A selection method of chickens with blue-eggshell and dwarf traits by molecular marker-assisted selection

Integration of whole genome resequencing and transcriptome sequencing to identify candidate genes for tall and short traits in Baicheng Fatty chickens

The tall and short traits of chickens are significant indicators for evaluating their growth and development. Tall chickens have longer growth cycles, allowing them to accumulate sufficient nutrients and resulting in superior meat quality. This study aims to investigate the tall and short traits of Baicheng Fatty chickens and to identify relevant candidate genes. A total of 25 Baicheng Fatty chickens were selected for this research, where whole genome resequencing was performed on all samples to uncover genetic variations influencing tall and short traits. Additionally, transcriptome sequencing was conducted on 15 of these chickens to identify important genes affecting these traits through combined analysis. Using methods such as population genetic structure analysis, principal component analysis (PCA), linkage disequilibrium analysis (LD), runs of homozygosity (ROH) analysis, as well as genetic differentiation index (FST ) and nucleotide diversity (θπ), a total of 1,019 candidate genes were identified through whole genome resequencing analysis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed on these candidates. From the transcriptome data, 253 differentially expressed genes (DEGs) were identified, including 229 upregulated and 24 downregulated genes. GO and KEGG enrichment analyses were conducted on these differential genes, and a protein-protein interaction network for the DEGs was constructed. Through the combined analysis of whole genome resequencing and transcriptome data, six intersecting genes were identified: KLF15, NRXN1, LOC107050638, MHCY11, HAO1, and BORCS6. KEGG enrichment analysis revealed significant involvement in the Glyoxylate and Dicarboxylate Metabolism pathway, Peroxisome pathway, Carbon Metabolism, and Cell Adhesion Molecules (CAMs) pathway. These genes may influence the growth and developmental patterns of skeletal structures, though their regulatory mechanisms require further investigation. This study provides new insights for further research into the genetic mechanisms underlying chicken skeletal development and growth, as well as potential molecular markers for poultry breeding.

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.

Circular RNA circRPS19 promotes chicken granulosa cell proliferation and steroid hormone synthesis by interrupting the miR-218-5p/INHBB axis

Ovarian follicle development is an important physiological activity for females and makes great significance in maintaining female health and reproduction performance. The development of ovarian follicle is mainly affected by the granulosa cells (GCs), whose growth is regulated by a variety of factors. Here, we identified a novel circular RNA (circRNA) derived from the Ribosomal protein S19 (RPS19) gene, named circRPS19, which is differentially expressed during chicken ovarian follicle development. Further explorations identified that circRPS19 promotes GCs proliferation and steroid hormone synthesis. Furthermore, circRPS19 was found to target and regulate miR-218-5p through a competitive manner with endogenous RNA (ceRNA). Functionals investigation revealed that miR-218-5p attenuates GCs proliferation and steroidogenesis, which is opposite to that of circRPS19. In addition, we also confirmed that circRPS19 upregulates the expression of Inhibin beta B subunit (INHBB) by binding with miR-218-5p to facilitate GCs proliferation and steroidogenesis. Overall, this study revealed that circRPS19 regulates GCs development by releasing the repression of miR-218-5p on INHBB, which suggests a novel mechanism in respect to circRNA and miRNA regulation in ovarian follicle development.

Bovine FRAS1: mRNA Expression Profile, Genetic Variations, and Significant Correlations with Ovarian Morphological Traits, Mature Follicle, and Corpus Luteum

The amelioration of bovine fertility caused by a multi-factorial problem has always been a hot topic, among which the detection of available target genes is the most crucial. It was hypothesized that the Fraser extracellular matrix complex subunit 1 (FRAS1) gene detected by GWAS is involved in physiological activities such as ovarian development. Herein, unilateral ovaries from 2111 cows were used to examine the mRNA expression profile and polymorphisms of bovine FRAS1 and their associations with fertility-related characteristics. Firstly, it was confirmed that FRAS1 gene transcripts are expressed in various bovine tissues. Then, among five potential insertion-deletion (indel) loci, the 20 bp (named P3-D20-bp) and 15 bp (P4-D15-bp) deletion mutations were confirmed to be polymorphic with linkage equilibrium. Secondly, the P3-D20-bp polymorphism was significantly associated with ovarian weight and corpus luteum diameter in the metaestrus phase and ovarian length in the dioestrum stage. Additionally, both ovarian length and mature follicle diameter in metaestrus are significantly correlated with different genotypes of P4-D15-bp. Thirdly, the transcriptional expression of the FRAS1 gene in groups with a minimum value of ovarian weight or volume was significantly higher than the expression in groups with a maximum value. Instead of that, the more corpus luteum and mature follicles there are, the higher the transcription expression of the FRAS1 gene is. Furthermore, FRAS1 expression in cows with a heterozygous genotype (ID) of P3-D20-bp was significantly higher than others. Eventually, P3-D20-bp deletion could disturb the binding efficiency of WT1-I and Sox2 to FRAS1 sequence according to binding prediction, indicating that mutation may affect gene expression and traits by influencing the binding of transcription factors. Overall, the polymorphisms of P3-D20-bp and P4-D15-bp of the bovine FRAS1 gene significantly correlated to follicle or ovarian traits that could be applied in optimizing female fertility in cow MAS breeding programs.

Transcriptome profiling reveals SLC5A5 regulates chicken ovarian follicle granulosa cell proliferation, apoptosis, and steroid hormone synthesis

The egg-laying performance of hens holds significant economic importance within the poultry industry. Broody inheritance of the parent stock of chickens can result in poor options for the improvement of egg production, and is a phenomenon influenced by multiple genetic factors. However, few studies have been conducted to delineate the molecular mechanism of ovarian regression in brooding chickens. Here, we explored the pivotal genes responsible for the regulation of ovarian follicles in laying hens, using RNA-sequencing analysis on the small ovarian follicles from broody and laying chickens. Sequencing data analysis revealed the differential expression of 200 genes, with a predominant enrichment in biological processes related to cell activation and metabolism. Among these genes, we focused on solute carrier family 5 member 5 (SLC5A5), which exhibited markedly higher RNA expression levels in follicles from laying compared with broody chickens. Subsequent cellular function studies with knockdown of SLC5A5 in chicken ovarian follicle granulosa cells (GCs) led to the down-regulation of genes associated with cell proliferation and steroid hormone synthesis, and concurrent promotion of gene expression linked to apoptosis. These findings indicated that SLC5A5 deficiency led to the inhibition of proliferation, steroid hormone synthesis and secretion, and promotion of apoptosis in chicken GCs. Our study demonstrated a pivotal role for SLC5A5 in the development and function of chicken GCs, shedding light on its potential significance in the broader context of chicken ovarian follicle development, and providing a prospective target to improve the egg-laying performance of chickens via molecular marker-assisted breeding technology.

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.

Investigating the heat tolerance and production performance in local chicken breed having normal and dwarf size

Heat stress significantly impairs the growth performance of broilers, which causes serious losses to the poultry industry every year. Thus, understanding the performance of indigenous chicken breeds under such environment is crucial to address heat stress problem. The purpose of this study was to investigate the effects of heat stress (HS) on production performance, tissue histology, heat shock response (HSP70, HSP90), and muscle growth-related genes (GHR, IGF-1, and IGF-1R) of Normal yellow chicken (NYC) and Dwarf yellow chicken (DYC). Seventy-two female birds from each strain were raised under normal environmental conditions up to 84 days, with birds from each strain being divided into two groups (HS and control). In the HS group, birds were subjected to high temperature at 35 ± 1 °C for 8 h daily and lasted for a week, while in the control group, birds were raised at 28 ± 1 °C. At 91 days old, bird's liver, hypothalamus, and breast muscle tissues were collected to evaluate the gene expression, histological changes, and the production performance. The Feed intake, weight gain ratio, total protein intake and protein efficiency ratio showed a significant reduction in the treatments (P < 0.01) and treatment × strain interaction (P < 0.05) with breast muscle rate significantly reducing among the treatments (P < 0.01) after 7 days of HS. Correspondingly, total abdominal fat showed significant change among treatment and strain (P < 0.01, P < 0.05), respectively. Besides, HS markedly upregulated the mRNA expression of HSP70 and HSP90 in the pectoralis major of both chicken strains, but no significant increase (P < 0.05) was found in mRNA expression of HSP90 in liver and hypothalamus tissues of both chicken strains. Moreover, HS significantly upregulated (P < 0.05) the expression of lipogenic genes (FASN, ACC) in liver tissues of NYC, while mRNA expression of these genes showed no variation in DYC. Similarly, HS downregulated the mRNA expression of muscle growth-related genes (GHR, IGF-1, and IGF-1R). Consequently, the histopathological analysis showed that histological changes were accompanied by inflammatory cell infiltration in liver tissues of both chicken strains; however, histopathological changes were more severe in NYC than dwarf chicken strain. Conclusively, this study depicted that the production performance and growth rate varied significantly between treatment and control group of NYC. However, heat treatment in DYC has not shown significant damaging consequences as compared to the control group that signifies the vital role of the dwarf trait in thermal tolerance.

Expression and polymorphisms of CD8B gene and its associations with body weight and size traits in sheep

The growth traits are economically important traits in sheep. Improving growth rates will increase the profitability of producers. The aim of this study was to identify alleles of CD8B (encoding T-cell surface glycoprotein CD8 beta chain) that are aberrantly expressed in different tissues and to assess the effects and associations of its different genotypes on weight and size traits in sheep. Using quantitative real-time reverse transcription PCR arrays, expression profiling of CD8B was performed in various organs and tissues. CD8B was ubiquitously expressed, with very high expression in the lung, spleen, lymph, duodenum, and liver. One intronic mutation (chr3:62,718,030 (Oar_rambouillet_v1.0, same below) G > A) was identified using pooled DNA sequencing. Subsequently, the variants (AA, AG, and GG) were genotyped using the KASPar^® PCR single nucleotide polymorphism (SNP) genotyping system. The results of association analysis with body weight and body size traits in 1304 sheep showed that increases in multiple phenotypic traits correlated with the AA genotype (body weight, p < 0.05; body length, p < 0.05). Thus, SNP chr3:62,718,030 G > A is a promising molecular marker for marker-assisted selection in sheep breeding.

Circular PPP1R13B RNA Promotes Chicken Skeletal Muscle Satellite Cell Proliferation and Differentiation via Targeting miR-9-5p

Skeletal muscle plays important roles in animal locomotion, metabolism, and meat production in farm animals. Current studies showed that non-coding RNAs, especially the circular RNA (circRNA) play an indispensable role in skeletal muscle development. Our previous study revealed that several differentially expressed circRNAs among fast muscle growing broilers (FMGB) and slow muscle growing layers (SMGL) may regulate muscle development in the chicken. In this study, a novel differentially expressed circPPP1R13B was identified. Molecular mechanism analysis indicated that circPPP1R13B targets miR-9-5p and negatively regulates the expression of miR-9-5p, which was previously reported to be an inhibitor of skeletal muscle development. In addition, circPPP1R13B positively regulated the expression of miR-9-5p target gene insulin like growth factor 2 mRNA binding protein 3 (IGF2BP3) and further activated the downstream insulin like growth factors (IGF)/phosphatidylinositol 3-kinase (PI3K)/AKT serine/threonine kinase (AKT) signaling pathway. The results also showed that the knockdown of circPPP1R13B inhibits chicken skeletal muscle satellite cells (SMSCs) proliferation and differentiation, and the overexpression of circPPP1R13B promotes the proliferation and differentiation of chicken SMSCs. Furthermore, the overexpression of circPPP1R13B could block the inhibitory effect of miR-9-5p on chicken SMSC proliferation and differentiation. In summary, our results suggested that circPPP1R13B promotes chicken SMSC proliferation and differentiation by targeting miR-9-5p and activating IGF/PI3K/AKT signaling pathway.

Integrative Analyses of mRNA Expression Profile Reveal SOCS2 and CISH Play Important Roles in GHR Mutation-Induced Excessive Abdominal Fat Deposition in the Sex-Linked Dwarf Chicken

Sex-linked dwarf (SLD) chicken, which is caused by a recessive mutation of the growth hormone receptor (GHR), has been widely used in the Chinese broiler industry. However, it has been found that the SLD chicken has more abdominal fat deposition than normal chicken. Excessive fat deposition not only reduced the carcass quality of the broilers but also reduced the immunity of broilers to diseases. To find out the key genes and the precise regulatory pathways that were involved in the GHR mutation-induced excessive fat deposition, we used high-fat diet (HFD) and normal diet to feed the SLD chicken and normal chicken and analyzed the differentially expressed genes (DEGs) among the four groups. Results showed that the SLD chicken had more abdominal fat deposition and larger adipocytes size than normal chicken and HFD can promote abdominal fat deposition and induce adipocyte hypertrophy. RNA sequencing results of the livers and abdominal fats from the above chickens revealed that many DEGs between the SLD and normal chickens were enriched in fat metabolic pathways, such as peroxisome proliferator-activated receptor (PPAR) signaling, extracellular matrix (ECM)-receptor pathway, and fatty acid metabolism. Importantly, by constructing and analyzing the GHR-downstream regulatory network, we found that suppressor of cytokine signaling 2 (SOCS2) and cytokine-inducible SH2-containing protein (CISH) may involve in the GHR mutation-induced abdominal fat deposition in chicken. The ectopic expression of SOCS2 and CISH in liver-related cell line leghorn strain M chicken hepatoma (LMH) cell and immortalized chicken preadipocytes (ICP) revealed that these two genes can regulate fatty acid metabolism, adipocyte differentiation, and lipid droplet accumulation. Notably, overexpression of SOCS2 and CISH can rescue the hyperactive lipid metabolism and excessive lipid droplet accumulation of primary liver cell and preadipocytes that were isolated from the SLD chicken. This study found some genes and pathways involved in abdominal fat deposition of the SLD chicken and reveals that SOCS2 and CISH are two key genes involved in the GHR mutation-induced excessive fat deposition of the SLD chicken.