| In modern pig production,15%～20% of newborn piglets are intrauterine growth retardation(IUGR).The occurrence of IUGR pigs and its adverse effects have severely restricted the development of China’s pig industry.As a class of epigenetic regulators,non-codingRNAs(ncRNA)are one of the important ways in which animal genetic material responds to environmental effects.The research on ncRNA will help to deepen the understanding of the occurrence of IUGR in pigs and the differential characteristics of IUGR pigs.And provide reference for reducing the occurrence of IUGR in pigs and improving the production performance of IUGR pigs.This study systematically analyzed the factors affecting the occurrence of IUGR in pig farms,the differences in production performance and the characteristics of skeletal muscle amino acid metabolism between IUGR pigs and normal pigs.This study carried out research from two dimensions of ncRNA type and skeletal muscle development stage.Taking miRNA as the main research object,we focused on the expression characteristics of miRNAs in normal and IUGR pig skeletal muscle at different developmental stages.Taking postnatal 35 days as an important stage,we explored the expression characteristics and regulatory networks of different ncRNAs.In addition,functional verification and feasibility application exploration were carried out for key regulatory factors.The main results of this study are as follows:1.The results of heritability evaluation showed that the key indicator traits affecting the occurrence of IUGR in pigs were all low heritability traits.Based on the analysis of pig farm production data,it was found that the mating combination,farrowing parity,gestational days,boar semen quality and sex were important influencing factors of piglet birth weight,while farrowing season had no significant effect on piglet birth weight.2.The Gompertz model is the best growth curve fitting model for IUGR pigs and normal pigs.Compared with normal pigs,the maximum daily gain of IUGR pigs was reduced by 141.67 g.Pigs were slaughtered at 180 days,and IUGR pigs had lower body weights than normal pigs(21.12 kg).In addition,carcass length,shoulder backfat thickness,and eye muscle area were significantly lower than normal pigs.In terms of meat quality traits,drip loss and p H drop rate within 24 h were significantly higher than normal pigs;and the cooked meat rate,intramuscular fat content(IMF),L1* and a1* values were significantly lower than normal pigs.3.The amino acid analysis of skeletal muscle showed that the internal correlation characteristics of each amino acid in pig skeletal muscle at different stages were different.Branched-chain amino acids were positively correlated with each other in different stages,MET,PHE,THR,TRP,TYR and ARG were also positively correlated with each other,while GLN and branched-chain amino acids had negative correlations.4.mRNA sequencing analysis showed that compared with normal pigs,886 genes were up-regulated and 1005 genes were down-regulated in IUGR pig skeletal muscle at neonatal stage(1 d);874 genes were up-regulated and 625 genes were down-regulated in IUGR pig skeletal muscle at postnatal stage 35 days.1743 genes were up-regulated and375 genes were down-regulated in IUGR pig skeletal muscle at embryonic day 63(GSE169092).Differential genes in the three stages were significantly enriched in 12 biological processes including muscle tissue development and striated muscle tissue development,and 9 signaling pathways including PI3K-AKT signaling pathway and Protein digestion and absorption.5.miRNA sequencing showed that in the skeletal muscle of embryonic 63-day pigs,15 were up-regulated and 9 were down-regulated in IUGR pig muscle.In embryonic90-day pig skeletal muscle,IUGR pigs up-regulated 43 miRNAs and down-regulated 63 miRNAs.In pig skeletal muscle on postnatal day 1,IUGR pigs up-regulated 16 miRNAs and down-regulated 22 miRNAs.In pig skeletal muscle at postnatal day 35,IUGR pigs up-regulated 55 miRNAs and down-regulated 32 miRNAs.In pig skeletal muscle at postnatal day 180,IUGR pigs up-regulated 124 miRNAs and down-regulated 57 miRNAs.Differential miRNAs were mainly involved in cell responses to stimuli(especially responses to starvation)at embryonic 63 d,and were mainly involved in protein catabolism at embryonic 90 d.Differential miRNAs were mainly involved in the process of fiber and protein polymerization in the neonatal stage,mainly involved in the transcriptional regulation process at 35 days after birth,and mainly involved in lipid metabolism and autophagy-related processes at 180 days after birth.6.A total of 586 tsRNAs were identified based on the analysis of tRNA-derived smallRNAs(tsRNA)from 35-day porcine skeletal muscle.The t RF-5c type tsRNA was mainly highly expressed in porcine skeletal muscle.Differential analysis showed that 19 tsRNAs were down-regulated and 9 were up-regulated in skeletal muscle of IUGR pigs.Functional enrichment analysis showed that highly expressed tsRNAs were mainly involved in embryonic development,and differentially expressed tsRNAs were mainly involved in intracellular signal transduction and protein phosphorylation.In addition,differential tsRNAs were mainly enriched in m TOR signaling pathway and AMPK signaling pathway.7.A total of 8367 lncRNAs were identified in the skeletal muscle of normal and IUGR pigs at 35 days,208 lncRNAs were up-regulated and 131 lncRNAs were down-regulated in IUGR pigs.A total of 24,047 circRNAs were identified,of which 152 circRNAs were up-regulated and 117 circRNAs were down-regulated in the skeletal muscle of IUGR pigs.Differential lncRNAs are mainly involved in nucleotide metabolism and homeostatic processes.Differential circRNAs are mainly involved in skeletal muscle function and material transport processes.8.Based on the differential miRNA and mRNA analysis of skeletal muscle and umbilical cord blood exosomes from embryonic to newborn piglets,a regulatory pathway was constructed: umbilical cord blood exosomes → miR-29 family → IGF1/CCND1 →cell proliferation and protein degradation.Based on postnatal phenotypic characteristics and multiple transcriptome analyses,it was found that muscle atrophy was a common feature of IUGR pigs at all stages,and miR-222 was highly expressed in various muscle atrophy models.In addition,genistein was found to act as a natural regulator of miR-222 to alleviate muscle atrophy.According to the meat quality characteristics of IUGR pigs,the analysis found that the miR-152→PKM→lactate pathway may be the main pathway that affects the rapid decrease of muscle p H in IUGR pigs.The co-analysis of tsRNA and amino acids found that the production of tsRNA may affect the ability of host tRNA to transport the corresponding amino acid.t RF-Glu-TTC-047 may affect IUGR pig skeletal muscle development through IGF1.In conclusion,this study analyzed the factors affecting the occurrence of IUGR pigs in pig farms and the differences in production performance and skeletal muscle amino acid metabolism between IUGR pigs and normal pigs,and improved the differential miRNA expression signature library of normal and IUGR pigs at important stages(primary muscle fiber formation,secondary muscle fiber formation,newborn,early fattening to slaughter)of skeletal muscle development.In this study,tsRNA expression profiles in normal and IUGR pig skeletal muscle were constructed,supplemented with information on the expression characteristics of lncRNA and circRNA in normal and IUGR pigs.The miR-29 family,miR-222,miR-152 and t RF-Glu-TTC-047 were identified and preliminarily verified as representative ncRNAs in the regulation of porcine skeletal muscle development.In addition,based on these key ncRNAs,functional small molecules such as glycine(Gly),glutamine(Gln)and genistein on the regulation of related ncRNAs and their effects on the growth of IUGR animals were initially explored.These results not only provide basic data for further understanding of the skeletal muscle development characteristics of IUGR pigs,but also provide new insights and references for improving the production performance of IUGR pigs. |
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