Mining Key Genes In The Number Of Thoracic Vertebrae Of Lijiang Pigs Based On Whole Genome Resequencing

Lijiang pig is a national identification pig breed resource in 2015,and the number of thoracic vertebrae in the population varies,with some individuals having 15 or more thoracic vertebrae.However,the reasons for the difference in thoracic vertebra numbers of Lijiang pigs need to be investigated.In this study,there were 44 Lijiang pigs with differences in the number of thoracic vertebrae were used for whole-genome resequencing,including 27 Lijiang pigs with ≥15 thoracic vertebrae and 17 Lijiang pigs with ≤13 thoracic vertebrae,and the genes affecting the number of thoracic vertebrae were mined by genomics and bioinformatics.The main findings were as follows.(1)Whole genome resequencing of 44 Lijiang pigs detected 40,343,967 SNPs and7,851,569 Indels.After gene annotation,there were 17150 missense mutated genes and4798 shift mutated genes.We found genes that were associated with the number of thoracic vertebrae in pigs were NR6A1,PROX2,FOS,VRTN,LTBP2,VSX2,GREB1 L,MIB1,ABCD4,TGFβ3 and other genes.The missense mutated genes and shift mutated genes were respectively annotated with GO and KEGG,these genes were mainly enriched in the calcium signaling pathway,Wnt signaling pathway,Notch signaling pathway and other pathways.(2)The genome-wide signal of Lijiang pigs was analyzed by combining Fst and PI ratio,and 4556 selected regions were detected and 902 genes were screened.In Lijiang pigs with multiple thoracic vertebrae,a total of 470 genes were annotated in2095 selected regions,and the genes related to the number of thoracic vertebrae were TCF7 and CER1,etc.In Lijiang pigs with few thoracic vertebrae,432 genes were annotated in 2461 selected regions,and the genes related to the number of thoracic vertebrae were LTBP2 and SYNDIG1 L,etc.These genes were significantly enriched in Notch signaling pathway,Wnt signaling pathway,calcium signaling pathway,osteoblast differentiation,etc.(3)A total of 879 genes were found in GWAS analysis.A total of 32 candidate genes were screened according to literature and functional enrichment.The protein of candidate genes interaction showed that AKT3,FOS,PROX2,SMURF1,GRIN2 B,VSX2,LTBP2,and NUMB proteins were in the core position.AKT3,SMURF1,GRIN2 B,NUMB,and BMP6 were potential candidates for thoracic vertebrae number in Lijiang pigs.The genome-wide signal scan was enriched with GWAS for 80 genes,and candidate genes such as LTBP2,NUMB,SYNDIG1 L,EDIL3,MAML2,PKDCC may be potentially correlated with different thoracic vertebrae number variations.(4)The results of gene exchange showed that there was gene exchange between European commercial pigs and Lijiang pigs,and there was European commercial pigs infiltration located on chromosome 7 and chromosome 10 in Lijiang pigs,and the infiltrated region included genes related to thoracic vertebrae such as LTBP2,VRTN etc.In this paper,based on the resequencing data of the extreme population of Lijiang pigs,a total of 43 genes related to the number of thoracic vertebrae were screened by selection signaling,genome-wide association,population genetic and gene flow analysis.11 genes,including NR6A1,PROX2,FOS,VRTN and LTBP2,were most likely to be closely related to the number of thoracic vertebrae in Lijiang pigs,while 32 genes,including SMURF1,NUMB,EDIL3,PKDCC,etc.,were found to affect the variation of thoracic vertebrae number in Lijiang pigs.In conclusion,this study provides a basis for the subsequent excavation and analysis of the number of thoracic vertebrae affecting Lijiang pigs,and also provides a basis for the conservation and improvement of Lijiang pigs.