Screening And Identification Of Candidate Genes Related To The Meat Quality Based On Genomic Structure Variation Of Xiang Pig

Genomic structural variation was detected using SoftSV and Pindel softwares based on the resequencing data of Xiang pig genome.The frequencies of population genotype distribution of nine structural variation(SV)were detected by PCR method using Xiang pig and Large White pig as samples.The effect of different SV genotypes on gene expression was analyzed by qPCR method.The main results were as follows:1.The meat quality was measured on 29 Xiang pigs and 18 Large White pigs.The meat color,pH1 and intramuscular fat content of Xiang pigs were obviously higher than Large White pigs.The values of pH24,backfat thickness,shear force,drip loss,eye muscle area and other indicators in Xiang pig were obviously lower than that of Large White pig.By spearman correlation analysis,there present a significant correlationship between pH1,pH24 and flesh color,and the drip loss was significantly correlated with intramuscular fat content.2.Screening the results of resequencing data of Xiang pig,Large White pig and Landrace pig,29,088 SVs were found from Xiang pig,related with 6350 genes;1987SVs from Large White pig and related with 705 genes;10668 SVs were found from Landrace pigs,affecting 3,48 genes.By comparison,it was found that Xiang pig contained 20,349 SVs,related with 5351 genes,and enriched into 33 pathways,from which nine candidate structural variants were chosen to be further investigated the population distribution in pig breeds.3.The SV CD9-I1-SV308 was located in the intron 1 of CD9 gene and in the QTL interval of average gluten thickness and fleshy traits.There was no significant difference in the distribution frequency of structural variation CD9-I1-SV308 between Large White pig and Xiang pig population;the expression level of CD9 gene in adipose tissue with deletion genotype DD was significantly lower than that of normaltype Ⅱ.4.Structural variation HADH-I2-SV282 presented a 292 bp deletion in the second intron of HADH gene,and located in the QTL interval related to meat quality traits such as abdominal fat weight and percentage of steroid fat area.There was a significant difference in the allelic and genotype frequencies of HADH-I2-SV282 locus between Xiang pig and Large White pig populations.The expression levels of different genotypes in adipose tissue were detected,and the expression level of HADH gene with deletion genotype DD was significantly lower than that of normal type Ⅱ.5.The structural variation ADH5-I2-SV296 located in the intron 2 of the ADH5 gene,and the QTL of meat quality,eye muscle area and tenth rib fat.The frequency distribution of alleles between the two groups was extremely significant.The expression of adipose tissue was detected in the normal(type Ⅱ)and deletion(DD)genotypes of SV,and the expression of ADH5 gene with DD-type was significantly lower than that of type Ⅱ.6.The 312 bp deletion was found in the ACAA1-I3-SV312 locus,located in the ACAA1 gene intron 3.The QTL analysis mapped the SV to the QTL related to the fleshy traits such as the succulent score,the backfat weight,and the fat/muscle ratio region.The distribution of alleles and genotypes in the ACAA1-I3-SV312 locus between Xiang and Large White pigs was extremely significant.7.Structural variation ACAT1-I10-SV274 located in 10 introns of ACAT1 gene.The proportion of genotype Ⅱ in Large White population was predominant.The highest,Ⅱ,ID type frequency presented in the Xiang pig group.Through allele frequency analysis,the difference in genotype distribution and allele frequency between the two populations was extremely significant.8.Structural variation ACACA-5flank-SV286 located at the upstream of ACACA gene.The allele distribution frequency was significant between Xiang and Large White pig populations.9.The structural variation ACADSB-I1-SV278 located in the intron 1 of ACADSB gene.The population test showed that all three genotypes in Large Whitepig were detected,among which the normal type Ⅱ was the most significant.The frequency of heterozygous type was the highest in Xiang pigs.In the allelic distribution,Large White pigs were dominated with allele I,while Xiang pig were rich in allele D.10.Structural variation RHEB-I2-SV293 contained a 293 bp deletion,located in the intron 2 of the RHEB gene,the QTL interval of the meat loss traits including drip loss and final rib fat.In the population detection,the difference in allelic distribution of RHEB-I2-SV29 locus between Xiang pig and Large White pig population was extremely significant.The expression of RHEB gene in adipose tissue showed that RHEB gene in DD-deficient samples was significantly lower than that of normal type Ⅱ.11.The structural variation PIK3R5-I4-SV297 located in the intron 4 of the PIK3R5 gene.The 297 bp variant fragment was found by sequencing alignment.The population polymorphism test showed that there was no significant difference in the distribution of alleles and genotypes between Large White and Xiang pigs.In summary,Xiang pig showed higher tenderness,strong hydraulic power and high intramuscular fat content compared with Large White pigs.The frequencies of eight structural variant sites of CD9-I1-SV308,HADH-I2-SV282,ADH5-I2-SV296,ACAA-I3-SV312,ACAT1-I10-SV275,ACACA-5flank-SV286,ACADSB-I1-SV278 and RHEB-I2-SV293,were significantly different between Xiang pig and Large White pig.As a molecular markers,these SVs might be helpful to identify Xiang pigs and Large White pig breeds.Four loci of CD9-I1-SV308,CD9-I1-SV308,ADH5-I2-SV296,and RHEB-I2-293 SV with deletion genotypes affected the gene expression in adipose tissue of pigs.