| Shenxian pig is the only local pig in Hebei Province.It not only brings delicious pork,but also stimulates the development of the surrounding economy.At the same time,it also contributes helps to research local pig breeds in China.physical conformation traits are important considerations in the selection of breeding pigs.It is also closely related to many economies and affects the interests of the farm.Therefore,the physical conformation traits of pigs gradually become an important economic trait.Therefore,the study of physical conformation traits of the Shenxian pig became the key research in pig breeding at the present stage and became the current hot spot.With the completion of swine whole-genome sequencing and the development of swine high-density commercial chips,genome-wide association analysis has become the main tool for finding mutation sites that affect various economic traits in pigs.This study collected venous blood samples from 68 healthy Shenxian pigs,genotyped the samples using an Illumina Porcine 80 K SNP chip,and passed stringent quality tests,60 125 effective SNPs and 68 samples were obtained that used for Genome-wide association analysis(GWAS).The phenotypic traits analysed in this study were the six-month-old physical conformation traits,including five indicators of body weight,body length,body height,chest circumference and tube circumference.The purpose of this study was to find the genetic variation associated with the somatic physical conformation traits of the six-month-old Shenxian pig.This study was based on high-density SNP microarrays and performed a genome-wide association analysis of five six-month-old somatic traits in 68 Shenxian pigs.In this study,a mixed linear model was used to consider the stratification and inter-individual kinship in Shenxian pigs.The results show that:1.The descriptive statistical analysis of physical conformation traits in the Shenxian pig population can be seen from the analysis of the epiphenome.The mean values were: 55.92 kg,103.29 cm,58.91 cm,99.09 cm,and 16.32 cm;The coefficients of variation were:13.34,7.80,10.49,8.25,and 6.45.2.GWAS were performed for body weight,body length,body height,chest circumference and tube circumference by PLINK software and based on high-density SNP chip in Shenxian pig individual,there were 37,23 and 26 sites that significantly affected body weight,body length,and chest circumference,respectively.NO significant SNPs were detected for body height and tube circumference.3.According the database information from NCBI,Ensembl,and biological informatics,the genes function that the vicinity genes of all ralated significant SNPs of physical conformation traits were annotated.Four candidates genes,PDZD2,MTMR12,NPR3,and TARS were identified by gene function annotations and significant locus rankings,and candidate genes related to physical conformation traits were initially located.4.Haplotype analysis of all significant SNPs were done by using haplo.stats of R-language environment and HAPLOVIEW 4.2 software,we found that there were 3 haplotype blocks on chromosome 16,all of which were significantly associated with body weight,body length and chest circumference.Thus it can position five candidate genes--PDZD2,MTMR12,NPR3,ADAMTS12 and TARS genes.Therefore,five genes PDZD2,MTMR12,NPR3,ADAMTS12 and TARS were initially selected as key candidate genes for physical conformation traits.5.In summary,it was found that the four candidate genes ranked by significant locus ranking are identical to the four candidate genes in the haplotype-annotated genes,so four genes--PDZD2,MTMR12,NPR3 and TARS genes are were initially selected key candidate genes for physical conformation traits.The results of this study provide a theoretical basis to study Shenxian pigs and discover new SNPs and candidate genes that affect the physical conformation traits of pigs,laying the foundation for subsequent verification of functional genes.It also provides molecular theoretical basis for the breeding of new strains of Shenzhen pigs. |
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