Insights into the architecture of human-induced polygenic selection in Duroc pigs

Background:As one of the most utilized commercial composite boar lines,Duroc pigs have been introduced to China and undergone strongly human-induced selection over the past decades.However,the efficiencies and limitations of previous breeding of Chinese Duroc pigs are largely understudied.The objective of this study was to uncover directional polygenic selection in the Duroc pig genome,and investigate points overlooked in the past breeding process.Results:Here,we utilized the Generation Proxy Selection Mapping(GPSM)on a dataset of 1067 Duroc pigs with 8,766,074 imputed SNPs.GPSM detected a total of 5649 putative SNPs actively under selection in the Chinese Duroc pig population,and the potential functions of the selection regions were mainly related to production,meat and carcass traits.Meanwhile,we observed that the allele frequency of variants related to teat number(NT)relevant traits was also changed,which might be influenced by genes that had pleiotropic effects.First,we identified the direction of selection on NT traits by G,and further pinpointed large-effect genomic regions associated with NT relevant traits by selection signature and GWAS.Combining results of NT relevant traits-specific selection signatures and GWAS,we found three common genome regions,which were overlapped with QTLs related to production,meat and carcass traits besides“teat number”QTLs.This implied that there were some pleiotropic variants underlying NT and economic traits.We further found that rs346331089 has pleiotropic effects on NT and economic traits,e.g.,litter size at weaning(LSW),litter weight at weaning(LWW),days to 100 kg(D100),backfat thickness at 100 kg(B100),and loin muscle area at 100 kg(L100)traits.Conclusions:The selected loci that we identified across methods displayed the past breeding process of Chinese Duroc pigs,and our findings could be used to inform future breeding decision.

DNA methylation in poultry:a review

As an important epigenetic modification,DNA methylation is involved in many biological processes such as animal cell differentiation,embryonic development,genomic imprinting and sex chromosome inactivation.As DNA methylation sequencing becomes more sophisticated,it becomes possible to use it to solve more zoological problems.This paper reviews the characteristics of DNA methylation,with emphasis on the research and application of DNA methylation in poultry.

Semen extracellular vesicles mediate vertical transmission of subgroup J avian leukosis virus

Subgroup J avian leukosis virus(ALV-J) is a highly oncogenic retrovirus that has been devastating the global poultry industry since the late 1990s. The major infection model of ALV-J is vertical transmission, which is responsible for the congenital infection of progeny from generation to generation. Increasing evidence has suggested that extracellular vesicles(EVs) derived from virus-infected cells or biological fluids have been thought to be vehicles of transmission for viruses. However, the role of EVs in infection and transmission of ALV-J remains obscure. In the present study, semen extracellular vesicles(SE) were isolated and purified from ALV-J-infected rooster seminal plasma(SE-ALV-J), which was shown to contain ALV-J genomic RNA and partial viral proteins, as determined by RNA sequencing, reverse transcription-quantitative PCR and Western blotting. Furthermore, SE-ALV-J was proved to be able to transmit ALV-J infection to host cells and establish productive infection.More importantly, artificial insemination experiments showed that SE-ALV-J transmitted ALV-J infection to SPF hens, and subsequently mediated vertical transmission of ALV-J from the SPF hens to the progeny chicks. Taken together, the results of the present study suggested that ALV-J utilized host semen extracellular vesicles as a novel means for vertical transmission, enhancing our understanding on mechanisms underlying ALV-J transmission.