Microchromosomes are prevalent in nonmammalian vertebrates [P. D. Waters et al. , Proc. Natl. Acad. Sci. U.S.A. 118 (2021)], but a few of them are missing in bird genome assemblies. Here, we present a new chicken reference genome containing all autosomes, a Z and a W chromosome, with all gaps closed except for the W. We identified ten small microchromosomes (termed dot chromosomes) with distinct sequence and epigenetic features, among which six were newly assembled. Those dot chromosomes exhibit extremely high GC content and a high level of DNA methylation and are enriched for housekeeping genes. The pericentromeric heterochromatin of dot chromosomes is disproportionately large and continues to expand with the proliferation of satellite DNA and testis-expressed genes. Our analyses revealed that the 41-bp CNM repeat frequently forms higher-order repeats (HORs) at the centromeres of acrocentric chromosomes. The centromere core regions where the kinetochore attaches often encompass telomeric sequence (TTAGGG)n, and in a one of the dot chromosomes, the centromere core recruits an endogenous retrovirus (ERV). We further demonstrate that the W chromosome shares some common features with dot chromosomes, having large arrays of hypermethylated tandem repeats. Finally, using the complete chicken chromosome models, we reconstructed a fine picture of chordate karyotype evolution, revealing frequent chromosomal fusions before and after vertebrate whole-genome duplications. Our sequence and epigenetic characterization of chicken chromosomes shed insights into the understanding of vertebrate genome evolution and chromosome biology.

The present study was conducted to evaluate the effects of different rearing methods and stocking densities on carcass yield and proximate composition of meat in small-sized meat ducks. A total of 555 one-day-old birds were randomly allocated to six treatment groups (three replicates per treatment, sex ratio 1/1) with a 2 × 3 factorial arrangement of two rearing methods (reared in cage or net) and three stocking densities (5 [low], 7 [medium], or 9 [high] birds/m2) until day 70. Five male and five female birds from each replicate were randomly selected and processed to determine the carcass yield. Proximate composition was determined by proximate analysis using the breast and thigh muscles. There was no interaction effect between the rearing method and stocking density on carcass yield. The rearing method affected the thigh muscle rate, which was higher in the cage groups (P < 0.05). The final BW and abdominal fat rate decreased with increasing density (P < 0.05), whereas the thigh muscle rate increased (P < 0.05). There were significant interaction effects (P < 0.05) between the rearing method and stocking density on the content of protein, fat, and collagen. The content of fat and moisture was greater and lower, respectively, in the cage groups (P < 0.05). The content of moisture, fat, and collagen with a medium density was higher (P < 0.05). In addition, the content of protein and fat was lower in the ducks fed in nets at low and high densities (P < 0.05), respectively; the collagen content of breast and thigh muscle was lower in the ducks fed in cages and nets, respectively, at a low density (P < 0.05). Our findings provide valuable insights into the single and interactive effects of the rearing method and stocking density on duck slaughter performance and proximate composition of meat. The results indicate that a rearing system with a cage pattern and a medium density is better than other arrangements for small-sized meat ducks.

Frequencies of up to 3% of beak deformity (normally a crossed beak) occur in some indigenous chickens in China, such as and Beijing-You. Chickens with deformed beaks have reduced feed intake, growth rate, and abnormal behaviors. Beak deformity represents an economic as well as an animal welfare problem in the poultry industry. Because the genetic basis of beak deformity remains incompletely understood, the present study sought to identify important genes and metabolic pathways involved in this phenotype. Digital gene expression analysis was performed on deformed and normal beaks collected from Beijing-You chickens to detect global gene expression differences. A total of >11 million cDNA tags were sequenced, and 5,864,499 and 5,648,877 clean tags were obtained in the libraries of deformed and normal beaks, respectively. In total, 1,156 differentially expressed genes (DEG) were identified in the deformed beak with 409 being up-regulated and 747 down-regulated in the deformed beaks. qRT-PCR using eight genes was performed to verify the results of DGE profiling. Gene ontology (GO) analysis highlighted that genes of the keratin family on GGA25 were abundant among the DEGs. Pathway analysis showed that many DEGs were linked to the biosynthesis of unsaturated fatty acids and glycerolipid metabolism. Combining the analyses, 11 genes (MUC, LOC426217, BMP4, ACAA1, LPL, ALDH7A1, GLA, RETSAT, SDR16C5, WWOX, and MOGAT1) were highlighted as potential candidate genes for beak deformity in chickens. Some of these genes have been identified previously, while others have unknown function with respect to thus phenotype. To the best of our knowledge, this is the first genome-wide study to investigate the transcriptome differences in the deformed and normal beaks of chickens. The DEGs identified here are worthy of further functional characterization.

Given an increasing trend in slaughter and chilling for the sale of chickens in China, it is important to determine the marketable age of chickens for chilled sales. This study determined the effects of two marketable ages on the body measurements, carcass traits, and meat quality of yellow-feathered chickens. A total of 360 healthy one-day-old male Xueshan chickens were raised in six pens (straw-covered floor, numbered 1 to 6) and treated in the same manner (free access to food and water) until day 100. Sixty chickens from pens numbered 1 to 3 and 4 to 6 were selected to determine the body measurements, carcass traits, and meat quality at two slaughter ages (90 and 100 days), respectively. One hundred-day-old chickens had a higher body slope, cockscomb, keel, shank lengths, and higher live and dressed weights (p < 0.05). The abdomen skin follicle density, a*(redness) and b*(yellowness) values were higher in 100-day-old chickens (p < 0.05), whereas the 90-day-old chickens were characterized by better spotted skin. For the breast muscle, pH, shear force, a*, moisture, and protein and intramuscular fat contents were lower; moreover, L*(lightness) and b* were higher in 90-day-old chickens. In leg muscles, the pH, shear force, L*, b* and collagen content were lower; furthermore, the a* and moisture contents were higher in 90-day-old chickens (p < 0.05). These findings indicate that two marketable ages both have pros and cons, but 90 days chickens perform better on carcass appearance, and producers can adjust the marketable age to meet needs of different consumers. This study provides a unique idea and theoretical reference for breeding and marketing yellow-feathered chickens.

Comparative population genomics and genome-wide association studies (GWAS) offer opportunities to discover human-driven detectable signatures within the genome. From the point of view of evolutionary biology, the identification of genes associated with the domestication of traits is of interest for the elucidation of the selection of these traits. To this end, an F₂ population of ducks, consisting of 275 ducks, was genotyped using a whole genome re-sequence containing 12.6 Mb single nucleotide polymorphisms (SNPs) and four plumage colors. GWAS was used to identify the candidate and potential SNPs of four plumage colors in ducks (white, spot, grey, and black plumage). In addition, FST and genetic diversity (π ratio) were used to screen signals of the selective sweep, which relate to the four plumage colors. Major genomic regions associated with white, spotted, and black feathers overlapped with their candidate selection regions, whereas no such overlap was observed with grey plumage. In addition, MITF and EDNRB2 are functional candidate genes that contribute to white and black plumage due to their indirect involvement in the melanogenesis pathway. This study provides new insights into the genetic factors that may influence the diversity of plumage color.

Totally, 315 42-day-old male Xueshan chickens were allocated into 3 caging densities, 14, 21 and 28 birds/m². Each treatment was represented by 5 replicates. The body weight (BW), slaughter performance, meat quality, behavioral assessment, and the cecal microorganisms were detected at the market age. The results showed that the BW of broilers in the low- and medium-density groups was significantly higher (p < 0.05) than that of the high-density group from the age of 10 weeks. Only the feather quality of the broilers in the low-density group improved significantly (p < 0.05) compared with those of the other two groups. And, the abdominal fat percentage and the fat content of thigh muscle of broilers in the low- and medium-density groups were higher (p < 0.05) than those in the high-density group. No significant difference (p > 0.05) was noted in the other traits. The abundance of some microbial like Akkermansiaceae, Lactobacillaceae and Faecalibacterium may be correlated with the BW and fat content of broilers. The findings of this study suggest that increasing the stocking density decreased the final BW, fat content and the feather quality, whereas no evidence was found that stocking density caused changes in other parameters.