Difference Characteristics Of RFI-related MRNA And LncRNA In Beef Cattle And Genetic Effect Analysis Of Candidate Gene MTNR1A

Improvements in feed efficiency are essential for improving the economic performance of livestock producers and for the sustainable development of livestock farming.Residual feed intake（RFI）is one of the ideal indicators of feed efficiency and can be used to evaluate animal feed conversion rates,herd metabolism levels and breed selection.Individual livestock with low RFI have higher feed efficiency,and artificial selection for high feed efficiency livestock is of great practical importance for livestock development.To investigate the relationship between differentially expressed genes and differential lncRNAs and the phenotypic variation of RFI in beef cattle,five cattle with extreme high RFI（HRFI）and five cattle with low RFI（LRFI）were selected from this study,and RNA was extracted from hypothalamus tissues and transcriptome sequencing was performed to screen the differentially expressed genes and differential lncRNAs related to RFI in beef cattle through bioinformatics analysis.Association analysis was performed on the polymorphic loci of the candidate target genes with RFI.The main results were as follows.（1）Differential analysis of mRNA in hypothalamic tissue of high and low RFI Qinchuan cattleA total of 1538 differentially expressed genes were identified in the hypothalamus tissue of beef cattle in the HRFI and LRFI groups,of which 762 genes were up-regulated and 776 genes were downregulated in the LRFI group.feeding-related genes such as AGRP and PMCH and metabolism-related genes GH1,MTNR1A,RYR2,ADCY4 and FGFR1 and differentially expressed genes were mainly enriched in the calcium signaling pathway The FGFR1 gene may play a role in feed efficiency through its involvement in the biology of feeding and glucose metabolism via the brain-intestinal axis in beef cattle.Six randomly selected differentially expressed genes were validated by RT-qPCR,demonstrating that the quantitative analysis was in general agreement with the sequencing analysis.（2）Differential analysis of lncRNAs in hypothalamic tissue from high and low RFI Qinchuan cattleCompared with mRNA,the average length of lncRNA was 2846 bp,shorter than the average length of mRNA（18222 bp）;the average number of exons was 2.8,lower than that of mRNA（average 4.4 exons）;the ORF length of mRNA was significantly larger than that of lncRNA.1,406 differentially expressed lncRNAs were identified.The top 5 most highly expressed lncRNAs in the LRFI group had 191 trans target genes and 65 cis target genes.81 trans target genes and 11 cis target genes were identified in the top 5 most expressed lncRNAs in the HRFI group.lncRNAs The differentially expressed target genes were involved in neuroactive ligand receptor interactions,metabolic-related pathways including retinol metabolism,steroid hormone biosynthesis and metabolism,and immune-related pathways such as graftversus-host disease,malaria and autoimmune thyroid disease.TCONS₀0226900,which was specifically highly expressed in the LRFI group,was co-expressed with the candidate gene MTNR1A and could be used as a candidate lncRNA for further study.Seven randomly selected differentially expressed lncRNAs were validated by RT-qPCR and demonstrated that the quantitative analysis was consistent with the sequencing analysis.（3）Correlation analysis of MTNR1A coding region polymorphism and residual feed intake in beef cattleThe SNP1（g.G489A）locus of MTNR1A showed a more favourable GG genotype in both the Qinchuan and Angus cattle populations.SNP2（g.A497G）locus showed a higher RFI in individuals with the AA genotype of Qinchuan cattle than the other two genotypes,and individuals with the GG genotype of Angus cattle were better than the other two genotypes.The two polymorphic loci of MTNR1A had significant effects on growth traits in Angus cattle,which may affect the growth and development of beef cattle.