Genome-wide analyses based on a novel donkey 40K liquid chip reveal the gene responsible for coat color diversity in Chinese Dezhou donkey.

Dezhou donkey is one of the representative local breeds in China, which is mainly divided into two strains: Sanfen and Wutou. There are obvious differences in coat color between the two strains. The former shows light points around the eyes, around the muzzle and under the belly, while the latter is completely solid black. In this study, genome-wide association analysis was performed for the differences in coat color traits between the Sanfen (n = 97) and Wutou (n = 108) strains using a novel donkey 40K liquid chip developed based on GenoBaits technology, to identify genomic regions and causal genes that could explain this variation. We also used FST and The cross-population composite likelihood ratio test (XPCLR) analyses to explore selected regions related to coat color differences. We identified one significant region on chromosome 15, with the most significant SNP located within the agouti signaling protein (ASIP) gene. At the same time, both FST and XPCLR methods detected the same selected region on chromosome 15, and ASIP was the gene with the strongest signal. ASIP and melanocortin 1 receptor (MC1R) control the ratio of eumelanin to pheomelanin through their protein activity. They are deeply involved in the process of melanosome organation and melanogenesis, thus affecting mammals' coat color variation. We used a range of genome-wide approach to identify the genetic basis of coat color variation in Dezhou donkeys. The results provide a supplement to the color variation study in Chinese donkeys at the genome-wide level, and preliminarily verified the reliability of the Molbreeding Donkey No. 1 40K liquid chip.

Single nucleotide polymorphisms (rs3736228 and rs4988321) in low-density lipoprotein receptor-related protein-5 gene with predisposition to rheumatoid arthritis.

BACKGROUND: LRP5 (Lipoprotein Receptor 5) is one of the representatives of the low-density lipoprotein receptors family that play a crucial role in the process of bone homeostasis and bone remodeling. The role of LRP5 single nucleotide polymorphisms (SNPs) rs3736228 and rs4988321 has been associated with the susceptibility to osteoporosis and bone fracture. The frequency of mentioned LRP5 SNPs is unknown among RA (Rheumatoid Arthritis) patients. The case-control study was designed to determine the association of targeted SNPs among RA patients. METHODOLOGY: Patients were selected by ACR/EULAR 2010 criteria. After ethical approval blood samples of patients and healthy individuals were collected. DNA was extracted from the whole blood followed by amplification of the targeted region by T-ARMS PCR (Tetra-primer Amplification Refractory Mutation System) obtained product was observed on agarose gel electrophoresis. The data were analyzed by statistical and bioinformatic tools. RESULTS: It was observed that the SNPs rs3736228 and rs4988321 showed significant association with the risk of RA [χ2 = 44, p =< 0.001, O.R 95 % CI = 2.495, (1.865 âˆ¼ 3.337), p =< 0.001] and [χ2 = 85, p =< 0.001, O.R 95 % CI = 2.05, (1.571 âˆ¼ 2.69), p =< 0.001] respectively. Haplotypes AT, GC, and GT were found to be significantly associated with the risk of RA. Furthermore, both SNPs were in 40 % LD (Linkage Disequilibrium). CONCLUSIONS: The study revealed that SNPs rs3736228 and rs4988321 were significantly associated with the increased susceptibility to RA. The study serves as the baseline data considering targeted SNPs and their association with the progression of the disease. The study might be utilized for the development of potential biomarker for diagnostic purposes and in the precision medicine approach.

Metabolic changes before and after weaning in Dezhou donkey foals in relation to gut microbiota.

Weaning is undoubtedly one of the most crucial stages in the growth and development of all mammalian animals, including donkey foals. Weaning is a dynamic and coordinated process of the body, which is closely associated with the health, nutrition, and metabolism of the host. Many studies have shown that the intestinal microbiota and serum metabolites of mammals exhibit different changes during lactation, weaning, and postweaning. However, the alterations in serum metabolites in donkey foals before and postweaning and the correlation between serum metabolites and intestinal microbiota are largely unknown. This study is based on the fecal 16S rRNA and serum metabolomes of Dezhou donkey foals. In total, 10 samples (fecal and serum) were collected during the following three stages: before weaning (F.M.1), during weaning (F.M.3), and postweaning (F.M.6). To study the alterations in intestinal microflora, serum metabolites, and their correlation before and postweaning. We found that with the growth and weaning progress of donkey foals, the intestinal microbiota of donkey foals underwent obvious changes, and the diversity of fecal bacteria increased (Chao1 and Shannon indexes). The main intestinal microbial flora of donkey foals include Bacteroides and Firmicutes. We found many microbiota that are associated with immunity and digestion in the postweaning group, such as Verrucomicrobiales, Clostridia, Oscillospiraceae, Akkermansia, and Rikenellaceae, which can be considered microbial markers for the transition from liquid milk to solid pellet feed. Clostridia and Oscillospiraceae can produce organic acids, including butyric acid and acetic acid, which are crucial for regulating the intestinal microecological balance of donkeys. Furthermore, the metabolome showed that the serum metabolites enriched before and postweaning were mainly related to arachidonic acid metabolism and riboflavin metabolism. Riboflavin was associated with the development of the small intestine and affected the absorption of the small intestine. We also found that the changes in the gut microbiome of the foals were significantly correlated with changes in serum metabolites, including lysophosphatidylcholine (LPC; 12,0) and positively correlated with Lachnoclostridium and Roseburia. To summarize, this study provides theoretical data for the changes in the intestinal microbiome and serum metabolism during the entire weaning period of donkey foals.

Growth performance, haematological assessment and chemical composition of Nile tilapia, Oreochromis niloticus (Linnaeus, 1758) fed different levels of Aloe vera extract as feed additives in a closed aquaculture system.

A 105-day experimental trial was conducted to assess different levels of dietary Aleo vera extract supplementation on water quality parameters, proximate composition, growth performance and haematological parameters of fry Oreochromis niloticus. Four different percentages of dietary leaf extract powder of Aleo vera (ALE) with a basal feed, designated as, i.e., T0 (Control group; without ALE), T1 (1% ALE), T2 (2% ALE), and T3 (3% ALE). Fish fry was reared in concrete tanks (7.0 m, 1.6 m, 1.0: L, W, H; water volume 11.2 m3/tank), with an average initial weight 4.04 ± 0.03 g/ fry, and each treatment was triplicated. Fry was randomly distributed at a stocking rate of 450 individuals/ tanks. The water quality parameters revealed that temperature, pH, salinity, dissolved oxygen (DO) and nitrates were found in a promising range as given by FAO/WHO limits. However, the record values obtained for Electric Conductivity (EC), Total dissolved solids (TDS), and alkalinities were not found in all tanks' suitable range according to FAO/WHO limits. The results revealed a significant impact of different percentages of dietary ALE supplementation on fry's body composition and haematological parameters. Moreover, the final body weight, final body length, average daily weight gain (g), net weight gain (g) and specific growth rate (%) were significantly higher (p < 0.05) in T1 and T2 compared with T0 and T3 treatments. The poorest feed conversion ratio was recorded in the T2 group compared with other treatments. Thus, the current study provides information about the nutritional quality of Nile tilapia culturing in Pakistan.