Significant genomic introgression from grey junglefowl (Gallus sonneratii) to domestic chickens (Gallus gallus domesticus)

BACKGROUND

Chicken is one of the most numerous and widely distributed species around the world, and many studies support the multiple ancestral origins of domestic chickens. The research regarding the yellow skin phenotype in domestic chickens (regulated by BCO2) likely originating from the grey junglefowl serves as crucial evidence for demonstrating the multiple origins of chickens. However, beyond the BCO2 gene region, much remains unknown about the introgression from the grey junglefowl into domestic chickens. Therefore, in this study, based on whole-genome data of 149 samples including 4 species of wild junglefowls and 13 local domestic chicken breeds, we explored the introgression events from the grey junglefowl to domestic chickens.

RESULTS

We successfully detected introgression regions besides BCO2, including two associated with growth trait (IGFBP2 and TKT), one associated with angiogenesis (TIMP3) and two members of the heat shock protein family (HSPB2 and CRYAB). Our findings suggest that the introgression from the grey junglefowl may impact the growth performance of chickens. Furthermore, we revealed introgression events from grey junglefowl at the BCO2 region in multiple domestic chicken breeds, indicating a phenomenon where the yellow skin phenotype likely underwent strong selection and was retained. Additionally, our haplotype analysis shed light on BCO2 introgression event from different sources of grey junglefowl into domestic chickens, possibly suggesting multiple genetic flows between the grey junglefowl and domestic chickens.

CONCLUSIONS

In summary, our findings provide evidences of the grey junglefowl contributing to the genetic diversity of domestic chickens, laying the foundation for a deeper understanding of the genetic composition within domestic chickens, and offering new perspectives on the impact of introgression on domestic chickens.

Molecular characterization of Oxyspirura mansoni and Philophthalmus gralli collected from the eyes of domestic chickens in Bangladesh

A variety of helminths have been found in domestic chickens in Bangladesh, but little is known about their gene sequences. Here, parasitic nematodes and trematodes were collected from the eyes of domestic chickens and analyzed for their morphological and morphometric characteristics, and characterized molecularly. The helminths were identified as Oxyspirura mansoni and Philophthalmus gralli. The ITS1 and ITS2 sequences of O. mansoni were 532 bp and 306 bp in length, respectively, and showed low identity (50.7-62.7%) with those of O. petrowi and O. conjunctivalis. Furthermore, the O. mansoni CO1 sequences (393 bp) showed five haplotypes (97.5-99.5% similarity) that formed a monophyletic clade. With respect to P. gralli, the ITS1 (452 bp) and ITS2 (736 bp) sequences showed 100% similarity with the reference sequences in GenBank. Both the ND1 and CO1 phylograms showed that P. gralli from Bangladesh, Costa Rica and Peru form a monophyletic clade, distinct from the clades of P. lucipetus and P. lacrymosus. Our data show that, Philophthalmus gralli isolates from Bangladesh, Costa Rica and Peru are genetically close to each other.

A within-host mathematical model of H9N2 avian influenza infection and type-I interferon response pathways in chickens

Chickens infected with avian influenza virus (AIV) transmit the virus via respiratory and cloacal shedding. While previous mathematical models have shown that the innate immune response is necessary for the early suppression of virus production in infected respiratory cells, the different pathways by which the innate immune response can affect cloacal viral shedding have not been studied in chickens. The present study aims to evaluate the sensitivity of H9N2 low pathogenic AIV shedding in chicken gastrointestinal cells to different type-I interferon (IFN) response pathways, and to determine the impact of a cellular eclipse phase (latent period) on the time to peak virus shedding using a mathematical model describing within host viral kinetics. Our model results demonstrate that a mechanistic model that incorporates 1) the intracellular antiviral effects of type-I IFN on virus production, 2) destruction of infected cells by type-I IFN activated Natural Killer cells, and 3) an eclipse phase is most consistent with experimental cloacal virus shedding data. These results provide a potential mechanistic explanation for the delay to peak cloacal virus shedding observed in experimental studies conducted in chickens, as well as an improved understanding of the primary type-I IFN pathways involved in the control of cloacal virus shedding, which may lead to the development of more targeted vaccine candidates.

Prevalence of Eimeria species in domestic chickens in Anhui province, China

Prevalence studies can adequately assist in the design of prophylaxis strategies for disease control. Here, the prevalence of Eimeria species in chickens was investigated in Anhui province, China, from July to September 2016. A total of 171 samples were tested by microscopic examination and molecular methods. The prevalence of coccidiosis in Anhui province was found to be 87.75% (150/171). Eimeria tenella was the most prevalent species (80.67%, 121/150), and Eimeria necatrix, Eimeria mitis, Eimeria maxima, Eimeria brunetti and Eimeria acervulina were 68% (102/150), 55.33% (83/150), 54.67% (82/150), 44.67% (67/150) and 2.67% (4/150), respectively. Eimeria praecox was not detected at all. The most common combinations are E. tenella, E. maxima, E. necatrix, E. brunetti and E. mitis (26.67%, 40/150), followed by E. tenella, E. maxima and E. necatrix (19.33%, 29/150). Eimeria necatrix exhibited the highest participation in multiple infections. The results of the present study suggested that Eimeria infection is mixed, severe and widespread in chickens, Therefore, integrated strategies should be performed to prevent and control coccidial infection in chickens in Anhui province.