Exploring Genomic Variants And Genes Related To Residual Feed Intake In Chickens By High-throughput Sequencing

As with most animal production systems,the cost of feed in chicken meat production is a high proportion of the total farming expense,being nearly 70% of the total cost of poultry production.Selection of more efficient animals reduces production costs,improves economic returns,and reduces environmental impact of nitrogen and phosphorus excretion resulting from the digestion/metabolic processes.In order to develop the marker-or gene-assisted selection for the improvement of feed efficiency in broiler,variants and genes for residual feed intake(RFI)were explored using high-throughput sequencing.Trial 1: Construction of the test groups and analysis of the relationship between RFI and production performanceThe relationship of RFI and production performance were explored using Beijing-You and Cobb chickens.400 Beijing-You chickens and 800 Cobb chickens were used to analyze the correlation of these traits.The results show that: 1)In Beijing-You,the difference value(D-value)of the highest and lowest RFI were 60.81 g/d in male group and 34.83 g/d in female group.In Cobb,the D-values were65.10 g/d in male group and 61.58 g/d in female group respectively.2)In Beijing-You,RFI had positive correlation with feed conversion ratio(FCR),daily feed intake(DFI)(P<0.01).RFI was positive correlated with percentage of abdominal fat(P<0.05)and negative correlation with percentage of breast and thigh muscle in male chickens(P<0.01),and was negative correlation with percentage of thigh muscle in female chickens(P<0.01).In Cobb,RFI was positive correlated with FCR,DFI and percentage of abdominal fat(P<0.01).All of these results mean that selection for low RFI may increase the deposition of muscle and decrease the deposition of abdominal fat.Trial 2: Exploring genomic variants related to residual feed intake in chickens by whole genomic resequencing(WGS)Genomic DNA was isolated from whole blood samples collected from 48 high RFI and 48 low RFI chickens,within each breed,using the phenol–chloroform method.Sequencing of six DNA pools for each breed revealed 6288 reliable single-nucleotide polymorphisms(SNPs)including 1137 genes in Beijing-You chickens and 448 genes with 1000 SNPs in Cobb chickens.Only 127 enriched genes were common to the two breeds.The number of SNPs and genes identified in Beijing-You was more than twice that of Cobb chickens,which reflected the differences in genetic background and impact of selection between the two breeds.Functions annotation indicated that RFI-related genes in Beijing-You were enriched in lipid and carbohydrate metabolism as well as the PTEN signaling pathway.In Cobb,however,RFI-related genes were enriched in the feed behavior process and CREB signaling pathway.For both breeds,organismal development physiological processes were enriched.In Beijing-You,the enrichment of n NOS signaling in skeletal muscle cells as the significant pathway supported the important role played by organismal development for the RFI trait.In Cobb,the enrichment of Rac andthe actin cytoskeleton signaling were consistent with the important role played by organismal development in the RFI trait.Trial 3: Exploring differential expressed genes related to residual feed intake in duodenum of chickens by RNA-SeqTissues of duodenum were collected from three high RFI and three low RFI Cobb chickens,respectively.An analysis of RNA-Seq was used to investigate the differential expressed genes and related signaling pathways involved in RFI.Results showed that: There were 24624 genes expressed in chicken duodenum,in which 599 genes were differential expressed(DEGs)between high-and low-RFI chickens with the criterion of P-value <0.05 and fold change ?1.5 or ?0.67.Compared to high RFI ones,there were 309 up-regulated genes and 290 down-regulated genes in low RFI ones.Function annotation and pathway enrichment showed that the DEGs involved in metabolism and immune processes.CCK,MPEG1,EPHB2,SERPINH1,VANGL2,CYFIP2,PCDH19,TGBI,SCUBE3 and CATHL1 were identified in the results of WGS and RNA-Seq,which involved in feed intake,metabolism,digestion and immune.Therefore,these genes that differentially expressed in duodenum maintained the good function and health of the gastrointestinal tract,which may result in the different feed efficiency in chickens...