Study On The Runs Of Homozygosity (ROH) Of Baoshan Pigs Based On Whole Genome Resequencing

In order to accurately assess the inbreeding level of Baoshan pig population,screen the candidate genes which are regulated with good traits from the pure genomic regions of Baoshan pigs,and to gain insight into the structure and function of the candidate genes to reveal the molecular mechanism of the genes regulating the good traits of Baoshan pigs.In this study,12 Baoshan pigs were selected for whole genome resequencing,the length,number and distribution of ROH in Baoshan pigs were counted,the inbreeding coefficients were calculated based on lineage and ROH information,the inbreeding levels of Baoshan pigs were assessed,ROH islands were captured,GO and KEGG enrichment analysis and mapping results of QTLs loci were performed in the islands,and key genes closely related to economic traits were selected for SNP screening and bioinformatics analysis,and the results were as follows:（1）Whole genome resequencing of Baoshan pigs yielded 22,633,391 SNPs,and a total of 254 ROHs were detected from 532,450 SNPs after quality control,with the most ROHs were medium-length ROHs（1-5 Mb）（98.43%）,the least ROHs were long ROHs（>5 Mb）（1.57%）,indicating that mainly inbreeding were occurred in Baoshan pigs in the distant generations,the F_ROHcalculated from the total length of ROH was 0.0178 and the F_PEDcalculated from the lineage was 0.0268,with a positive correlation between the two methods,and the population inbreeding level of Baoshan pigs was assessed to be low;（2）A total of 40 ROH islands containing 505 genes and 1073 QTLs loci were identified in Baoshan pigs,and significantly enriched genes were obtained by GO and KEGG analysis.development（COL1A2,DLX5,DKK1,WNT2）,fat deposition（ACSM3,ECI1,CD36,KLF6）,meat quality traits（ROCK1,CACNA2D1）,reproductive traits（NPW,TSHR,AHR,BMP7）,diseases（MBL2,CAV1）,etc;（3）Among the 19 candidate genes,the CD36 gene related to fat deposition and the BMP7 gene related to reproductive performance were screened for bioinformatics analysis,and the results showed that there were two missense mutations and two synonymous mutations in the CD36 gene and five synonymous mutations in the BMP7 gene in Baoshan pigs,the synonymous mutations did not change the amino acid sequence and the missense mutations did not cause changes in protein structure and function.The specific biological functions of the two candidate genes in regulating fat deposition and reproductive performance of Baoshan pigs need to be further investigated.In this study,the ROH length and number statistics and inbreeding coefficients were calculated to find that the low inbreeding level of Baoshan pigs,and several candidate genes related to the performance of reproduction,growth and meat quality were screened in genetically pure regions of Baoshan pigs,which can provide reference basis for the conservation,selection,population inbreeding control and breeding plan of Baoshan pigs,is important for the conservation of Baoshan pigs.