Jindong Ren

Analysis of miRNAs and their target genes associated with lipid metabolism in duck liver.

Fat character is an important index in duck culture that linked to local flavor, feed cost and fat intake for costumers. Since the regulation networks in duck lipid metabolism had not been reported very clearly, we aimed to explore the potential miRNA-mRNA pairs and their regulatory roles in duck lipid metabolism. Here, Cherry-Valley ducks were selected and treated with/without 5% oil added in feed for 2 weeks, and then fat content determination was performed on. The data showed that the fat contents and the fatty acid ratios of C17:1 and C18:2 were up-regulated in livers of oil-added ducks, while the C12:0 ratio was down-regulated. Then 21 differential miRNAs, including 10 novel miRNAs, were obtain from the livers by sequencing, and 73 target genes involved in lipid metabolic processes of these miRNAs were found, which constituted 316 miRNA-mRNA pairs. Two miRNA-mRNA pairs including one novel miRNA and one known miRNA, N-miR-16020-FASN and gga-miR-144-ELOVL6, were selected to validate the miRNA-mRNA negative relation. And the results showed that N-mir-16020 and gga-miR-144 could respectively bind the 3′-UTRs of FASN and ELOVL6 to control their expressions. This study provides new sights and useful information for future research on regulation network in duck lipid metabolism.

Paternity assessment: application on estimation of breeding value in body-weight at first egg trait of egg-laying duck (Anas platyrhynchos)

Paternity index was analyzed using five microsatellite loci among Chinese egg-laying ducks (Anas platyrhynchos). Based on the paternity relationship that was identified by paternity index analysis, the estimated breeding value (EBV) was calculated using BLUP (best linear unbiased predictor) method. Body weight at first egg (BWF) is the only considered trait in this study. In total, 12 sires, 31 dams and 77 daughters were involved in the EBV calculation. The results demonstrated that five microsatellite loci’s polymorphism information content (PIC) ranged from 0.795 in locus AY493338 to 0.957 in locus AY493264 with average 0.899; the parent–offspring relationships were built by these microsatellites’ genotype, 12 families of half sibling and 2 families of full sibling were involved, and the relationship error is smaller than 10−7. The EBV results suggest that the average EBV was significantly higher in females (average EBV is 10.234 and 0.1045 for mother and daughter, respectively) than males (average EBV is just −26.44). The EBV results on BWF were in good agreement with the principle of GH (growth hormone) expression in poultry. These results show that paternity analyses of Chinese egg-laying ducks were basically resolved using the five microsatellite loci selected. The paternity relationships can apply in Chinese egg-laying duck breeding to quicken the improvement of genetic progress.

Identification of Egg White Proteins and Divergence in the Regulatory Region of the Ovalbumin Gene in Avians

Egg white proteins play an important role in avian reproductive systems and are an ideal resource for bioreactor construction. In this study, 1D electrophoresis and MALDI-TOF-MS were performed to analyze egg white proteins in four species. In total, 18, 11, 28, and 13 proteins were identified in the egg whites of the chicken, duck, goose, and pigeon, respectively. Egg white proteins in chickens have been studied previously; therefore, we focused on the proteins in goose and duck egg whites. Based on the amino acid sequence analysis and a comparison of the unique peptides, high similarity was observed between the goose and duck egg whites. Diversity in the regulatory region of the ovalbumin gene explained the higher ovalbumin expression in the duck and goose than in the chicken. These data clarify the evolutionary processes underlying to the unique peptides contributing to the differential expression of ovalbumin in avians.

Divergently expressed gene identification and interaction prediction of long noncoding RNA and mRNA involved in duck reproduction

Long noncoding RNAs (lncRNAs) and divergently expressed genes exist widely in different tissues of mammals and birds, in which they are involved in various biological processes. However, there is limited information on their role in the regulation of normal biological processes during differentiation, development, and reproduction in birds. In this study, whole transcriptome strand-specific RNA sequencing of the ovary from young ducks (60days), first-laying ducks (160days), and old ducks, i.e., ducks that stopped laying eggs (490days) was performed. The lncRNAs and mRNAs from these ducks were systematically analyzed and identified by duck genome sequencing in the three study groups. The transcriptome from the duck ovary comprised 15,011 protein-coding genes and 2905 lncRNAs; all the lncRNAs were identified as novel long noncoding transcripts. The comparison of transcriptome data from different study groups identified 2240 divergent transcription genes and 135 divergently expressed lncRNAs, which differed among the groups; most of them were significantly downregulated with age. Among the divergent genes, 38 genes were related to the reproductive process and 6 genes were upregulated. Further prediction analysis revealed that 52 lncRNAs were closely correlated with divergent reproductive mRNAs. More importantly, 6 remarkable lncRNAs were correlated significantly with the conversion of the ovary in different phases. Our results aid in the understanding of the divergent transcriptome of duck ovary in different phases and the underlying mechanisms that drive the specificity of protein-coding genes and lncRNAs in duck ovary.

Genetic parameter estimation for growth traits of Pacific white shrimp(Litopenaeus vannamei)

Eighteen half-sib families and fifty-four full-sib families were constructed using methods of nest design and artificial insemination,in which each male mated three females.Sixty 5-month-old shrimp were measured for nine growth traits including the body weight(BW),the total length(TL),the body length(BL),the carapace length(CL),the carapace width(CW),the carapace depth(CD),the first abdominal segment depth(FASD),the third abdominal segment depth(TASD),and first abdominal segment width(FASW).According to quantitative genetics theory,the heritability of each growth trait,and the genetic and phenotypic correlation among the traits were statistically studied utilizing the method of variance and covariance analysis.The results showed that the heritability estimates in the narrow sense from intra-group correlation of paternal half-sib were precise and unbiased,and the heritability values for the above nine traits were 0.460,0.392,0.303,0.234,0.251,0.330,0.282,0.321 and 0.356,respectively.All of them belonged to moderate and high heritability,thus showed a high potential for selective breeding.The estimates of genetic correlation coefficients were 0.750-0.976,where the highest(0.976)was that between the BW and the TL,while the lowest(0.750)was seen between the TL and the TASD.The estimates of phenotypic correlation coefficients were 0.507-0.947,where the highest(0.947)was seen between the BW and the TL,while the lowest(0.507)was that between the FASD and the CD.Very significant difference was detected by t-test(P0.01)among the nine growth traits for both genetic and phenotypic correlation coefficients,which indicate all the nine traits may respond favorably to direct and indirect selection for growth.