Single-cell transcriptomic reveals a cell atlas and diversity of chicken amygdala responded to social hierarchy.

Amygdala serves as a highly cellular, heterogeneous brain region containing excitatory and inhibitory neurons and is involved in the dopamine and serotoninergic neuron systems. An increasing number of studies have revealed the underpinned mechanism mediating social hierarchy in mammal and vertebrate, however, there are rare studies conducted on how amygdala on social hierarchy in poultry. In this study, we conducted food competition tests and determined the social hierarchy of the rooster. We performed cross-species analysis with mammalian amygdala, and found that cell types of human and rhesus monkeys were more closely related and that of chickens were more distant. We identified 26 clusters and divided them into 10 main clusters, of which GABAergic and glutamatergic neurons were associated with social behaviors. In conclusion, our results provide to serve the developmental studies of the amygdala neuron system and new insights into the underpinned mechanism of social hierarchy in roosters.

Genetic assessment and candidate genes identification for breed-specific characteristics of Qingyuan partridge chicken based on runs of homozygosity.

BACKGROUND: Several core breeding and supporting lines of the Qingyuan partridge chicken, a representative local chicken breed in China, have been developed over 20 years. Consequently, its economic traits related to growth and reproduction have been significantly improved by breeding selection and commercial utilization, but some characteristic traits, such as partridge feathers, high meat quality and sufficient flavor, have always been retained. However, effective methods for genetic assessment and functional gene exploration of similar trait groups are lacking. The presence of identical haplotype fragments transmitted from parent to offspring results in runs of homozygosity (ROH), which offer an efficient solution. In this study, genomes of 134 Qingyuan partridge chickens representing two breeding populations and one preserved population were re-sequenced to evaluate the genetic diversity and explore functional genes by analyzing the diversity, distribution, and frequency of ROH. RESULTS: The results showed a low level of genomic linkage and degree of inbreeding within both the bred and preserved populations, suggesting abundant genetic diversity and an adequate genetic potential of the Qingyuan partridge chicken. Throughout the long-term selection process, 21 genes, including GLI3, ANO5, BLVRA, EFNB2, SLC5A12, and SVIP, associated with breed-specific characteristics were accumulated within three ROH islands, whereas another 21 genes associated with growth traits including IRX1, IRX2, EGFR, TPK1, NOVA1, BDNF and so on were accumulated within five ROH islands. CONCLUSIONS: These findings provide new insights into the genetic assessment and identification of genes with breed-specific and selective characteristics, offering a solid genetic basis for breeding and protection of Qingyuan partridge chickens.

Genome-wide association study identifies a novel candidate gene for egg production traits in chickens.

Qingyuan partridge chicken is a renowned indigenous yellow broiler breed in China. Egg production traits are important economic traits for chickens. With the decreasing cost of whole genome resequencing, identifying candidate genes with more precision has become possible. In order to identify molecular markers and candidate genes associated with egg production traits, we conducted genome-wide association studies based on the resequencing data of 287 female Qingyuan partridge chickens. For each hen, age at first egg and egg laying rate were recorded and calculated, respectively. With a univariate linear mixed model, we detected one genome-wide significant single nucleotide polymorphism (SNP) and three chromosome-wide significant SNPs associated with egg laying rate. MTA2 is highly likely to be a functional gene for egg laying rate. Our study identifies MTA2 as the first time to be associated with egg laying rate. Findings in our study will advance our understanding of the genetic basis of egg production and have the potential to improve the efficiency of genomic selection in chickens.

Estimation of genetic parameters for important traits using a multi-trait model in late-feathering Qingyuan partridge hens in China.

Qingyuan partridge chicken is one of the most well-known Chinese indigenous yellow broilers. In breeding programmes, five traits are usually selected when the chickens are 105 days old, namely body weight (BW), comb height (CH), shank length (SL), shank girth (SG) and feather maturity (FM). The objective of this study was to estimate the genetic parameters of these five traits, especially direct additive genetic correlations, to lay the foundation for balanced selection of Qingyuan partridge chickens. Approximately 9600 records were used for estimation. Variance components for these five traits were estimated using three multi-trait models incorporating different effects via Gibbs sampling. Based on model 1 in which the random effects included direct additive genetic effects and residuals, the estimated direct heritabilities for BW, CH, SL, SG and FM were 0.29 ± 0.04, 0.53 ± 0.04, 0.47 ± 0.04, 0.43 ± 0.05 and 0.18 ± 0.03, respectively. The direct genetic correlations ranged from -0.08 to 0.46. When additionally considering maternal additive genetic effects (model 2), the estimates of direct heritabilities and absolute values of direct additive genetic correlations were smaller. The heritabilities were 0.14 ± 0.04, 0.40 ± 0.02, 0.34 ± 0.05, 0.27 ± 0.05 and 0.12 ± 0.03 for BW, CH, SL, SG and FM, respectively. The direct additive genetic correlations ranged from -0.33 to 0.36. More specifically, the direct additive genetic correlations between BW and CH, SL, SG and FM were 0.19 ± 0.13, 0.15 ± 0.15, 0.36 ± 0.15 and - 0.33 ± 0.21, respectively. The genetic correlations of FM with SL, SG and CH were - 0.15 ± 0.15, -0.08 ± 0.17 and 0.18 ± 0.15, respectively. The direct genetic correlations between CH and SG and SL were - 0.02 ± 0.11 and - 0.20 ± 0.11, respectively, and that between SL and SG was 0.19 ± 0.11. The total heritabilities and maternal additive genetic correlations ranged from 0.16 to 0.44 and from -0.13 to 0.61, respectively. The third model also included the maternal permanent environmental effect for BW. The estimates of direct heritability, direct additive genetic correlation, total heritability and maternal additive genetic correlation were only slightly different from those based on the second model. Therefore, the maternal additive genetic effect has a large effect on the estimation of genetic parameters, and it is better to consider this effect in the genetic evaluation of these five traits. Relatively high direct and maternal additive genetic correlations for most trait pairs suggested that it is better to jointly evaluate these five traits in breeding programmes.

Versatile, vigilance, and gut microbiome support the priority of high-ranking hens.

Dominance hierarchy exists in social animals and shows profound impacts on animals' survival, physical and mental health, and reproductive success. Aggressive interaction, as the main indicator used to calculate social hierarchy, however, is not found in some female animals. In this study, we aimed to figure out the establishment of social hierarchy in hens that almost perform aggressive behaviors and investigated the interactions of social hierarchy with production performance and gut microbiome. Forty 49-day-old Qingyuan hens were randomly divided into four groups. The social hierarchy of hens was calculated by the relative position around the feeder. The rank 1 (R1), R2, R3, R4, R5, R6, R7, R8, R9, and R10 birds were determined in ascending order. Then, R1 and R2 birds (four duplicates, n = 8) were named as the high-ranking hens (HR) group, while R9 and R10 individuals were named as the low-ranking hens (LR) group (four duplicates, n = 8). The heart index (p = 0.01), number of visits per day, daily feed intake, and occupation time per day were higher in the HR group than LR group, but the LR group had a higher feed intake per visit than the HR group. The alpha diversity was significantly lower in the HR group than the LR group (p = 0.05). The relative abundance of phylum Firmicutes was higher while that of phylum Deferribacterota was lower in the HR group than LR group (p < 0.05). At the genus level, the relative abundance of Succinatimonas, Eubacterium hallii group, and Anaerostipes were higher in HR group than in LR group. The relative abundance of Bacteroides, Mucispirillum, Subdoligranulum, and Barnesiellaceae unclassified was higher in the LR group than HR group (p < 0.05). In conclusion, the rank of hens could be calculated by the relative position around the feeder when they compete for food. The dominant hens have a versatile. Moreover, they are more vigilant and have priority when foraging. Low-ranking hens adopt strategies to get enough food to sustain themselves. Hens of high-rank possess beneficial bacteria that use favorable substances to maintain the balance of the gut environment.

Specific Microbial Taxa and Functional Capacity Contribute to Chicken Abdominal Fat Deposition.

Genetically selected chickens with better growth and early maturation show an incidental increase in abdominal fat deposition (AFD). Accumulating evidence reveals a strong association between gut microbiota and adiposity. However, studies focusing on the role of gut microbiota in chicken obesity in conventional breeds are limited. Therefore, 400 random broilers with different levels of AFD were used to investigate the gut microbial taxa related to AFD by 16S rRNA gene sequencing of 76 representative samples, and to identify the specific microbial taxa contributing to fat-related metabolism using shotgun metagenomic analyses of eight high and low AFD chickens. The results demonstrated that the richness and diversity of the gut microbiota decrease as the accumulation of chicken abdominal fat increases. The decrease of Bacteroidetes and the increase of Firmicutes were correlated with the accumulation of chicken AFD. The Bacteroidetes phylum, including the genera Bacteroides, Parabacteroides, and the species, B. salanitronis, B. fragilis, and P. distasonis, were correlated to alleviate obesity by producing secondary metabolites. Several genera of Firmicutes phylum with circulating lipoprotein lipase activity were linked to the accumulation of chicken body fat. Moreover, the genera, Olsenella and Slackia, might positively contribute to fat and energy metabolism, whereas the genus, Methanobrevibacter, was possible to enhance energy capture, and associated to accumulate chicken AFD. These findings provide insights into the roles of the gut microbiota in complex traits and contribute to the development of effective therapies for the reduction of chicken fat accumulation.

Genetic parameters and direct and maternal effects for important traits in late-feathering Qingyuan partridge hens in China.

Qingyuan partridge chicken is an important indigenous chicken in China. In its breeding schemes, chickens are usually selected at the age of 105-day-old for five traits, including body weight (BW), shank length (SL), shank girth (SG), comb height (CH) and feather maturity (FM). At present, genetic parameters of the aforementioned traits have still not been studied in Qingyuan partridge chickens. The objectives of this study were the following: (1) to investigate whether the optimal statistical models of these traits need to consider maternal genetic and permanent environmental effects in late-feathering Qingyuan partridge hens, and (2) to estimate genetic parameters for these traits based on the optimal models. The numbers of records for BW, SL, SG, CH and FM were 13,721, 13,671, 13,670, 13,669 and 13,672, respectively. Variance components were estimated using average information-restricted maximum likelihood method, and the optimal model was determined based on Bayesian information criterion. More specifically, the optimal model for BW considered maternal genetic and permanent environmental effects in addition to direct additive genetic effect; SL, SG and FM considered direct and maternal genetic effects; and CH considered direct and maternal genetic effects, and the covariance between them. The direct heritabilities of these traits estimated using the optimal models were 0.21 ± 0.04, 0.30 ± 0.05, 0.40 ± 0.05, 0.59 ± 0.09 and 0.09 ± 0.04, respectively; the maternal heritabilities were 0.01 ± 0.04, 0.05 ± 0.05, 0.04 ± 0.05, 0.09 ± 0.09 and 0.03 ± 0.04, respectively. Maternal genetic effect evidently played an important part in FM and maternal heritability accounted for 30 per cent of total heritability. Furthermore, the direct and maternal genetic effects for CH were estimated to be negatively and moderately correlated (-0.51 ± 0.11). For all traits, neglecting existent maternal effects biased the estimation of direct heritability. Therefore, to implement optimum breeding strategies for improvement of these traits in Qingyuan partridge hens, maternal effects should be taken into consideration.

The association of SNPs in Hsp90ß gene 5' flanking region with thermo tolerance traits and tissue mRNA expression in two chicken breeds.

Thermo stress induces heat shock proteins (HSPs) expression and HSP90 family is one of them that has been reported to involve in cellular protection against heat stress. But whether there is any association of genetic variation in the Hsp90ß gene in chicken with thermo tolerance is still unknown. Direct sequencing was used to detect possible SNPs in Hsp90ß gene 5' flanking region in 3 chicken breeds (n = 663). Six mutations, among which 2 SNPs were chosen and genotypes were analyzed with PCR-RFLP method, were found in Hsp90ß gene in these 3 chicken breeds. Association analysis indicated that SNP of C.-141G>A in the 5' flanking region of the Hsp90ß gene in chicken had some effect on thermo tolerance traits, which may be a potential molecular marker of thermo tolerance, and the genotype GG was the thermo tolerance genotype. Hsp90ß gene mRNA expression in different tissues detected by quantitative real-time PCR assay were demonstrated to be tissue dependent, implying that different tissues have distinct sensibilities to thermo stress. Besides, it was shown time specific and varieties differences. The expression of Hsp90ß mRNA in Lingshan chickens in some tissues including heart, liver, brain and spleen were significantly higher or lower than that of White Recessive Rock (WRR). In this study, we presume that these mutations could be used in marker assisted selection for anti-heat stress chickens in our breeding program, and WRR were vulnerable to tropical thermo stress whereas Lingshan chickens were well adapted.