Discovering And Analysing Important Genes Affecting Intramuscular Content In Pigs In Genome

Pig is considered as an important meat animal in our country,its meat quality has always been the focus for many consumers.The important issue for improvement the meat quality of pigs is how to effectively reduce the thickness of the backfat but with simultaneously increase the intramuscular fat content(IMF).Among a large number of factors affecting IMF deposition in pigs,genetic factor is the leading factor.Particularly,the phenotypic differences of the IMF deposition is more obvious among different pig breeds.Therefore,exploring the molecular basis and the mechanism of IMF deposition in pigs has become a hot research field.In recent years,with the rapid development of sequencing technology,the detection of genetic variation has changed from a single,local gene or fragment to the study of the whole genome.High-speed,high-throughput,and cost-effective sequencing technologies,such as,simplified genome sequencing,transcriptome sequencing,and genome resequencing,are playing a role in improving pig germplasm traits.In addition,the Pig QTL database provides a large amount of avaiable information for us,so that more and more researchers can analyse in depth via integrating different omics data.Therefore,this study conducted in-depth exploration and analysis on genetic variation and important genes affecting the IMF content in pigs at the genomic level.The results were as follows:1.Comparing the genetic differences between Chinese and foreign pig breeds based on genome re-sequencingIn order to understand the variation information of genetic differences between domestic and foreign pigs with different IMF content,we downloaded the original data of the whole genome re-sequencing in pigs from public databases.Among them,there are 4 Chinese indigenous pig brees with high IMF content(6 Laiwu pigs,13 Meishan pigs,8 Rongchang pigs,and 5 Erhualian pigs)and 2 western pig breeds with low IMF content(18 Landrace pigs and 15 Pietrain pigs),which were divided into two different populations.Then the signature of selection in Chinese and foreign pigs were identified.After data filtering,a total of 9,465,463 high-quality SNPs(nucleotide polymorphism sites)were obtained on autosomes for subsequent analysis.To accurately obtain the information related to IMF traits,we combined the IMF QTLs and the differentially selection regions using the top 5%SNPs of FST value,and finally identified 3,002 potential candidate genes,thus laying a foundation for further study.2.Identifying the candidate genes related to intramuscular fat content using SLAFsequencing technologyIn order to further clarify the candidate genes related to the IMF content of pigs,SLAFseq technology was used to dig the genetic variation and important genes affecting IMF deposition between the high and low IMF content groups.Using the enzyme comination of RsaⅠ+HaeⅢ,more than 1,000,000 SLAFs were discovered.After quality control,a total of 173,154 high-quality SNPs were selected for the futher analysis.Based on the FST method,341 differentially selected regions including 210 differential genes were identified from these SNPs,which contained a large number of important candidates related to fat traits,such as DDHD1、COL22A1、CRISPLD2、STK32B、EPHA5、TUB、DUSP10、SORBS2、PDZD2、NPR3、DAB2、KIF16B、ANK1、KIF16B,etc.Functional enrichment analysis revealed that the function of these genes were mainly involved in oxytocin signaling,ECM receptor interaction,chemokines,relaxin signaling,pi3k-akt signaling,and other signaling pathways related to IMF content.Combined with the above genome resequencing results,we found that TRIM54,ANK1,COL22A1,etc.as common genes in the two datasets,which are expected to be important candidate genes affecting the IMF content in pigs.In summary,this study integrated different methods to reveal the genomic differences between the Chinese and foreign pig breeds with different IMF content/between hybridization pigs in high and low IMF groups,and identified a number of important candidate genes related to IMF trait of pigs.These results could provide an available genetic material for the subsequent molecular improvement of IMF trait of pigs and a scientific basis for improving pork quality.