Publications by authors named "Xinkai Tong"

Genetic variants can influence complex traits by altering gene expression through changes to regulatory elements. However, the genetic variants that affect the activity of regulatory elements in pigs are largely unknown, and the extent to which these variants influence gene expression and contribute to the understanding of complex phenotypes remains unclear. Here, we annotate 90,991 high-quality regulatory elements using acetylation of histone H3 on lysine 27 (H3K27ac) ChIP-seq of 292 pig livers.

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Article Synopsis
  • The study involves high-quality whole-genome resequencing of 740 pigs and combines data from 149 previous resequencing efforts to analyze a total of 1096 genomes from 43 different pig breeds.
  • Researchers construct a comprehensive panel of 1,874 haploid genomes that contain over 41 million genetic variants, enabling better understanding of genetic diversity and inheritance.
  • Key findings include the identification of five new genetic loci related to intramuscular fat content and improved breeding value accuracy by 36.7%, highlighting the study's significance in pig genetics and breeding.
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Low microbial biomass in the lungs, high host-DNA contamination and sampling difficulty limit the study on lung microbiome. Therefore, little is still known about lung microbial communities and their functions. Here, we perform a preliminary exploratory study to investigate the composition of swine lung microbial community using shotgun metagenomic sequencing and compare the microbial communities between healthy and severe-lesion lungs.

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Article Synopsis
  • The intestinal microbiome composition differs greatly among individuals and is linked to overall health, making it important to explore the role of host genetics in these variations.
  • A study on a diverse pig population found that certain genetic traits are heritable and can significantly influence the presence of specific bacteria in the gut.
  • Researchers identified a genetic deletion related to the ABO blood group that impacts levels of certain bacteria by altering gut biochemistry, providing insights applicable to understanding similar mechanisms in humans.
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In pig-to-human xenotransplantation, the transmission risk of porcine endogenous retroviruses (PERVs) is of great concern. However, the distribution of PERVs in pig genomes, their genetic variation among Eurasian pigs, and their evolutionary history remain unclear. We scanned PERVs in the current pig reference genome (assembly Build 11.

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Background: Short tandem repeats (STRs) are genetic markers with a greater mutation rate than single nucleotide polymorphisms (SNPs) and are widely used in genetic studies and forensics. However, most studies in pigs have focused only on SNPs or on a limited number of STRs.

Results: This study screened 394 deep-sequenced genomes from 22 domesticated pig breeds/populations worldwide, wild boars from both Europe and Asia, and numerous outgroup Suidaes, and identified a set of 878,967 polymorphic STRs (pSTRs), which represents the largest repository of pSTRs in pigs to date.

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Swine respiratory disease (SRD) causes massive economic losses in the swine industry and is difficult to control and eradicate on pig farms. Here, we employed population genetics and transcriptomics approaches to decipher the molecular mechanism of host adaptation to swine respiratory disease. We recorded two SRD-related traits, the enzootic pneumonia-like (EPL) score and lung lesion (LL) levels, and performed four body weight measurements, at ages of 150, 180, 240, and 300 days, in a Chinese Bamaxiang pig herd ( = 314) raised under consistent indoor rearing conditions.

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Under natural farming, environmental pathogenic microorganisms may invade and affect swine lungs, further resulting in lung lesions. However, few studies on swine lung microbiota and their potential relationship with lung lesions were reported. Here, we sampled 20 pigs from a hybrid herd raised under natural conditions; we recorded a lung-lesion phenotype and investigated lung microbial communities by sequencing the V3-V4 region of 16S rRNA gene for each individual.

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