metabolism pathway. This study sheds light on the potential mechanisms that contribute to the improved meat quality and flavor. SIGNIFICANCE: Shuxing No.1 rabbit is a new breed of meat rabbit in the Chinese market. In meat marketing, meat quality usually determines the purchase intention of consumers. Determining the biological and molecular mechanisms of meat quality in meat rabbit is essential for developing strategies to improve meat quality. According to the tested rabbit parameters, this study ascertained that the slaughter performance and meat quality of Shuxing No.1 rabbit surpasses that of IRA rabbit. The present study profiled the transcriptome, proteome, widely targeted metabolome, and volatilome of longissimus dorsi from Shuxing No.1 rabbit and IRA rabbit. The study found that meat quality and flavor-related tryptophan metabolism pathway is enriched with many DEGs/DAPs (including ALDH, RAB3D, and CAT), as well as a DAM, melatonin. This study sheds light on the potential mechanisms that contribute to the improved meat quality and flavor.

Medium chain triglycerides improve the growth performance, immune and antioxidant functions, and intestinal health of weaned rabbits.

The purpose is to study the effects of different doses of medium chain triglyceride (MCT) on growth performance, immune and oxidative functions, and intestinal health of weaned rabbits. A total of 600 weaned rabbits weighing about 993.26 g and at 35 d of age were randomly divided into five groups. The control group was fed a basal diet containing 2400 mg/kg soybean oil, and the experimental group was substituted with 600, 1200, 1800, and 2400 mg/kg MCT. The whole trial period lasted for 48 d. The results showed that treatment with 2400 mg/kg MCT significantly increased the weaning survival rate and crude fat digestibility (p < 0.05) and dramatically raised the levels of serum immunoglobulin (Ig)A, IgG, IgM, catalase, superoxide dismutase, and total antioxidant capability (p < 0.05). The villus height and crypt depth in 1800 mg/kg MCT group were observably enhanced (p < 0.05). The abundance of Bacteroidetes was significantly increased in 1800 and 2400 mg/kg MCT groups (p < 0.05). In conclusion, 1800 and 2400 mg/kg MCT substituting soybean oil in the diet of weaned rabbits can improve the growth performance and intestinal barrier function of weaned rabbits.

Trait Analysis in Domestic Rabbits (Oryctolagus cuniculus f. domesticus) Using SNP Markers from Genotyping-by-Sequencing Data.

The domestic rabbit (Oryctolagus cuniculus f. domesticus) is a very important variety in biomedical research and agricultural animal breeding. Due to the different geographical areas in which rabbit breeds originated, and the long history of domestication/artificial breeding, rabbits have experienced strong selection pressure, which has shaped many traits of most rabbit varieties, such as color and weight. An efficient genome-wide single-nucleotide polymorphism (SNP) detection strategy is genotyping-by-sequencing (GBS), which has been widely used in many organisms. This study attempted to explore bi-allelic SNPs associated with fur color and weight-related traits using GBS in five rabbit breeds. The data consisted of a total 831,035 SNPs in 150 individuals from Californian rabbits (CF), German Zika rabbits (ZK), Qixing rabbits (QX), Sichuan grey rabbits (SG), and Sichuan white rabbits (SW). In addition, these five breeds of rabbits were obviously independent populations, with high genetic differentiation among breeds and low genetic diversity within breeds. A total of 32,144 SNP sites were identified by selective sweep among the different varieties. The genes that carried SNP loci in these selected regions were related to important traits (fur color and weight) and signal pathways, such as the MAPK/ERK signaling pathway and the Hippo signaling pathway. In addition, genes related to fur color and weight were identified, such as ASIPs, MITFs and KITs, ADCY3s, YAPs, FASs, and ACSL5s, and they had more SNP sites. The research offers the foundation for further exploration of molecular genetic markers of SNPs that are related to traits.

Transcriptome Comparison of Chorion-Attached and Non-chorion-attached Endometrium in Mid-gestation of Rabbit.

Background: The chorion from the placenta is directly attached to the endometrium (CA) after embryo implantation while some parts of the endometrium are not chorion-attached (NCA). The differences in gene expression between the CA and NCA endometrium mid-gestation are unknown. Our objective was to compare the gene expression profiles of the CA and NCA endometrium of rabbit, to identify the differentially expressed genes (DEGs), and correlate the differences with the physiological state of the endometrium at mid-gestation of rabbit. Methods: We used transcriptome sequencing to reveal the differences in gene expression between CA and NCA endometrium (n = 3), and then determined the concentration of inflammatory cytokines in CA and NCA tissue and serum by ELISA. Results: Six Hundred and Forty-Six DEGs were identified between the CA and NCA endometrium [p < 0.05, |log2 (fold change) |≥ 2], The expression levels of 590 DEGs were higher in the NCA endometrium than in the CA endometrium, while the expression level of only 56 DEGs were higher in CA than in NCA. The DEGs were enriched in gene ontology (GO) terms and pathways related to immune regulation and cellular adhesions. Six hub-genes related to inflammatory mediator regulation of transient receptor potential (TRP) channels and chemokine signaling pathways had a lower expression level in the CA endometrium compared to the NCA endometrium, and the expression levels of genes related to focal adhesion and extracellular matrix (ECM)-receptors were significantly higher in NCA endometrium than in CA endometrium. The level of pro-inflammatory cytokines accumulated in the CA endometrium, and high abundance of integrin-ß and THBS1 were localized in the luminal epithelium of the NCA endometrium, but not in the CA endometrium. Conclusions: Our study reveals differences in gene expression between the CA and NCA endometrium at mid-gestation of rabbit, and suggests implications for endometrial physiological function. The CA endometrium showed relative low-level gene expression compared to the NCA endometrium, while the NCA endometrium performed physiological functions related to focal adhesion and ECM-receptor interaction.

Circular RNA, microRNA and Protein Profiles of the Longissimus Dorsi of Germany ZIKA and Sichuan White Rabbits.

Due to the dietetic properties and remarkable nutritive value of rabbit meat, its industry is increasing rapidly. However, the association between circular RNAs, microRNAs, and proteins and muscle fiber type, and meat quality of rabbit is still unknown. Here, using deep sequencing and iTRAQ proteomics technologies we first identified 3159 circRNAs, 356 miRNAs, and 755 proteins in the longissimus dorsi tissues from Sichuan white (SCWrabs) and Germany great line ZIKA rabbits (ZIKArabs). Next, we identified 267 circRNAs, 3 miRNAs, and 29 proteins differentially expressed in the muscle tissues of SCWrabs and ZIKArabs. Interaction network analysis revealed some key regulation relationships between noncoding RNAs and proteins that might be associated with the muscle fiber type and meat quality of rabbit. Further, miRNA isoforms and gene variants identified in SCWrabs and ZIKArabs revealed some pathways and biological processes related to the muscle development. This is the first study of noncoding RNA and protein profiles for the two rabbit breeds. It provides a valuable resource for future studies in rabbits and will improve our understanding of the molecular regulation mechanisms in the muscle development of livestock. More importantly, the output of our study will benefit the researchers and producers in the rabbit breeding program.

Whole transcriptome sequencing reveals that non-coding RNAs are related to embryo morphogenesis and development in rabbits.

The roles of long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) in embryonic development remain unclear. We performed a comprehensive analysis of lncRNA and circRNA profiles in rabbit embryos at different stages by whole transcriptome sequencing. We identified 719 lncRNAs and 744 circRNAs that were differentially expressed between stages S1, S2 and S3. A total of 241 differentially expressed lncRNAs and 166 differentially expressed circRNAs were significantly involved in embryonic morphogenesis and development. An RNA network was established and of the embryonic development-associated RNAs, the lncRNAs TCONS_00009253 and TCONS_00010436 were persistently downregulated, while circRNA_07129, circRNA_15209, and circRNA_12526 were persistently upregulated, and their co-expressed mRNAs TBX1, WNT3 and FGFR2 were persistently downregulated during embryonic development. These candidate RNAs were mainly involved in the Wnt, PI3K-Akt, and calcium signaling pathways. This study reports candidate lncRNAs and circRNAs that may be indispensable for the morphogenesis and development of rabbit embryos.

Comparative analysis of host resistance to Sarcoptes scabiei var. cuniculi in two different rabbit breeds.

BACKGROUND: Scabies, caused by infestation of the mite Sarcoptes scabiei, is one of the most severe ectoparasitic diseases in rabbits. Scabies seriously affects the commercial rabbit breeding, causing severe economic losses. Host resistance to S. scabiei is an important factor in further development of the rabbit industry. In the present study, we compared the host resistance to S. scabiei var. cuniculi of a new breed of domestic rabbit propagated by the Sichuan Animal Sciences Academy (QiXing rabbit, QX) compared with that of a traditional rabbit breed in the domestic rabbit industry (IRA rabbit, IRA). METHODS: Both QX and IRA rabbits were experimentally infested with live S. scabiei var. cuniculi mites for 48 h. Then, during the course of four-week experimental infestation period, the body weight of rabbits was recorded every two weeks for calculating body-weight variations in comparison to the non-infested control rabbits. Skin lesions in the foot area were assessed on weekly basis and serum samples were tested weekly for the estimation of changes in the total antibody levels (IgG, IgE and IgM). Moreover, DNA extracted from the blood samples was amplified for analysis of the genetic diversity in the major histocompatibility complex, class II, DQ Alpha (MHC-DQA) gene. RESULTS: Compared to the IRA rabbits, the QX rabbits showed a significantly higher (P < 0.05) relative body weight gain compared to the non-infested control rabbits and significantly lower (P < 0.05) scores for foot skin lesions and higher levels of IgG, IgE and IgM at weeks 1 to 4, week 2 and week 1 post-infestation, respectively. Furthermore, a polymorphism site at position 103 bp of exon two of MHC-DQA gene and a different gene frequency were found between two rabbit breeds, suggesting the genetic basis for the differential host resistance to the S. scabiei var. cuniculi between two rabbit breeds. CONCLUSIONS: The QX rabbits showed higher host resistance to S. scabiei var. cuniculi compared to the IRA rabbits at the clinical, immunological and genetic levels. These results provide a reference for the breeding of rabbits with adequately improved and sustained host resistance to scabies in the domestic rabbit industry.

Identification of Long Non-Coding RNAs Related to Skeletal Muscle Development in Two Rabbit Breeds with Different Growth Rate.

Skeletal muscle development plays an important role in muscle quality and yield, which decides the economic value of livestock. Long non-coding RNAs (lncRNAs) have been reported to be associated with skeletal muscle development. However, little is revealed about the function of lncRNAs in rabbits' muscle development. LncRNAs and mRNAs in two rabbit breeds (ZIKA rabbits (ZKR) and Qixin rabbits (QXR)) with different growth rates at three developmental stages (0 day, 35 days, and 84 days after birth) were researched by transcriptome sequencing. Differentially expressed lncRNAs and mRNAs were identified for two rabbit breeds at the same stages by DESeq package. Co-expression correlation analysis of differentially expressed lncRNAs and mRNAs were performed to construct lncRNA⁻mRNA pairs. To explore the function of lncRNAs, Gene Ontology (GO) analysis of co-expression mRNAs in lncRNA⁻mRNA pairs were performed. In three comparisons, there were 128, 109, and 115 differentially expressed lncRNAs, respectively. LncRNAs TCONS_00013557 and XR_518424.2 differentially expressed in the two rabbit breeds might play important roles in skeletal muscle development, for their co-expressed mRNAs were significantly enriched in skeletal muscle development related GO terms. This study provides potentially functional lncRNAs in skeletal muscle development of two rabbit breeds and might be beneficial to the production of rabbits.

Expression profiles of myostatin, myogenin, and Myosin heavy chain in skeletal muscles of two rabbit breeds differing in growth rate.

The purpose of the present study was to compare mRNA levels of myostatin (MSTN), myogenin (MyoG), and fiber type compositions in terms of myosin heavy chain (MyHC) in skeletal muscles of two rabbit breeds with different body sizes and growth rates. Longissimus dorsi and biceps femoris muscles of 16 Californian rabbits (CW) and 16 Germany great line of ZIKA rabbits (GZ) were collected at the ages of 35d and 84d (slaughter age). The results showed that the live weights of GZ rabbits of 35d and 84d old were approximately 36% and 26% greater than those of CW rabbits, respectively. Quantitative real-time PCR analysis revealed that at the age of 84d GZ rabbits contained significantly lower MSTN mRNA level and higher MyoG mRNA level in both longissimus dorsi and biceps femoris muscles than CW rabbits, and mRNA levels of MSTN and MyoG exhibited opposite changes from the age of 35d to 84d, suggesting that GZ rabbits were subjected to less growth inhibition from MSTN at slaughter age, which occurred most possibly in skeletal muscles. Four types of fiber were identified by real-time PCR in rabbit muscles, with MyHC-1 and MyHC-2D, MyHC-2B were the major types in biceps femoris and longissimus dorsi muscles, respectively. At the age of 84d, GZ rabbits contained greater proportion of MyHC-1 and decreased proportion of MyHC-2D and decreased lactate dehydrogenase activity in biceps femoris than CW rabbits, and the results were exactly opposite in longissimus dorsi, suggesting that GZ rabbits show higher oxidative capacity in biceps femoris muscle than CW rabbits. In conclusion, the trends of mRNA levels of MSTN and fiber types in GZ rabbits' skeletal muscles might be consistent with the putative fast growth characteristic of GZ rabbits compared to CW rabbits.

High-altitude adaptation of yak based on genetic variants and activity of lactate dehydrogenase-1.

This study investigates the molecular mechanism by which yaks (Bos grunniens) adapt to hypoxia based on lactate dehydrogenase (LDH). Three LDH1 variants of the yak were revealed in tissue extracts by electrophoresis, including LDH1-F, LDH1-M, and LDH1-S. Kinetic analysis using purified LDH1 variants showed that the yak LDH1-M variant exhibited a similar K (m) (NADH) and the same mobility on a gel as bovine LDH1, and the LDH1-F variant showed significant differences in K (m) values for NADH or pyruvate from the other two variants of yak LDH1 and bovine LDH1. Among the three muscles assayed, yak longissimus dorsi showed the highest LDH activity and the lowest malate dehydrogenase (MDH) activity; heart muscle was exactly the opposite. Our results suggest that the three LDH1 variants might play an important role in the adaptation to hypoxia.