Selection Signal Analysis Reveals Hainan Yellow Cattle Are Being Selectively Bred for Heat Tolerance.

Hainan yellow cattle are indigenous Zebu cattle from southern China known for their tolerance of heat and strong resistance to disease. Generations of adaptation to the tropical environment of southern China and decades of artificial breeding have left identifiable selection signals in their genomic makeup. However, information on the selection signatures of Hainan yellow cattle is scarce. Herein, we compared the genomes of Hainan yellow cattle with those of Zebu, Qinchuan, Nanyang, and Yanbian cattle breeds by the composite likelihood ratio method (CLR), Tajima's D method, and identifying runs of homozygosity (ROHs), each of which may provide evidence of the genes responsible for heat tolerance in Hainan yellow cattle. The results showed that 5210, 1972, and 1290 single nucleotide polymorphisms (SNPs) were screened by the CLR method, Tajima's D method, and ROH method, respectively. A total of 453, 450, and 325 genes, respectively, were identified near these SNPs. These genes were significantly enriched in 65 Gene Ontology (GO) functional terms and 11 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways (corrected p < 0.05). Five genes-Adenosylhomocysteinase-like 2, DnaJ heat shock protein family (Hsp40) member C3, heat shock protein family A (Hsp70) member 1A, CD53 molecule, and zinc finger and BTB domain containing 12-were recognized as candidate genes associated with heat tolerance. After further functional verification of these genes, the research results may benefit the understanding of the genetic mechanism of the heat tolerance in Hainan yellow cattle, which lay the foundation for subsequent studies on heat stress in this breed.

Sex Differences in Intestinal Microbial Composition and Function of Hainan Special Wild Boar.

The gut microbiome plays an important role in the health and disease status of the host. Research on the effect of sex on animal intestinal microorganisms is still limited; and the effect of castration on the gut microbiome of male pigs has not been fully investigated. In this study, 30 Hainan special wild boars at the same growth stage were divided into three groups (10 entire males, 10 females, and 10 castrated males). High-throughput 16S rRNA sequencing was used to investigate the fecal microbiota of the Hainan special wild boar. Firmicutes, Bacteroidetes, Actinobacteria, Spirochaetes, and Proteobacteria were the five dominant phyla found in the specimens. The relative abundance of Bacteroidetes was higher in the microbiota of female pigs than in male pigs, while Firmicutes was on the contrary. The percentage of Streptococcus and Lactobacillus was higher in males than females. The microbial diversity of females was significantly higher compared to males; castration increased the intestinal microbial diversity of males. Functional prediction showed that male fecal microorganisms were rich in membrane transport and carbohydrate metabolism; energy metabolism, glycan biosynthesis, and metabolism of cofactors and vitamins were rich in the female group; the fecal microorganisms of castrated males had higher membrane transport abundance.

Characterization of the cecal microbiome composition of Wenchang chickens before and after fattening.

The cecum of poultry harbors a complex and dynamic microbial community which plays important roles in preventing pathogen colonization, detoxifying harmful substances, nutrient processing, and harvesting of the ingestion. Understanding and optimizing microbial communities could help improve agricultural productivity. In this study, we analyzed the composition and function of cecal microbiota of Wenchang chicken (a native breed of Bantam) before and after fattening, using high throughput sequencing technology. High-throughput sequencing of the 16S rRNA genes V3-V4 hypervariable regions was used to characterize and compare the cecal microbiota of Wenchang chicken before fattening (free-range in hill) and after fattening (cage raising). Sixteen phyla were shared by the 20 samples. Firmicutes and Bacteroidetes were the top two abundant phyla being 80% of the total microbiota. Samples of chickens prior to fattening were more dispersed than those after fattening. Twenty four microbes could be considered as biomarkers and 3 phyla revealed differences by variance analysis which could distinguish the two groups. Cecal microbiota in the before fattening group had higher abundance of functions involved in digestive system and biosynthesis of other secondary metabolites. The composition and function of cecal microbiota in Wenchang chicken before and after fattening under the two feeding modes, free range in hillside and cage raising, were found to be different. These results can be attributed to the differences in feeding modes and growth stages. In-depth study on the functions and interactions of intestinal microbiota can help us in developing strategies for raising Wenchang chickens and provide valuable information for the study of microbiota in the chicken gut.

Studying the variations in differently expressed serum proteins of Hainan black goat during the breeding cycle using isobaric tags for relative and absolute quantitation (iTRAQ) technology.

The Hainan black goat is a high-quality local goat breed in Hainan Province of China. It is resistant to high temperatures, humidity, and disease. Although the meat of this breed is tender and delicious, its reproductive performance and milk yield are low. In this study, isobaric tags for relative and absolute quantitation (iTRAQ) technology was used to analyze the differentially expressed proteins in the serum of female Hainan black goats during the reproductive cycle (empty pregnant, estrus, gestation, and lactation). The pathway enrichment analysis results showed that most of the differentially expressed proteins between each period belonged to the complement and coagulation cascades. Analysis of the differential protein expression and function revealed seven proteins that were directly associated with reproduction, namely pre-SAA21, ANTXR2, vWF, SFRP3, ß4GalT1, pre-IGFBP2 and Ran. This study revealed the changing patterns of differentially expressed proteins in the reproductive cycle of the Hainan black goat. pre-SAA21, ANTXR2, vWF, SFRP3, ß4GalT1, pre-IGFBP2, and Ran were identified as candidate proteins for mediating the physiological state of Hainan black goats and regulating their fertility. This study elucidated the changes in expression levels of differentially expressed proteins during the reproductive cycle of Hainan black goats and also provides details about its breeding pattern.

Molecular identification of the Danzhou chicken breed in China using DNA barcoding.

Mitochondrial cytochrome C oxidase subunit I (COI) has been used as a DNA barcode to identify population genetic diversity and distinguish animal species as it is variable enough to distinguish between species, yet suitably conserved. A new native chicken breed, named Danzhou chicken was discovered in Hainan, China in 2014, although identification is difficult by morphological examination alone. The mitochondrial COI genes of six chicken breeds, including four local and two imported breeds (Danzhou, Wenchang, Bawang, Beijing-You, Hy-Line Brown, and Ross) were compared and assessed in terms of their efficacy for DNA barcoding. The results showed that the number of COI gene variants in Danzhou chickens was less than those of other breeds, except Bawang and the genetic structure was relatively stable. The Kimura 2-parameter genetic distance between Danzhou chickens and the five other breeds was from ∼0.001 to 0.734. The genetic distance of the six breeds was ∼0.001-0.339, with that of Danzhou being the highest (0.339). Danzhou chickens clustered with Bawang and Wenchang chickens in the phylogenetic tree due to geographic closeness. Danzhou chickens could be identified more accurately using COI barcoding. Multiple molecular markers combined with morphological differences were more persuasive for identifying species.

Effects of cathelicidin-derived peptide from reptiles on lipopolysaccharide-induced intestinal inflammation in weaned piglets.

Cathelicidins are the largest family of antimicrobial peptides. C-BF, which is short for Cathelicidin-Bungarus Fasciatus, was isolated from snake venom. C-BF was found to be the most potential substitutes for antibiotics. In this study, we analyzed the effects of cathelicidin-derived peptide C-BF, on lipopolysaccharide (LPS)-induced intestinal damage in weaned piglets, to evaluate the therapeutic effect of C-BF on infectious disease of piglets. Twenty-four piglets were randomly assigned into four groups: control, C-BF, LPS, and C-BF+LPS. The LPS and C-BF+LPS groups were intraperitoneally injected with LPS at fixed timepoints, while the control and C-BF groups were injected with equal volumes of saline. The C-BF and C-BF+LPS groups were then intraperitoneally injected with antimicrobial peptide C-BF, while the control and LPS groups were injected with equal volumes of saline. All piglets were observed for 15days and then sacrificed for analysis. The results showed that C-BF significantly improved the growth performance of weaned piglets compared with LPS-treated animals (P<0.05), and that C-BF could ameliorate the structural and developmental damage to the small intestine caused by LPS treatment. Further, the level of apoptosis in the LPS group was significantly higher than in the other three groups (P<0.05), as was the invasion of inflammatory cells into the intestinal mucosa of the jejunum (P<0.05), leading to increased secretion of pro-inflammatory cytokines. In conclusion, the study indicates that C-BF treatment may be a potential therapy for LPS/pathogen-induced intestinal injury in piglets.

Transcriptome Analysis of HepG2 Cells Expressing ORF3 from Swine Hepatitis E Virus to Determine the Effects of ORF3 on Host Cells.

Hepatitis E virus- (HEV-) mediated hepatitis has become a global public health problem. An important regulatory protein of HEV, ORF3, influences multiple signal pathways in host cells. In this study, to investigate the function of ORF3 from the swine form of HEV (SHEV), high-throughput RNA-Seq-based screening was performed to identify the differentially expressed genes in ORF3-expressing HepG2 cells. The results were validated with quantitative real-time PCR and gene ontology was employed to assign differentially expressed genes to functional categories. The results indicated that, in the established ORF3-expressing HepG2 cells, the mRNA levels of CLDN6, YLPM1, APOC3, NLRP1, SCARA3, FGA, FGG, FGB, and FREM1 were upregulated, whereas the mRNA levels of SLC2A3, DKK1, BPIFB2, and PTGR1 were downregulated. The deregulated expression of CLDN6 and FREM1 might contribute to changes in integral membrane protein and basement membrane protein expression, expression changes for NLRP1 might affect the apoptosis of HepG2 cells, and the altered expression of APOC3, SCARA3, and DKK1 may affect lipid metabolism in HepG2 cells. In conclusion, ORF3 plays a functional role in virus-cell interactions by affecting the expression of integral membrane protein and basement membrane proteins and by altering the process of apoptosis and lipid metabolism in host cells. These findings provide important insight into the pathogenic mechanism of HEV.