Research On Candidate Genes And QTL Fine Mapping On The Chromosome 12 Affecting Litter Size Of Erhualian Pigs

The litter size can reflect the reproductive performance of the sow,and its level is directly related to the economic benefits of the pig industry.As one of the most important production traits,the litter size has low heritability and it is a complex trait controlled by micro-effect and multi-gene.It has a long interval between generations by using the traditional breeding method,and the pig’s litter performance is progressing slowly.Therefore,it is very important to identify and utilize new gene markers to improve pig litter performance.The pig breeds in the Taihu Lake Region are known for their high fecundity,and the Erhualian pigs are the representative which the litter performance is even better.However,in recent years,due to the decrease in the population of Erhualian pigs,there is a large variation in litter size in the population.Therefore,it is very important and meaningful to identify the key genes and functional locus affecting the variation of litter size in Erhualian pigs and to recover the litter size performance based on molecular markers.In this study,the AHR gene,which is infiltrated into European white pig from Asian pigs to affect the litter size,was identified as the candidate gene affecting the litter size of Erhualian pigs.In addition,we identified a QTL that significantly affected the litter size on pig chromosome 12 by using the Fst method of the extremely high-and low-yield population of Erhualian in the early research of our laboratory.Therefore,this study was designed to carry out QTL fine-mapping on 12 chromosome in pigs by increasing the density of markers and the number of populations to dentify the causal loci of the QTL.In the first part,we made a statistics for CV of litter size by using the Erhualian pigs.It was found that there was a large variation of the litter size in Erhualian pig population and the value of CV was greater than 23%,which means that is has larger room for selection and improvement.As the candidate gene that may be infiltrated into Asian white pigs from Asian pigs to affect litter size,AHR gene was used to identify whether it is a causal gene affecting litter size in Erhualian pigs.By PCR amplification of the specific fragments and sequencing analysis,we found that there was polymorphism in AHR gene rs339939442 among Erhualian pigs.Subsequently,the association analysis between rs339939442 locus and NBA and TNB was carried out by SAS software,one-way ANOVA for the genotype of rs339939442 locus and the EBV of NBA&TNB was performed by SPSS software and regression analysis for the genotype of rs339939442 locus and litter size was performed by GEMMA software were carried out to vitified the result.However,none of the three analyses found that AHR gene rs339939442 locus was significant associated with the litter size of Erhualian pigs.In addition,the Correlation analysis also carried out in Meishan pig,Suhuai pig,Taiwanese line Landrace,American line Large White,Canadian line Large White pig and French line Large White to verify whether the AHR gene can affect litter size.The AHR gene rs339939442 loucs was found significantly associated with the litter size in Suhuai and French line Large White population,and the TT genotype is the dominant genotype,while rs339939442 loucs was failed to found significantly associated the litter size in Meishan pig,Taiwanese line Landrace pig,American line Large White,Canadian line Large White population.The result showed that the effect on litter size of AHR gene rs339939442 locus is heterogeneous.The rs339939442 may not be a causal locus affecting litter size,and the true causal locus may be a locus tightly linked with the rs339939442 locus on or adjacent to the AHR gene.In the second part,due to the low density which is about one marker per 100 Kb and the fewer populations,we increased the number of markers(64)in the target range of 500 Kb upstream and downstream of the most significant rs81434499 locus on the chromosome 12.Furthermore,we performed multiplex PCR amplification in 334 Erhualian pigs and 269 Meishan pigs which have similar blood to Erhualian pig.Then,correlation analysis between the SNP locus and the corrected litter size phenotype and LDLA were performed in the Erhualian pig population and the Meishan pig population.Finally,we used meta-analysis to fine-map QTLs and candidate genes affecting litter size.Through the above three analytical methods,we successfully mapped the QTLs affecting NBA of latter parities,TNB of all parities,NBA of all parities and TNB of all parities to 37558824-37426181 bp(70.36 Kb),37276185-37372919 bp(96.74 Kb),37384450-37489433 bp(105.98 Kb)and 37276185-37438766 bp(162.58 Kb)on 12 chromosome.The RPS6KB1,TUBD1 and a predicted uncommented LOC102157559 gene was identified as the candidate gene affecting litter size.