The First Crested Duck Genome Reveals Clues to Genetic Compensation and Crest Cushion Formation.

The Chinese crested (CC) duck is a unique indigenous waterfowl breed, which has a crest cushion that affects its survival rate. Therefore, the CC duck is an ideal model to investigate the genetic compensation response to maintain genetic stability. In the present study, we first generated a chromosome-level genome of CC ducks. Comparative genomics revealed that genes related to tissue repair, immune function, and tumors were under strong positive selection, indicating that these adaptive changes might enhance cancer resistance and immune response to maintain the genetic stability of CC ducks. We also assembled a Chinese spot-billed (Csp-b) duck genome, and detected the structural variations (SVs) in the genome assemblies of three ducks (i.e., CC duck, Csp-b duck, and Peking duck). Functional analysis revealed that several SVs were related to the immune system of CC ducks, further strongly suggesting that genetic compensation in the anti-tumor and immune systems supports the survival of CC ducks. Moreover, we confirmed that the CC duck originated from the mallard ducks. Finally, we revealed the physiological and genetic basis of crest traits and identified a causative mutation in TAS2R40 that leads to crest formation. Overall, the findings of this study provide new insights into the role of genetic compensation in adaptive evolution.

Embryonic morphology observation and HOXC8 gene expression in crest cushions of Chinese Crested duck.

The Chinese Crested duck (Fengtou duck) reappeared in China recently. Along with white feathers and a black bill and feet, the Fengtou duck has a high feather crest. This breed can be used for ornamental purposes or as a model organism; however, little is known about the genetic basis and development of its distinct morphological features. In this study, we observed the skull and feather crest of Fengtou duck in the embryonic stages. As a result, the protuberances of the head integument could be clearly observed at embryonic stage E9, and small perforations in the skull were first visible at E13 and were clearer at E15. Besides, intracranial fat in a small number of individuals was found starting at E15, and a small number of osteophytes was found at E18. In addition, hematoxylin-eosin (HE) and Oil Red-O staining of the crest cushion and intracranial tissue revealed fat tissue accumulation. Previous studies demonstrated that homeobox c8 (HOXC8) played a critical role in chicken crest formation. Here, we cloned the HOXC8 from Fengtou duck and determined that its transcript was highly expressed in the crest cushion; moreover, HOXC8 was detected in this tissue with a molecular weight of 38 kDa in the Fengtou duck. In conclusion, embryos of Fengtou duck have different small protuberances and perforations in the skull, including accumulation of intracranial tissue and osteophytes in some cases. Furthermore, HOXC8 may regulate the formation of the crest. These findings provide novel insight into the ontogenesis of the crest cushion in crested ducks and a basis for future studies on their evolutionary origins.

The differentiation of preadipocytes and gene expression related to adipogenesis in ducks (Anas platyrhynchos).

Meat quality is closely related to adipose tissues in ducks, and adipogenesis is controlled by a complex network of transcription factors tightly acting at different stages of differentiation especially in ducks. The aim of this study was to establish the preadipocyte in vitro culture system and understand the biological characteristics of expansion of duck adipocyte tissue at the cellular and molecular level. We isolated pre-adipocytes from the subcutaneous fat of three breeds of duck and differentiated them into mature adipocytes using a mixture of insulin, rosiglitazone, dexamethasone, 3-isobutyl-1-methylxanthine, and oleic acid over 0,2, 4, 6, and 8 days. Successful differentiation was confirmed from the development of lipid droplets and their response to Oil Red O, and increasing numbers of lipid droplets were stained red over time. The expression of key marker genes, including peroxisome proliferator activated receptor γ (PPARγ), CCAAT/enhancer binding protein-α (C/EBPα), adipocyte fatty acid binding protein 4 (FABP4), and fatty acid synthetase (FAS), gradually increased during pre-adipocyte differentiation. Furthermore, it was verified by interference experiments that the knockdown of PPARγ directly reduced lipid production. Meanwhile we analyzed the role of unsaturated fatty acids in the production of poultry fat using different concentrations of oleic acid and found that lipid droplet deposition was highest when the concentration of oleic acid was 300 µM. We also compared the level of differentiated pre-adipocytes that were isolated from Jianchang ducks (fatty-meat duck), Cherry Valley ducks (lean-meat duck) and White-crested ducks (egg-producing duck). The proliferation and differentiation rate of pre-adipocytes derived from Jianchang ducks was higher than that of White-crested ducks. These results provide the foundation for further research into waterfowl adipogenesis.

Comparative characterization of bacterial communities in geese fed all-grass or high-grain diets.

BACKGROUND: Gut microbial composition is dependent on diet. Geese are herbivores and can digest crude fibre, but the relationship between composition of the microbiota and a fibre-rich diet in geese is not well understood. RESULTS: Here, caecal and faecal samples were collected simultaneously from all-grass-fed geese and high-grain-fed geese and the hypervariable V3-V4 regions of the bacterial 16S rRNA gene were sequenced. The results was identified that high-grass-fed geese possessed significantly higher alpha diversity both in caecum and faeces compared with that in all-grain-fed geese. In addition, the composition of dominant bacterium occurred remarkable shifting due to different diet patterns, Firmicutes were more abundant in all-grass-fed geese, whereas Bacteroidetes were abundant in high-grain-fed geese. Fusobacteria and Deferribacteres were obviously present in high-grain-fed geese and few in all-grass-fed geese. Most importantly, some specific microorgnisms such as Ruminococcaceae, Lachnospiraceae and Bacteroidaceae which may associated with cellulose-degrading that were characterized to show distinctly diverse between the two diet patterns. PICRUSt analysis revealed the metabolic pathways such as carbohydrate and amino acid metabolism were overrepresented in all-grass-fed geese. CONCLUSIONS: In conclusion, Firmicutes and Bacteroidetes were identified abundantly when the geese was fed with all-grass feed and high-grain feed, respectively. And Ruminococcaceae, Lachnospiraceae and Bacteroidaceae were recognized as main cellulose-degrading bacteria in the geese. The functional profiles of gut microbiota revealed the dominant microbiota communities were involved mainly in the carbohydrate metabolism in all-grass-fed geese.