Genome-wide Analysis Of Selective Regions And Identification Of Excellent Germplasm Related Functional Genes In Anqing Six-end-white Pig Breed

As a famous native Chinese breed which exhibits disease resistance and high meat quality,Anqing six-end-white pig（AQ pig）represents a valuable germplasm resource for pig development.But in a long-time,AQ pigs have been in small population size lead to inbreeding depression such as:slower growth rate,less lean meat,unconspicuous fertility advantage,poor stability with meat quality.In this study,SSR markers were used to identify genetic distance in AQ pigs.Then,24 AQ pigs which were in distantly blood relationship and 6 Asian Wild Boar（AWB）were chosen to perform 10X deep genome re-sequencing.Signatures of selection and runs of homozygosity were analyzed for exploring the genetic basis of its germplasm characteristics and identifying execellent germplasm related functional genes based on NGS data.The main results were as follows:（1）All of the 14 microsatellite loci were polymorphic in AQ pigs,the average number of alleles was 8.5,effective number of alleles ranged from 3.1927 to 7.1078,observed heterozygosity ranged from 3.1927 to 7.1078,SW963,SW122,S0255,S0386,S0355,SW2156 microsatellite loci deviated from Hard-Weinberg equilibrium,SW240,SW72,S0101,S0090,SW24,S0026 were in Hard-Weinberg equilibrium,the combined probability of exclusion reached 99%of 14 microsatellite loci.Genetic distance results of microsatellite loci were similar to genetic relationship which showed animals were not related in this work.（2）A total of 49,289,052 SNP and 6,186,123 Indel were detected across the genome in thirty pigs.Most of the genetic variations were synonym mutation and existed in intergene region.275 selected regions（Top 1%）harboring 85 genes were identified by applying the genetic differentiation(F_ST)and polymorphism levels（πratio）based cross approaches.Some genes were found to be positively selected in AQ pig’s breeding.SMPD4,DDX18 genes were involved in immune response for PPR and PRRSV virus.BCL6,P2RX6 genes were involved in biological regulation of immune T cells and phagocytes.SLC7A4,SPACA4 genes were related to reproductive performance.MSTN,HIF1A genes were related to fat deposition and muscle development.（3）Compared with AWB,AQ pigs have higher ROH number,long ROH rate and F_ROHvalues which revealed that artificial selection has influence in ROH distribution and genome inbreeding level.Total of 307 and 205 ROH islands were identified in AQ and AWB pigs,respectively.The ROH islands harboring genes of AQ pigs were significantly enriched in Chemokine signaling pathway,Epstein-Barr virus infection and Fc gamma R-mediated phagocytosis by functional enrichment analysis.（4）138 overlapping regions were detected in selected regions and ROH islands of AQ pigs.Moreover,we found the majority of QTLs in overlapping regions were related to back fat thickness,meat color,p H value,fatty acid content,number of immune cells,parasitic immunity,bacterial immunity.Three missense mutation loci in exon region of SLC7A4 and INSIG2 genes were detected polymorphism in AQ pigs,these loci have been found in mutational which are agreed with re-sequencing results.In this work,we analyzed the family relationship and determined sample selection based on SSR molecular marker.AWB pigs were chosen as a reference population to analyse signatures of selection for AQ pigs,the results indicated that there were several candidate genes in selected regions which related to germplasm characteristics.The results of ROH detection in two pig breeds indicated that distribution of ROH is related to selection pressure,AQ pigs（with high-intensity of selection）have higher ROH abundance,length,F_ROHvalues than AWB pig（with low-intensity of selection）.We further performed molecular genetic basis of germplasm characteristics（disease resistance and excellent meat quality）based on functional enrichment analysis and QTLs mapping.These findings are a reliable resource for conserving germplasm resources conservation and exploiting molecular marker of AQ pigs.