Study On The Genomic Copy Number Variation Of Guizhou Local Pig Breeds Based On Resequencing Technology

Copy Number Variation?CNV?is a genomic structural variation between individuals or groups.It is an important component of genomic genetic variation and is mainly related to some complex traits,disease susceptibility and evolution.Guizhou local pigs have some disadvantages of small size,slow growth rate,low lean meat rate,thick backfat and low fertility.The advantages of strong stress resistance and tender meat are outstanding,but the molecular mechanism of these phenotypes is still unclear.Therefore,this paper uses the Read Depth method to perform genomic CNV detection based on genome resequencing data.The variation feature of CNV in pigs,the effects of CNV on Guizhou local pigs traits,and the association of CNV with the subcutaneous adipose tissue and skin wrinkle phenotype of wrinkled Xiang pigs were explored from the genomic level.The research results are as follows:Based on genome-wide resequencing data,3,814 non-redundant CNVRs were identified using the Read Depth method.The length variation ranged from 4.36 kb to 912.80 kb,with a median of 21.77 kb,covering a genome length of 121.08 Mb and a coverage rate of 5.06%.There were 1,778?46.62%?CNVRs overlapping with known CNVR,and 2,036?53.38%?were detected for the first time in this study.A total of nine CNVRs were validated using qPCR method.CNVRs were consisted of two types of events,copy number deletion and copy number duplication,with the deletion as dominant type.In addition,the distribution density of CNVRs on chromosomes is unrelated to the chromosome length.CNV often presented in gene-rich regions and regions with high G + C content.Cluster analysis and principal co-ordinates analysis?PCoA?showed that there were large differences among different breeds,which might be resulted from the unique CNV of those pig populations.The number of CNVs in European pigs was much higher than that of Guizhou local pigs?European pigs: 2,582,Guizhou local pigs: 475?,which was deduced to be the main reason for the difference in phenotype between Guizhou local pigs and European pigs.It suggested that the genetic variation of the populations with different origin was great.The difference between the Xiang pig and the other four pig breeds was the most obvious among the five Guizhou local pigbreeds.Based on GO and KEGG functional enrichment analysis on each local Guizhou pig breed using unique CNVR overlapping genes,as input,it was significantly enriched in growth,reproduction and immune-related signaling pathways and GO term.Among the Guizhou local pig breeds,it identified a number of candidate genes that might affect the corresponding traits,including MAOB,SMAD1,PLCG2,KIT,MAPK8,PIK3R3,SOX3,NTF4.The copy number duplication of monoamine oxidase B?MAOB?might promote the growth and development of Guanling pigs.The copy number deletion of SMAD1 gene may be related to the slow growth of Luobu pigs.Phospholipase C gamma 2?PLCG2?might play an important role in the immune regulation of Luobu pigs.Deletion of MAPK8 copy number might affect the differentiation of embryonic stem cells by down-regulating JNK signal by dose reduction effect,which has an important influence on the phenotype of Qianbei black pig.Under the condition of PIK3R3 with copy number deletion,its expression was decreased,PIK3/AKT signaling pathway can't be activated,PI3K/Akt signaling pathway was negatively regulated,cell proliferation was inhibited,and apoptosisis promoted.It might play an important role in regulating the growth and immunity of Kele pigs.The lower fertility of the Xiang pigs might be related to the loss of function due to the deletion of copy number of SOX3.Deletion of copy number of NTF4 might affect the development of the taste system.Comparing the CNVRs of wrinkled Xiang pigs,normal Xiang pigs and two European pig breeds,the KEGG and GO enrichment and QTL quantitative traits were used to analyze the CNVR overlapping genes unique to normal Xiang pigs and wrinkled Xiang pigs.The genes affecting the skin traits and subcutaneous fat traits were identified,including five genes that may be involved in fat deposition?MPC1,RPS6KA2/RSK3,PECR,PDHB and PGM1?,four of which might be associated with skin folds,Genes?CCL17,CX3CL1,MID1 and ANTXR1?.Among them,MPC1 and RPS6KA2/RSK3 in the copy number deletion event CNVR₀012,which might be associated with subcutaneous fat deposition.PECR had a high affinity for 16 carbon fatty acids,and duplication mutations in PECR copy number might result in increased deposition of subcutaneous fat in the normal Xiang pigs.PDHB is enriched in signaling pathways such as tricarboxylic acid cycle?TCA cycle?,pyruvate metabolism,and glycolysis/gluconeogenesis,which have important effects on energy metabolism.Overexpression of PDHB inhibits cell growth,and the normal copy number in wrinkled Xiang pigs might be responsible for the reduction ofsubcutaneous fat deposition.PGM1 is a widely-existing group of enzymes.When PGM1 is lack,there shows two two different types of metabolic disorders that can lead to inborn glycosylation disorders?CDG?and glycogen storage disease,and resulting in short stature.PGM1 deletion might hinder the growth of wrinkled Xiang pigs.The expression level of CX3CL1 is up-regulated in the affected skin of patients with systemic sclerosis?SSc?,and can lead to excessive collagen in the skin of the mice and cause skin fibrosis.The expression level of CCL17 gene is elevated in the skin of damaged parts of patients with psoriasis,and the expression level of patients with acute allergic contact dermatitis?ACD?is increased by 90-fold and CCL17 protein is increased by 50-fold.The copy number duplication of CX3CL1 and CCL17 in wrinkled pigs might be related to the formation of skin wrinkles.The anthrax toxin receptor 1 encoded by the ANTXR1 gene is a type I transmembrane protein that binds to the extracellular matrix?ECM?component and has an important relationship with skin regulation.Deletion of ANTXR1 in wrinkled Xiang pigs might cause skin wrinkles.In summary,this paper studied the genomic copy number variation of five Guizhou local pig breeds based on genome resequencing technology,and constructed the copy number variation map of Guizhou local pig breeds.The pattern of genomic copy number variation in Guizhou pig population was analyzed,and the copy number variation of 8 genes might affecte the growth and reproduction traits of Guizhou local pigs.Nine genes were associated with subcutaneous fat and skin wrinkle phenotype in wrinkled Xiang pigs.