Establishment Of An Efficient Method To Determine KIT Genotypes And A Further Look At Genetic Mapping Of QTL For The Traits Of Growth And Fatness In Pigs

In modern swine industry,the purity of coat color,fast growth(body weight and daily gain)and low fatness deposition(back fat thickness,plate oil weight and abdominal fat weight)are very important indicators during pig breeding.This study majorly focused on these three important traits.First,molecular genetics was used to analyze the causes of coat color separation in Duroc ×(Landrace × Yorkshire)(DLY)hybrids pigs.The QTL affecting the growth and fat deposition were further refined in F3 generation pigs.The results provided reference to and help for the frontline breeding works in pigs.Coat color is an important breed characteristic in pigs.Coat colors are often segregating DLY hybrids pigs.To uncover the reason for this phenomena,we genotyped103 DLY pigs using porcine 80 K SNP chips and conducted genome-wide association study(GWAS)for the segregated coat color phenotype.As a result,we detected that KIT gene is most likely the gene responsible for the segregated coat color phenotype in the DLY hybrid pigs.To provide further evidence for the GWAS result,we collected the different coat color skin samples from DLY hybrid pigs to perform transcriptome sequencing.No splicing mutation was found in intron 17 of the KIT gene in these colored DLY pigs,indicating that these individuals do not carry the dominant white allele I at the KIT locus and thus show colored phenotypes.In this study,we also explored competitive allele specific PCR(KASP)to genotype the splicing mutation(G>A)in intron 17 of the KIT gene.We found that the KASP assay can be used to detect the presence/absence of the splicing mutation in intron 17 of the KIT gene,while cannot distinguish i from Ip allele in individuals of the I/-genotype.To establish an accurate method for detecting KIT genotypes and efficiently identifying individuals that carry i or Ip allele,we made a close examination on sequence of a tandem repeat(DUP3)representing different KIT alleles.The nested PCR was explored to genotype a large number of individuals(n=2959)from 9 nucleus populations of Landrace and Yorkshire pigs.The results shows that i or Ip carrier was found in Landrace pigs is more than Yorkshire.we confirmed the accuracy and efficiency of this nested PCR assay.In the part two of this study,we collected the phenotypic data of 22 growth and 7fat-related traits for 473 individuals from the F3 generation population crossing by white Duroc × Erhualian.Phenotypic correlation analysis showed that:(1)Significant positive correlation exhibits in the body weights along the whole growth periods;(2)Strong positive correlation exhibits in the fatness traits at different sites ranging from 0.46 to 0.94;(3)Fat deposition is more and more correlated to body weight with the increase of growth age.On this basis Genome wide association analyses of 29 growth and fatness traits using pig 50 K SNP chip data in this F3 generation population.8 significant loci were identified for growth and fatness related traits.Seven major QTL haplotypes were identified in this F3 population using related pedigree information.Two recombinant Q haplotypes(q1q2and q2q1)were newly identified.Subsequently,high-density genotypes of 473 individuals were imputated using the haplotypes constructed from 287 genome-wide re-sequenced individuals representing 18 breeds as the reference genomic genotypes.As a result,40 new QTL loci were found for all 29 phenotypes.To further explore the genetic differences of growth and fatness traits between males and females,our study conducted a sex-stratification GWAS.It was found that 29 QTL loci were only detected in boar population.35 QTL loci were only detected in sow population.For example,the body weight at the age of 46-day-old had sex dimorphism.In summary,this study mainly focused on the practical problem in pig production,through the establishment of an accurate and efficient method for detecting KIT alleles.This method could be explored to efficiently identify i or Ip alleles carrier,which enable the breeder and farmers to eradicate colored pigs from commercial hybrid populations.Meanwhile,we refined the QTL loci affecting the growth and fatness traits in pigs,as well as the sex-stratification using the methods of molecular genetics.These results enhanced people understanding of the genetic mechanism of porcine growth and fat deposition related traits,and provide a reference to the selection of pig growth and fatness related traits.