Total Transcriptomic Analysis Of Rumen Tissue Of Calves Under Different Feed Structures

Choosing the right feed structure and understanding the gastrointestinal digestive mechanism could help the growth and health of calves in intensive farming.To achieve this,calves are fed solid feed a few days after birth to increase productivity,fertility and milk production.So far,the effects of different feed structure on rumen development have been studied only at the nutritional level,and its genetic basis and regulatory mechanism remain unclear.In this study,7-day-old Holstein male calves were randomly divided into GF group,GFF group and TMR group using three different dietary structures(concentrate,concentrate + hay and concentrate + alfalfa +oat grass)and fed to 80 d.Rumen tissue and blood were collected to study the effects of different dietary structures on papillae development and digestive enzyme activities of rumen tissue of calves.At the same time,complete transcriptomic sequencing of rumen tissue was conducted to explore the regulatory mechanism of different dietary structures on genes in rumen tissue of calves and to select the best feed structure.The main results are as follows:(1)The papillae width,height and serum of Holstein male rumen tissue fed three different feed structure were measured in this experiment,and the width of posterior abdominal papillae was significantly different among the three groups(p<0.01);the height and width of dorsal sac and abdominal sac papilla in GF group were significantly higher than those in GFF(concentrate + hay)(alfalfa + oat =3:2)group and TMR(concentrate + alfalfa + oat+ water =0.30:0.12:0.08:0.50)group(p<0.05);the content of α-amylase and the activity of cupric protein in TMR group were significantly higher than those in GFFand GF(concentrate)groups(p<0.01).(2)A total of 1210 mRNAs,132 lncRNAs,666 circRNAs and 27 miRNAs were identified by differential expression analysis of total transcriptomics.The function and pathway enrichment of the selected target genes with differentially expressed miRNAs,lncRNAs and circRNAs were analyzed using GO and KEGG databases.The GF group genes are mainly concentrated in B cell receptor signaling pathway,oxytocin signaling pathway and Fcγr mediated phagocytosis pathway,which may be related to insulin resistance and inflammation.The genes of GFF group were mainly enriched in immune system and glucolipid metabolic pathways such as alcoholism,DNA repair and PPAR signaling pathway.Target genes differentially expressing miRNA and LncRNA in TMR group were enriched in Ras,VEGF,Hippo,Wnt signaling pathways and protein and fat absorption signaling pathways.(3)Correlation analysis was conducted on differentially expressed lncRNA,circRNA,miRNA,and mRNA,and multiple circRNAs/lncRNA-miRNAs-mRNAs that may be involved in rumen growth structure and developmental function were screened.Endogenous competitive network interaction(CeRNA)maps were constructed.In conclusion,TMR feed structure could improve rumen digestive enzyme activities,promote energy homeostasis and microenvironmental balance related gene expression,and promote rumen growth and development better than GF and GFF groups.Besides,important candidate genes such as PADI3 and CLEC6A,important miRNAs such as bta-miR-11975,bta-miR-2890,and novel＿circ＿0002471,TCONS＿00946152 were screened,which provided a new idea for further revealing the molecular genetic mechanism of rumen development in calves.