Polymorphism of Structural Variation DKK2-I1-sv89 in the DKK2 Gene of Five Pig Breeds

LONG Juyan; LU Shengfei; TIAN Jiao; NIU Xi; CHEN Xia; HUANG Shihui; RAN Xueqin; WANG Jiafu

doi:10.15933/j.cnki.1004-3268.2025.04.013

Abstract：A structural variation measuring 89 bp,designated as DKK2-I1-sv89,was identified in intron 1 of the DKK2 gene of pigs through preliminary genomic analysis.To investigate the polymorphism distribution of this structural variation(SV)and its potential impact on gene expression,specific primers targeting the SV sequence were designed for this study.The population distribution of DKK2-I1-sv89 was subsequently evaluated using polymerase chain reaction(PCR)across four Guizhou indigenous pig breeds(Xiang pig,Qianbeihei pig,Kele pig,and Jiangkouluobo pig)and one European pig breed(Large White pig).The gene expression difference of DKK2 among the various genotypes was determined by using real time quantitative PCR(RT-qPCR).Additionally,bioinformatics analyses were employed to assess the functional elements within the structural variation region of DKK2-I1-sv89.The findings demonstrated that in the Xiang pig and Qianbeihei pig,three genotypes(insertional genotype Ⅱ,heterozygous genotype DI,and wild-type genotype DD)were found,while only one genotype(DD)was found in Large White pig,however in Kele pig and Jiangkouluobo pig,two genotypes(DI and DD)were found.Comparative analysis across the five breeds demonstrated that the four Guizhou local pig breeds(including Xiang pig,Qianbeihei pig,Kele pig,and Jiangkouluobo pig)had a higher frequency of the insertional allele(I allele)compared to the Large White pig.Bioinformatics analysis revealed that the DKK2-I1-sv89 contained one intronic splicing enhancer(ISE)and 13 RNA binding protein(RBP)binding sites.Quantitative trait locus(QTL)analysis demonstrated that the QTL at this SV locus was associated with reproduction,meat quality,and health-related traits.Further analysis of DKK2 gene expression in ovarian tissues of Xiang pigs with different genotypes(Ⅱ,DI,and DD)revealed that Ⅱ genotype pigs exhibited significantly higher expression levels compared to both the DI and DD genotypes.The results indicated a notable difference in the distribution frequency of this polymorphism between Large White pig and Guizhou local pigs.Additionally,the SV was found to be beneficial for the expression of DKK2 gene in the ovary and could serve as an early molecular marker for distinguishing between Large White pig and Guizhou local pigs.