Xiaoting Yao

Goats are essential to the dairy industry in Shaanxi, China, with udder traits playing a critical role in determining milk production and economic value for breeding programs. However, the direct measurement of these traits in dairy goats is challenging and resource-intensive. This study leveraged genotyping imputation to explore the genetic parameters and architecture of udder traits and assess the efficiency of genomic prediction methods. Using data from 635 Saanen dairy goats, genotyped for over 14,717,075 SNP markers and phenotyped for three udder traits, heritability was 0.16 for udder width, 0.32 for udder depth, and 0.13 for teat spacing, with genetic correlations of 0.79, 0.70, and 0.45 observed among the traits. Genome-wide association studies (GWAS) revealed four candidate genes with selection signatures linked to udder traits. Predictive models, including GBLUP, kernel ridge regression (KRR), and Adaboost.RT, were evaluated for genomic estimated breeding value (GEBV) prediction. Machine learning models (KRR and Adaboost.RT) outperformed GBLUP by 20% and 11% in predictive accuracy, showing superior stability and reliability. These results underscore the potential of machine learning approaches to enhance genomic prediction accuracy in dairy goats, providing valuable insights that could contribute to improvements in animal health, productivity, and economic outcomes within the dairy goat industry.

The attenuated Orf virus (ORFV) strain (aFX0910), derived from continuous passages of wild-type strain FX0910 in vitro , displays obviously lower virulence in kids. However, the latent virulence determinants and intracellular mechanisms for the attenuated variant remain unknown. In this study, we constructed a comprehensive analysis of the ORFV and goat lip fibroblasts transcriptomes during viral infection using RNA sequencing. Focusing on the host transcriptome, we performed gene expression analysis, Gene Ontology analysis, and biological pathway analysis, among others. This integrated analysis allowed us to assess potential changes in mRNA expression and single nucleotide polymorphisms (SNPs) in both viral and host genes. In general, the global patterns of immune gene expression induced by different ORFV isolates were mostly shared. However, host transcripts and non-synonymous of viral genes differed between the wild-type and attenuated ORFV strains. Notably, the natural ORFV isolate (FX0910) predominantly triggered an innate immune response in host cells, while aFX0910 downregulated innate immune response and antiviral response. Analysis of viral transcriptomes manifested that FX0910 and aFX0910 had different SNP events in multiple functional genes. Collectively, our findings highlighted novel insights into virus-host interactions and shed light on the molecular basis of ORFV virulence at the genomic level. Furthermore, this study may contribute to the development of targeted intervention strategies and the advancement of vaccine research in the field of ORFV. IMPORTANCE: Currently, the only available commercial vaccines for Orf virus (ORFV) are live attenuated vaccines, which present a potential risk of reversion to virulence. Therefore, understanding the pathogenic mechanisms of different virulent strains of ORFV and host immune responses triggered by these viruses is crucial for developing new vaccines and interventions. In this study, we found that the attenuated strain downregulates the host innate immune response and antiviral activity. In addition, we noted that the wild-type strain can induce the immune response pattern centered on interferon-stimulated genes and interferon regulatory factor gene family. We predicted that STAT1 and STAT2 are the main transcription factors upstream of target gene promoters through gene regulatory networks and exert significant regulatory effects on co-expressed genes. Our study elucidated the complex interaction between ORFV strains and host cell immune responses, providing new insights into vaccine research for ORFV.

Background: The gut microbiome is a large and complex organic assemblage with subtle and close relationships with the host. This symbiotic mechanism is important for the health and adaptability of the host to the environment. Compared with other ruminants, there are few studies on yak intestinal microbes. The study of the gut microbiota of the yak will help us better understand the correlation between the microbiota and the environmental adaptability of the host. In this study, we adapted 16S rDNA sequencing technology to investigate the diversity and composition of the intestinal microbial community in free-range yaks and captive yaks living on the Qinghai–Tibet Plateau (QTP). Results: Sequencing results showed that the intestinal microbial community diversity was significantly different between free-range yaks and captive yaks. Firmicutes and Bacteroidetes were the dominant bacteria in both free-range and captive yaks. However, there were differences between the microbes of the two analyzed feeding styles in different classification levels. Compared with the captive type, free-range yaks had a higher abundance of Ruminococcaceae, Eubacteriaceae, Desulfovibrionaceae, Elusimicrobium, and Oscillibacter, while the abundance of Succinivibrionaceae, Clostridiales, Lachnospiraceae, Prevotellaceae, Roseburia, and Barnesiella was relatively low. The feeding method may be the key factor for the formation of intestinal flora differences in yaks, while altitude did not significantly affect Qinghai yak. Conclusions: In this study, we used 16S rDNA sequencing technology to investigate the composition of intestinal flora in free-range and captive yaks living on the QTP. The exploration of dietary factors can provide a theoretical basis for scientifically and rationally breeding yaks and provides a new direction for the development of prebiotics and microecological agents.

Background: Pulmonary arterial hypertension (PAH) is a life-threatening chronic cardiopulmonary disease. However, there are limited studies reflecting the available biomarkers from separate gene expression profiles in PAH. This study explored two microarray datasets by an integrative analysis to estimate the molecular signatures in PAH.Methods: Two microarray datasets (GSE53408 and GSE113439) were exploited to compare lung tissue transcriptomes of patients and controls with PAH and to estimate differentially expressed genes (DEGs). According to common DEGs of datasets, gene and protein overrepresentation analyses, protein–protein interactions (PPIs), DEG–transcription factor (TF) interactions, DEG–microRNA (miRNA) interactions, drug–target protein interactions, and protein subcellular localizations were conducted in this study.Results: We obtained 38 common DEGs for these two datasets. Integration of the genome transcriptome datasets with biomolecular interactions revealed hub genes (HSP90AA1, ANGPT2, HSPD1, HSPH1, TTN, SPP1, SMC4, EEA1, and DKC1), TFs (FOXC1, FOXL1, GATA2, YY1, and SRF), and miRNAs (hsa-mir-17-5p, hsa-mir-26b-5p, hsa-mir-122-5p, hsa-mir-20a-5p, and hsa-mir-106b-5p). Protein–drug interactions indicated that two compounds, namely, nedocromil and SNX-5422, affect the identification of PAH candidate biomolecules. Moreover, the molecular signatures were mostly localized in the extracellular and nuclear areas.Conclusions: In conclusion, several lung tissue-derived molecular signatures, highlighted in this study, might serve as novel evidence for elucidating the essential mechanisms of PAH. The potential drugs associated with these molecules could thus contribute to the development of diagnostic and therapeutic strategies to ameliorate PAH.

Parapoxvirus (PPV) has been identified in some mammals and poses a great threat to both the livestock production and public health. However, the prevalence and evolution of this virus are still not fully understood. Here, we performed an in silico analysis to investigate the genomic features and evolution of PPVs. We noticed that although there were significant differences of GC contents between orf virus (ORFV) and other three species of PPVs, all PPVs showed almost identical nucleotide bias, that is GC richness. The structural analysis of PPV genomes showed the divergence of different PPV species, which may be due to the specific adaptation to their natural hosts. Additionally, we estimated the phylogenetic diversity of seven different genes of PPV. According to all available sequences, our results suggested that during 2010–2018, ORFV was the dominant virus species under the selective pressure of the optimal gene patterns. Furthermore, we found the substitution rates ranged from 3.56 × 10⁻⁵ to 4.21 × 10⁻⁴ in different PPV segments, and the PPV VIR gene evolved at the highest substitution rate. In these seven protein-coding regions, purifying selection was the major evolutionary pressure, while the GIF and VIR genes suffered the greatest positive selection pressure. These results may provide useful knowledge on the virus genetic evolution from a new perspective which could help to create prevention and control strategies.

Goat milk is essential for the initial development of kids by providing a great source of commensal bacteria. In this study, we analyzed the microbiota of the milk of 30 healthy Saanen dairy goats. The 30 samples comprised 15 colostrum and 15 mature milk samples, collected from three different farms of Shaanxi Province. Colostrum samples were collected daily for five days post-delivery and mature milk was collected on the 7th, 10th, 20th, 30th, and 40th days. The result showed that microbial alpha diversity was higher in the mature milk compared with that in the colostrum. Linear discriminant analysis effect size (LEfSe) was performed to detect differentially abundant taxa in colostrum and goat milk. According to taxonomy results, Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were the predominant bacteria phyla in both colostrum and mature milk. In addition, lactation stage noticeably influenced the composition of milk microbiota. Specifically, Novosphingobium, Brachybacterium, Psychrobacter, Lactobacillus, Yersinia, Roseateles, Rothia, Sanguibacter, Cloacibacterium, Variovorax, Sphingobacterium, and Coxiella were enriched in the colostrum, while Georgenia, Peptostreptococcus, Bacteroidales, Yaniella, Planomicrobium, Cloacibacterium, Azospirillum, Turicibacter, Cupriavidus, Herbaspirillum, Rhodobacteraceae, and Aeromonadales were the dominant genera in the mature milk. The enriched metabolic functions of the goat milk microbiota were predicted by PICRUSt and classified by KEGG pathway. Moreover, the abundances of environmental information processing, cellular processes pathway, genetic information processing pathway, organismal systems pathway, and metabolism pathway were significantly different between microbiota of colostrum and mature milk. Altogether, our study disclosed the significant difference between the microbial communities of colostrum and mature milk and provided grounds for further research in dairy microbiology.

Background: The recent emergence of viral pneumonia was caused by the novel coronavirus (SARS-Cov-2), which has spread to many countries and threated the global public health.Results: In the current study, we provide a primary evolutionary analysis based on the codon usage patterns of SARS-Cov-2 genome sequences. We employed bioinformatics technologies to measure the nucleotide compositions, the relative synonymous codon usage (RSCU), the codon adaptation index (CAI), and other indices. Our results reflected that there were some similarities of codon usage bias between SARS-Cov-2 and its natural reservoirs, suggesting that SARS-Cov-2 was tended to evolve its codon usage which was comparable to that of its hosts. Additionally, various degree of adaptation to the SARS-Cov-2 host and vector were estimated, even different genes have different codon adaptation to their reservoirs. We further suggested that SARS-Cov-2 isolates were evolving at a rapid substitution rate under their translation selection pressure of their hosts.Conclusions: The findings of the present study will provide help for the understanding of the elements leading to viral evolution and adaptation to reservoirs.

Background: Gut microbiota play important roles in their co-evolution with mammals. However, little is understood about gut bacterial community of Tibetan sheep compared with other sheep breeds. In this study, we investigated the gut bacterial community in 4 different sheep breeds living in the Qinghai-Tibetan Plateau (QTP) of China using high-throughput sequencing (HTS) technique. Results: The results suggested that bacterial community abundance and breeds diversity of Tibetan sheep (TS) were significantly lower than that of the other three breeds of sheep [Dorset sheep (DrS), Dorper sheep (DrS) and Small Tail Han sheep (STHS)] (p < 0.05). Principal coordinates analysis (PCoA) and nonmetric multidimensional scaling (NMDS) analysis indicated that microbiome composition of TS was significantly different from that of other three sheep breeds (p < 0.01). Firmicutes was the most predominant microbial phylum in the gut, followed by Bacteroidetes. The gut bacterial community of TS showed higher proportions of phylum Spirochaetes, Proteobacteria and Verrucomicrobia, compared to the other three sheep breeds, but the Deferribacteres was absent in TS. At the genus level, Treponema, Succinivibrio, 5-7 N15 and Prevotella showed significantly higher abundance in TS than in the other three sheep breeds (p < 0.05). Conclusions: In this study, we first employed HTS to understand the gut microbiomes among different sheep breeds in QTP of China.

Parapoxvirus (PPV) has been identified in most mammals and poses a great threat to both the livestock production and public health. However, it is still not fully understood the viral prevalence and evolution of PPV coding sequences. Here, we performed a comparative approach integrating viral genetics, molecular selection pressure and genomic structure to investigate the genomic features and evolution of PPVs. We noticed that although there were significant differences of GC contents between ORFV and other three species of PPVs, all PPVs showed almost identical nucleotide bias, that is GC richness. This reflected a common mechanism which determines GC compositions for virus with similar life cycles. The structural analysis of PPV genomes showed the divergence of different PPV species, which may due to the specific adaptation to their natural hosts. Additionally, we estimated the phylogenetic diversity of segmented genome of PPV. Our results suggested that during the 2010 – 2018 outbreak, the orf virus has been the dominant species under the selective pressure of the optimal gene patterns. Furthermore, we found the mean substitution rates were between 3.56×10^-5 to 4.21×10^-4 in different PPV segments, and the PPV VIR gene was evolved at the highest substitution rate. In these protein-coding regions, purifying selection was the major evolutionary pressure, while the GIF and VIR genes suffered the greatest positive selection pressure. These results may provide useful knowledge on the virus genetic evolution from a new perspective which could help create prevention and control strategies.

Background: Gut microbiota play important roles in their co-evolution with mammals. However, little is understood about gut bacterial community of Tibetan sheep compared with other sheep breeds. In this study, we investigated the gut bacterial community in 4 different sheep breeds living in the Qinghai-Tibetan Plateau (QTP) of China using high-throughput sequencing (HTS) technique. Results: The results suggested that bacterial community abundance and breeds diversity of Tibetan sheep (TS) were significantly lower than that of the other three breeds of sheep [Dorset sheep (DrS), Dorper sheep (DrS) and Small Tail Han sheep (STHS)] (p < 0.05). Principal coordinates analysis (PCoA) and nonmetric multidimensional scaling (NMDS) analysis indicated that microbiome composition of TS was significantly different from that of other three sheep breeds (p < 0.01). Firmicutes was the most predominant microbial phylum in the gut, followed by Bacteroidetes. The gut bacterial community of TS showed higher proportions of phylum Spirochaetes, Proteobacteria and Verrucomicrobia, compared to the other three sheep breeds, but the Deferribacteres was absent in TS. At the genus level, Treponema, Succinivibrio, 5-7N15 and Prevotella showed significantly higher abundance in TS than in the other three sheep breeds (p < 0.05). Conclusions: In this study, we first employed HTS to understand the gut microbiomes among different sheep breeds in QTP of China.