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

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.

Analysis of merged transcriptomic and genomic datasets to identify genes and pathways underlying residual feed intake in growing pigs

“…In this way, one of the transcription factor coding genes located in QTL-1, AHR, can explain the differential expression of 65 DE genes. The AHR gene has been considered a candidate gene for reproductive traits in previous studies (37)(38)(39). SNP calling based on RNA-seq data revealed four missense mutations in the protein-coding part of the AHR gene.…”

Analysis of merged transcriptomic and genomic datasets to identify genes and pathways underlying residual feed intake in growing pigs

“…In this way, a transcription factor encoding gene located in QTL-1, AHR, may explain the differential expression of nine out of 17 DE-genes. The AHR gene has to our knowledge not been linked to FE before, but it has been considered a candidate gene for reproductive traits in previous studies [31][32][33] . SNP calling based on RNA-seq data revealed four missense mutations in the protein-coding part of the AHR gene.…”

Retrotransposon Insertion Polymorphisms (RIPs) in Pig Reproductive Candidate Genes

“…Meishan sows have a larger uterine capacity than Large White sows and this allows them to maintain their higher number of attached embryos throughout the gestation period [ 40 ]. The SuJiang and Sushan breeds are Chinese indigenous pig breeds hybridized with Taihu breeds and commercial varieties [ 23 ], while the breeds of Bama and Wuzhishan are well-known minipigs in China with less TNB and NBA [ 41 , 42 , 43 ].…”