Genome-wide association study identified candidate genes for egg production traits in the Longyan Shan-ma duck

Genome-wide association study revealed candidate genes associated with egg-laying time traits in layer chicken

In modern intensive caged laying hen production, variations in egg-laying time (ELT) among layers often increase the workload for egg collection, thereby raising the costs of labor or power and reducing overall efficiency. For management purpose, early and synchronized ELT is also advantageous, particularly to large-scale layer farm. However, the underlying genetic mechanisms of ELT remain unclear. In this study, through the development of video and artificial intelligence-based software, ELT records during the peak laying period (27-32 weeks) from 507 layers, and their earlier laying performance (21-32 weeks) were collected. Via whole genome sequencing data of all the individuals, the estimated heritabilities of traditional egg production traits ranged from 0.23 to 0.36, consistent with previous reports. The heritability of average egg-laying time (AELT) was estimated as 0.46. Furthermore, individuals with earlier AELT tended to exhibit superior egg production performance. Genome-wide association study revealed three SNPs associated with AELT traits, located at 170,867,650 bp on chromosome 1, at 5,548,087 and 5,817,488 bp on chromosome 9. Across the region of 5.4 to 7.0 Mb on chromosome 9, mutations were also identified to be strongly linked with the two AELT-associated SNPs. Genes located in this region may be responsible for the differences in AELT among hens. These results indicate that ELT has the potential to be integrated into the production system of caged layers. If ELT is to be included as a breeding objective in the future, its reliability needs to be validated in larger populations and over longer periods.

Statistical Analysis of Reproductive Traits in Jinwu Pig and Identification of Genome-Wide Association Loci

BACKGROUND

The Jinwu pig is a novel breed created by crossbreeding Jinhua and Duroc pigs, displaying superior meat quality, strong adaptability to coarse feed, high production performance, and a rapid growth rate. However, research on its reproductive traits and genomic characteristics has not been systematically reported.

METHODS

In this study, we investigated the genetic basis of reproductive traits in Jinwu pigs us-ing a genome-wide association study. We analyzed 2831 breeding records from 516 Jinwu sows to evaluate the effects of fixed factors (farrowing season, parity, and mated boar) on six reproductive traits: the total number of births (TNB), number born alive (NBA), number of healthy offspring produced (NHOP), weak litter size (WLS), number of stillbirths (NS), and number of mummies (NM).

RESULTS

A total of 771 genome-wide significant single-nucleotide polymorphisms (SNPs) and ten potential candidate genes associated with pig reproductive traits were identified: VOPP1, PGAM2, TNS3, LRFN5, ORC1, CC2D1B, ZFYYE9, TUT4, DCN, and FEZF1. TT-genotype-carrier individuals of the pleiotropic SNP rs326174997 exhibited significantly higher TNB, NBA, and NHOP trait-related phenotypic values.

CONCLUSIONS

These findings provide a foundation for the reproductive breeding of Jinwu pigs and offer new insights into molecular genetic breeding in pigs.

A genome-wide association study identified candidate genes associated with egg quality traits in Muscovy duck

BACKGROUND

Egg quality directly determines embryo development in meat-type poultry. However, it is difficult to directly select the egg quality of Muscovy duck. The genes and SNPs associated with egg quality screened by GWAS can be used for molecular breeding and accelerate the progress of selection in Muscovy duck.

RESULT

295 Muscovy ducks were used for whole genome sequencing, and a total of 6,131,623 SNPs were obtained for further analysis. The heritability of egg quality ranged from 0.01 to 0.41, in which egg weight (EW) was 0.19, albumen weight (AW) was 0.16 and the yolk weight (YW) was 0.27. The genetic correlation of EW and AW, EW and YW, and eggshell thickness (EST) and eggshell strength (ESS) were 0.65, 0.51, and 0.74, respectively. Phenotypic correlations between egg quality ranged from - 0.13 to 0.17. A total of 68 SNPs significantly associated with EW were located within the genes PSMG4, SLC22A23, DNAH5, FABP6, ADAMST17, IGF1R, NTRK3, and SCAI. The linkage disequilibrium (LD) analysis identified 2_75684453_C > G, 2_76305509_A > G, 2_76350118_T > A, 11_3834664_C > T, 11_4339778_C > T, and 11_8079686_C > T as tagSNPs to represent the significant SNPs. Fifty SNPs significantly associated with YW were located within the genes XKR6, DNAJC24, SNCB, UNC5A, MAD1L1, NOTCH1, and WDR7. The SNPs 14_9186714_C > T, 14_9199818_A > G, 15_5452098_C > T, and 18_9038052_C > T were selected as tagSNPs. Fifty-four SNPs significantly associated with albumen height were located within the genes LIN9 and NID1. The SNP 3_17718980_A > G was selected as the tagSNP. The significant SNPs associated with eggshell strength were located within the genes CLPX, EPHA5, ZBTB44, NOL6, and UBAP1. The SNPs 25_1996726_A > C and 25_2078328_A > G were selected as tagSNPs. Genes associated with egg quality were significantly enriched in the positive regulation of the BMP signaling pathway in the GO enrichment analysis of biological processes. The KEGG enrichment analysis suggested that the SNPs located genes were significantly enriched in Axon guidance, Endocrine resistance, and Progesterone-mediated oocyte maturation.

CONCLUSION

Some tagSNPs were identified that may be useful for molecular breeding of egg quality. RNF423, RNF220, IGF1R, SLC22A23, WDR7, and NTRK3 may be candidate genes for egg quality traits in Muscovy duck.

Folic acid alleviates the negative effects of dexamethasone induced stress on production performance in Hyline Brown laying hens

Multiple stressors are believed to deteriorate production performance and cause substantial economic losses in commercial poultry farming. Folic acid (FA) is an antioxidant compound that can improve oocyte function and regulate gut microbiota composition. The current study was conducted to investigate the role of FA in alleviating stress and improving production performance. Sixty Hyline Brown laying hens at 21 weeks of age were randomly divided into three groups, with 10 replicates in each group and each replicate containing two chickens. Each group received basic diet and saline injection (Con group), basic diet with dexamethasone (DXM) injection (DXM group), or basic diet supplemented with FA (13 mg/kg in the premix) with DXM injection (FA group). The feeding trial lasted five weeks. Birds in the DXM and FA groups receiving subcutaneous DXM injections at a dosage of 4.50 mg/kg per day during the first seven days of the trial. Results showed that the levels of corticosterone, triglyceride, total cholesterol, and malondialdehyde in serum were significantly increased in the DXM group (P < 0.05), while the concentrations of FA and 5-methyltetrahydrofolate were decreased in the DXM group (P < 0.05). Laying hens in the DXM group had lower laying rates and egg quality, including egg weight, eggshell thickness, eggshell strength, albumen height, and Haugh units (P < 0.05). Conversely, FA alleviated these negative impacts. Through transcriptome analysis, a total of 247 and 151 differentially expressed genes were identified among the three groups, and 32 overlapped genes were further identified. Moreover, 44 and 59 differential metabolites were influenced by DXM and FA, respectively. Kyoto Encyclopedia of Genes and Genomes enrichment from the transcriptome and metabolomics showed that the reduced production performance may be due to the disturbance of oocyte production, calcium metabolism, and oxidative stress. Analysis of 16S rRNA gene amplicon sequences revealed the differential microbial composition and potential functional changes among the different groups. LEfSe analysis showed that Mucispirillum and Nautella were the predominant bacteria in the DXM group, while Clostridium was the predominant bacteria in the FA group. Functional prediction demonstrated that stressors enhanced fatty acid biosynthesis, while betaine biosynthesis and retinol metabolism were elevated in the FA group. Dietary FA reversed the elevated levels of bile acids (BA), including cholic acid, taurodeoxycholic acid, and taurochenodeoxycholic acid (P < 0.05). The DXM group showed an overall decrease in short-chain fatty acids (SCFA), but FA restored the concentrations of acetic acid, propionic acid, and isobutyric acid (P < 0.05). In conclusion, this study reveals that dietary FA can alleviate the degradation of production performance caused by stress through improving circulating antioxidant capacity, maintaining intestinal microbiota homeostasis, and regulating SCFA and BA biosynthesis. Thus, highlighting the prominent role of gut microbe-host interactions in alleviating multi-stresses.

Identification of Candidate Genes for Sebum Deposition in Pekin Ducks Using Genome-Wide Association Studies

BACKGROUND

Sebum deposition is a vital trait influencing meat quality and production efficiency in Pekin ducks. Providing insights into the genetic basis of fat deposition could help improve breeding strategies aimed at producing high-quality meat ducks. This study aimed to identify the genetic mechanisms and lipid metabolism pathways regulating subcutaneous and intramuscular fat deposition in two Pekin duck strains: Nankou No. 1 and Jingdian.

METHODS

A total of 72 male ducks, Nankou No. 1 (n = 36) and Jingdian (n = 36), were raised under controlled conditions for 42 days. On days 28, 35, and 42, ducks from each group were selected and slaughtered, and their subcutaneous and liver tissues were collected to analyze lipid enzyme activities. On day 42, additional ducks from each strain were slaughtered and evaluated for carcass performance, as well as intramuscular and sebum yield. Genome-wide association analysis (GWAS) was conducted in the Nankou No. 1 strain.

CONCLUSION

Our results showed statistically significant differences in intramuscular and subcutaneous fat yield between the two strains, with Nankou No. 1 exhibiting a higher yield than Jingdian (p < 0.05). The GWAS results identified 96 significant single nucleotide polymorphisms (SNPs), associated with sebum deposition. Functional annotation identified ALDH7A1 as a key candidate gene involved in lipid metabolism and fat storage regulation in Pekin ducks, Nankou No. 1 strain. Enzyme activity assays in liver and subcutaneous tissues revealed breed-specific differences in lipid metabolism, aligning with genetic findings. The activities of the lipid enzymes changed over time, suggesting changes in the developmental stages. The results on fat yield and enzymatic activities further align with molecular findings from the GWAS, which identified variations in lipid metabolism pathways. These results highlight genetic markers and biochemical pathways related to fat deposition in Pekin ducks, offering new insights for selective breeding programs aimed at optimizing fat content in meat production. Further research is needed to clarify the specific role of ALDH7A1 in lipid metabolism and its potential to enhance fat deposition traits in poultry.