Whole-genome SNP allele frequency differences between Tibetan and Large white pigs reveal genes associated with skeletal muscle growth.

BACKGROUND: The skeletal muscle growth rate and body size of Tibetan pigs (TIB) are lower than Large white pigs (LW). However, the underlying genetic basis attributing to these differences remains uncertain. To address this knowledge gap, the present study employed whole-genome sequencing of TIB (slow growth) and LW (fast growth) individuals, and integrated with existing NCBI sequencing datasets of TIB and LW individuals, enabling the identification of a comprehensive set of genetic variations for each breed. The specific and predominant SNPs in the TIB and LW populations were detected by using a cutoff value of 0.50 for SNP allele frequency and absolute allele frequency differences (△AF) between the TIB and LW populations. RESULTS: A total of 21,767,938 SNPs were retrieved from 44 TIB and 29 LW genomes. The analysis detected 2,893,106 (13.29%) and 813,310 (3.74%) specific and predominant SNPs in the TIB and LW populations, and annotated to 24,560 genes. Further GO analysis revealed 291 genes involved in biological processes related to striated and/or skeletal muscle differentiation, proliferation, hypertrophy, regulation of striated muscle cell differentiation and proliferation, and myoblast differentiation and fusion. These 291 genes included crucial regulators of muscle cell determination, proliferation, differentiation, and hypertrophy, such as members of the Myogenic regulatory factors (MRF) (MYOD, MYF5, MYOG, MYF6) and Myocyte enhancer factor 2 (MEF2) (MEF2A, MEF2C, MEF2D) families, as well as muscle growth inhibitors (MSTN, ACVR1, and SMAD1); KEGG pathway analysis revealed 106 and 20 genes were found in muscle growth related positive and negative regulatory signaling pathways. Notably, genes critical for protein synthesis, such as MTOR, IGF1, IGF1R, IRS1, INSR, and RPS6KA6, were implicated in these pathways. CONCLUSION: This study employed an effective methodology to rigorously identify the potential genes associated with skeletal muscle development. A substantial number of SNPs and genes that potentially play roles in the divergence observed in skeletal muscle growth between the TIB and LW breeds were identified. These findings offer valuable insights into the genetic underpinnings of skeletal muscle development and present opportunities for enhancing meat production through pig breeding.

PRNP gene polymorphism frequencies for comparing possible vulnerability to BSE in Chinese bovine population.

Among the numerous transmissible spongiform encephalopathies (TSEs), bovine spongiform encephalopathy (BSE) is the most well-known TSEs. It is a potential Creutzfeldt-Jakob (CJD) disease mutation that can be transferred through cattle to humans. In several animals, the prion protein gene (PRNP) is recognized to take active part in TSE vulnerability or tolerance. Previous studies have found indels polymorphism in PRNP gene promoter and intron1 region linked to BSE vulnerability. It's linked with 23 bp indels polymorphism in putative promoter and 12 bp indel in intron 1 of the PRNP gene. The aim of this study was to compare the allele, genotype and haplotype frequencies of PRNP indel polymorphisms in Zhongdian Yak (Bos grunniens) (YK), Zhongdian Yellow cattle (Bos taurus) (YC) and Zhongdian Yakow (Bos primigenius taurus × Bos grunniens) (PK) with worldwide reported healthy or affected BSE cattle, in order to assess their potential resistance to BSE. A comparison of Chinese bovine populations with healthy and BSE-affected German and Swiss cattle from globally was conducted, and result indicating significant difference (p < .001) between healthy and affected cattle. Additionally, as compared to prior studies with Chinese bovine population, the significant results were found. In this study, the allelic frequency D23 finding high deletion in all analyzed Chinese bovine species, and haplotype D12-D23 exhibited a less significant inclination toward susceptibility to BSE.

Complete genome sequence of a Chuzan virus strain isolated for the first time in mainland China.

Chuzan virus (CHUV) belongs to the Palyam serogroup, causes bovine congenital disease, and is prevalent in Asia. To date, only one full Palyam virus (PALV) genome sequence, that of Japanese CHUV strain K47, has been reported. Sequence analysis indicates that PALV strains isolated from different geographical regions show significant diversity, which is mainly shaped by geographically independent evolution and genetic reassortment. Our understanding of the genetic characteristics of PALV is hampered by a very limited genomic sequence database. In this study, we report the complete genome sequence of CHUV strain SZ187, which was isolated for the first time in 2012 in mainland China. Sequence alignment and phylogenetic analysis demonstrate that SZ187 is closely related to other CHUV strains isolated in Taiwan and Japan, indicating that they may share a common ancestor. This new full-length CHUV genome sequence could help in the design of broader assays for epidemiological studies and facilitate the identification of new CHUV isolates in the future.

Complete genome sequence of the first bluetongue virus serotype 7 isolate from China: evidence for entry of African-lineage strains and reassortment between the introduced and native strains.

Bluetongue virus (BTV) mainly infects sheep but can be transmitted to other domestic and wild ruminants, resulting in a considerable financial burden and trade restriction. Our understanding of the origin, movement, and distribution of BTV has been hindered by the fact that this virus has a segmented genome with the possibility of reassortment, the existence of 27 identified serotypes, and a lack of complete sequences of viruses isolated from different parts of the world. BTV serotype 7 is one of the prevalent BTV serotypes in Asia. Nonetheless, no complete genomic sequence of an Asian isolate of this serotype is available. In an effort to understand the molecular epidemiology of BTV infection in China, for the first time, we report here the complete genome sequence of a BTV serotype 7 strain, GDST008, which was isolated in 2014 in China. This sequence also represents the first complete genome sequence of a BTV serotype 7 from Asia and the third one in the world. Sequence analysis suggests that GDST008 consists of segments from BTV viruses of African lineage as well as those from China. Together, these results improve our understanding of the origin, emergence/re-emergence, and movement of BTV and thus can be applied in the development of vaccines and diagnostics.

Investigation of SNPs in differentially expressed genes and proteins reveals the genetic basis of skeletal muscle growth differences between Tibetan and Large White pigs.

Objective: Skeletal muscle growth is an important economic trait for meat production, with notable differences between Tibetan pigs (TIBPs, a slow-growing breed) and Large White pigs (LWPs, a fast-growing breed). However, the genetic underpinnings of this disparity remain unclear. Methods: In the current study, we integrated differentially expressed genes (DEGs) and proteins (DEPs) from 60-day-old embryonic muscle tissue, along with whole-genome single nucleotide polymorphisms (SNPs) displaying absolute allele frequency differences (ΔAF) of 0.5 or more between the TIBP and LWP breeds, to unravel the genetic factors influencing skeletal muscle growth. Results: Our analysis revealed 3499 DEGs and 628 DEPs with SNPs having a ΔAF equal to or greater than 0.5. Further functional analysis identified 145 DEGs and 23 DEPs involved in biological processes related to skeletal muscle development, and 22 DEGs and 3 DEPs implicated in the mTOR signaling pathway, which is known for positively regulating protein synthesis. Among these genes, several DEGs and DEPs, enriched with TIPB-specific SNPs in regulatory or/and coding regions, showed marked ΔAF between the TIBP and LWP breeds, including MYF5, MYOF, ASB2, PDE9A, SDC1, PDGFRA, MYOM2, ACVR1, ZIC3, COL11A1, TGFBR1, EDNRA, TGFB2, PDE4D, PGAM2, GRK2, SCN4B, CACNA1S, MYL4, IGF1, and FOXO1. Additionally, genes such as CAPN3, MYOM2, and PGAM2, identified as both DEPs and DEGs related to skeletal muscle development, contained multiple TIBP-specific and LWP-predominant SNPs in regulatory and/or coding regions, underscoring significant ΔAF differences between the two breeds. Conclusion: s: This comprehensive investigation of SNPs in DEGs and DEPs identified a significant number of SNPs and genes related to skeletal muscle development during the prenatal stage. These findings not only shed light on potential causal genes for muscle divergence between the TIBP and LWP breeds but also offer valuable insights for pig breeding strategies aimed at enhancing meat production.

Comparative Analysis of PRNP Gene Indel Polymorphism and Expression among Zhongdian Yellow Cattle, Zhongdian Yak, and Their Hybrids.

Bovine spongiform encephalopathy (BSE) is a fatal disease in cattle caused by misfolded prion proteins and linked to indel polymorphisms in the promoter and intron 1 of the PRNP gene. The aim of this study was to determine the allele, genotype, and haplotype frequencies of PRNP indel polymorphisms and to investigate the effect of PRNP gene expressions of 23 bp and 12 bp indels via polymerase chain reaction (PCR) in Zhongdian Yak (Bos-grunniens) (YK), Zhongdian Yellow cattle (Bos-taurus) (YC), and Zhongdian Yakow (Bos-primigenius taurus × Bos-grunniens) (PK). Resultant high allelic frequencies were found in 23- and 12+, while haplotype frequencies were very low in 23+/12 in YK, YC, and PK. PRNP expression was higher in the +-/-- diplotype of the PK and (mean ± SE) was 3.6578 ± 1.85964. Furthermore, two variable sites were investigated-a 23 bp indel polymorphism holding AP1 binding site and a 12 bp indel polymorphism holding SP1 binding site. Additionally, reporter gene assays revealed a link between two proposed transcription factors and lower expression levels of the +/+ allele compared with the -/- allele. The expression level of PRNP was shown to be dependent on two indel polymorphisms in the bovine PRNP promoter, which includes binding sites for RP58 and SP1 transcription factors. These findings raised the possibility that the PRNP genotype may contribute to the high variation in PRNP expression.

Genetic diversity and genetic origin of Lanping black-boned sheep investigated by genome-wide single-nucleotide polymorphisms (SNPs).

Lanping black-boned sheep was first discovered in the 1950s in Lanping county of China and characterized by black pigmentation on skin and internal organs. Due to the novel and unique trait, the genetic background of Lanping black-boned sheep is of great interest. Here, we genotyped genome-wide SNPs (single nucleotide polymorphisms) of Lanping black-boned sheep and Lanping normal sheep using Illumina OvineSNP50 BeadChip to investigate the genetic diversity and genetic origin of Lanping black-boned sheep. We also downloaded a subset SNP dataset of two Tibet-lineage sheep breeds and four other sheep breeds from the International Sheep Genomics Consortium (ISGC) as a reference for interpreting. Lanping black-boned sheep had a lower genetic diversity level when compared to seven other sheep breeds. Principal component analysis (PCA) showed that Lanping black-boned sheep and Lanping normal sheep were clustered into the Asian group, but there was no clear separation between the two breeds. Structure analysis demonstrated a high ancestry coefficient in Lanping black-boned sheep and Lanping normal sheep. However, the two populations were separated into two distinct branches in a neighbor-joining (NJ) tree. We further evaluated the genetic divergence using population F ST , which showed that the genetic differentiation that existed between Lanping black-boned sheep and Lanping normal sheep was higher than that between Tibet sheep and Changthangi sheep, which revealed that Lanping black-boned sheep is a different breed from Lanping normal sheep on the genetic level. In addition, structure analysis and NJ tree showed that Lanping black-boned sheep had a relatively close relation with Tibet sheep. The results reported herein are a first step toward understanding the genetic background of Lanping black-boned sheep, and it will provide informative knowledge on the unique genetic resource conservation and mechanism of novel breed formation.

Deletion/insertion polymorphisms of the prion protein gene (PRNP) in gayal (Bos frontalis).

Resistance to fatal disease bovine spongiformencephalopathy (BSE), due to misfolded prion protein in cattle, is associated with a 23-bp indel polymorphism in the putative promoter and a 12-bp indel in intron 1 of the PRNP gene. Gayal (Bos frontalis) is an important semiwild bovid species and of great conservation concern, but till today these indel polymorphisms have not been evaluated in gayals. Therefore, we collected 225 samples of gayals and evaluated the genetic indel polymorphism in the two regions of this PRNP gene. The results revealed high allelic frequencies of insertions at these indel sites: 0.909 and 0.667 for, respectively, the 23 bp and 12 bp indels, both also with significant genotype frequencies (χ2: 9.81; 23 bp and χ2: 43.56; 12 bp). At the same time, the haplotype data showed indel polymorphisms with extremely low deletion (0.01) in both regions of the PRNP gene. We compared these data with those reported for healthy and BSE-affected cattle (Bos taurus) breeds from two European countries, Germany and Switzerland, and significant difference (P <0.001) was observed between BSE-affected as well as the healthy cattle. Further, our data were also extensively compared with previous reports on BSE and highly significant (P<0.001) outcomes were observed. This result suggested negligible genetic susceptibility to BSE in gayals. To the best of our knowledge, this study is the first comprehensive deciphering information about the PRNP indel polymorphisms of 23 bp and 12 bp in gayals, a semiwild species of China.