Song-Jia Lai

Single nucleotide polymorphisms in the FTO gene and their association with growth and meat quality traits in rabbits.

Fat mass and obesity associated (FTO) gene is an excellent candidate to affect the fatness and growth-related traits in pig and cattle. The aim of this study was to reveal the association between FTO and growth and meat quality traits in rabbits. A total of eight coding SNPs were detected, and four SNPs of them in exon 3 were further genotyped for association analysis in 442 rabbits from three breeds, including 248 New Zealand rabbits, 92 Ira rabbits, and 102 Champagne rabbits. Because there were significant differences for the allele and genotype frequencies among breeds, the association analysis was independently conducted in each breed only for these SNPs with minor allele frequency >5.0%. The results revealed that non-synonymous SNP c.499G>A (p.A167T) was significantly associated with body weight (BW) at 35, 70, and 84 days of age in New Zealand rabbits (P<0.01). The CC genotype of synonymous SNP c.660T>C was significantly associated with higher BW84, average daily weight gain, and intramuscular fat content of longissimus lumborum than TT and TC genotypes in Ira rabbits (P<0.05). There were no associations between the four SNPs and growth and meat quality traits in Champagne rabbits. Meanwhile, FTO SNPs were not associated with meat pH value. Our data indicated that FTO gene could be a candidate gene associated with growth and meat quality traits in rabbits. However, the breed-specific effect should be carefully taken into consideration.

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 (0.25<PIC<0.50) was present in both breeds. The association analysis revealed that genotypes GA and AA had higher 35 d body weight (BW) than genotype GG in both EWR (p<0.01) and NEW (p<0.05). For the 56 d BW and 70 d BW traits, genotypes AA and GA were higher than genotype GG in both two breeds, the difference was not significant (p>0.05). 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.

A transcriptome atlas of rabbit revealed by PacBio single-molecule long-read sequencing.

It is widely acknowledged that transcriptional diversity largely contributes to biological regulation in eukaryotes. Since the advent of second-generation sequencing technologies, a large number of RNA sequencing studies have considerably improved our understanding of transcriptome complexity. However, it still remains a huge challenge for obtaining full-length transcripts because of difficulties in the short read-based assembly. In the present study we employ PacBio single-molecule long-read sequencing technology for whole-transcriptome profiling in rabbit (Oryctolagus cuniculus). We totally obtain 36,186 high-confidence transcripts from 14,474 genic loci, among which more than 23% of genic loci and 66% of isoforms have not been annotated yet within the current reference genome. Furthermore, about 17% of transcripts are computationally revealed to be non-coding RNAs. Up to 24,797 alternative splicing (AS) and 11,184 alternative polyadenylation (APA) events are detected within this de novo constructed transcriptome, respectively. The results provide a comprehensive set of reference transcripts and hence contribute to the improved annotation of rabbit genome.

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.

Association of a synonymous mutation of the PGAM2 gene and growth traits in rabbits

Phosphoglycerate mutase (PGAM2) catalyzes the conversion of 3-phosphoglycerate into 2-phosphoglycerate and releases energy during glycolysis in muscle tissues. PGAM2 has been considered as a candidate gene to influence growth, development, and carcass traits in livestock. The aim of this study was to investigate the association between polymorphisms of PGAM2 and growth traits in rabbits. Three single nucleotide polymorphisms (SNPs) were identified by direct sequencing in 20 random individuals from three breeds, including c.-10C>T, c.195C>T, and c.414+17C>T. The c.195C>T was genotyped by PCR-RFLP in a total of 222 rabbits of three breeds (Tianfu black, 53 animals; Ira, 91 animals; Champagne, 78 animals). The average allele frequency among the breeds was 0.52 for allele T and 0.48 for C. The heterozygosity and effective number of alleles were 0.4992 and 1.996, respectively. The association results revealed the CT genotype of c.195C>T was associated significantly (P < 0.05) with greater body weight at 84 days of age (BW84) and with average daily weight gain (ADG). However, association of the genotypes with other production traits was not observed. The results of this study suggested PGAM2 is one of the candidate genes affecting BW84 and ADG in the rabbit.

A novel single nucleotide polymorphism of the POU1F1 gene associated with meat quality traits in rabbits

Abstract The purpose of this research was to investigate the effect of the POU1F1 gene on meat quality traits in the Hyla, Champagne, and Tianfu Black rabbit breeds. We detected one single nucleotide polymorphism and the SNP was located at 536 bp in intron 5 of this gene. Chi-square tests showed that the genotypic frequencies in the three rabbit populations were not in Hardy-Weinberg equilibrium. The PIC values indicated that the three populations had intermediate levels of genetic diversity. Rabbits with the CC genotype had a significantly greater pH0h than those with the CT genotype in the biceps femoris muscle. The least squares means for cooking loss in CT and CC rabbits were significantly higher than those for TT rabbits. Rabbits with the CC genotype had a significantly higher intramuscular fat content in the longissimus dorsi and biceps femoris muscles than those with genotype TT and CT. Thus, the results here indicate that this POU1F1 SNP may be of potential use in marker assisted selection for meat quality traits in rabbits.

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.

bioOTU: An Improved Method for Simultaneous Taxonomic Assignments and Operational Taxonomic Units Clustering of 16s rRNA Gene Sequences

Clustering of 16s rRNA amplicon sequences into operational taxonomic units (OTUs) is the most common bioinformatics pipeline for investigating microbial community by high-throughput sequencing technologies. However, the existing algorithms of OTUs clustering still remain to be improved at reliability. Here we propose an improved method (bioOTU) that first assigns taxonomy to unique tags at genus level for separating the error-free sequences of known species in reference database from artifacts, and then cluster them into OTUs by different strategies. The remaining tags, which fail to be clustered in the previous step, are further subjected to independent OTUs clustering by the optimized algorithm of heuristic clustering. The performance tests on both mock and real communities revealed that bioOTU is powerful for recovering the underlying profiles at both microbial composition and abundance, and it also produces comparable or less number of OTUs in comparison with the prevailing tools of Mothur and UPARSE. The bioOTU is implemented in C and Python languages with source codes freely available on the GitHub repository.

miR-221 modulates skeletal muscle satellite cells proliferation and differentiation

MicroRNAs (miRNAs) are a class of small non-coding RNA molecules, which play important roles in animals by targeting mRNA transcripts for translational repression. Many recent studies have shown that miRNAs are involved in the control of muscle development. In this study, the expression levels of miR-221 in different tissues and during rabbit skeletal muscle satellite cells (SMSCs) differentiation were detected. Gene ontology term enrichment was used to predict the potential biological roles of miR-221. A synthetic miR-221 mimic and a miR-221 inhibitor were used to investigate the functions of miR-221 during SMSCs proliferation and differentiation to further verify the functions of miR-221 in muscle development. In this report, we compared the expression levels of miR-221 in different tissues. The expression levels of miR-221 were upregulated after the induction of differentiation, and then were gradually downregulated during SMSCs differentiation. Overexpression of miR-221 promoted SMSCs proliferation, whereas inhibiting expression restrained proliferation in the EdU and CCK-8 assays. In addition, overexpression of miR-221 led to a decline in the expression levels of the differentiation marker genes MyoG and MHC. miR-221 overexpression suppressed SMSCs myotube formation. On the contrary, inhibition of miR-221 promoted myotube formation. Our data showed that miR-221 increased SMSCs proliferation and decreased differentiation.

Genetic effect of Myf5 gene in rabbit meat quality traits

The objective of this study was to investigate the effect of the polymorphism in the Myf5 gene on meat quality traits in the Ira and Tianfu Black rabbit breeds using polymerase chain reaction and DNA sequencing. A total of six SNPs and four haplotypes were found in Ira rabbits and only two SNPs were found in Tianfu Black rabbits. The two rabbit breeds had intermediate levels of genetic diversity according to their polymorphic information content values. The SNP association analysis in Ira indicated that SNP1-6 had a significant association with redness, yellowness and intramuscular fat values in the biceps femoris muscle, and also a significantly effect on redness in the longissimus dorsi muscle. The haplotype association analysis indicated that some haplotypes could be selected to get higher or lower meat redness, yellowness and intramuscular fat content in longissimus dorsi in Ira rabbits. Several SNPs and haplotypes of Myf5 identified here could be considered as molecular markers to improve the meat quality of Ira and Tianfu Black rabbits.