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 wholegenome 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.

Origins,timing and introgression of domestic geese revealed by whole genome data

Background Geese are among the most important poultry species in the world.The current generally accepted hypothesis is that the European domestic geese originated from greylag geese(Anser anser),and Chinese domestic geese have two origins,most of which originated from swan geese(Anser cygnoides),and the Yili goose originated from greylag geese.To explain the origin and demographic history of geese,we selected 14 goose breeds from Europe and China and wild populations of swan and greylag geese,and whole genome sequencing data were obtained for 74 samples.Results Population structure analysis and phylogenetic trees showed that the wild ancestor of Chinese domestic geese,except for Yili,is the swan geese,and the wild ancestor of Chinese Yili and European domestic geese is greylag geese.Analysis of the demographic history suggests that the domestication of Chinese geese occurred~3499 years ago and that of the European geese occurred~7552 years ago.Furthermore,gene flow was observed between domestic geese and their wild ancestors.Analysis of introgression showed that Yili geese had been introgressed by Chinese domestic geese,and the body size of Yili geese may be influenced by introgression events of some growthrelated genes,including IGF-1.Conclusions Our study provides evidence for the origin of geese at the genome-wide level and advances the understanding of the history of goose domestication and the traits affected by introgression events.

Transcriptome responses to heat stress in hypothalamus of a meat-type chicken

Background： Heat stress has resulted in great losses in poultry production. To address this issue, we systematically analyzed chicken hypothalamus transcriptome responses to thermal stress using a 44 k chicken Agilent microarray, Methods： Hypothalamus samples were collected from a control group reared at 25℃, a heat-stress group treated at 34℃ for 24 h, and a temperature-recovery group reared at 25℃ for 24 h following a heat-stress treatment. We compared the expression profiles between each pair of the three groups using microarray data. Results： A total of 1,967 probe sets were found to be differentially expressed in the three comparisons with P 〈 0.05 and a fold change （FC） higher than 1.5, and the genes were mainly involved in self-regulation and compensation required to maintain homeostasis. Consistent expression results were found for 11 selected genes by quantitative real-time PCR. Thirty-eight interesting differential expression genes were found from GO term annotation and those genes were related to meat quality, growth, and crucial enzymes. Using these genes for genetic network analysis, we obtained three genetic networks. Moreover, the transcripts of heat-shock protein, including Hsp 40 and Hsp 90, were significantly altered in response to thermal stress. Conclusions： This study provides a broader understanding of molecular mechanisms underlying stress response in chickens and discovery of novel genes that are regulated in a specific thermal-stress manner.

Correlation analysis of the total IgY level in hen serum, egg yolk and offspring serum

The correlation between IgY levels of the serum and the yolk has been well documented in wild and domestic birds. The levels of total yolk IgY can be an index of the general health status of birds and may contribute to breeding programs when fitness of the offspring is a concern. We measured the levels of total serum IgY and yolk IgY in three different breeds （White Leghorn, Silkie and Dongxiang blue-shell） using indirect ELISA, and found that there was a significantly positive correlation between the levels of total serum IgY and total yolk IgY in all three breeds （White Leghorn： r = 0.404, P 〈 0.001, n = 100; Silkie： r = 0.561, P 〈 0.001, n = 70; Dongxiang blue-shell： r = 0.619, P 〈 0.001, n = 30）. We also measured the total serum IgY levels in the 3-day-old offspring hatched from the Silkie hens and results were significantly correlated for serum IgY levels （r = 0.535, P 〈 0.001, n = 70） and the yolk IgY levels （r = 0.481, P 〈 0.001, n = 70）. The regression analysis showed simple linear regression between IgY levels in hen serum, yolk and offspring serum. Our results suggest that total IgY level could be used as an index for chicken fitness.