Unravelling The Major Genes And Key Mutations Of Teat Number In Duroc Pigs

Teat number is an important economic trait for a sow to rear a large number of piglets.A larger litter size in pigs requires sufficient teats for the lactating sow,and the lack thereof can affect the piglets’ weight gain and mortality.More teats are necessary for sows to nurse larger litters to provide immunity and nutrient for piglets prior to weaning.In order to identify major gene and key mutations affecting teat number in pigs,we used single marker method and four multi-locus genome-wide association studies to map key mutations and genes associated with teat number in two Duroc pig populations with different genetic backgrounds(S21 line and S22 line).A total of 5356 Duroc pigs were selected as experimental animals.Previous studies have reported the strong effect of an insertion mutation in the Vertebrae Development Associated(VRTN)gene on a quantitative trait locus(QTL)on Sus scrofa chromosome 7(SSC7)that increased the number of thoracic vertebrae and teat number in pigs.Whether VRTN is a causal gene affecting teat number in pigs is worth further investigation.We also performed association tests between the VRTN insertion(g.20311＿20312ins291)and teat number in the same populations(3521 Duroc pigs).The conclusions are as follows:(1)Single-locus and multi-locus totally detected 33 and 54 single nucleotide polymorphisms(SNPs)to be associated with teat number in S21 and S22 populations,respectively.In the S21 population,one,six and two SNPs were consistently detected with two,three and four multi-locus methods,respectively.In the S22 population,five,two and five SNPs were consistently detected with two,three and four multi-locus methods,respectively.Two multi-locus models identified one SNP on SSC14 was shared in both Duroc pigs.Moreover,26 SNPs were newly found by multi-locus methods to be associated with teat number.These SNPs each explained a small proportion of the phenotypic variance of teat number ranged from 0.17% to 3.59%.(2)We detected one consistent quantitative trait locus(QTL)on(SSC7)for teat number using single-locus and the top SNP(rs692640845)explained 8.68% phenotypic variances of teat number in the S22 pig population.However,no association on SSC7 for teat number in the S21 Duroc pigs was found.Population structure and Fst analyses showed that there were population differences between the two Duroc pigs,indicating that the existence of difference in genetic background can have substantial effect on genetic variant mapping.(3)Both S21 and S22 Duroc pigs were segregating for the VRTN mutation and the dominant allele frequencies(VRTN g.20311＿20312ins291)was 0.82 and 0.49,respectively.Associations between the VRTN mutation and teat number in the two Duroc pig populations were analyzed using single-locus model,which revealed that no association between the VRTN genotype and teat number in the S21 Duroc pigs.Although the VRTN insertion was strongly associated with teat number in the S22 population,the effect was weaker than the top SNP(rs692640845)identified in this population.To determine whether the signal in this QTL region(96.1-98.2 Mb)was caused by the VRTN mutation or the top SNP rs692640845,we conducted conditional analyses by adding the genotypes of these two variants at each locus in the mixed linear model as covariate.Association between the significant SNPs in this QTL region and teat number was greatly diminished in the presence of the VRTN mutation or rs692640845 as a covariate.Further analysis revealed that the VRTN insertion and the lead SNP rs692640845 were located in an 84 kb haplotype block(including VRTN)with high linkage disequilibrium(LD)pattern,implying that the effect of VRTN on teat number may be mediated by its LD with the true causal mutation.Based on large samples,the single-locus and multi-locus genome-wide association analyses identified a large number of new SNPs affecting teat number in pigs.our study demonstrated that VRTN insertion mutation on SSC7 may not be a strong causal mutation affecting teat number in pigs.These findings will advance our understanding of the genetic basis for teat number,and the identified SNPs will be useful for the genetic improvement of teat number in pigs by assigning higher weights to associated SNPs in genomic selection.