Association of Rs339939442 in the AHR Gene with Litter Size are Inconsistent among Chinese Indigenous Pigs and Western Commercial Pigs

SIMPLE SUMMARY: Litter size is one of the most important economic traits in pig production. However, it is slow to improve litter size by traditional breeding methods. It has been paid much 1attention to improving pig litter performance by using marker-assisted selection and genomic selection. Our research indicated that rs339939442 in the aryl hydrocarbon receptor (AHR) gene could be a marker to improve litter size in European commercial lines and Chinese Suhuai pigs containing genomic fragments of British Yorkshire pigs, and the litter size could be improved by selecting the individuals with favorable genotype (TT) of rs339939442 for pig breeding. ABSTRACT: Eastern and Southern Chinese pigs have been imported to Western countries to improve economic traits including fertility in Western pig breeds by intensive selecting Chinese advantage genes. It was reported that the selected Asian-derived non-synonymous mutations including rs339939442 (G > T) in the aryl hydrocarbon receptor (AHR) gene could increase litter size in multiple European commercial lines. The objective of this study is to identify whether rs339939442 in the AHR gene is polymorphic and has an influence on the litter size in 10 pig populations including five Chinese indigenous breeds, one cultivated breed, one lean-type breed, two North American lean-type breeds, and one European lean-type breed. We found that rs339939442 had polymorphism in all 10 populations, whereas rs339939442 was associated with litter size only in French Yorkshire (FRA-Y) and Chinese cultivated Suhuai (SH) pigs containing approximately 75% British Yorkshire pigs ancestry. Our results indicated that rs339939442 in the AHR gene was a potential marker to improve litter size in European commercial lines and the pigs containing ancestries of European commercial lines, whereas this locus maybe not a causal mutation affecting the litter size but only in linkage disequilibrium with the causal mutation for litter size.