Identification Of Functional Genes And NcRNA-mediated Genetic Regulation Affecting Residual Feed Intake In Chickens

The feed cost accounts for more than 70% of the total cost of poultry production.Residual feed intake(RFI)is one of the important indexes to measure feed efficiency of livestock and poultry.However,most of the research on RFI is still focused on commercial chickens,and there is a lack of in-depth research on RFI traits of native chicken.Therefore,the purpose of this study was to explore the transcriptional regulation mechanisms of key genes and pathways affecting RFI of native chicken and to explore the transcriptional regulatory mechanisms of associated non-coding RNAs(nc RNAs).A total of 1008 Wannan Yellow chickens were selected as the experimental materials to determine the growth performance and feed efficiency of 56-98 d old chickens.At 98 d of age,the RFI values were used to rank all the chickens.25 high RFI(HRFI),medium RFI(MRFI)and low RFI(LRFI)chickens were selected,and the carcass traits,meat quality,and blood variables of native chickens were measured.Our results found that selecting LRFI chickens was more conducive to reducing abdominal fat deposition in native chickens(P < 0.05)without affecting growth performance and meat quality.The blood levels of T3,ACTH,cortisol and LDL-C in the HRFI group were significantly lower than those in the LRFI group(P < 0.05),while the IGF-1,GLU and TG in the HRFI group were significantly higher than those in the LRFI group(P < 0.05).5 chickens were randomly selected from HRFI and LRFI groups for transcriptome sequencing.The function analysis of the differentially expressed genes(DEGs)showed that genes associated with inflammation and immune response were up-regulated in HRFI chickens,while genes associated with mitochondrial function were down-regulated in HRFI chickens.Among them,the ND2,ND4,CYTB,RAC2,VCAM1,CTSS and TLR4 were identified as key genes of RFI in native chickens,involving ROS production and inflammatory response."Phagocytic","cell adhesion molecules(CAMs)","citric acid cycle(TCA cycle)" and "oxidative phosphorylation" were identified as key pathways of feed efficiency in the native chickens.Moreover,the current study identified differentially expressed lnc RNAs(DELs),differentially expressed mi RNAs(DEMis),and differentially expressed circ RNAs(DECs)in the native chicken.The target genes of DEMis are mainly enriched in "stress response" and "immune system process pathways".The target genes of DECs are mainly enriched in "PI3K-AKT signaling pathway" and "thyroid hormone signaling pathway".We built and analyzed the lnc RNA-related ce RNA interaction network,and found that DELs may eliminate the inhibition of mi RNAs on immune-related genes by lnc RNAs competitive binding to mi RNAs.The target genes in ce RNA network are mainly involved in the response to signal,stimulus and immunity.Among them,gga-mir-133a-3p,gga-mir-133a-3p and mir-133-z were identified as key mi RNAs in lnc RNA-related ce RNA network.In addition,alternative splicing(AS)events between chickens between the different RFI chickens were analyzed.Out results found that about 39.7% of the expressed genes undergo AS events.Skipping Exon(SE)is the most common type of AS in the skeletal muscle of native chickens.Retention Intron(RI)is the rarest type of AS in the skeletal muscle of native chickens.Functional analysis of differently spliced genes(DSGs)revealed that DSGs mainly enriched three pathways,namely "Hedgehog signaling pathway","Glycerolipid metabolism" and "Pyruvate metabolism",which involved the lipid metabolism and glycolysis in the native chickens.Further analysis revealed six key DSGs(CREBBP,GAPDH,HDAC8,ARID4 A,ARID4B,and KDM6A),which involved the energy homeostatic state and reproductive performance in the native chickens.Circulating IGF-1,T3,cortisol and LDL-C can be used as candidate biological indicators of feed efficiency in the native chickens.The RNA sequencing results suggest that HRFI chickens may be exposed to more oxidative stress,leading to an increased inflammatory response,while LRFI chickens may be able to synthesize ATP more efficiently and control ROS production more strictly by enhancing skeletal muscle mitochondrial function.A series of key nc RNAs affecting RFI were identified by nc RNA sequencing.AS analysis indicated that local chicken RFI differences may affect lipid metabolism,energy homeostasis,and reproductive performance.Our research will provide a new perspective for further research on the potential molecular mechanism of RFI.These data provide reference information for the development of multi-trait selective breeding and molecular assisted breeding strategies of the native chickens.