Study On The AHR Gene Affecting Litter Size In Pigs

Litter size is one of the most important economic traits in the pig industry.More litters will bring more economic profit.Chinese local pig breeds especially Taihu pigs were renowned for high litter size?>15 piglets?.Previous studies identified several genes related to litter size including the AHR gene,which encodes a ligand-activated helix-loop-helix transcription factor involved in the regulation of biological responses to planar aromatic hydrocarbons.The AHR gene is conserved in mammals and plays a role in estrogen production and follicular development.It has been shown that Asian-derived non-synonymous mutations in the AHR gene are associated with increased litter size in several European commercial pig breeds,and the copy number variation of the AHR gene is related to the pig litter size.This study aims to verify the copy assembly of the AHR gene on the genome,identify AHR SNPs associated with litter size and uncover the origin of the beneficial mutations.First,we verified the assembly of the AHR gene on the genome.We show that the AHR gene has been correctly assembled in the pig genome database and the AHR gene has two copies on the pig genome--the first copy is an incomplete one with a length of 28 kb and is in a reverse orientation with the second copy.Subsequently,the AHR gene copy number was detected by using real-time quantitative PCR in Chinese wild boars,Erhualian,Tibetan,Min,Jinhua,Gansu Tibetan,Sichuan Tibetan and Duroc pigs.The result confirmed that the AHR gene has two copies on the pig genome.Then,we designed primers for four SNPs in exon 11 of the AHR gene?c.1993₂004ins12,c.2070C>T,c.2139A>G and c.2149G>T?that was reported to be associated with litter size,and condueted PCR amplification and sanger sequencing in a French Large White pig population.Only one shift frame mutation?c.1993₂004ins12?and one non-synonymous mutation?c.2149G>T?were segregated in this population.We tested associations of the two variate with estimated breeding value of litter size in this population.We found that both mutations are significantly associated with litter size,and c.2149G>T had a greater effect on litter size.To improve production traits in European local breeds,Chinese breeds were imported to Europe during the late 18 th and early 19 th century.To determine the origin of beneficial mutations for litter size on the AHR gene,we first analyzed the frequency of mutations c.1993₂004ins12 and c.2149G>T in Chinese and Western pig breeds.We found that the 12 bp insertion at the c.1993₂004 locus was fixed in Chinese local pigs but segregated in Western pig breeds,and the frequency of allele G at the 2149 G>T locus was significantly higher in chinese local pigs than that in Western pig breeds.These findings suggest that AHR mutations beneficial for litter size was possibly introgressed from Chinese pigs into European pigs.Subsequently,SNPs in a 5 kb region proximal to exon 11 of the AHR gene were explored to construct a haplotype phylogenetic tree,which verified the chinese origin of beneficial mutations on the AHR gene.In summary,we used a series of statistical analysis and experimental methods to confirm that two copies of AHR exist on the pig genome,the two copies are opposite and the first copy is incomplete.AHR c.1993₂004ins12 and c.2149G>T are significantly associated with the number of litter size in French Large White pigs,and AHR mutations beneficial for litter size was possibly introgressed from Chinese pigs into European pigs.