Transcriptome analysis of long noncoding RNAs ribonucleic acids from the livers of Hu sheep with different residual feed intake

Genetic diversity of United States Rambouillet, Katahdin and Dorper sheep

BACKGROUND

Managing genetic diversity is critically important for maintaining species fitness. Excessive homozygosity caused by the loss of genetic diversity can have detrimental effects on the reproduction and production performance of a breed. Analysis of genetic diversity can facilitate the identification of signatures of selection which may contribute to the specific characteristics regarding the health, production and physical appearance of a breed or population. In this study, breeds with well-characterized traits such as fine wool production (Rambouillet, N = 745), parasite resistance (Katahdin, N = 581) and environmental hardiness (Dorper, N = 265) were evaluated for inbreeding, effective population size (Ne), runs of homozygosity (ROH) and Wright's fixation index (FST) outlier approach to identify differential signatures of selection at 36,113 autosomal single nucleotide polymorphisms (SNPs).

RESULTS

Katahdin sheep had the largest current Ne at the most recent generation estimated with both the GONe and NeEstimator software. The most highly conserved ROH Island was identified in Rambouillet with a signature of selection on chromosome 6 containing 202 SNPs called in an ROH in 50 to 94% of the individuals. This region contained the DCAF16, LCORL and NCAPG genes that have been previously reported to be under selection and have biological roles related to milk production and growth traits. The outlier regions identified through the FST comparisons of Katahdin with Rambouillet and Dorper contained genes with known roles in milk production and mastitis resistance or susceptibility, and the FST comparisons of Rambouillet with Katahdin and Dorper identified genes related to wool growth, suggesting these traits have been under natural or artificial selection pressure in these populations. Genes involved in the cytokine-cytokine receptor interaction pathways were identified in all FST breed comparisons, which indicates the presence of allelic diversity between these breeds in genomic regions controlling cytokine signaling mechanisms.

CONCLUSIONS

In this paper, we describe signatures of selection within diverse and economically important U.S. sheep breeds. The genes contained within these signatures are proposed for further study to understand their relevance to biological traits and improve understanding of breed diversity.

Detection of single nucleotide polymorphism in HTR4 and its relationship with growth traits in sheep

In this study, a single nucleotide polymorphism of HTR4 (hydroxytryptamine receptor 4) was detected using DNA sequencing and KASPar (Kompetitive Allele-Specific PCR) technique with the aim of analyzing its effect on growth traits in 1102 sheep. A synonymous mutation g.101220 C > T located on the fifth intron of the ovis HTR4 gene was detected, and association analysis showed that this mutation was significantly associated with growth traits in sheep (p ＜.05), with TT genotypes having significantly lower body weight, height, length and chest circumference than TC and CC genotypes. It showed that the polymorphism of this locus was significantly associated with growth traits in sheep. In addition, qRT-PCR results showed that HTR4 was expressed in different tissues of sheep. It is highly expressed in the liver, spleen and duodenum. As important metabolic, immune and digestive absorption organs in animals, the above tissues can regulate the excitability of intestinal smooth muscle by participating in the body metabolism and nutrient metabolism of sheep, so that sheep can show better growth characteristics. In conclusion, the polymorphic locus identified in HTR4 gene can be used as candidate molecular marker in sheep breeding.

Combined transcriptome and metabolome analysis reveal key regulatory genes and pathways of feed conversion efficiency of oriental river prawn Macrobrachium nipponense

BACKGROUND

Oriental river prawn Macrobrachium nipponense is an economically important aquaculture species in China, Japan, and Vietnam. In commercial prawn farming, feed cost constitutes about 50 to 65% of the actual variable cost. Improving feed conversion efficiency in prawn culture will not only increase economic benefit, but also save food and protect the environment. The common indicators used for feed conversion efficiency include feed conversion ratio (FCR), feed efficiency ratio (FER), and residual feed intake (RFI). Among these, RFI is much more suitable than FCR and FER during the genetic improvement of feed conversion efficiency for aquaculture species.

RESULTS

In this study, the transcriptome and metabolome of hepatopancreas and muscle of M. nipponense from high RFI low RFI groups, which identified after culture for 75 days, were characterized using combined transcriptomic and metabolomic analysis. A total of 4540 differentially expressed genes (DEGs) in hepatopancreas, and 3894 DEGs in muscle were identified, respectively. The DEGs in hepatopancreas were mainly enriched in KEGG pathways including the metabolism of xenobiotics by cytochrome P450 (down-regulated), fat digestion and absorption (down-regulated) and aminoacyl-tRNA biosynthesis (up-regulated), etc. The DEGs in muscle were mainly enriched in KEGG pathways including the protein digestion and absorption (down-regulated), glycolysis/gluconeogenesis (down-regulated), and glutathione metabolism (up-regulated), etc. At the transcriptome level, the RFI of M. nipponense was mainly controlled in biological pathways such as the high immune expression and the reduction of nutrients absorption capacity. A total of 445 and 247 differently expressed metabolites (DEMs) were identified in the hepatopancreas and muscle, respectively. At the metabolome level, the RFI of M. nipponense was affected considerably by amino acid and lipid metabolism.

CONCLUSIONS

M. nipponense from higher and lower RFI groups have various physiological and metabolic capability processes. The down-regulated genes, such as carboxypeptidase A1, 6-phosphofructokinase, long-chain-acyl-CoA dehydrogenase, et. al., in digestion and absorption of nutrients, and the up-regulated metabolites, such as aspirin, lysine, et. al., in response to immunity could be potential candidate factors contributed to RFI variation for M. nipponense. Overall, these results would provide new insights into the molecular mechanism of feed conversion efficiency and assist in selective breeding to improve feed conversion efficiency in M. nipponense.

Drying of Food Waste for Potential Use as Animal Feed

A considerable part of food is wasted, causing investment capital loss as well as environmental pollution and health problems in humans. Indirect solar drying was applied to test the potential of drying and reusing this waste as a component of animal feed. The effect of weather changes on drying kinetics and the effective diffusion coefficient, dried feed nutritional composition, and microbiological analysis of the dried product were investigated. A convective laboratory dryer was used as a reference method. Weather conditions have a crucial effect on the use of solar drying; one sunny day with appropriate conditions can reduce the water activity of food waste to below 0.3 and moisture content to below 6%. Much better fitting of experimental and model drying curves was achieved considering sample shrinkage, applying a more complex solution of Fick’s second law combined with an optimization procedure. The studied food waste had a good combination of nutrients, such as protein, fat, and carbohydrates; however, the amount of protein in the dried food waste was found to be lower than that in regular feed, and therefore, adding a protein source is recommended. Autoclaving of fresh samples reduced the total microbial counts of dried samples by more than 50%.

Transcriptome analysis reveals the potential roles of long non-coding RNAs in feed efficiency of chicken

Feed efficiency is an important economic trait and reduces the production costs per unit of animal product. Up to now, few studies have conducted transcriptome profiling of liver tissue in feed efficiency-divergent chickens (Ross vs native breeds). Also, molecular mechanisms contributing to differences in feed efficiency are not fully understood, especially in terms of long non-coding RNAs (lncRNAs). Hence, transcriptome profiles of liver tissue in commercial and native chicken breeds were analyzed. RNA-Seq data along with bioinformatics approaches were applied and a series of lncRNAs and target genes were identified. Furthermore, protein-protein interaction network construction, co-expression analysis, co-localization analysis of QTLs and functional enrichment analysis were used to functionally annotate the identified lncRNAs. In total, 2,290 lncRNAs were found (including 1,110 annotated, 593 known and 587 novel), of which 53 (including 39 known and 14 novel), were identified as differentially expressed genes between two breeds. The expression profile of lncRNAs was validated by RT-qPCR. The identified novel lncRNAs showed a number of characteristics similar to those of known lncRNAs. Target prediction analysis showed that these lncRNAs have the potential to act in cis or trans mode. Functional enrichment analysis of the predicted target genes revealed that they might affect the differences in feed efficiency of chicken by modulating genes associated with lipid metabolism, carbohydrate metabolism, growth, energy homeostasis and glucose metabolism. Some gene members of significant modules in the constructed co-expression networks were reported as important genes related to feed efficiency. Co-localization analysis of QTLs related to feed efficiency and the identified lncRNAs suggested several candidates to be involved in residual feed intake. The findings of this study provided valuable resources to further clarify the genetic basis of regulation of feed efficiency in chicken from the perspective of lncRNAs.

Emerging Roles of Non-Coding RNAs in the Feed Efficiency of Livestock Species

A global population of already more than seven billion people has led to an increased demand for food and water, and especially the demand for meat. Moreover, the cost of feed used in animal production has also increased dramatically, which requires animal breeders to find alternatives to reduce feed consumption. Understanding the biology underlying feed efficiency (FE) allows for a better selection of feed-efficient animals. Non-coding RNAs (ncRNAs), especially micro RNAs (miRNAs) and long non-coding RNAs (lncRNAs), play important roles in the regulation of bio-logical processes and disease development. The functions of ncRNAs in the biology of FE have emerged as they participate in the regulation of many genes and pathways related to the major FE indicators, such as residual feed intake and feed conversion ratio. This review provides the state of the art studies related to the ncRNAs associated with FE in livestock species. The contribution of ncRNAs to FE in the liver, muscle, and adipose tissues were summarized. The research gap of the function of ncRNAs in key processes for improved FE, such as the nutrition, heat stress, and gut–brain axis, was examined. Finally, the potential uses of ncRNAs for the improvement of FE were discussed.