Polymorphisms of CRELD1 and DNAJC30 and their relationship with chicken carcass traits

Indigenous broilers in crossbreeding: impacts on meat quality and candidate gene screening

In the fierce market competition, high-quality chicken products often stand out. There are significant differences in meat quality between yellow and white feathered chickens. However, the underlying mechanisms that lead to the differences in their meat quality remain unclear. Single nucleotide polymorphisms (SNP) are effective molecular markers that can be utilized in marker-assisted breeding programs targeting chicken meat quality traits. Our research findings indicated that the bloodline of yellow-feathered chickens can significantly alter the meat quality traits of chickens, especially in terms of the shear force and meat color of the breast muscle. Additionally, through metabolomic, lipidomic, and RNA-seq, we identified differentially expressed metabolites, lipids, and genes that influence meat quality. Furthermore, we discovered a key gene, the purinergic receptor P2 × 5 (P2RX5), which significantly contributes to meat quality traits. We identified five SNP sites within the P2RX5 gene and conducted genotyping. Three of these SNP sites were found to be significantly associated with meat quality traits in chickens, such as the a*value and cooking loss. These results indicated that our findings provide potential molecular markers for changing meat quality traits in chickens. However, due to our small sample size and the absence of testing on males, the generalizability of the results may be insufficient.

EGR1 mRNA expression levels and polymorphisms are associated with slaughter performance in chickens

With the implementation of the policy of "centralized slaughtering and chilled to market" and the development of the livestock processing industry, numerous researchers have begun to focus on the selection and breeding of broilers bred for slaughter. The selection of breeds with excellent slaughtering performance and high meat production performance has become one of the most important selective breeding goals. In our previous study, we conducted transcriptome sequencing on chicken breast tissues with high and low breast muscle rates and found higher early growth response protein 1 (EGR1) expression in breast tissues with a low breast muscle ratio, thus hypothesizing that the EGR1 gene is involved in the growth and development process of chicken muscle tissues. Therefore, we analyzed the gene functions and polymorphisms of EGR1 to investigate its association with slaughter traits. We used various experimental methods, including RT-qPCR, Cell Counting Kit 8, 5-ethynyl-2'-deoxyuridine, western blot, flow cytometry, and immunofluorescence, to validate EGR1's role in chicken primary myoblasts. The results of our functional validation experiments indicate that EGR1 is highly expressed in breast tissues with a low breast muscle content and plays a key role in regulating of muscle growth and development by promoting proliferation and inhibiting the differentiation of chicken primary myoblasts. In addition, we explored the relationship between the EGR1 gene polymorphisms and slaughter traits using mixed linear models for the first time. In a population of Jiangfeng M3 lineage partridge chickens, we identified 4 EGR1 single-nucleotide polymorphisms, 2 of which were significantly associated with slaughter traits, including live weight, slaughter weight, semi-eviscerated weight, eviscerated weight, leg weight, wing weight, and breast muscle rate. In summary, ectopic expression of EGR1 promotes the proliferation and differentiation of chicken primary myoblasts. In addition, polymorphisms in EGR1 were associated with slaughter performance, providing a potential basis for further utilization of EGR1 as a breeding marker.

Large-scale transcriptomic and genomic analyses reveal a novel functional gene SERPINB6 for chicken carcass traits

BACKGROUND

Carcass traits are crucial indicators of meat production efficiency. However, the molecular regulatory mechanisms associated with these traits remain unclear.

RESULTS

In this study, we conducted comprehensive transcriptomic and genomic analyses on 399 Tiannong partridge chickens to identify key genes and variants associated with carcass traits and to elucidate the underlying regulatory mechanisms. Based on association analyses with the elastic net (EN) model, we identified 12 candidate genes (AMY1A, AP3B2, CEBPG, EEF2, EIF4EBP1, FGFR1, FOXD3, GOLM1, LOC107052698, PABPC1, SERPINB6 and TBC1D16) for 4 carcass-related traits, namely live weight, dressed weight, eviscerated weight, and breast muscle weight. SERPINB6 was identified as the only overlapping gene by 3 analyses, EN model analysis, weighted gene co-expression network analysis and differential expression analysis. Cell-level experiments confirmed that SERPINB6 promotes the proliferation of chicken DF1 cells and primary myoblasts. Further expression genome-wide association study and association analysis indicated that rs317934171 is the critical site that enhances SERPINB6 expression. Furthermore, a dual-luciferase reporter assay proved that gga-miR-1615 targets the 3'UTR of SERPINB6.

CONCLUSIONS

Collectively, our findings reveal that SERPINB6 serves as a novel gene for chicken carcass traits by promoting fibroblast and myoblast proliferation. Additionally, the downstream variant rs317934171 regulates SERPINB6 expression. These results identify a new target gene and molecular marker for the molecular mechanisms of chicken carcass traits.

LncEDCH1 g.1703613 T>C regulates chicken carcass traits by targeting miR-196-2-3p

Single nucleotide polymorphisms (SNPs) are valuable genetic markers that can provide insights into the genetic diversity and variation within chicken populations. In poultry breeding, SNP analysis is widely utilized to accelerate the selection of desirable traits, improving the efficiency and effectiveness of chicken breeding programs. In our previous research, we identified an association between LncEDCH1 and muscle development. To further investigate its specific mechanism, we conducted SNP detection and performed genotyping, linkage disequilibrium, and haplotype analysis. Our research findings indicate that 16 SNPs in the LncEDCH1. Among these SNPs, g.1703497 C>T and g.1704262 C>T were significantly associated with breast muscle weight percentage, g.1703497 C>T and g.1703613 T>C were significantly associated with leg weight percentage, and g.1703497 C>T, g.1703589 T>C, g.1703613 T>C, g.1703636 C>A, g.1703768 T>C, g.1704079 C>T, g.1704250 T>C, g.1704253 G>A were significantly associated with skin yellowness. Two haplotype blocks composed of 6 SNPs that were significantly associated with wing skin yellowness, breast skin yellowness, full-bore weight, and carcass weight percentage. Furthermore, through dual-luciferase reporter assays, biotin-coupled miRNA pull-down assays, 5-ethynyl-2'-deoxyuridine (EDU) assays, immunofluorescence, and quantitative real-time polymerase chain reaction (qPCR), it has been confirmed that miR-196-2-3p inhibits the expression of LncEDCH1 directly by binding to LncEDCH1 g.1703613T>C, thereby achieving indirect regulation of muscle development. These findings provide valuable molecular markers for chicken molecular breeding and broaden our understanding of the regulatory mechanisms.

Identification of central regulators related to abdominal fat deposition in chickens based on weighted gene co-expression network analysis

Abdominal fat (AF) is one of the most important economic traits in chickens. Excessive AF in chickens will reduce feed utilization efficiency and negatively affect reproductive performance and disease resistance. However, the regulatory network of AF deposition needs to be further elucidated. In the present study, 300 one-day-old female Wannan chickens were reared to 17 wk of age, and 200 Wannan hens were selected to determine the abdominal fat percentage (AFP). Twenty AF tissue samples with the lowest AFP were selected as the low abdominal fat group (L-AFG), and 20 AF tissue samples with the highest AFP were selected as the high abdominal fat group (H-AFG). Eleven samples from L-AFG and 14 samples from H-AFG were selected for RNA-seq and used for weighted gene co-expression network analysis (WGCNA). Among the 25 RNA-seq samples, 5 samples with the lowest and highest AFP values were selected for differential expression gene analysis. Compared with the L-AFG, 225 and 101 genes were upregulated and downregulated in the H-AFG, respectively. A total of 20,503 genes were used to construct the WGCNA, and 44 co-expression gene modules were identified. Among these modules, 3 modules including turquoise, darkorange2, and floralwhite were identified as significantly associated with AFP traits. Furthermore, several genes including acyl-CoA oxidase 1 (ACOX1), stearoyl-CoA desaturase (SCD), aldehyde dehydrogenase 6 family member A1 (ALDH6A1), jun proto-oncogene, AP-1 transcription factor subunit (JUN), and fos proto-oncogene, AP-1 transcription factor subunit (FOS) involved in the "PPAR signaling pathway," "fatty acid metabolism," and "MAPK signaling pathway" were identified as central regulators that contribute to AF deposition. These results provide valuable information for further understanding of the gene expression and regulation of AF traits and contribute to future molecular breeding for AF in chickens.

Exploring the association between fat-related traits in chickens and the RGS16 gene: insights from polymorphism and functional validation analysis

Introduction

Excessive fat deposition in chickens can lead to reduced feed utilization and meat quality, resulting in significant economic losses for the broiler industry. Therefore, reducing fat deposition has become an important breeding objective in addition to achieving high broiler weight, growth rate, and feed conversion efficiency. In our previous studies, we observed high expression of Regulators of G Protein Signaling 16 Gene (RGS16) in high-fat individuals. This led us to speculate that RGS16 might be involved in the process of fat deposition in chickens.

Methods

Thus, we conducted a polymorphism and functional analysis of the RGS16 gene to investigate its association with fat-related phenotypic traits in chickens. Using a mixed linear model (MLM), this study explored the relationship between RGS16 gene polymorphisms and fat-related traits for the first time. We identified 30 SNPs of RGS16 in a population of Wens Sanhuang chickens, among which 8 SNPs were significantly associated with fat-related traits, including sebum thickness (ST), abdominal fat weight (AFW), and abdominal fat weight (AFR). Furthermore, our findings demonstrated that AFW, AFR, and ST showed significant associations with at least two or more out of the eight identified SNPs of RGS16. We also validated the role of RGS16 in ICP-1 cells through various experimental methods, including RT-qPCR, CCK- 8, EdU assays, and oil red O staining.

Results

Our functional validation experiments showed that RGS16 was highly expressed in the abdominal adipose tissue of high-fat chickens and played a critical role in the regulation of fat deposition by promoting preadipocyte differentiation and inhibiting their proliferation. Taken together, our findings suggest that RGS16 polymorphisms are associated with fat-related traits in chickens. Moreover, the ectopic expression of RGS16 could inhibit preadipocyte proliferation but promote preadipocyte differentiation.

Discussion

Based on our current findings, we propose that the RGS16 gene could serve as a powerful genetic marker for marker-assisted breeding of chicken fat-related traits.