Analysis of long non-coding RNAs in skeletal muscle of Bama Xiang pigs in response to heat stress

Insights and implications for transcriptomic analysis of heat stress-induced intestinal inflammation in pigs

BACKGROUND

Heat stress (HS) can affect the physiology and metabolism of animals. HS-induced intestinal inflammation in pigs is a common disease, causing severe diarrhea, that can result in substantial economic losses to the pig industry, but the molecular mechanisms and pathogenicity of this disease are not fully understood. The objective of this study was to identify the differentially expressed genes (DEGs) and long noncoding RNAs (DELs) related to inflammation in the colon tissues of pigs under constant (1, 7, and 14 days) HS.

RESULTS

LncRNA and targeted gene interaction networks were constructed. GO annotation and KEGG pathway analyses were subsequently performed to determine the functions of the DEGs and DELs. The results revealed 57, 212, and 54 DEGs and 87, 79, and 55 DELs in the CON/H01, CON/H07, and CON/H14 groups, respectively. KRT85, CLDN1, S100A12, TM7SF2, CCN1, NR4A1, and several lncRNAs may be involved in regulating the development of intestinal inflammation. GO analysis indicated that the DEGs and DELs were enriched in a series of biological processes involved in the innate immune response, RAGE receptor binding, and positive regulation of the ERK1 and ERK2 cascades. KEGG pathways related to inflammation, such as the tight junction (TJ) and MAPK signaling pathways, were enriched in DEGs and DELs.

CONCLUSIONS

This study have expanded the knowledge about colon inflammation-related genes and lncRNA biology in pigs under HS; analyzed the the lncRNA‒mRNA interaction for HS-induced intestinal inflammation. These results may provide some references for our understanding of the molecular mechanism of the intestinal response to HS in pig.

Long non-coding RNA variability in porcine skeletal muscle

Recently, numerous studies including various tissues have been carried out on long non-coding RNAs (lncRNAs), but still, its variability has not yet been fully understood. In this study, we characterised the inter-individual variability of lncRNAs in pigs, in the context of number, length and expression. Transcriptomes collected from muscle tissue belonging to six Polish Landrace boars (PL1-PL6), including half-brothers (PL1-PL3), were investigated using bioinformatics (lncRNA identification and functional analysis) and statistical (lncRNA variability) methods. The number of lncRNA ranged from 1289 to 3500 per animal, and the total number of common lncRNAs among all boars was 232. The number, length and expression of lncRNAs significantly varied between individuals, and no consistent pattern has been found between pairs of half-brothers. In detail, PL5 exhibits lower expression than the others, while PL4 has significantly higher expression than PL2-PL3 and PL5-PL6. Noteworthy, comparing the inter-individual variability of lncRNA and mRNA expression, they exhibited concordant patterns. The enrichment analysis for common lncRNA target genes determined a variety of biological processes that play fundamental roles in cell biology, and they were mostly related to whole-body homeostasis maintenance, energy and protein synthesis as well as dynamics of multiple nucleoprotein complexes. The high variability of lncRNA landscape in the porcine genome has been revealed in this study. The inter-individual differences have been found in the context of three aspects: the number, length and expression of lncRNAs, which contribute to a better understanding of its complex nature.

Taming transposable elements in livestock and poultry: a review of their roles and applications

Livestock and poultry play a significant role in human nutrition by converting agricultural by-products into high-quality proteins. To meet the growing demand for safe animal protein, genetic improvement of livestock must be done sustainably while minimizing negative environmental impacts. Transposable elements (TE) are important components of livestock and poultry genomes, contributing to their genetic diversity, chromatin states, gene regulatory networks, and complex traits of economic value. However, compared to other species, research on TE in livestock and poultry is still in its early stages. In this review, we analyze 72 studies published in the past 20 years, summarize the TE composition in livestock and poultry genomes, and focus on their potential roles in functional genomics. We also discuss bioinformatic tools and strategies for integrating multi-omics data with TE, and explore future directions, feasibility, and challenges of TE research in livestock and poultry. In addition, we suggest strategies to apply TE in basic biological research and animal breeding. Our goal is to provide a new perspective on the importance of TE in livestock and poultry genomes.

Effect of mild intermittent cold stimulation on thymus immune function in broilers

This study aims to assess the effect of intermittent and mild cold stimulation (IMCS) on thymus function and the ability of 1-day-old male Ross 308 broilers to withstand cold. Four hundred broilers were reared under normal and mild cold temperatures at 3°C below the normal feeding temperature and were subjected to acute cold stress (ACS) at 10°C on d 50 at 7 am for 6 h, 12 h, and 24 h. We determined the expression levels of toll-like receptors (TLRs), cytokines and avian β-defencins (AvBDs), encoding genes in thymus of broilers at 22, 36, 43, and 50 d of age, and the serum ACTH and cortisol (CORT) levels at 50 d of age. At D22 and D36, the mRNA expression levels of TLRs and AvBDs genes in CS groups were generally significantly decreased (P < 0.05). The lowest expression levels were found in birds submitted to intermittent and mild cold stimulation training for 5 h (CS5 group) on d 22 and 36 of development (P < 0.05). At D43 and D49 after IMCS, mRNA expression levels of most TLRs and AvBDs were significantly lower than those in CC group (P < 0.05), and that mRNA expression levels of all TLRs and most AvBDs in CS5 group had the same change trend with age as those in CC group (P > 0.05). At D22 and D36, mRNA expression levels of different cytokines in each CS groups were different (P < 0.05). mRNA expression levels of IL-2, IL-4, IL-6, IL-8, IL-17, and IFN-α all reached the highest values in the CS5 group at D36 (P < 0.05). The levels of ACTH and CORT in all IMCS-treated birds changed in varying degrees after ACS, but there was no significant change in CS5 group (P > 0.05). Collectively, different cold stimulation schemes could modulate thymus immune function of broilers by maintaining homeostasis and enhancing cold resistance. In particular, the optimal cold adaptation scheme was at 3°C below the conventional feeding temperature for 5 h.

Micro-Coevolution of Genetics Rather Than Diet With Enterotype in Pigs

Based on the characteristic of low diarrhea in native Chinese breeds, we introduce the enterotype model for piglets, which is a new perspective to decipher the colonization and the transition of the gut microbiota among various pig breeds. After eliminating environmental influences represented by diet, the microbiota, mainly shaped by host genetics, is focused. Three representative enterotype clusters were identified, which were represented by Bacteroides, Streptococcus, and Lactobacillus. Chinese native breeds were distributed in enterotype 1 (E1) and E3, which collectively drove the diversification and functionality of the microbial community of various Chinese pig breeds. Next, the Lactobacillus reuteri (L. reuteri), which is the representative strain of E3, was specifically isolated in all three enterotypes. The excellent stress-resistance of L. reuteri-E3 not only highlighted the stronger disease resistance of Chinese breeds but also had a great potential to intervene in weaned piglet diseases. Enterotype classification based on host genetics is much more deterministic and predictable, clarifying the driver of the host-microbiome dynamics and constructing the picture of the micro-coevolution of human host genetics with the gut microbiome.