Genome-Wide Association Study and Transcriptome Differential Expression Analysis of the Feather Rate in Shouguang Chickens

The feather rate phenotype in chicks, including early-feathering and late-feathering phenotypes, are widely used as a sexing system in the poultry industry. The objective of this study was to obtain candidate genes associated with the feather rate in Shouguang chickens. In the present study, we collected 56 blood samples and 12 hair follicle samples of flight feathers from female Shouguang chickens. Then we identified the chromosome region associated with the feather rate by genome-wide association analysis (GWAS). We also performed RNA sequencing and analyzed differentially expressed genes between the early-feathering and late-feathering phenotypes using HISAT2, StringTie, and DESeq2. We identified a genomic region of 10.0–13.0 Mb of chromosome Z, which is statistically associated with the feather rate of Shouguang chickens at one-day old. After RNA sequencing analysis, 342 differentially expressed known genes between the early-feathering (EF) and late-feathering (LF) phenotypes were screened out, which were involved in epithelial cell differentiation, intermediate filament organization, protein serine kinase activity, peptidyl-serine phosphorylation, retinoic acid binding, and so on. The sperm flagellar 2 gene (SPEF2) and prolactin receptor (PRLR) gene were the only two overlapping genes between the results of GWAS and differential expression analysis, which implies that SPEF2 and PRLR are possible candidate genes for the formation of the chicken feathering phenotype in the present study. Our findings help to elucidate the molecular mechanism of the feather rate in chicks.</p

Delay-agnostic Asynchronous Distributed Optimization

Existing asynchronous distributed optimization algorithms often use diminishing step-sizes that cause slow practical convergence, or fixed step-sizes that depend on an assumed upper bound of delays. Not only is such a delay bound hard to obtain in advance, but it is also large and therefore results in unnecessarily slow convergence. This paper develops asynchronous versions of two distributed algorithms, DGD and DGD-ATC, for solving consensus optimization problems over undirected networks. In contrast to alternatives, our algorithms can converge to the fixed-point set of their synchronous counterparts using step-sizes that are independent of the delays. We establish convergence guarantees under both partial and total asynchrony. The practical performance of our algorithms is demonstrated by numerical experiments

Genetic comparison of transmissible gastroenteritis coronaviruses

Transmissible gastroenteritis virus (TGEV) is a porcine coronavirus that threatens animal health and remains elusive despite years of research efforts. The systematical analysis of all available full-length genomes of TGEVs (a total of 43) and porcine respiratory coronaviruses PRCVs (a total of 7) showed that TGEVs fell into two independent evolutionary phylogenetic clades, GI and GII. Viruses circulating in China (until 2021) clustered with the traditional or attenuated vaccine strains within the same evolutionary clades (GI). In contrast, viruses latterly isolated in the USA fell into GII clade. The viruses circulating in China have a lower similarity with that isolated latterly in the USA all through the viral genome. In addition, at least four potential genomic recombination events were identified, three of which occurred in GI clade and one in GII clade. TGEVs circulating in China are distinct from the viruses latterly isolated in the USA at either genomic nucleotide or antigenic levels. Genomic recombination serves as a factor driving the expansion of TGEV genomic diversity

Multiple potential recombination events among Newcastle disease virus genomes in China between 1946 and 2020

IntroductionNewcastle Disease Virus (NDV) is a highly adaptable virus with large genetic diversity that has been widely studied for its oncolytic activities and potential as a vector vaccine. This study investigated the molecular characteristics of 517 complete NDV strains collected from 26 provinces across China between 1946-2020.MethodsHerein, phylogenetic, phylogeographic network, recombination, and amino acid variability analyses were performed to reveal the evolutionary characteristics of NDV in China.Results and discussionsPhylogenetic analysis revealed the existence of two major groups: GI, which comprises a single genotype Ib, and GII group encompassing eight genotypes (I, II, III, VI. VII. VIII, IX and XII). The Ib genotype is found to dominate China (34%), particularly South and East China, followed by VII (24%) and VI (22%). NDV strains from the two identified groups exhibited great dissimilarities at the nucleotide level of phosphoprotein (P), matrix protein (M), fusion protein (F), and haemagglutinin-neuraminidase (HN) genes. Consistently, the phylogeographic network analysis revealed two main Network Clusters linked to a possible ancestral node from Hunan (strain MH289846.1). Importantly, we identified 34 potential recombination events that involved mostly strains from VII and Ib genotypes. A recombinant of genotype XII isolated in 2019 seems to emerge newly in Southern China. Further, the vaccine strains are found to be highly involved in potential recombination. Therefore, since the influence of recombination on NDV virulence cannot be predicted, this report’s findings need to be considered for the security of NDV oncolytic application and the safety of NDV live attenuated vaccines

The epithelial transcriptome and mucosal microbiota are altered for goats fed with a low-protein diet

IntroductionFeeding low protein (LP) diet to animals impose severe challenge to animals' immune homeostasis. However, limited knowledge about the underlying adaption mechanism of host and ruminal microbiota responding to LP diet were well understood. Herein, this study was performed to examine the changes in relative abundance of ruminal microbiota and host ruminal mucosal transcriptome profiles in response to a LP diet.MethodsA total of twenty-four female Xiangdong balck goats with similar weight (20.64 ± 2.40 kg) and age (8 ± 0.3 months) were randomly assigned into two groups, LP (5.52% crude protein containing diet) and CON (10.77% crude protein containing diet) groups. Upon completion of the trial, all goats were slaughtered after a 16-hour fasting period in LiuYang city (N 28°15′, E 113°63′) in China. HE staining, free amino acids measurement, transcriptome analysis and microbiome analysis were applied to detect the morphology alterations, free amino acids profile alterations and the shift in host ruminal mucosal transcriptome and ruminal microbiota communities.ResultsFirstly, the results showed that feeding LP diet to goats decreased the rumen papilla width (P = 0.043), surface area (P = 0.013) and total ruminal free amino acids concentration (P = 0.016). Secondly, microbiome analysis indicated that 9 microbial genera, including Eubacterium and Prevotella, were enriched in LP group while 11 microbial genera, including Butyrivibrio and Ruminococcus, were enriched in CON group. Finally, in terms of immune-related genes, the expression levels of genes involved in tight junction categories (e.g., MYH11, PPP2R2C, and MYL9) and acquired immunity (e.g., PCP4 and CXCL13) were observed to be upregulated in the LP group when compared to the CON group.ConclusionUnder the LP diet, the rumen exhibited increased relative abundance of pathogenic microbiota and VFA-degrading microbiota, leading to disruptions in immune homeostasis within the host's ruminal mucosa. These findings indicate that the ruminal microbiota interacts with host results in the disruption in animals' immune homeostasis under LP diet challenge

Effects of hypoxia on serum hepatic chemistries of Tibet chicken and Shouguang chicken

Hypoxia is a major factor that affects the subsistence and development of multicellular organisms. Tibet chicken, as a unique native chicken breed in altiplano, shows genetic adaptation to hypoxia comparing with the breeds at the low altitude. In the present study, to explore effects of hypoxia on chicken fetal livers, eggs of Tibet chicken and Shouguang chicken were collected and the samples from each breed were divided into two groups, incubated in hypoxia and in normoxia respectively. The blood of embryos on the 16th day of incubation was collected and the serum chemistry  parameters indicating liver metabolism were determined, which included glutamic-pyruvic transaminase (GPT), aspartate aminotransferase (GOT), total bilirubin (TB), direct bilirubin (DB), total bile acid (TBA), gamma glutamyltransferase (GGT), alkaline phosphatease (ALP), lactate dehydrogenase (LDH), creatine kinase (CK), glucose and creatinine. The results show that biochemical indices varied significantly between hypoxia and normoxia except for GPT and glucose. Moreover, the concentration of ALP and LDH showed significant differences between the breeds and the incubations. The results suggest that the livers of both Shouguang chicken and Tibet chicken suffered damages in hypoxia, but the former was more serious. The results of this study support the opinion that Tibet chicken had better genetic adaptability on hypoxia, and made a good basis for further study of the genetic mechanism of adaptation to hypoxia.Key words: Hypoxia adaptation, liver metabolism, serum chemistry, Tibet chicken, chicken embryo

A Novel α-Galactosidase A Splicing Mutation Predisposes to Fabry Disease

Fabry disease (FD) is a rare X-linked α-galactosidase A (GLA) deficiency, resulting in progressive lysosomal accumulation of globotriaosylceramide (Gb3) in a variety of cell types. Here, we report a novel splicing mutation (c.801 + 1G &gt; A) that results in alternative splicing in GLA of a FD patient with variable phenotypic presentations of renal involvement. Sequencing of the RT-PCR products from the patient’s blood sample reveals a 36-nucleotide (nt) insertion exists at the junction between exons 5 and 6 of the GLA cDNA. Splicing assay indicates that the mutated minigene produces an alternatively spliced transcript which causes a frameshift resulting in an early termination of protein expression. Immunofluorescence shows puncta in cytoplasm for mutated GLA whereas uniform staining small dots evenly distributed inside cytoplasm for wild type GLA in transfected HeLa cells. The increased senescence and decreased GLA enzyme activity suggest that the abnormalities might be due to the altered localization which further might result from the lack of the C-terminal end of GLA. Our study reveals the pathogenesis of splicing mutation c.801 + 1G &gt; A to FD and provides scientific foundation for accurate diagnosis and precise medical intervention for FD