| In livestock production,feed efficiency is a complex,multi-trait composite characterisation and is one of the most important economic traits for pigs.It is one of the most important economic traits of pigs.Genetic improvement of pig feed efficiency through optimal selection and breeding strategies can significantly improve the economic efficiency and sustainability of the entire pig industry.Genomic selection technologies can help to investigate complex traits that are difficult to select for by traditional breeding techniques,with the advantage of high efficiency and low cost.Currently,genome-wide association studies have identified many genetic variant loci associated with complex traits,but most of the genetic variant loci are located in non-coding regions,and single GWAS studies cannot further elucidate the regulatory role of these loci on phenotypes.In order to further elucidate the effects of these genetic variant loci,a comprehensive annotation of the functional components of the non-coding regions of the genome is required,and the regulatory mechanisms of key functional variants need to be elucidated through integrated multi-omics analysis.In this study,multi-omics analysis was performed using ATAC-seq and RNA-seq techniques,and in combination with genetic variant loci significantly associated with feed efficiency,to screen key functional variants to reveal their role in pig feed efficiency.The main findings of this study are as follows:1.Transcriptome sequencing of duodenal and muscle tissues from high and low feed efficiency pigs screened for 264 and 270 differentially expressed genes in duodenum and muscle from high and low feed efficiency pigs,respectively.Compared to the low feed efficiency group,141 up-regulated and 123 down-regulated differentially expressed genes were identified in duodenal tissues and 187 upregulated and 83 down-regulated differentially expressed genes were identified in muscle tissue.Functional enrichment analysis showed that the differentially expressed genes were mainly involved in digestion and absorption,carbohydrate and unsaturated fatty acid metabolism in duodenal tissues;and in muscle tissues,they were mainly involved in lipid metabolism and energy metabolism.In this study,we identified several genes related to feed efficiency,including GUCA2B,AQPs,SLCs,CYPs,PPP1R3G and LIPG.2.Chromatin openings in duodenal and muscle tissues from pigs in the high and low feed efficiency groups were compared by ATAC-seq,and 18,295 and 45,052 differentially open chromatin regions were screened in the two tissues,respectively.Compared to the low feed efficiency group,10,270 up-regulated peaks and 8025 down-regulated peaks were identified in duodenal tissues;27,941 up-regulated peaks and 17,111 down-regulated peaks were identified in muscle tissues in the high feed efficiency group.These transcription factors are involved in the processes of glycolytic metabolism and fatty acid metabolism.The functional enrichment results showed that the genes near the differentially open chromatin region were mainly involved in glucose uptake,fatty acid oxidation and energy metabolism.3.In this study,80 K functional locus gene chip data from 3866 boars were directly populated into the genome sequence of 288 pigs to assess the accuracy of genotype populations using high-depth sequencing typing results of the same individuals as a standard.Genome-wide association analysis using populated sequence data screened 211 SNP loci for significant association with feed efficiency traits(P<4.55E-08).Candidate genes associated with feed efficiency traits within 1M each upstream and downstream of the first 15 SNP loci were selected,and three candidate genes associated with feed efficiency traits were obtained,namely PPP1R14C,TH and KCNQ1,located near 1:15865487,2:1502986 and 2:1787269,respectively.4.Using ATAC-seq and GWAS data,GWAS signals were found to be significantly enriched in differentially open chromatin regions in duodenal and muscle tissues of high feed efficiency pigs,and six key functional variants were screened(2:1500985,2:1509128,2:1510539,2:1509641,2:1509458 and 2.1509676),the ATAC-seq signal in the 2:1500985-2:1509676 region was significantly enriched in duodenal tissue from high feed efficiency pigs,with no significant enrichment observed in muscle tissue.In order to narrow down the search for target genes,this study draws on published Hi-C data to locate genes within the same TAD region near the SNP locus.Because the boundary of TAD is an isolation mechanism,it can regulate the physical contact between enhancers and promoters within the domain,playing an important role to control gene expression.High expression of the CTSD gene in duodenal tissue from high feed efficiency pigs was identified by RNA-seq data.We speculate that the five SNP loci in the 2:1500985-2:1509676 region may enhance the transcriptional activity of the promoter or enhancer of the CTSD gene and promote the expression of the CTSD gene in duodenal tissues of high feed efficiency pigs,and that the CTSD gene may be a target gene related to feed efficiency in pigs.In conclusion,by integrating RNA-seq,ATAC-seq,GWAS data and multi-omics analysis with the help of published Hi-C data,this study screened some key functional variants and target genes related to feed efficiency,providing a reference basis for exploring the regulatory mechanisms of feed efficiency and providing a genetic basis for achieving the breeding goal of breeding food-saving pig breeds. |
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