A reduced incidence of digestive disorders in rabbits is associated with allelic diversity at the TLR4 locus

Comparative Analysis of Intestinal TLR4 Gene Expression and Functional Verification in Lepus yarkandensis and Oryctolagus cuniculus

Lepus yarkandensis live year-round in harsh desert environments and are less susceptible to enteritis. The living conditions of Oryctolagus cuniculus in captivity were suitable, but they were highly susceptible to death by Gram-negative bacteria infected with inflammatory bowel disease complex.TLR4 is closely related to the occurrence of enteritis, and the neighbor-joining topology based on the 12S rDNA sequences showed that the relationship between O. cuniculus and L. yarkandensis is as high as 98%.Therefore, we chose O. cuniculus and L. yarkandensis for comparative study.The purpose of this study was to investigate the role of Toll-like receptor 4 (TLR4) in the regulation of immunity and inflammation in the intestinal tract of L. yarkandensis. In this study, the TLR4 gene was cloned for the first time in the colon of L. yarkandensis. The expression of TLR4 in the intestinal tissues of L. yarkandensis and O. cuniculus was detected by histological observation, real-time fluorescence quantification PCR(qRT-PCR), and protein blotting (Western blot).An LPS-induced cell inflammation model was constructed in vitro, and ELISA was used to examine the effect of pEGFP-N1-TLR4 and siRNA knockout on the anti-inflammatory ability of the TLR4 gene. The results showed that the open reading frame of the L. yarkandensis TLR4 gene was 2520 bp in length. Compared with the sequence of O. cuniculus, there were 15 differences in the TLR4 amino acid sequence of L. yarkandensis, 12 of which occurred in the LRR domain and 2 in the TIR domain, and the sequence changed from G to D at position 298. Immunohistochemistry showed that TLR4 was mainly expressed in the epithelial cells of the colon L. yarkandensis, and the expression level of TLR4 in the cecum and colon was significantly lower compared with that of O. cuniculus. qRT-PCR and Western blot results showed that the expression level of TLR4 in the colon of L. yarkandensis was significantly lower than that of O. cuniculus. At the cellular level, ELISA showed that overexpression of the TLR4 protein in L. yarkandensis could reduce the LPS-induced inflammatory response. Therefore, according to the above results, the protein structure and function of L. yarkandensis TLR4 may be different due to the change of nucleotide, which affects its binding with LPS and the activation of downstream molecules, so that L. yarkandensis is not prone to enteritis and can adapt to the harsh desert environment for a long time. This study also laid the foundation for improving the disease resistance of O. cuniculus and promoting the development and utilization of genes in L. yarkandensis.

Genome-wide association studies for diarrhoea outcomes identified genomic regions affecting resistance to a severe enteropathy in suckling rabbits

Selection and breeding strategies to improve resistance to enteropathies are essential to reaching the sustainability of the rabbit production systems. However, disease heterogeneity (having only as major visible symptom diarrhoea) and low disease heritability are two barriers for the implementation of these strategies. Diarrhoea condition can affect rabbits at different life stages, starting from the suckling period, with large negative economic impacts. In this study, from a commercial population of suckling rabbits (derived from 133 litters) that experienced an outbreak of enteropathy, we first selected a few animals that died with severe symptoms of diarrhoea and characterized their microbiota, using 16S rRNA gene sequencing data. Clostridium genus was consistently present in all affected specimens. In addition, with the aim to identify genetic markers in the rabbit genome that could be used as selection tools, we performed genome-wide association studies for symptoms of diarrhoea in the same commercial rabbit population. These studies were also complemented with FST analyses between the same groups of rabbits. A total of 332 suckling rabbits (151 with severe symptoms of diarrhoea, 42 with mild symptoms and 129 without any symptoms till the weaning period), derived from 45 different litters (a subset of the 133 litters) were genotyped with the Affymetrix Axiom OrcunSNP Array. In both genomic approaches, rabbits within litters were paired to constitute two groups (susceptible and resistant, including the mildly affected in one or the other group) and run case and control genome-wide association analyses. Genomic heritability estimated in the designed experimental structure integrated in a commercial breeding scheme was 0.19-0.21 (s.e. 0.09-0.10). A total of eight genomic regions on rabbit chromosome 2 (OCU2), OCU3, OCU7, OCU12, OCU13, OCU16 and in an unassembled scaffold had significant single nucleotide polymorphisms (SNPs) and/or markers that trespassed the FST percentile distribution. Among these regions, three main peaks of SNPs were identified on OCU12, OCU13 and OCU16. The QTL region on OCU13 encompasses several genes that encode members of a family of immunoglobulin Fc receptors (FCER1G, FCRLA, FCRLB and FCGR2A) involved in the immune innate system, which might be important candidate genes for this pathogenic condition. The results obtained in this study demonstrated that resistance to an enteropathy occurring in suckling rabbits is in part genetically determined and can be dissected at the genomic level, providing DNA markers that could be used in breeding programmes to increase resistance to enteropathies in meat rabbits.

Identification of two novel single nucleotide polymorphism sites in the Myostatin (MSTN) gene and their association with carcass traits in meat-type rabbits (Oryctolagus cuniculus)

<p>Two unknown single nucleotide polymorphism (SNP) sites in exons 1 (c.194C&gt;T) and 2 (c.445T&gt;A) of meat-type rabbit <em>MSTN</em> gene were identified in the study. Our objective was to analyse the population genetics structure of the two novel SNP sites in 230 individuals from six breeds and their associations with carcass traits of rabbits. We found that live body weight (BW), cold carcass weight (CCW), reference carcass weight (RCW), CCW percentage (P_CCW) and RCW percentage (P_RCW) of the rabbits with the genotype CC at the c.194C&gt;T of exon 1 or AA at the c.445T&gt;A of exon 2 were significantly higher than those with other genotypes. Diplotype significantly affected BW, RCW, CCW, P_RCW (<em>P</em>&lt;0.01) and P_CCW and P_CM (<em>P</em>&lt;0.05). CC/AA was the advantageous diplotype for BW, RCW, CCW and P_CM, and TT/AA was the advantageous diplotype for P_CCW and P_RCW. In contrast, TT/TT was the negative diplotype for BW, CCW, RCW, P_CCW and P_RCW, and TT/AA was the negative diplotype for P_CM. The results suggest that the two new mutations of <em>MSTN</em> gene significantly affected BW, CCW, RCW, P_CCW and P_RCW of rabbits, and <em>MSTN</em> may be an important candidate gene of carcass traits in meat-type rabbits.</p>

Gut microbiota profiling with differential tolerance against the reduced dietary fibre level in rabbit

Dietary fibre is well acknowledged to be critical in maintaining the gut homeostasis in human and other monogastric animals. As a small monogastric herbivorous animal, rabbit is much sensitive to the reduced intake of dietary fibre and more interestingly shows individual difference in clinical tolerance. In the present study, we fed rabbits with fibre-deficiency diet for two weeks and successfully distinguished the individual tolerances according to clinical signs and gastrointestinal gross lesions. A total of 40 treatments were classified into three groups of the full health (N = 10), moderate intestinal disorder (N = 11) and severe intestinal disorder (N = 19). Together with three controls, 43 individuals were subjected to gut microbiota profiling by 16S rRNA gene sequencing. It was revealed that the Firmicutes/Bacteroidetes ratio steadily decreased from 1.74 in healthy group to 1.03 in severe group. However, the healthy individuals that showed complete tolerance still remained a comparable Firmicutes/Bacteroidetes ratio with controls. Notably, the class Alphaproteobacteria was found to be higher abundance in healthy group than controls and other treatment groups. The results would improve our understanding of the relationship among dietary fibre, gut microbiota and host health.

Investigation of significant microRNA-mRNA pairs associated with nonspecific digestive disorder in rabbits

Nonspecific digestive disorders (NSDD) are one of the major intestinal problems in rabbit, with considerable economic losses in industrial rabbit farms. MicroRNAs (miRNAs), as small non-coding RNAs, have significant biological involvement in intestinal disorders. In this study, we investigated the expression levels of 25 genes and 25 miRNAs in ileum, rabbit sacculus rotundus (RSR) and colon tissues from 9 rabbits with different severity of NSDD. These molecules have been found to be related to NSDD or inflammatory bowel disease, which will help recognise the miRNA-mRNA pairs. Finally, 108 possible pairs of miRNA-mRNA pairs with an anti-correlation were identified by Pearson’s correlation analysis between differentially expressed 25 miRNAs and 23 mRNAs. Ninety-five of these miRNA-mRNA pairs were hitherto unexplored, and their roles in NSDD biology require further elucidation. Our results give a clue to the potential miRNA-mRNA pairs for the NSDD that can further improve the understanding of the pathogenesis of NSDD in rabbit.

A synonymous mutation of uncoupling protein 2 (UCP2) gene is associated with growth performance, carcass characteristics and meat quality in rabbits

Background

Uncoupling proteins 2 (UCP2) plays an important role in energy regulation, previous studies suggested that UCP2 is an excellent candidate gene for human obesity and growth-related traits in cattle and chicks. The current study was designed to detect the genetic variation of UCP2 gene, and to explore the association between polymorphism of UCP2 gene and growth, carcass and meat quality traits in rabbits.

Results

A synonymous mutation in exon 1 and four variants in the first intron of the UCP2 gene were identified by using PCR-sequencing. The synonymous mutation c.72G>A was subsequently genotyped by MassArray system (Sequenom iPLEXassay) in 248 samples from three meat rabbit breeds (94 Ira rabbits, 83 Champagne rabbits, and 71 Tianfu black rabbits). Association analysis suggested that the individuals with AA and AG genotypes showed greater 70 d body weight (P < 0.05), 84 d body weight (P < 0.01), ADG from 28 to 84 days of age (P < 0.05), eviscerated weight (P < 0.01), semi-eviscerated weight (P < 0.01) and semi-eviscerated slaughter percentage (P < 0.05), respectively. Additionally, the individuals with AA and AG genotype had a lower pH value of longissimus muscle (P < 0.01) and hind leg muscle (P < 0.05) after slaughter 24 h.

Conclusions

These findings indicated that UCP2 could be a candidate gene that associated with growth performance, body composition and meat quality in rabbits, and this would contribute to advancements in meat rabbit breeding practice.

Single Nucleotide Polymorphisms of NLRP12 Gene and Association with Non-specific Digestive Disorder in Rabbit

The NLRP12 (NLR family, pyrin domain containing 12) serves as a suppressor factor in the inflammatory response and protects the host against inflammation-induced damage. In the present study, we aimed to study the polymorphisms of NLRP12 gene and its association with susceptibility to non-specific digestive disorder (NSDD) in rabbits. We re-sequenced the entire coding region of the rabbit NLRP12 gene and detected a total of 19 SNPs containing 14 synonymous and five non-synonymous variations. Among them, the coding SNP (c.1682A>G), which would carry a potential functional implication, was subsequently subjected to genotyping for case-control association study (272 cases and 267 controls). The results revealed that allele A was significantly protective against NSDD with an odds ratio value of 0.884 (95% confidence interval, 0.788 to 0.993; p = 0.038). We also experimentally induced NSDD in growing rabbits by feeding a fibre-deficient diet and subsequently investigated NLRP12 mRNA expression. The mRNA expression of NLRP12 in healthy status was significantly higher than that in severe NSDD (p = 0.0016). The highest expression was observed in individuals carrying the protective genotype AA (p = 0.0108). These results suggested that NLRP12 was significantly associated with the NSDD in rabbits. However, the precise molecular mechanism of NLRP12 involving in the development of rabbit NSDD requires further research.

Polymorphism of NLRP3 Gene and Association with Susceptibility to Digestive Disorders in Rabbit

NLR family pyrin domain containing 3 (NLRP3) is a key component of the inflammasome, whose assembly is a crucial part of the innate immune response. The aim of the present study was to evaluate the association between exon 3 polymorphisms of NLRP3 and the susceptibility to digestive disorders in rabbits. In total, five coding single-nucleotide polymorphisms (cSNPs) were identified; all of which are synonymous. Among them, c.456 C> and c.594 G> were further genotyped for association analysis based on case-control design (n =162 vs n =102). Meanwhile, growing rabbits were experimentally induced to digestive disorders by feeding a fiber-deficient diet, subsequently they were subjected to mRNA expression analysis. Association analysis revealed that haplotype H1 (the two cSNPs: GT) played a potential protective role against digestive disorders (p<0.001). The expression of NLRP3 in the group H1HX₁ (H1HX₁ is composed of H1H1, H1H3 and H1H4) was the lowest among four groups which were classified by different types of diplotypes. Those results suggested that the NLRP3 gene was significantly associated with susceptibility to digestive disorders in rabbit.

Effects of variants in proopiomelanocortin and neuropeptide y genes on growth, carcass, and meat quality traits in rabbits

Appetite-related neuropeptides proopiomelanocortin (POMC) and Neuropeptide Y (NPY) are essential for regulating feeding behavior and energy homeostasis. The objective of this study was to evaluate the effects of variants in POMC and NPY genes on growth, carcass and meat quality traits in rabbits. A total of six SNPs were identified for POMC (n = 2) and NPY (n = 4) genes by direct sequencing. Three SNPs were subsequently genotyped by using MassArray system (Sequenom iPLEXassay) in 235 individuals, which belong to three meat rabbit breeds, including 93 Ira rabbits; 81 Champagne rabbits and 61 Tianfu black rabbits. The SNP c.112-12G>T was in intron-exon boundaries (intron 1) of POMC gene, and the association analysis showed that individuals with TT genotype had a greater 84 d body weight (BW84), eviscerated weight and semi-eviscerated weight than those with GT genotype (p<0.05); the TT individuals were also higher than those GG in the ripe meat ratio (RMR) (p<0.05). The g.1778G>C SNP, which was in complete linkage with other three SNPs (g.1491G>A, g.1525G>T and g.1530C>T) in intron 1 of NPY gene, was significantly correlated with eviscerated slaughter percentage and semi-eviscerated slaughter percentage in rabbits, and the individuals with CC genotype had a better performance than CG genotype (p<0.05). These findings would provide primary clues for the biological roles of POMC and NPY underlying the rabbit growth-related traits.

Rapid Genotyping of MSTN Gene Polymorphism Using High-resolution Melting for Association Study in Rabbits

The myostatin (MSTN) gene, as a negative regulator of skeletal muscle growth, has been proposed to be associated with production traits in farm animals. In the present study, a T/C variant at −125 bp (relative to ATG start codon) of 5’regulatory region of rabbit MSTN was identified by direct sequencing. Two hundred and twenty two rabbits, which were randomly sampled from 3 breeds (Ira rabbits, Champagne rabbits and Tianfu black rabbits), were genotyped by high-resolution melting (HRM). Comparing the genotyping results of 47 samples with direct sequencing, the HRM showed high sensitivity (0.96) and high specificity (0.98). In the three rabbit breeds, the allele C was the predominant allele. The polymorphic site showed high heterozygosity (He = 0.48) and high effective number of alleles (Ne = 1.91). The genetic diversity was reasonably informative (0.25<PIC<0.50). The association analysis showed that the genotype TC had significant effect on the 84-d-weight of rabbits compared with genotype CC (p = 0.047). In contrast, the genotypes had no significant effect on other production traits. These results showed that HRM could be effectively used for genotyping analysis of MSTN gene. The T/C variant in 5’regulatory region of MSTN might be one of the candidate SNP loci affecting the trait of 84-d-weight.

Investigation of JAK1 and STAT3 polymorphisms and their gene-gene interactions in nonspecific digestive disorder of rabbits

Acting in a cellular signaling pathway, Janus kinase 1 (JAK1) and signal transducer and activator of transcription 3 (STAT3) play critical roles in several kinds of physiological and pathological responses, including inflammatory response. In this study, we detected three coding single nucleotide polymorphisms (cSNPs) of JAK1 and four cSNPs of STAT3 in New Zealand White rabbits. We analyzed their association with genetic resistance to nonspecific digestive disorder (NSDD) based on a case-control study (253 cases and 227 controls). The rabbits were genotyped for c.1421 C>T and c.3036 G>A in JAK1 using restriction fragment length polymorphisms and for c.831 T>C and c.399 G>A of STAT3 using high-resolution melting technology. The frequencies of the alleles and genotypes differed significantly between the case and control groups (P<0.05). The case-control association analysis revealed that in JAK1, allele C increased the risk of NSDD (OR: 1.60, 95% CI 1.166-2.185, P=0.003), whereas allele A played a potentially protective role against NSDD (OR: 0.74, 95% CI 0.572-0.952, P=0.019). We used five inheritance models to evaluate the importance of the associated genotypes. Under the dominant inheritance model, the association analysis suggested that the CT/TT genotype increased the risk of NSDD (OR: 1.65, 95% CI 1.13-2.40, P=0.009). A haplotype analysis showed that allele H2 (the two cSNPs: CG; OR: 1.354, 95% CI 1.050-1.747, P=0.019) markedly increased the risk of the disorder. The association analysis revealed that in STAT3, allele G played a potentially protective role against NSDD (OR: 0.74; 95% CI 0.569-0.951; P=0.019), whereas allele C increased the risk of NSDD (OR: 1.37; 95% CI 1.059-1.760; P=0.016). Recessive inheritance was shown to be the best fitting model for c.399 and c.831. Under the recessive inheritance model, the association analysis suggested that the G/G genotype increased the risk of NSDD (OR: 1.73; 95% CI 1.07-2.80; P=0.025). A haplotype analysis showed that H1' (the two cSNPs: AC; OR: 1.365; CI 1.059-1.760; P=0.016) significantly increased the risk of the disorder. The CATMOD program (SAS 9.2) and the multifactor dimensionality reduction method were used to analyze the genetic interactions between JAK1 and STAT3. Data on the genetic interactions revealed that the JAK1 and STAT3 risk alleles described above contribute to NSDD susceptibility in combination with each other, and that model (c1421, c3036, c831) was the best model (OR: 2.7262; 95% CI: 4.7408-5.1986; P<0.0001). To our knowledge, this is the first report of the genetic polymorphisms of the JAK1 and STAT3 genes and their associations with the incidence of NSDD in rabbits.

Identification and Association of SNPs in TBC1D1 Gene with Growth Traits in Two Rabbit Breeds

The TBC1D1 plays a key role in body energy homeostasis by regulating the insulin-stimulated glucose uptake in skeletal muscle. The present study aimed to identify the association between genetic polymorphisms of TBC1D1 and body weight (BW) in rabbits. Among the total of 12 SNPs detected in all 20 exons, only one SNP was non-synonymous (c.214G>A. p.G72R) located in exon 1. c.214G>A was subsequently genotyped among 491 individuals from two rabbit breeds by the high-resolution melting method. Allele A was the predominant allele with frequencies of 0.7780 and 0.6678 in European white rabbit (EWR, n = 205) and New Zealand White rabbit (NZW, n = 286), respectively. The moderate polymorphism information content (0.250.05). Our results implied that the c.214G>A of TBC1D1 gene might be one of the candidate loci affecting the trait of 35 d BW in the rabbit.

Dectin-1 gene polymorphism is associated with susceptibility to nonspecific digestive disorders and cytokine expression in rabbits

Dectin-1 plays a critical role in the pathogenesis of intestinal inflammation by recognizing the pathogenic agents and mediating cytokine responses. The objective of this study was to establish the association between dectin-1 polymorphisms and susceptibility to nonspecific digestive disorders (NSDD) and cytokine expression in rabbits. A total of 7 coding SNP were detected in dectin-1 gene. The genetic association between SNP (ss707197675A > G) and susceptibility to NSDD was evaluated using a case-control study (178 cases and 174 controls). The results revealed that the A allele was associated with an increased risk of developing NSDD in rabbits. The AA genotype significantly increased the genetic susceptibility to NSDD with odds ratio of 4.76 (95% confidence interval, 1.92-12.50, P = 0.0002) compared with GG and GA genotypes. We also experimentally induced NSDD in another independent growing rabbit population by feeding a low-fiber diet and subsequently investigated the cytokine mRNA expression. Among the 4 studied cytokines, the expression of interferon-γ, IL-17F, and IL-22 were increased 2.8 to 6.0-fold in AA genotype compared with GG genotype (P < 0.01). The greater IL-17F and IL-22 mRNA expressions indicated a positive correlation with severe intestinal inflammation (P < 0.05). The decreased expression of IL-10 was associated with severe intestinal inflammation (P = 0.006), but IL-10 expression was not influenced by dectin-1 genotype. In conclusion, polymorphism ss707197675 of dectin-1 is related with susceptibility to NSDD and increased expression of proinflammatory cytokines, and dectin-1 could be an important candidate gene associated with NSDD in rabbits.

Case-control study and mRNA expression analysis reveal the MyD88 gene is associated with digestive disorders in rabbit

As in humans, significant associations between Toll-like receptor 4 (TLR4) and digestive disorders have been identified in rabbit and dog. However, as an essential adaptor downstream of TLR4, the genetic variation of myeloid differentiating factor 88 (MyD88) and its association with digestive disorders have remained unknown. In this study, we detected 10 single nucleotide polymorphisms (SNPs) in the entire genomic region of rabbit MyD88. The genetic variation in susceptibility to digestive disorders for the only coding SNP (synonymous c.699T>C) was studied in Yaan (183 cases and 142 controls) and Chengdu populations (145 cases and 140 controls). A case-control association study revealed that individuals with the C allele had significant protection against digestive disorders in the Yaan population (OR = 0.71; 95% CI, 0.51-0.99; P < 0.05), the Chengdu population (OR = 0.55; 95% CI, 0.39-0.78; P < 0.01) and for joint analysis (OR = 0.62; 95% CI, 0.49-0.79; P < 0.01). We also experimentally induced digestive disorders by feeding a fiber-deficient diet and found that increased susceptibility was significantly associated with higher MyD88 mRNA expression (P < 0.05). The lowest MyD88 mRNA expression was observed in individuals carrying the protective CC genotype. These results suggest that MyD88 is one of the most plausible candidate genes in relation to digestive disorders in rabbit. Further studies are required to explore the biological implications of MyD88 in the pathogenesis of digestive disorders.

A synonymous mutation in NOD2 gene was significantly associated with non-specific digestive disorder in rabbit

Nucleotide-binding oligomerization domain containing 2 (NOD2) plays a pivotal role in the host innate and adaptive immunity by recognizing the pathogenic agents. Therefore, its genetic polymorphisms and association with susceptibility to infectious diseases have been widely reported in human and farm animals. In the present study, we investigated the genetic polymorphisms in 3171 bp coding region of NOD2 gene and association with non-specific digestive disorder (NSDD) in rabbit. A total of four coding single-nucleotide polymorphisms (cSNPs) were detected. Among them, c.2961C>T was further genotyped for case (n=176) and control (n=130) based on association analysis, which revealed that C allele carried the potential protective role for susceptibility to NSDD with the odds ratio (OR) values of 0.52 (95% confidence interval (CI) 0.37-0.73, P<0.01). Under the dominant inheritance model, CC genotype was associated with decreased susceptibility to NSDD (OR=0.38, 95% CI 0.24-0.60, P<0.01). Along with the aggravation of NSDD, we observed higher mRNA expression of NOD2 gene (P<0.05). However, the mRNA expression pattern of CC genotype would be interacted by the different status of NSDD, which only showed the significantly increased level in severe NSDD group (P<0.05). These results revealed by genetic association and gene expression analysis suggested that the NOD2 gene was associated with the susceptibility to NSDD in rabbit. However, the causative mutations linked to c.2961C>T and corresponding functional depiction should be further explored by performing exhaustive genetic studies.

[Functional analysis of SNPs in porcine TLR4 gene]

Toll-like receptor 4 (TLR4) plays an important role in immune response and the polymorphism in it might affect protein signaling and host resistance/susceptibility to disease. This study was designed to characterize the functional relevance of 3 nonsynonymous single nucleotide polymorphisms (SNPs), c.611 T>A (p.Leu204His), c.1027 C>A (p.Gln343Lys), and c.1605 G>T (p.Leu535Phe), which were selected based on our previous studies. RT-PCR method was used to clone the complete coding sequence of porcine TLR4 gene and the PCR-based method was used to introduce the point mutation. The effects of 3 SNPs on the ligand recognition and signaling of porcine TLR4 were investigated in transiently transfected PK-15 cells using dual-luciferase reporter system and Western blotting method. At the same time, the distribution of c.1605 G>T among pig populations composed of Min pig, Yorkshire, Landrace, and Wild boar from northeastern China was studied by created restriction site PCR-RFLP method. The complete coding sequence of TLR4 gene in Min pig and 3 variants with single point mutations were obtained. Eukaryotic expression vectors containing different alleles of porcine TLR4 were constructed. SNP c.1605 G>T significantly decreased the TLR4 signaling (P<0.01) and the polymorphism only existed in Min pig and Wild boar from northeastern China with high frequencies. SNP c.1605 G>T in porcine TLR4 might affect the receptor function and host resistance/susceptibility to diseases.