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Background Duck is an ancient domesticated animal with high economic value, used for its meat, eggs, and feathers. However, the origin of indigenous Chinese ducks remains elusive. To address this question, we performed whole-genome resequencing to first explore the genetic relationship among variants of these domestic ducks with their potential wild ancestors in eastern China, as well as understand how the their genomes were shaped by different natural and artificial selective pressures. Results Here, we report the resequencing of 60 ducks from Chinese spot-billed ducks (Anas zonorhyncha), mallards (Anas platyrhnchos), Fenghua ducks, Shaoxing ducks, Shanma ducks and Cherry Valley Pekin ducks of eastern China (ten from each population) at an average effective sequencing depth of ~ 6× per individual. The results of population and demographic analysis revealed a deep phylogenetic split between wild (Chinese spot-billed ducks and mallards) and domestic ducks. By applying selective sweep analysis, we identified that several candidate genes, important pathways and GO categories associated with artificial selection were functionally related to cellular adhesion, type 2 diabetes, lipid metabolism, the cell cycle, liver cell proliferation, and muscle functioning in domestic ducks. Conclusion Genetic structure analysis showed a close genetic relationship of Chinese spot-billed ducks and mallards, which supported that Chinese spot-billed ducks contributed to the breeding of domestic ducks. During the long history of artificial selection, domestic ducks have developed a complex biological adaptation to captivity.

Ochratoxin A (OTA) is a widespread mycotoxin, that has strong thermal stability, and is difficult to remove from feed. OTA is nephrotoxic, hepatotoxic, teratogenic, immunotoxic, and enterotoxic to several species of animals. The gut is the first defense barrier against various types of mycotoxins present in feed that enter the body, and it is closely connected to other tissues through enterohepatic circulation. Compared with mammals, poultry is more sensitive to OTA and has a lower absorption rate. Therefore, the gut is an important target tissue for OTA in poultry. This review comprehensively discusses the role of OTA in gut health and the gut microbiota of poultry, focusing on the effect of OTA on digestive and absorptive processes, intestinal barrier integrity, intestinal histomorphology, gut immunity, and gut microbiota. According to the studies described to date, OTA can affect gut dysbiosis, including increasing gut permeability, immunity, and bacterial translocation, and can eventually lead to gut and other organ injury. Although there are many studies investigating the effects of OTA on the gut health of poultry, further studies are needed to better characterize the underlying mechanisms of action and develop preventative or therapeutic interventions for mycotoxicosis in poultry., Graphical abstract

Additional file 1: Figure S1. The number of unique and shared SNPs among six duck groups shown by a venn diagram. Figure S2. Principal component analysis (PCA). Figure S3. Demographic history of ducks. Figure S4. Distribution of KEGG pathway of domestic ducks is shown as a bar chart. Figure S5. Gene ontology (GO) classification for positively selected genes in domestication. Figure S6. The number of differential expression genes in muscle, liver and cerebellum. Figure S7. Function classifications of Gene Ontology terms of differential expression genes in muscle. Figure S8. Function classifications of Gene Ontology terms of differential expression genes in liver. Figure S9. Function classifications of Gene Ontology terms of differential expression genes in cerebellum. Figure S10. Venn diagram of selected genes (blue) and significantly expressed genes in muscle (yellow), liver (red) and cerebellum (green) of Shaoxing ducks. Table S1. Breeds included in the study and phenotypic description. Table S2. Statistics of genomic sequencing of six duck populations. Table S3. Summary of mapping and coverage of six duck populations. Table S4. Summary of SNPs of six duck populations included in the analyses. Table S5. Summary of the functional annotation statistics of SNP in ducks by ANNOVAR. Table S6. θπ and θW for six duck populations. Table S7. Summary statistics for genomic nucleotide diversity in different species. Table S8. List of CDRs with top 5% highest FST values and log2 (θπ ratio) in domestic ducks. Table S9. The KEGG pathway of the loci under selections in domestic ducks (Top 20). Table S10. The GO classification of the loci under selections in domestic ducks. Table S11. Summarize of sequence mapping of three tissues in Shaoxing ducks and mallards. Table S12. Pathway of KEGG differentially expressed gene in muscle of Shaoxing ducks. Table S13. The down-regulated genes in muscle of Shaoxing ducks (top 20). Table S14. The up-regulated genes in muscle of Shaoxing ducks (top 20). Table S15. The down-regulated genes in liver of Shaoxing ducks (top 20). Table S16. The up-regulated genes in liver of Shaoxing ducks (top 20). Table S17. The down-regulated genes in liver of Shaoxing ducks. Table S18. The up-regulated genes in liver of Shaoxing ducks.